From bdfea88a85446110477c567454de9a0ad74837bf Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Wed, 8 Feb 2023 13:45:56 -0500
Subject: [PATCH 01/48] Update import sorting for all tasks (#15)

* Add isort to dev dependencies

* Update import order for all tasks
---
 .github/workflows/lint.yml                    |  5 +++++
 poetry.lock                                   | 22 +++++++++----------
 pyproject.toml                                |  8 +++++--
 .../input/convert_to_cells_file.py            |  4 ++--
 .../input/convert_to_locations_file.py        |  4 ++--
 .../input/generate_setup_file.py              |  4 ++--
 .../input/merge_region_samples.py             |  4 ++--
 .../output/parse_cells_file.py                |  2 +-
 .../output/parse_locations_file.py            |  2 +-
 tox.ini                                       |  1 +
 10 files changed, 33 insertions(+), 23 deletions(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index dad3cb9..d6deb55 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -44,6 +44,11 @@ jobs:
         source .venv/bin/activate
         black -l 100 --check src/ tests/
 
+    - name: Check with isort
+      run: |
+        source .venv/bin/activate
+        isort -l 100 --check src/ tests/
+
     - name: Check with mypy
       run: |
         source .venv/bin/activate
diff --git a/poetry.lock b/poetry.lock
index e8c0ef6..1681aa3 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -422,7 +422,7 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "fsspec"
-version = "2022.8.2"
+version = "2022.10.0"
 description = "File-system specification"
 category = "main"
 optional = false
@@ -610,17 +610,17 @@ python-versions = "*"
 
 [[package]]
 name = "isort"
-version = "5.10.1"
+version = "5.12.0"
 description = "A Python utility / library to sort Python imports."
 category = "dev"
 optional = false
-python-versions = ">=3.6.1,<4.0"
+python-versions = ">=3.8.0"
 
 [package.extras]
-colors = ["colorama (>=0.4.3,<0.5.0)"]
-pipfile_deprecated_finder = ["pipreqs", "requirementslib"]
+colors = ["colorama (>=0.4.3)"]
+pipfile-deprecated-finder = ["pip-shims (>=0.5.2)", "pipreqs", "requirementslib"]
 plugins = ["setuptools"]
-requirements_deprecated_finder = ["pip-api", "pipreqs"]
+requirements-deprecated-finder = ["pip-api", "pipreqs"]
 
 [[package]]
 name = "Jinja2"
@@ -1595,7 +1595,7 @@ testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools"
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.9"
-content-hash = "089eb617978b397a05734a73aa827940560426a8c607e03a4127f6f2ec88225e"
+content-hash = "0072f8e0773f1f98a03e9b3eb09f46c8fb72b798a5f2c195291884e229d472a5"
 
 [metadata.files]
 aiofiles = [
@@ -2049,8 +2049,8 @@ frozenlist = [
     {file = "frozenlist-1.3.1.tar.gz", hash = "sha256:3a735e4211a04ccfa3f4833547acdf5d2f863bfeb01cfd3edaffbc251f15cec8"},
 ]
 fsspec = [
-    {file = "fsspec-2022.8.2-py3-none-any.whl", hash = "sha256:6374804a2c0d24f225a67d009ee1eabb4046ad00c793c3f6df97e426c890a1d9"},
-    {file = "fsspec-2022.8.2.tar.gz", hash = "sha256:7f12b90964a98a7e921d27fb36be536ea036b73bf3b724ac0b0bd7b8e39c7c18"},
+    {file = "fsspec-2022.10.0-py3-none-any.whl", hash = "sha256:6b7c6ab3b476cdf17efcfeccde7fca28ef5a48f73a71010aaceec5fc15bf9ebf"},
+    {file = "fsspec-2022.10.0.tar.gz", hash = "sha256:cb6092474e90487a51de768170f3afa50ca8982c26150a59072b16433879ff1d"},
 ]
 google-auth = [
     {file = "google-auth-2.12.0.tar.gz", hash = "sha256:f12d86502ce0f2c0174e2e70ecc8d36c69593817e67e1d9c5e34489120422e4b"},
@@ -2169,8 +2169,8 @@ iniconfig = [
     {file = "iniconfig-1.1.1.tar.gz", hash = "sha256:bc3af051d7d14b2ee5ef9969666def0cd1a000e121eaea580d4a313df4b37f32"},
 ]
 isort = [
-    {file = "isort-5.10.1-py3-none-any.whl", hash = "sha256:6f62d78e2f89b4500b080fe3a81690850cd254227f27f75c3a0c491a1f351ba7"},
-    {file = "isort-5.10.1.tar.gz", hash = "sha256:e8443a5e7a020e9d7f97f1d7d9cd17c88bcb3bc7e218bf9cf5095fe550be2951"},
+    {file = "isort-5.12.0-py3-none-any.whl", hash = "sha256:f84c2818376e66cf843d497486ea8fed8700b340f308f076c6fb1229dff318b6"},
+    {file = "isort-5.12.0.tar.gz", hash = "sha256:8bef7dde241278824a6d83f44a544709b065191b95b6e50894bdc722fcba0504"},
 ]
 Jinja2 = [
     {file = "Jinja2-3.1.2-py3-none-any.whl", hash = "sha256:6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61"},
diff --git a/pyproject.toml b/pyproject.toml
index 4ed04b4..717c760 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,15 +16,19 @@ pandas = "^1.5.1"
 
 [tool.poetry.group.dev.dependencies]
 black = "^22.8.0"
+isort = "^5.12.0"
+mypy = "^0.971"
 pylint = "^2.15.2"
-tox = "^3.26.0"
 pytest = "^7.2.0"
 pytest-cov = "^3.0.0"
 pytest-subtests = "^0.8.0"
 Sphinx = "^5.1.1"
-mypy = "^0.971"
 sphinx-rtd-theme = "^1.0.0"
 sphinx_mdinclude = "^0.5.2"
+tox = "^3.26.0"
+
+[tool.isort]
+profile = "black"
 
 [build-system]
 requires = ["poetry-core"]
diff --git a/src/arcade_collection/input/convert_to_cells_file.py b/src/arcade_collection/input/convert_to_cells_file.py
index 2731118..65593a1 100644
--- a/src/arcade_collection/input/convert_to_cells_file.py
+++ b/src/arcade_collection/input/convert_to_cells_file.py
@@ -1,7 +1,7 @@
-from typing import List, Dict, Tuple
+from typing import Dict, List, Tuple
 
-from prefect import task
 import pandas as pd
+from prefect import task
 
 
 @task
diff --git a/src/arcade_collection/input/convert_to_locations_file.py b/src/arcade_collection/input/convert_to_locations_file.py
index ae367da..bd2ff8e 100644
--- a/src/arcade_collection/input/convert_to_locations_file.py
+++ b/src/arcade_collection/input/convert_to_locations_file.py
@@ -1,7 +1,7 @@
-from typing import List, Dict, Tuple, Optional
+from typing import Dict, List, Optional, Tuple
 
-from prefect import task
 import pandas as pd
+from prefect import task
 
 
 @task
diff --git a/src/arcade_collection/input/generate_setup_file.py b/src/arcade_collection/input/generate_setup_file.py
index 9ecda91..87a5713 100644
--- a/src/arcade_collection/input/generate_setup_file.py
+++ b/src/arcade_collection/input/generate_setup_file.py
@@ -1,9 +1,9 @@
-from typing import List, Tuple, Optional
 import xml.etree.ElementTree as ET
+from typing import List, Optional, Tuple
 
-from prefect import task
 import numpy as np
 import pandas as pd
+from prefect import task
 
 
 @task
diff --git a/src/arcade_collection/input/merge_region_samples.py b/src/arcade_collection/input/merge_region_samples.py
index 0772b92..35c013d 100644
--- a/src/arcade_collection/input/merge_region_samples.py
+++ b/src/arcade_collection/input/merge_region_samples.py
@@ -1,8 +1,8 @@
-from typing import Tuple, Optional
+from typing import Optional, Tuple
 
-from prefect import task
 import numpy as np
 import pandas as pd
+from prefect import task
 
 
 @task
diff --git a/src/arcade_collection/output/parse_cells_file.py b/src/arcade_collection/output/parse_cells_file.py
index 03e6de7..8d2634c 100644
--- a/src/arcade_collection/output/parse_cells_file.py
+++ b/src/arcade_collection/output/parse_cells_file.py
@@ -1,6 +1,6 @@
-from typing import List, Union
 import json
 import tarfile
+from typing import List, Union
 
 import pandas as pd
 from prefect import task
diff --git a/src/arcade_collection/output/parse_locations_file.py b/src/arcade_collection/output/parse_locations_file.py
index d23b3fe..5065d5b 100644
--- a/src/arcade_collection/output/parse_locations_file.py
+++ b/src/arcade_collection/output/parse_locations_file.py
@@ -1,6 +1,6 @@
-from typing import List, Union
 import json
 import tarfile
+from typing import List, Union
 
 import numpy as np
 import pandas as pd
diff --git a/tox.ini b/tox.ini
index 4e1f860..eacdfcb 100644
--- a/tox.ini
+++ b/tox.ini
@@ -11,6 +11,7 @@ commands =
 [testenv:linter]
 commands =
     poetry run black -l 100 src/ tests/
+    poetry run isort -l 100 src/ tests/
     poetry run pylint --ignore-patterns=test.*?py src/ tests/
 
 [testenv:mypy]

From 5d6f0bb2a68fa59e49437176925d62c656096749 Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Mon, 13 Feb 2023 11:30:59 -0500
Subject: [PATCH 02/48] Add convert units task (#16)

* Add convert model units task

* Update convert units task for variable input

* Update pytest cov version
---
 poetry.lock                                   |  8 ++--
 pyproject.toml                                |  2 +-
 src/arcade_collection/output/__init__.py      |  1 +
 .../output/convert_model_units.py             | 39 +++++++++++++++++++
 4 files changed, 45 insertions(+), 5 deletions(-)
 create mode 100644 src/arcade_collection/output/convert_model_units.py

diff --git a/poetry.lock b/poetry.lock
index 1681aa3..1155cbd 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1043,7 +1043,7 @@ testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.
 
 [[package]]
 name = "pytest-cov"
-version = "3.0.0"
+version = "4.0.0"
 description = "Pytest plugin for measuring coverage."
 category = "dev"
 optional = false
@@ -1595,7 +1595,7 @@ testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools"
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.9"
-content-hash = "0072f8e0773f1f98a03e9b3eb09f46c8fb72b798a5f2c195291884e229d472a5"
+content-hash = "f56de737e88527afb41253ce99c72bb9cc7241f47bed0480674a0eabb33146f4"
 
 [metadata.files]
 aiofiles = [
@@ -2618,8 +2618,8 @@ pytest = [
     {file = "pytest-7.2.0.tar.gz", hash = "sha256:c4014eb40e10f11f355ad4e3c2fb2c6c6d1919c73f3b5a433de4708202cade59"},
 ]
 pytest-cov = [
-    {file = "pytest-cov-3.0.0.tar.gz", hash = "sha256:e7f0f5b1617d2210a2cabc266dfe2f4c75a8d32fb89eafb7ad9d06f6d076d470"},
-    {file = "pytest_cov-3.0.0-py3-none-any.whl", hash = "sha256:578d5d15ac4a25e5f961c938b85a05b09fdaae9deef3bb6de9a6e766622ca7a6"},
+    {file = "pytest-cov-4.0.0.tar.gz", hash = "sha256:996b79efde6433cdbd0088872dbc5fb3ed7fe1578b68cdbba634f14bb8dd0470"},
+    {file = "pytest_cov-4.0.0-py3-none-any.whl", hash = "sha256:2feb1b751d66a8bd934e5edfa2e961d11309dc37b73b0eabe73b5945fee20f6b"},
 ]
 pytest-subtests = [
     {file = "pytest-subtests-0.8.0.tar.gz", hash = "sha256:46eb376022e926950816ccc23502de3277adcc1396652ddb3328ce0289052c4d"},
diff --git a/pyproject.toml b/pyproject.toml
index 717c760..0443cd7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -20,7 +20,7 @@ isort = "^5.12.0"
 mypy = "^0.971"
 pylint = "^2.15.2"
 pytest = "^7.2.0"
-pytest-cov = "^3.0.0"
+pytest-cov = "^4.0.0"
 pytest-subtests = "^0.8.0"
 Sphinx = "^5.1.1"
 sphinx-rtd-theme = "^1.0.0"
diff --git a/src/arcade_collection/output/__init__.py b/src/arcade_collection/output/__init__.py
index cac6837..048cbfa 100644
--- a/src/arcade_collection/output/__init__.py
+++ b/src/arcade_collection/output/__init__.py
@@ -1,3 +1,4 @@
+from .convert_model_units import convert_model_units
 from .extract_tick_json import extract_tick_json
 from .get_location_voxels import get_location_voxels
 from .merge_parsed_results import merge_parsed_results
diff --git a/src/arcade_collection/output/convert_model_units.py b/src/arcade_collection/output/convert_model_units.py
new file mode 100644
index 0000000..0d88385
--- /dev/null
+++ b/src/arcade_collection/output/convert_model_units.py
@@ -0,0 +1,39 @@
+from typing import Optional, Union
+
+import pandas as pd
+from prefect import task
+
+
+@task
+def convert_model_units(
+    data: pd.DataFrame, ds: float, dt: float, regions: Optional[Union[list[str], str]] = None
+) -> None:
+    data["time"] = round(dt * data["TICK"], 2)
+
+    if "NUM_VOXELS" in data.columns:
+        data["volume"] = ds * ds * ds * data["NUM_VOXELS"]
+
+    if "MAX_Z" in data.columns and "MIN_Z" in data.columns:
+        data["height"] = ds * (data["MAX_Z"] - data["MIN_Z"] + 1)
+
+    if "CX" in data.columns:
+        data["cx"] = ds * data["CX"]
+
+    if "CY" in data.columns:
+        data["cy"] = ds * data["CY"]
+
+    if "CZ" in data.columns:
+        data["cz"] = ds * data["CZ"]
+
+    if regions is None:
+        return
+
+    if isinstance(regions, str):
+        regions = [regions]
+
+    for region in regions:
+        if region == "DEFAULT":
+            continue
+
+        data[f"volume.{region}"] = ds * ds * ds * data[f"NUM_VOXELS.{region}"]
+        data[f"height.{region}"] = ds * (data[f"MAX_Z.{region}"] - data[f"MIN_Z.{region}"])

From 2fe5aa13c7f7959bc509108aa6bf0d273244d265 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Mon, 13 Feb 2023 12:04:18 -0500
Subject: [PATCH 03/48] Release v0.5.0 (#17)

Co-authored-by: jessicasyu <15913767+jessicasyu@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 0443cd7..96b9051 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "arcade-collection"
-version = "0.4.0"
+version = "0.5.0"
 description = "Collection of tasks for working with ARCADE."
 authors = [
     "Jessica S. Yu <jesyu@uw.edu>"

From cacec0320eda50ee6c8b6a8e1101230b12026b93 Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Wed, 15 Feb 2023 17:56:07 -0500
Subject: [PATCH 04/48] Add convert format tasks (#18)

* Add convert to images task

* Add convert to meshes task

* Update init to load tasks

* Update dependencies

* Update mypy to ignore skimage

* Add convert to simularium task

* Rename tar input for clarity

* Update dependencies and config files
---
 .pylintrc                                     |   2 +-
 mypy.ini                                      |   6 +
 poetry.lock                                   | 342 +++++++++++++++++-
 pyproject.toml                                |   2 +
 src/arcade_collection/output/__init__.py      |   3 +
 .../output/convert_to_images.py               |  72 ++++
 .../output/convert_to_meshes.py               |  85 +++++
 .../output/convert_to_simularium.py           | 131 +++++++
 8 files changed, 641 insertions(+), 2 deletions(-)
 create mode 100644 src/arcade_collection/output/convert_to_images.py
 create mode 100644 src/arcade_collection/output/convert_to_meshes.py
 create mode 100644 src/arcade_collection/output/convert_to_simularium.py

diff --git a/.pylintrc b/.pylintrc
index f59eae6..97718afd 100644
--- a/.pylintrc
+++ b/.pylintrc
@@ -4,7 +4,7 @@
 disable=missing-module-docstring
 
 # Set good names.
-good-names=i,j,x,y,z
+good-names=i,j,x,y,z,ds,dt
 
 [DESIGN]
 
diff --git a/mypy.ini b/mypy.ini
index 7441e4a..60276d5 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -5,3 +5,9 @@ namespace_packages = True
 
 [mypy-pandas.*]
 ignore_missing_imports = True
+
+[mypy-simulariumio.*]
+ignore_missing_imports = True
+
+[mypy-skimage.*]
+ignore_missing_imports = True
diff --git a/poetry.lock b/poetry.lock
index 1155cbd..adf72db 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -576,6 +576,35 @@ category = "main"
 optional = false
 python-versions = ">=3.5"
 
+[[package]]
+name = "imageio"
+version = "2.25.1"
+description = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats."
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+numpy = "*"
+pillow = ">=8.3.2"
+
+[package.extras]
+all-plugins = ["astropy", "av", "imageio-ffmpeg", "opencv-python", "psutil", "tifffile"]
+all-plugins-pypy = ["av", "imageio-ffmpeg", "psutil", "tifffile"]
+build = ["wheel"]
+dev = ["black", "flake8", "fsspec[github]", "invoke", "pytest", "pytest-cov"]
+docs = ["numpydoc", "pydata-sphinx-theme", "sphinx (<6)"]
+ffmpeg = ["imageio-ffmpeg", "psutil"]
+fits = ["astropy"]
+full = ["astropy", "av", "black", "flake8", "fsspec[github]", "gdal", "imageio-ffmpeg", "invoke", "itk", "numpydoc", "opencv-python", "psutil", "pydata-sphinx-theme", "pytest", "pytest-cov", "sphinx (<6)", "tifffile", "wheel"]
+gdal = ["gdal"]
+itk = ["itk"]
+linting = ["black", "flake8"]
+opencv = ["opencv-python"]
+pyav = ["av"]
+test = ["fsspec[github]", "invoke", "pytest", "pytest-cov"]
+tifffile = ["tifffile"]
+
 [[package]]
 name = "imagesize"
 version = "1.4.1"
@@ -774,6 +803,21 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "networkx"
+version = "3.0"
+description = "Python package for creating and manipulating graphs and networks"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+
+[package.extras]
+default = ["matplotlib (>=3.4)", "numpy (>=1.20)", "pandas (>=1.3)", "scipy (>=1.8)"]
+developer = ["mypy (>=0.991)", "pre-commit (>=2.20)"]
+doc = ["nb2plots (>=0.6)", "numpydoc (>=1.5)", "pillow (>=9.2)", "pydata-sphinx-theme (>=0.11)", "sphinx (==5.2.3)", "sphinx-gallery (>=0.11)", "texext (>=0.6.7)"]
+extra = ["lxml (>=4.6)", "pydot (>=1.4.2)", "pygraphviz (>=1.10)", "sympy (>=1.10)"]
+test = ["codecov (>=2.1)", "pytest (>=7.2)", "pytest-cov (>=4.0)"]
+
 [[package]]
 name = "numpy"
 version = "1.23.4"
@@ -853,6 +897,35 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 python-dateutil = ">=2.6,<3.0"
 pytzdata = ">=2020.1"
 
+[[package]]
+name = "Pillow"
+version = "9.4.0"
+description = "Python Imaging Library (Fork)"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[package.extras]
+docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinxext-opengraph"]
+tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
+
+[[package]]
+name = "Pint"
+version = "0.20.1"
+description = "Physical quantities module"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+
+[package.extras]
+babel = ["babel (<=2.8)"]
+dask = ["dask"]
+numpy = ["numpy (>=1.19.5)"]
+pandas = ["pint-pandas (>=0.3)"]
+test = ["pytest", "pytest-cov", "pytest-mpl", "pytest-subtests"]
+uncertainties = ["uncertainties (>=3.1.6)"]
+xarray = ["xarray"]
+
 [[package]]
 name = "platformdirs"
 version = "2.5.2"
@@ -1108,6 +1181,17 @@ category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
+[[package]]
+name = "PyWavelets"
+version = "1.4.1"
+description = "PyWavelets, wavelet transform module"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+
+[package.dependencies]
+numpy = ">=1.17.3"
+
 [[package]]
 name = "pywin32"
 version = "304"
@@ -1208,6 +1292,46 @@ python-versions = ">=3.6,<4"
 [package.dependencies]
 pyasn1 = ">=0.1.3"
 
+[[package]]
+name = "scikit-image"
+version = "0.19.3"
+description = "Image processing in Python"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+imageio = ">=2.4.1"
+networkx = ">=2.2"
+numpy = ">=1.17.0"
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+
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+category = "main"
+optional = false
+python-versions = ">=3.8"
+
+[package.dependencies]
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+
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+
 [[package]]
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 version = "65.4.1"
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+
 [[package]]
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 version = "1.16.0"
@@ -1431,6 +1580,20 @@ category = "main"
 optional = false
 python-versions = "*"
 
+[[package]]
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+description = "Read and write TIFF files"
+category = "main"
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+
+[package.extras]
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+
 [[package]]
 name = "toml"
 version = "0.10.2"
@@ -1595,7 +1758,7 @@ testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools"
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 python-versions = "^3.9"
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+    {file = "scipy-1.9.3-cp38-cp38-macosx_12_0_arm64.whl", hash = "sha256:545c83ffb518094d8c9d83cce216c0c32f8c04aaf28b92cc8283eda0685162d5"},
+    {file = "scipy-1.9.3-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:0d54222d7a3ba6022fdf5773931b5d7c56efe41ede7f7128c7b1637700409108"},
+    {file = "scipy-1.9.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:cff3a5295234037e39500d35316a4c5794739433528310e117b8a9a0c76d20fc"},
+    {file = "scipy-1.9.3-cp38-cp38-win_amd64.whl", hash = "sha256:2318bef588acc7a574f5bfdff9c172d0b1bf2c8143d9582e05f878e580a3781e"},
+    {file = "scipy-1.9.3-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:d644a64e174c16cb4b2e41dfea6af722053e83d066da7343f333a54dae9bc31c"},
+    {file = "scipy-1.9.3-cp39-cp39-macosx_12_0_arm64.whl", hash = "sha256:da8245491d73ed0a994ed9c2e380fd058ce2fa8a18da204681f2fe1f57f98f95"},
+    {file = "scipy-1.9.3-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:4db5b30849606a95dcf519763dd3ab6fe9bd91df49eba517359e450a7d80ce2e"},
+    {file = "scipy-1.9.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c68db6b290cbd4049012990d7fe71a2abd9ffbe82c0056ebe0f01df8be5436b0"},
+    {file = "scipy-1.9.3-cp39-cp39-win_amd64.whl", hash = "sha256:5b88e6d91ad9d59478fafe92a7c757d00c59e3bdc3331be8ada76a4f8d683f58"},
+    {file = "scipy-1.9.3.tar.gz", hash = "sha256:fbc5c05c85c1a02be77b1ff591087c83bc44579c6d2bd9fb798bb64ea5e1a027"},
+]
 setuptools = [
     {file = "setuptools-65.4.1-py3-none-any.whl", hash = "sha256:1b6bdc6161661409c5f21508763dc63ab20a9ac2f8ba20029aaaa7fdb9118012"},
     {file = "setuptools-65.4.1.tar.gz", hash = "sha256:3050e338e5871e70c72983072fe34f6032ae1cdeeeb67338199c2f74e083a80e"},
 ]
+simulariumio = [
+    {file = "simulariumio-1.7.0-py3-none-any.whl", hash = "sha256:fda7df6fcf9368be4bbdf607fbecd73ee4d48eb8074784e3a7051bfaacacb965"},
+    {file = "simulariumio-1.7.0.tar.gz", hash = "sha256:2addf919174ba967479c4fd1f7d94290cd9a08905b0461ff8acfcc301d71fcf4"},
+]
 six = [
     {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
     {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
@@ -2818,6 +3154,10 @@ text-unidecode = [
     {file = "text-unidecode-1.3.tar.gz", hash = "sha256:bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93"},
     {file = "text_unidecode-1.3-py2.py3-none-any.whl", hash = "sha256:1311f10e8b895935241623731c2ba64f4c455287888b18189350b67134a822e8"},
 ]
+tifffile = [
+    {file = "tifffile-2023.2.3-py3-none-any.whl", hash = "sha256:6df45c1eab632eadb9384994c8ae8bc424cd3c26e9508481a345dbef1dcfd480"},
+    {file = "tifffile-2023.2.3.tar.gz", hash = "sha256:458df5ad9a5217f668edd636dc19fbc736062bf78aac823ab84cdbae9de8eaa6"},
+]
 toml = [
     {file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"},
     {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"},
diff --git a/pyproject.toml b/pyproject.toml
index 96b9051..14d0c44 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,6 +13,8 @@ python = "^3.9"
 prefect = "^2.6.0"
 numpy = "^1.23.4"
 pandas = "^1.5.1"
+scikit-image = "^0.19.3"
+simulariumio = "^1.7.0"
 
 [tool.poetry.group.dev.dependencies]
 black = "^22.8.0"
diff --git a/src/arcade_collection/output/__init__.py b/src/arcade_collection/output/__init__.py
index 048cbfa..a3dd5a2 100644
--- a/src/arcade_collection/output/__init__.py
+++ b/src/arcade_collection/output/__init__.py
@@ -1,4 +1,7 @@
 from .convert_model_units import convert_model_units
+from .convert_to_images import convert_to_images
+from .convert_to_meshes import convert_to_meshes
+from .convert_to_simularium import convert_to_simularium
 from .extract_tick_json import extract_tick_json
 from .get_location_voxels import get_location_voxels
 from .merge_parsed_results import merge_parsed_results
diff --git a/src/arcade_collection/output/convert_to_images.py b/src/arcade_collection/output/convert_to_images.py
new file mode 100644
index 0000000..ba34307
--- /dev/null
+++ b/src/arcade_collection/output/convert_to_images.py
@@ -0,0 +1,72 @@
+import tarfile
+
+import numpy as np
+from prefect import task
+
+from arcade_collection.output.extract_tick_json import extract_tick_json
+from arcade_collection.output.get_location_voxels import get_location_voxels
+
+
+@task
+def convert_to_images(
+    series_key: str,
+    data_tar: tarfile.TarFile,
+    frame_spec: tuple[int, int, int],
+    regions: list[str],
+    box: tuple[int, int, int],
+    chunk_size: int,
+    binary: bool,
+) -> list[tuple[int, int, np.ndarray]]:
+    length, width, height = box
+    frames = list(np.arange(*frame_spec))
+    array = np.zeros((len(frames), len(regions), height, width, length), "uint16")
+
+    for index, frame in enumerate(frames):
+        locations = extract_tick_json.fn(data_tar, series_key, frame, "LOCATIONS")
+
+        for location in locations:
+            location_id = location["id"]
+
+            for channel, region in enumerate(regions):
+                voxels = [
+                    (z, y, x)
+                    for x, y, z in get_location_voxels.fn(
+                        location, region if region != "DEFAULT" else None
+                    )
+                ]
+                array[index, channel][tuple(np.transpose(voxels))] = 1 if binary else location_id
+
+    return split_array_chunks(array, chunk_size)
+
+
+def split_array_chunks(array: np.ndarray, chunk_size: int) -> list[tuple[int, int, np.ndarray]]:
+    chunks = []
+    length = array.shape[4]
+    width = array.shape[3]
+
+    # Calculate chunk splits.
+    length_section = (
+        [0, chunk_size + 1] + (int(length / chunk_size) - 2) * [chunk_size] + [chunk_size + 1]
+    )
+    length_splits = np.array(length_section, dtype=np.int32).cumsum()
+    width_section = (
+        [0, chunk_size + 1] + (int(width / chunk_size) - 2) * [chunk_size] + [chunk_size + 1]
+    )
+    width_splits = np.array(width_section, dtype=np.int32).cumsum()
+
+    # Iterate through each chunk split.
+    for i in range(len(length_splits) - 1):
+        length_start = length_splits[i]
+        length_end = length_splits[i + 1]
+
+        for j in range(len(width_splits) - 1):
+            width_start = width_splits[j]
+            width_end = width_splits[j + 1]
+
+            # Extract chunk from full contents.
+            chunk = array[:, :, :, length_start:length_end, width_start:width_end]
+
+            if np.sum(chunk) != 0:
+                chunks.append((i, j, chunk))
+
+    return chunks
diff --git a/src/arcade_collection/output/convert_to_meshes.py b/src/arcade_collection/output/convert_to_meshes.py
new file mode 100644
index 0000000..7926c42
--- /dev/null
+++ b/src/arcade_collection/output/convert_to_meshes.py
@@ -0,0 +1,85 @@
+import tarfile
+
+import numpy as np
+from prefect import task
+from skimage import measure
+
+from arcade_collection.output.extract_tick_json import extract_tick_json
+from arcade_collection.output.get_location_voxels import get_location_voxels
+
+
+@task
+def convert_to_meshes(
+    series_key: str, data_tar: tarfile.TarFile, frame_spec: tuple[int, int, int], regions: list[str]
+) -> list[tuple[int, int, str, str]]:
+    frames = list(np.arange(*frame_spec))
+    meshes = []
+
+    for frame in frames:
+        locations = extract_tick_json.fn(data_tar, series_key, frame, "LOCATIONS")
+
+        for location in locations:
+            location_id = location["id"]
+
+            for region in regions:
+                voxels = [
+                    (z, y, x)
+                    for x, y, z in get_location_voxels.fn(
+                        location, region if region != "DEFAULT" else None
+                    )
+                ]
+                array = make_mesh_array(voxels)
+                mesh = make_mesh_object(array)
+
+                meshes.append((frame, location_id, region, mesh))
+
+    return meshes
+
+
+def make_mesh_array(voxels: list[tuple[int, int, int]]) -> np.ndarray:
+    mins = np.min(voxels, axis=0)
+    maxs = np.max(voxels, axis=0)
+    height, width, length = np.subtract(maxs, mins) + 3
+    array = np.zeros((height, width, length), dtype=np.uint8)
+
+    voxels_transposed = [voxel - mins + 1 for voxel in voxels]
+    array[tuple(np.transpose(voxels_transposed))] = 7
+
+    # Get set of zero neighbors for all voxels.
+    offsets = [(-1, 0, 0), (1, 0, 0), (0, -1, 0), (0, 1, 0), (0, 0, -1), (0, 0, 1)]
+    neighbors = {
+        (z + i, y + j, x + k)
+        for z, y, x in voxels_transposed
+        for k, j, i in offsets
+        if array[z + k, y + j, x + i] == 0
+    }
+
+    # Remove invalid neighbors on borders.
+    neighbors = {
+        (z, y, x)
+        for z, y, x in neighbors
+        if x != 0 and y != 0 and z != 0 and x != length - 1 and y != width - 1 and z != height - 1
+    }
+
+    # Smooth array levels based on neighbor counts.
+    for z, y, x in neighbors:
+        array[z, y, x] = sum(array[z + k, y + j, x + i] == 7 for k, j, i in offsets) + 1
+
+    return array
+
+
+def make_mesh_object(array: np.ndarray) -> str:
+    verts, faces, normals, _ = measure.marching_cubes(array, level=3, allow_degenerate=False)
+    mesh = ""
+    faces = faces + 1
+
+    for item in verts:
+        mesh += f"v {item[0]} {item[1]} {item[2]}\n"
+
+    for item in normals:
+        mesh += f"vn {item[0]} {item[1]} {item[2]}\n"
+
+    for item in faces:
+        mesh += f"f {item[2]}//{item[2]} {item[1]}//{item[1]} {item[0]}//{item[0]}\n"
+
+    return mesh
diff --git a/src/arcade_collection/output/convert_to_simularium.py b/src/arcade_collection/output/convert_to_simularium.py
new file mode 100644
index 0000000..13d9df8
--- /dev/null
+++ b/src/arcade_collection/output/convert_to_simularium.py
@@ -0,0 +1,131 @@
+import tarfile
+
+import numpy as np
+from prefect import task
+from simulariumio import (
+    DISPLAY_TYPE,
+    AgentData,
+    CameraData,
+    DimensionData,
+    DisplayData,
+    MetaData,
+    ModelMetaData,
+    TrajectoryConverter,
+    TrajectoryData,
+    UnitData,
+)
+
+from arcade_collection.output.extract_tick_json import extract_tick_json
+
+
+@task
+def convert_to_simularium(
+    series_key: str,
+    cells_data_tar: tarfile.TarFile,
+    locations_data_tar: tarfile.TarFile,
+    frame_spec: tuple[int, int, int],
+    box: tuple[int, int, int],
+    ds: float,
+    dt: float,
+    phase_colors: dict[str, str],
+) -> str:
+    length, width, height = box
+    frames = list(np.arange(*frame_spec))
+
+    meta_data = get_meta_data(series_key, length, width, height, ds)
+    agent_data = get_agent_data(series_key, cells_data_tar, frames)
+    agent_data.display_data = get_display_data(phase_colors)
+
+    for index, frame in enumerate(frames):
+        agent_data.times[index] = float(frame) * dt
+        convert_cells_tar(agent_data, cells_data_tar, series_key, frame, index)
+        convert_locations_tar(
+            agent_data, locations_data_tar, series_key, frame, index, length, width, height, ds
+        )
+
+    return TrajectoryConverter(
+        TrajectoryData(
+            meta_data=meta_data,
+            agent_data=agent_data,
+            time_units=UnitData("hr"),
+            spatial_units=UnitData("um"),
+        )
+    ).to_JSON()
+
+
+def get_meta_data(series_key: str, length: int, width: int, height: int, ds: float) -> MetaData:
+    meta_data = MetaData(
+        box_size=np.array([length * ds, width * ds, height * ds]),
+        camera_defaults=CameraData(
+            position=np.array([10.0, 0.0, 200.0]),
+            look_at_position=np.array([10.0, 0.0, 0.0]),
+            fov_degrees=60.0,
+        ),
+        trajectory_title=f"ARCADE - {series_key}",
+        model_meta_data=ModelMetaData(
+            title="ARCADE",
+            version="3.0",
+            description=(f"Agent-based modeling framework ARCADE for {series_key}."),
+        ),
+    )
+
+    return meta_data
+
+
+def get_agent_data(series_key: str, cells_tar: tarfile.TarFile, frames: list[int]) -> AgentData:
+    total_frames = len(frames)
+
+    max_agents = 0
+    for frame in frames:
+        cells = extract_tick_json.fn(cells_tar, series_key, frame, "CELLS")
+        max_agents = max(max_agents, len(cells))
+
+    return AgentData.from_dimensions(DimensionData(total_frames, max_agents))
+
+
+def get_display_data(phase_colors: dict[str, str]) -> DisplayData:
+    display_data = {}
+
+    for phase, color in phase_colors.items():
+        display_data[phase] = DisplayData(name=phase, color=color, display_type=DISPLAY_TYPE.SPHERE)
+
+    return display_data
+
+
+def convert_cells_tar(
+    data: AgentData,
+    tar: tarfile.TarFile,
+    series_key: str,
+    frame: int,
+    index: int,
+) -> None:
+    cells = extract_tick_json.fn(tar, series_key, frame, "CELLS")
+    data.n_agents[index] = len(cells)
+
+    for i, cell in enumerate(cells):
+        data.unique_ids[index][i] = cell["id"]
+        data.types[index].append(cell["phase"])
+        data.radii[index][i] = (cell["voxels"] ** (1.0 / 3)) / 1.5
+
+
+def convert_locations_tar(
+    data: AgentData,
+    tar: tarfile.TarFile,
+    series_key: str,
+    frame: int,
+    index: int,
+    length: int,
+    width: int,
+    height: int,
+    ds: float,
+) -> None:
+    locations = extract_tick_json.fn(tar, series_key, frame, "LOCATIONS")
+
+    for i, location in enumerate(locations):
+        data.positions[index][i] = np.array(
+            [
+                (location["center"][0] - length / 2) * ds,
+                (width / 2 - location["center"][1]) * ds,
+                (location["center"][2] - height / 2) * ds,
+            ]
+        )

From 794f7adfa011d4329342df5b5c03a1a75f0c8283 Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Wed, 15 Feb 2023 18:05:12 -0500
Subject: [PATCH 05/48] Fix type hints (#19)

---
 .../input/convert_to_cells_file.py            | 40 +++++++++----------
 .../input/convert_to_locations_file.py        | 10 ++---
 .../input/generate_setup_file.py              | 14 +++----
 .../input/merge_region_samples.py             |  6 +--
 .../output/parse_cells_file.py                |  4 +-
 .../output/parse_locations_file.py            |  4 +-
 6 files changed, 38 insertions(+), 40 deletions(-)

diff --git a/src/arcade_collection/input/convert_to_cells_file.py b/src/arcade_collection/input/convert_to_cells_file.py
index 65593a1..e48cf56 100644
--- a/src/arcade_collection/input/convert_to_cells_file.py
+++ b/src/arcade_collection/input/convert_to_cells_file.py
@@ -1,5 +1,3 @@
-from typing import Dict, List, Tuple
-
 import pandas as pd
 from prefect import task
 
@@ -8,13 +6,13 @@
 def convert_to_cells_file(
     samples: pd.DataFrame,
     reference: pd.DataFrame,
-    volume_distributions: Dict[str, tuple[float, float]],
-    height_distributions: Dict[str, tuple[float, float]],
-    critical_volume_distributions: Dict[str, tuple[float, float]],
-    critical_height_distributions: Dict[str, tuple[float, float]],
-    state_thresholds: Dict[str, float],
-) -> List[Dict]:
-    cells: List[Dict] = []
+    volume_distributions: dict[str, tuple[float, float]],
+    height_distributions: dict[str, tuple[float, float]],
+    critical_volume_distributions: dict[str, tuple[float, float]],
+    critical_height_distributions: dict[str, tuple[float, float]],
+    state_thresholds: dict[str, float],
+) -> list[dict]:
+    cells: list[dict] = []
     samples_by_id = samples.groupby("id")
 
     for i, (cell_id, group) in enumerate(samples_by_id):
@@ -39,11 +37,11 @@ def convert_to_cell(
     cell_id: int,
     samples: pd.DataFrame,
     reference: dict,
-    volume_distributions: Dict[str, tuple[float, float]],
-    height_distributions: Dict[str, tuple[float, float]],
-    critical_volume_distributions: Dict[str, tuple[float, float]],
-    critical_height_distributions: Dict[str, tuple[float, float]],
-    state_thresholds: Dict[str, float],
+    volume_distributions: dict[str, tuple[float, float]],
+    height_distributions: dict[str, tuple[float, float]],
+    critical_volume_distributions: dict[str, tuple[float, float]],
+    critical_height_distributions: dict[str, tuple[float, float]],
+    state_thresholds: dict[str, float],
 ) -> dict:
     """
     Convert samples to ARCADE .CELLS json format.
@@ -121,10 +119,10 @@ def convert_to_cell_region(
     region: str,
     region_samples: pd.DataFrame,
     reference: dict,
-    volume_distributions: Dict[str, tuple[float, float]],
-    height_distributions: Dict[str, tuple[float, float]],
-    critical_volume_distributions: Dict[str, tuple[float, float]],
-    critical_height_distributions: Dict[str, tuple[float, float]],
+    volume_distributions: dict[str, tuple[float, float]],
+    height_distributions: dict[str, tuple[float, float]],
+    critical_volume_distributions: dict[str, tuple[float, float]],
+    critical_height_distributions: dict[str, tuple[float, float]],
 ) -> dict:
     region_volume = len(region_samples)
     region_height = region_samples.z.max() - region_samples.z.min()
@@ -151,7 +149,7 @@ def convert_to_cell_region(
 def get_cell_state(
     volume: float,
     critical_volume: float,
-    threshold_fractions: Dict[str, float],
+    threshold_fractions: dict[str, float],
 ) -> str:
     """
     Estimates cell state based on cell volume.
@@ -187,8 +185,8 @@ def get_cell_state(
 
 def convert_value_distribution(
     value: float,
-    source_distribution: Tuple[float, float],
-    target_distribution: Tuple[float, float],
+    source_distribution: tuple[float, float],
+    target_distribution: tuple[float, float],
 ) -> float:
     """
     Estimates target value based on source value and source and target distributions.
diff --git a/src/arcade_collection/input/convert_to_locations_file.py b/src/arcade_collection/input/convert_to_locations_file.py
index bd2ff8e..c1b97e9 100644
--- a/src/arcade_collection/input/convert_to_locations_file.py
+++ b/src/arcade_collection/input/convert_to_locations_file.py
@@ -1,12 +1,12 @@
-from typing import Dict, List, Optional, Tuple
+from typing import Optional
 
 import pandas as pd
 from prefect import task
 
 
 @task
-def convert_to_locations_file(samples: pd.DataFrame) -> List[Dict]:
-    locations: List[Dict] = []
+def convert_to_locations_file(samples: pd.DataFrame) -> list[dict]:
+    locations: list[dict] = []
     samples_by_id = samples.groupby("id")
 
     for i, (_, group) in enumerate(samples_by_id):
@@ -49,7 +49,7 @@ def convert_to_location(cell_id: int, samples: pd.DataFrame) -> dict:
     return location
 
 
-def get_center_voxel(samples: pd.DataFrame) -> Tuple[int, int, int]:
+def get_center_voxel(samples: pd.DataFrame) -> tuple[int, int, int]:
     """
     Gets coordinates of center voxel of samples.
 
@@ -72,7 +72,7 @@ def get_center_voxel(samples: pd.DataFrame) -> Tuple[int, int, int]:
 
 def get_location_voxels(
     samples: pd.DataFrame, region: Optional[str] = None
-) -> List[Tuple[int, int, int]]:
+) -> list[tuple[int, int, int]]:
     """
     Get list of voxel coordinates from samples dataframe.
 
diff --git a/src/arcade_collection/input/generate_setup_file.py b/src/arcade_collection/input/generate_setup_file.py
index 87a5713..b8ad602 100644
--- a/src/arcade_collection/input/generate_setup_file.py
+++ b/src/arcade_collection/input/generate_setup_file.py
@@ -1,5 +1,5 @@
 import xml.etree.ElementTree as ET
-from typing import List, Optional, Tuple
+from typing import Optional
 
 import numpy as np
 import pandas as pd
@@ -8,7 +8,7 @@
 
 @task
 def generate_setup_file(
-    samples: pd.DataFrame, margins: Tuple[int, int, int], potts_terms: List[str]
+    samples: pd.DataFrame, margins: tuple[int, int, int], potts_terms: list[str]
 ) -> str:
     init = len(samples["id"].unique())
     bounds = calculate_sample_bounds(samples, margins)
@@ -18,8 +18,8 @@ def generate_setup_file(
 
 
 def calculate_sample_bounds(
-    samples: pd.DataFrame, margins: Tuple[int, int, int]
-) -> Tuple[int, int, int]:
+    samples: pd.DataFrame, margins: tuple[int, int, int]
+) -> tuple[int, int, int]:
     """
     Calculate transformed sample bounds including margin.
 
@@ -46,9 +46,9 @@ def calculate_sample_bounds(
 
 def make_setup_file(
     init: int,
-    bounds: Tuple[int, int, int],
-    terms: List[str],
-    regions: Optional[List[str]] = None,
+    bounds: tuple[int, int, int],
+    terms: list[str],
+    regions: Optional[list[str]] = None,
 ) -> str:
     """
     Create ARCADE setup file.
diff --git a/src/arcade_collection/input/merge_region_samples.py b/src/arcade_collection/input/merge_region_samples.py
index 35c013d..4fc0c93 100644
--- a/src/arcade_collection/input/merge_region_samples.py
+++ b/src/arcade_collection/input/merge_region_samples.py
@@ -1,4 +1,4 @@
-from typing import Optional, Tuple
+from typing import Optional
 
 import numpy as np
 import pandas as pd
@@ -7,7 +7,7 @@
 
 @task
 def merge_region_samples(
-    samples: dict[str, pd.DataFrame], margins: Tuple[int, int, int]
+    samples: dict[str, pd.DataFrame], margins: tuple[int, int, int]
 ) -> pd.DataFrame:
     default_samples = samples["DEFAULT"]
     all_samples = tranform_sample_coordinates(default_samples, margins)
@@ -33,7 +33,7 @@ def merge_region_samples(
 
 def tranform_sample_coordinates(
     samples: pd.DataFrame,
-    margins: Tuple[int, int, int],
+    margins: tuple[int, int, int],
     reference: Optional[pd.DataFrame] = None,
 ) -> pd.DataFrame:
     """
diff --git a/src/arcade_collection/output/parse_cells_file.py b/src/arcade_collection/output/parse_cells_file.py
index 8d2634c..b83a33e 100644
--- a/src/arcade_collection/output/parse_cells_file.py
+++ b/src/arcade_collection/output/parse_cells_file.py
@@ -1,6 +1,6 @@
 import json
 import tarfile
-from typing import List, Union
+from typing import Union
 
 import pandas as pd
 from prefect import task
@@ -20,7 +20,7 @@
 
 @task
 def parse_cells_file(tar: tarfile.TarFile, regions: list[str]) -> pd.DataFrame:
-    all_cells: List[List[Union[str, int]]] = []
+    all_cells: list[list[Union[str, int]]] = []
 
     for member in tar.getmembers():
         timepoint = int(member.name.replace(".CELLS.json", "").split("_")[-1])
diff --git a/src/arcade_collection/output/parse_locations_file.py b/src/arcade_collection/output/parse_locations_file.py
index 5065d5b..fdd1c34 100644
--- a/src/arcade_collection/output/parse_locations_file.py
+++ b/src/arcade_collection/output/parse_locations_file.py
@@ -1,6 +1,6 @@
 import json
 import tarfile
-from typing import List, Union
+from typing import Union
 
 import numpy as np
 import pandas as pd
@@ -23,7 +23,7 @@
 
 @task
 def parse_locations_file(tar: tarfile.TarFile, regions: list[str]) -> pd.DataFrame:
-    all_locations: List[List[Union[str, int]]] = []
+    all_locations: list[list[Union[str, int]]] = []
 
     for member in tar.getmembers():
         timepoint = int(member.name.replace(".LOCATIONS.json", "").split("_")[-1])

From a76f4fbcde7c3df871924d04eb24cb5ee18c83ce Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Wed, 15 Feb 2023 18:08:51 -0500
Subject: [PATCH 06/48] Release v0.6.0 (#20)

Co-authored-by: jessicasyu <15913767+jessicasyu@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 14d0c44..0e87f3d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "arcade-collection"
-version = "0.5.0"
+version = "0.6.0"
 description = "Collection of tasks for working with ARCADE."
 authors = [
     "Jessica S. Yu <jesyu@uw.edu>"

From c822834687ba96be4fdb5f1d7f6a8c5e87d460f6 Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Wed, 22 Feb 2023 11:56:15 -0500
Subject: [PATCH 07/48] Upgrade prefect and update dependencies (#21)

---
 poetry.lock    | 2317 +++++++++++++++++++++++++-----------------------
 pyproject.toml |   16 +-
 2 files changed, 1204 insertions(+), 1129 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index adf72db..5abc82b 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,64 +1,22 @@
-[[package]]
-name = "aiofiles"
-version = "22.1.0"
-description = "File support for asyncio."
-category = "main"
-optional = false
-python-versions = ">=3.7,<4.0"
-
-[[package]]
-name = "aiohttp"
-version = "3.8.3"
-description = "Async http client/server framework (asyncio)"
-category = "main"
-optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-aiosignal = ">=1.1.2"
-async-timeout = ">=4.0.0a3,<5.0"
-attrs = ">=17.3.0"
-charset-normalizer = ">=2.0,<3.0"
-frozenlist = ">=1.1.1"
-multidict = ">=4.5,<7.0"
-yarl = ">=1.0,<2.0"
-
-[package.extras]
-speedups = ["Brotli", "aiodns", "cchardet"]
-
-[[package]]
-name = "aiosignal"
-version = "1.2.0"
-description = "aiosignal: a list of registered asynchronous callbacks"
-category = "main"
-optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-frozenlist = ">=1.1.0"
-
 [[package]]
 name = "aiosqlite"
-version = "0.17.0"
+version = "0.18.0"
 description = "asyncio bridge to the standard sqlite3 module"
 category = "main"
 optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-typing_extensions = ">=3.7.2"
+python-versions = ">=3.7"
 
 [[package]]
 name = "alabaster"
-version = "0.7.12"
+version = "0.7.13"
 description = "A configurable sidebar-enabled Sphinx theme"
 category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "alembic"
-version = "1.8.1"
+version = "1.9.4"
 description = "A database migration tool for SQLAlchemy."
 category = "main"
 optional = false
@@ -73,7 +31,7 @@ tz = ["python-dateutil"]
 
 [[package]]
 name = "anyio"
-version = "3.6.1"
+version = "3.6.2"
 description = "High level compatibility layer for multiple asynchronous event loop implementations"
 category = "main"
 optional = false
@@ -86,17 +44,18 @@ sniffio = ">=1.1"
 [package.extras]
 doc = ["packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
 test = ["contextlib2", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (<0.15)", "uvloop (>=0.15)"]
-trio = ["trio (>=0.16)"]
+trio = ["trio (>=0.16,<0.22)"]
 
 [[package]]
 name = "apprise"
-version = "1.1.0"
+version = "1.2.1"
 description = "Push Notifications that work with just about every platform!"
 category = "main"
 optional = false
 python-versions = ">=3.6"
 
 [package.dependencies]
+certifi = "*"
 click = ">=5.0"
 markdown = "*"
 PyYAML = "*"
@@ -105,18 +64,18 @@ requests-oauthlib = "*"
 
 [[package]]
 name = "asgi-lifespan"
-version = "1.0.1"
+version = "2.0.0"
 description = "Programmatic startup/shutdown of ASGI apps."
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
 sniffio = "*"
 
 [[package]]
 name = "astroid"
-version = "2.12.11"
+version = "2.14.2"
 description = "An abstract syntax tree for Python with inference support."
 category = "dev"
 optional = false
@@ -124,50 +83,44 @@ python-versions = ">=3.7.2"
 
 [package.dependencies]
 lazy-object-proxy = ">=1.4.0"
-typing-extensions = {version = ">=3.10", markers = "python_version < \"3.10\""}
+typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
 wrapt = [
     {version = ">=1.11,<2", markers = "python_version < \"3.11\""},
     {version = ">=1.14,<2", markers = "python_version >= \"3.11\""},
 ]
 
-[[package]]
-name = "async-timeout"
-version = "4.0.2"
-description = "Timeout context manager for asyncio programs"
-category = "main"
-optional = false
-python-versions = ">=3.6"
-
 [[package]]
 name = "asyncpg"
-version = "0.26.0"
+version = "0.27.0"
 description = "An asyncio PostgreSQL driver"
 category = "main"
 optional = false
-python-versions = ">=3.6.0"
+python-versions = ">=3.7.0"
 
 [package.extras]
-dev = ["Cython (>=0.29.24,<0.30.0)", "Sphinx (>=4.1.2,<4.2.0)", "flake8 (>=3.9.2,<3.10.0)", "pycodestyle (>=2.7.0,<2.8.0)", "pytest (>=6.0)", "sphinx-rtd-theme (>=0.5.2,<0.6.0)", "sphinxcontrib-asyncio (>=0.3.0,<0.4.0)", "uvloop (>=0.15.3)"]
+dev = ["Cython (>=0.29.24,<0.30.0)", "Sphinx (>=4.1.2,<4.2.0)", "flake8 (>=5.0.4,<5.1.0)", "pytest (>=6.0)", "sphinx-rtd-theme (>=0.5.2,<0.6.0)", "sphinxcontrib-asyncio (>=0.3.0,<0.4.0)", "uvloop (>=0.15.3)"]
 docs = ["Sphinx (>=4.1.2,<4.2.0)", "sphinx-rtd-theme (>=0.5.2,<0.6.0)", "sphinxcontrib-asyncio (>=0.3.0,<0.4.0)"]
-test = ["flake8 (>=3.9.2,<3.10.0)", "pycodestyle (>=2.7.0,<2.8.0)", "uvloop (>=0.15.3)"]
+test = ["flake8 (>=5.0.4,<5.1.0)", "uvloop (>=0.15.3)"]
 
 [[package]]
 name = "attrs"
-version = "22.1.0"
+version = "22.2.0"
 description = "Classes Without Boilerplate"
 category = "main"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
 
 [package.extras]
-dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"]
-docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"]
-tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "zope.interface"]
-tests_no_zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins"]
+cov = ["attrs[tests]", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"]
+dev = ["attrs[docs,tests]"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope.interface"]
+tests = ["attrs[tests-no-zope]", "zope.interface"]
+tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=0.971,<0.990)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+tests_no_zope = ["cloudpickle", "hypothesis", "mypy (>=0.971,<0.990)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
 
 [[package]]
 name = "Babel"
-version = "2.10.3"
+version = "2.11.0"
 description = "Internationalization utilities"
 category = "dev"
 optional = false
@@ -178,7 +131,7 @@ pytz = ">=2015.7"
 
 [[package]]
 name = "black"
-version = "22.10.0"
+version = "22.12.0"
 description = "The uncompromising code formatter."
 category = "dev"
 optional = false
@@ -200,7 +153,7 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "cachetools"
-version = "5.2.0"
+version = "5.3.0"
 description = "Extensible memoizing collections and decorators"
 category = "main"
 optional = false
@@ -208,7 +161,7 @@ python-versions = "~=3.7"
 
 [[package]]
 name = "certifi"
-version = "2022.9.24"
+version = "2022.12.7"
 description = "Python package for providing Mozilla's CA Bundle."
 category = "main"
 optional = false
@@ -227,14 +180,11 @@ pycparser = "*"
 
 [[package]]
 name = "charset-normalizer"
-version = "2.1.1"
+version = "3.0.1"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 category = "main"
 optional = false
-python-versions = ">=3.6.0"
-
-[package.extras]
-unicode_backport = ["unicodedata2"]
+python-versions = "*"
 
 [[package]]
 name = "click"
@@ -249,7 +199,7 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
 [[package]]
 name = "cloudpickle"
-version = "2.2.0"
+version = "2.2.1"
 description = "Extended pickling support for Python objects"
 category = "main"
 optional = false
@@ -257,26 +207,15 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "colorama"
-version = "0.4.5"
+version = "0.4.6"
 description = "Cross-platform colored terminal text."
 category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-
-[[package]]
-name = "commonmark"
-version = "0.9.1"
-description = "Python parser for the CommonMark Markdown spec"
-category = "main"
-optional = false
-python-versions = "*"
-
-[package.extras]
-test = ["flake8 (==3.7.8)", "hypothesis (==3.55.3)"]
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 
 [[package]]
 name = "coolname"
-version = "1.1.0"
+version = "2.2.0"
 description = "Random name and slug generator"
 category = "main"
 optional = false
@@ -284,7 +223,7 @@ python-versions = "*"
 
 [[package]]
 name = "coverage"
-version = "6.5.0"
+version = "7.1.0"
 description = "Code coverage measurement for Python"
 category = "dev"
 optional = false
@@ -298,7 +237,7 @@ toml = ["tomli"]
 
 [[package]]
 name = "croniter"
-version = "1.3.7"
+version = "1.3.8"
 description = "croniter provides iteration for datetime object with cron like format"
 category = "main"
 optional = false
@@ -309,7 +248,7 @@ python-dateutil = "*"
 
 [[package]]
 name = "cryptography"
-version = "38.0.1"
+version = "39.0.1"
 description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
 category = "main"
 optional = false
@@ -319,20 +258,41 @@ python-versions = ">=3.6"
 cffi = ">=1.12"
 
 [package.extras]
-docs = ["sphinx (>=1.6.5,!=1.8.0,!=3.1.0,!=3.1.1)", "sphinx-rtd-theme"]
+docs = ["sphinx (>=5.3.0)", "sphinx-rtd-theme (>=1.1.1)"]
 docstest = ["pyenchant (>=1.6.11)", "sphinxcontrib-spelling (>=4.0.1)", "twine (>=1.12.0)"]
-pep8test = ["black", "flake8", "flake8-import-order", "pep8-naming"]
+pep8test = ["black", "check-manifest", "mypy", "ruff", "types-pytz", "types-requests"]
 sdist = ["setuptools-rust (>=0.11.4)"]
 ssh = ["bcrypt (>=3.1.5)"]
-test = ["hypothesis (>=1.11.4,!=3.79.2)", "iso8601", "pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-subtests", "pytest-xdist", "pytz"]
+test = ["hypothesis (>=1.11.4,!=3.79.2)", "iso8601", "pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-shard (>=0.1.2)", "pytest-subtests", "pytest-xdist", "pytz"]
+test-randomorder = ["pytest-randomly"]
+tox = ["tox"]
+
+[[package]]
+name = "dateparser"
+version = "1.1.7"
+description = "Date parsing library designed to parse dates from HTML pages"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+python-dateutil = "*"
+pytz = "*"
+regex = "<2019.02.19 || >2019.02.19,<2021.8.27 || >2021.8.27"
+tzlocal = "*"
+
+[package.extras]
+calendars = ["convertdate", "hijri-converter"]
+fasttext = ["fasttext"]
+langdetect = ["langdetect"]
 
 [[package]]
 name = "dill"
-version = "0.3.5.1"
+version = "0.3.6"
 description = "serialize all of python"
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
+python-versions = ">=3.7"
 
 [package.extras]
 graph = ["objgraph (>=1.7.2)"]
@@ -347,7 +307,7 @@ python-versions = "*"
 
 [[package]]
 name = "docker"
-version = "6.0.0"
+version = "6.0.1"
 description = "A Python library for the Docker Engine API."
 category = "main"
 optional = false
@@ -365,7 +325,7 @@ ssh = ["paramiko (>=2.4.3)"]
 
 [[package]]
 name = "docutils"
-version = "0.17.1"
+version = "0.18.1"
 description = "Docutils -- Python Documentation Utilities"
 category = "dev"
 optional = false
@@ -373,7 +333,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [[package]]
 name = "exceptiongroup"
-version = "1.0.0"
+version = "1.1.0"
 description = "Backport of PEP 654 (exception groups)"
 category = "dev"
 optional = false
@@ -384,7 +344,7 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "fastapi"
-version = "0.85.0"
+version = "0.92.0"
 description = "FastAPI framework, high performance, easy to learn, fast to code, ready for production"
 category = "main"
 optional = false
@@ -392,37 +352,29 @@ python-versions = ">=3.7"
 
 [package.dependencies]
 pydantic = ">=1.6.2,<1.7 || >1.7,<1.7.1 || >1.7.1,<1.7.2 || >1.7.2,<1.7.3 || >1.7.3,<1.8 || >1.8,<1.8.1 || >1.8.1,<2.0.0"
-starlette = "0.20.4"
+starlette = ">=0.25.0,<0.26.0"
 
 [package.extras]
-all = ["email-validator (>=1.1.1,<2.0.0)", "itsdangerous (>=1.1.0,<3.0.0)", "jinja2 (>=2.11.2,<4.0.0)", "orjson (>=3.2.1,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "pyyaml (>=5.3.1,<7.0.0)", "requests (>=2.24.0,<3.0.0)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)", "uvicorn[standard] (>=0.12.0,<0.19.0)"]
-dev = ["autoflake (>=1.4.0,<2.0.0)", "flake8 (>=3.8.3,<6.0.0)", "pre-commit (>=2.17.0,<3.0.0)", "uvicorn[standard] (>=0.12.0,<0.19.0)"]
-doc = ["mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-markdownextradata-plugin (>=0.1.7,<0.3.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "pyyaml (>=5.3.1,<7.0.0)", "typer (>=0.4.1,<0.7.0)"]
-test = ["anyio[trio] (>=3.2.1,<4.0.0)", "black (==22.8.0)", "databases[sqlite] (>=0.3.2,<0.7.0)", "email-validator (>=1.1.1,<2.0.0)", "flake8 (>=3.8.3,<6.0.0)", "flask (>=1.1.2,<3.0.0)", "httpx (>=0.23.0,<0.24.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.971)", "orjson (>=3.2.1,<4.0.0)", "passlib[bcrypt] (>=1.7.2,<2.0.0)", "peewee (>=3.13.3,<4.0.0)", "pytest (>=7.1.3,<8.0.0)", "pytest-cov (>=2.12.0,<4.0.0)", "python-jose[cryptography] (>=3.3.0,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "pyyaml (>=5.3.1,<7.0.0)", "requests (>=2.24.0,<3.0.0)", "sqlalchemy (>=1.3.18,<1.5.0)", "types-orjson (==3.6.2)", "types-ujson (==5.4.0)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)"]
+all = ["email-validator (>=1.1.1)", "httpx (>=0.23.0)", "itsdangerous (>=1.1.0)", "jinja2 (>=2.11.2)", "orjson (>=3.2.1)", "python-multipart (>=0.0.5)", "pyyaml (>=5.3.1)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0)", "uvicorn[standard] (>=0.12.0)"]
+dev = ["pre-commit (>=2.17.0,<3.0.0)", "ruff (==0.0.138)", "uvicorn[standard] (>=0.12.0,<0.21.0)"]
+doc = ["mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-markdownextradata-plugin (>=0.1.7,<0.3.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "pyyaml (>=5.3.1,<7.0.0)", "typer[all] (>=0.6.1,<0.8.0)"]
+test = ["anyio[trio] (>=3.2.1,<4.0.0)", "black (==22.10.0)", "coverage[toml] (>=6.5.0,<8.0)", "databases[sqlite] (>=0.3.2,<0.7.0)", "email-validator (>=1.1.1,<2.0.0)", "flask (>=1.1.2,<3.0.0)", "httpx (>=0.23.0,<0.24.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.982)", "orjson (>=3.2.1,<4.0.0)", "passlib[bcrypt] (>=1.7.2,<2.0.0)", "peewee (>=3.13.3,<4.0.0)", "pytest (>=7.1.3,<8.0.0)", "python-jose[cryptography] (>=3.3.0,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "pyyaml (>=5.3.1,<7.0.0)", "ruff (==0.0.138)", "sqlalchemy (>=1.3.18,<1.4.43)", "types-orjson (==3.6.2)", "types-ujson (==5.6.0.0)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)"]
 
 [[package]]
 name = "filelock"
-version = "3.8.0"
+version = "3.9.0"
 description = "A platform independent file lock."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-docs = ["furo (>=2022.6.21)", "sphinx (>=5.1.1)", "sphinx-autodoc-typehints (>=1.19.1)"]
-testing = ["covdefaults (>=2.2)", "coverage (>=6.4.2)", "pytest (>=7.1.2)", "pytest-cov (>=3)", "pytest-timeout (>=2.1)"]
-
-[[package]]
-name = "frozenlist"
-version = "1.3.1"
-description = "A list-like structure which implements collections.abc.MutableSequence"
-category = "main"
-optional = false
-python-versions = ">=3.7"
+docs = ["furo (>=2022.12.7)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.5)"]
+testing = ["covdefaults (>=2.2.2)", "coverage (>=7.0.1)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-timeout (>=2.1)"]
 
 [[package]]
 name = "fsspec"
-version = "2022.10.0"
+version = "2023.1.0"
 description = "File-system specification"
 category = "main"
 optional = false
@@ -453,7 +405,7 @@ tqdm = ["tqdm"]
 
 [[package]]
 name = "google-auth"
-version = "2.12.0"
+version = "2.16.1"
 description = "Google Authentication Library"
 category = "main"
 optional = false
@@ -468,38 +420,43 @@ six = ">=1.9.0"
 [package.extras]
 aiohttp = ["aiohttp (>=3.6.2,<4.0.0dev)", "requests (>=2.20.0,<3.0.0dev)"]
 enterprise_cert = ["cryptography (==36.0.2)", "pyopenssl (==22.0.0)"]
-pyopenssl = ["pyopenssl (>=20.0.0)"]
+pyopenssl = ["cryptography (>=38.0.3)", "pyopenssl (>=20.0.0)"]
 reauth = ["pyu2f (>=0.1.5)"]
+requests = ["requests (>=2.20.0,<3.0.0dev)"]
 
 [[package]]
 name = "greenlet"
-version = "1.1.3.post0"
+version = "2.0.2"
 description = "Lightweight in-process concurrent programming"
 category = "main"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
 
 [package.extras]
-docs = ["Sphinx"]
+docs = ["Sphinx", "docutils (<0.18)"]
+test = ["objgraph", "psutil"]
 
 [[package]]
 name = "griffe"
-version = "0.22.2"
+version = "0.25.5"
 description = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API."
 category = "main"
 optional = false
 python-versions = ">=3.7"
 
+[package.dependencies]
+colorama = ">=0.4"
+
 [package.extras]
 async = ["aiofiles (>=0.7,<1.0)"]
 
 [[package]]
 name = "h11"
-version = "0.12.0"
+version = "0.14.0"
 description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [[package]]
 name = "h2"
@@ -523,16 +480,16 @@ python-versions = ">=3.6.1"
 
 [[package]]
 name = "httpcore"
-version = "0.15.0"
+version = "0.16.3"
 description = "A minimal low-level HTTP client."
 category = "main"
 optional = false
 python-versions = ">=3.7"
 
 [package.dependencies]
-anyio = ">=3.0.0,<4.0.0"
+anyio = ">=3.0,<5.0"
 certifi = "*"
-h11 = ">=0.11,<0.13"
+h11 = ">=0.13,<0.15"
 sniffio = ">=1.0.0,<2.0.0"
 
 [package.extras]
@@ -541,7 +498,7 @@ socks = ["socksio (>=1.0.0,<2.0.0)"]
 
 [[package]]
 name = "httpx"
-version = "0.23.0"
+version = "0.23.3"
 description = "The next generation HTTP client."
 category = "main"
 optional = false
@@ -550,7 +507,7 @@ python-versions = ">=3.7"
 [package.dependencies]
 certifi = "*"
 h2 = {version = ">=3,<5", optional = true, markers = "extra == \"http2\""}
-httpcore = ">=0.15.0,<0.16.0"
+httpcore = ">=0.15.0,<0.17.0"
 rfc3986 = {version = ">=1.3,<2", extras = ["idna2008"]}
 sniffio = "*"
 
@@ -615,7 +572,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "importlib-metadata"
-version = "5.0.0"
+version = "6.0.0"
 description = "Read metadata from Python packages"
 category = "main"
 optional = false
@@ -625,17 +582,17 @@ python-versions = ">=3.7"
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
 testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"]
 
 [[package]]
 name = "iniconfig"
-version = "1.1.1"
-description = "iniconfig: brain-dead simple config-ini parsing"
+version = "2.0.0"
+description = "brain-dead simple config-ini parsing"
 category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7"
 
 [[package]]
 name = "isort"
@@ -655,7 +612,7 @@ requirements-deprecated-finder = ["pip-api", "pipreqs"]
 name = "Jinja2"
 version = "3.1.2"
 description = "A very fast and expressive template engine."
-category = "dev"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 
@@ -684,9 +641,25 @@ category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
+[[package]]
+name = "jsonschema"
+version = "4.17.3"
+description = "An implementation of JSON Schema validation for Python"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+attrs = ">=17.4.0"
+pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2"
+
+[package.extras]
+format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
+format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]
+
 [[package]]
 name = "kubernetes"
-version = "24.2.0"
+version = "26.1.0"
 description = "Kubernetes python client"
 category = "main"
 optional = false
@@ -709,15 +682,15 @@ adal = ["adal (>=1.0.2)"]
 
 [[package]]
 name = "lazy-object-proxy"
-version = "1.7.1"
+version = "1.9.0"
 description = "A fast and thorough lazy object proxy."
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [[package]]
 name = "Mako"
-version = "1.2.3"
+version = "1.2.4"
 description = "A super-fast templating language that borrows the best ideas from the existing templating languages."
 category = "main"
 optional = false
@@ -745,9 +718,30 @@ importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
 [package.extras]
 testing = ["coverage", "pyyaml"]
 
+[[package]]
+name = "markdown-it-py"
+version = "2.2.0"
+description = "Python port of markdown-it. Markdown parsing, done right!"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+mdurl = ">=0.1,<1.0"
+
+[package.extras]
+benchmarking = ["psutil", "pytest", "pytest-benchmark"]
+code_style = ["pre-commit (>=3.0,<4.0)"]
+compare = ["commonmark (>=0.9,<1.0)", "markdown (>=3.4,<4.0)", "mistletoe (>=1.0,<2.0)", "mistune (>=2.0,<3.0)", "panflute (>=2.3,<3.0)"]
+linkify = ["linkify-it-py (>=1,<3)"]
+plugins = ["mdit-py-plugins"]
+profiling = ["gprof2dot"]
+rtd = ["attrs", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
+testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
+
 [[package]]
 name = "MarkupSafe"
-version = "2.1.1"
+version = "2.1.2"
 description = "Safely add untrusted strings to HTML/XML markup."
 category = "main"
 optional = false
@@ -761,22 +755,22 @@ category = "dev"
 optional = false
 python-versions = ">=3.6"
 
+[[package]]
+name = "mdurl"
+version = "0.1.2"
+description = "Markdown URL utilities"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
 [[package]]
 name = "mistune"
-version = "2.0.4"
+version = "2.0.5"
 description = "A sane Markdown parser with useful plugins and renderers"
 category = "dev"
 optional = false
 python-versions = "*"
 
-[[package]]
-name = "multidict"
-version = "6.0.2"
-description = "multidict implementation"
-category = "main"
-optional = false
-python-versions = ">=3.7"
-
 [[package]]
 name = "mypy"
 version = "0.971"
@@ -797,11 +791,11 @@ reports = ["lxml"]
 
 [[package]]
 name = "mypy-extensions"
-version = "0.4.3"
-description = "Experimental type system extensions for programs checked with the mypy typechecker."
+version = "1.0.0"
+description = "Type system extensions for programs checked with the mypy type checker."
 category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.5"
 
 [[package]]
 name = "networkx"
@@ -820,15 +814,15 @@ test = ["codecov (>=2.1)", "pytest (>=7.2)", "pytest-cov (>=4.0)"]
 
 [[package]]
 name = "numpy"
-version = "1.23.4"
-description = "NumPy is the fundamental package for array computing with Python."
+version = "1.24.2"
+description = "Fundamental package for array computing in Python"
 category = "main"
 optional = false
 python-versions = ">=3.8"
 
 [[package]]
 name = "oauthlib"
-version = "3.2.1"
+version = "3.2.2"
 description = "A generic, spec-compliant, thorough implementation of the OAuth request-signing logic"
 category = "main"
 optional = false
@@ -841,7 +835,7 @@ signedtoken = ["cryptography (>=3.0.0)", "pyjwt (>=2.0.0,<3)"]
 
 [[package]]
 name = "orjson"
-version = "3.8.0"
+version = "3.8.6"
 description = "Fast, correct Python JSON library supporting dataclasses, datetimes, and numpy"
 category = "main"
 optional = false
@@ -849,18 +843,15 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "packaging"
-version = "21.3"
+version = "23.0"
 description = "Core utilities for Python packages"
 category = "main"
 optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
+python-versions = ">=3.7"
 
 [[package]]
 name = "pandas"
-version = "1.5.1"
+version = "1.5.3"
 description = "Powerful data structures for data analysis, time series, and statistics"
 category = "main"
 optional = false
@@ -868,8 +859,9 @@ python-versions = ">=3.8"
 
 [package.dependencies]
 numpy = [
-    {version = ">=1.21.0", markers = "python_version >= \"3.10\""},
     {version = ">=1.20.3", markers = "python_version < \"3.10\""},
+    {version = ">=1.21.0", markers = "python_version >= \"3.10\""},
+    {version = ">=1.23.2", markers = "python_version >= \"3.11\""},
 ]
 python-dateutil = ">=2.8.1"
 pytz = ">=2020.1"
@@ -879,7 +871,7 @@ test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"]
 
 [[package]]
 name = "pathspec"
-version = "0.10.1"
+version = "0.11.0"
 description = "Utility library for gitignore style pattern matching of file paths."
 category = "main"
 optional = false
@@ -928,15 +920,15 @@ xarray = ["xarray"]
 
 [[package]]
 name = "platformdirs"
-version = "2.5.2"
-description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+version = "3.0.0"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx (>=4)", "sphinx-autodoc-typehints (>=1.12)"]
-test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"]
+docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.22,!=1.23.4)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest (>=7.2.1)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"]
 
 [[package]]
 name = "pluggy"
@@ -952,19 +944,17 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "prefect"
-version = "2.6.3"
+version = "2.8.2"
 description = "Workflow orchestration and management."
 category = "main"
 optional = false
 python-versions = ">=3.7"
 
 [package.dependencies]
-aiofiles = ">=0.7.0"
-aiohttp = ">=3.8.1"
 aiosqlite = ">=0.17.0"
 alembic = ">=1.7.5"
 anyio = ">=3.4.0"
-apprise = ">=1.0.0"
+apprise = ">=1.1.0"
 asgi-lifespan = ">=1.0"
 asyncpg = ">=0.23"
 click = ">=8.0,<8.2"
@@ -972,13 +962,16 @@ cloudpickle = ">=2.0"
 coolname = ">=1.0.4"
 croniter = ">=1.0.12"
 cryptography = ">=36.0.1"
+dateparser = ">=1.1.1"
 docker = ">=4.0"
 fastapi = ">=0.70"
 fsspec = ">=2022.5.0"
 griffe = ">=0.20.0"
-httpx = {version = ">=0.23", extras = ["http2"]}
+httpx = {version = ">=0.23,<0.23.2 || >0.23.2", extras = ["http2"]}
 importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
+jinja2 = ">=3.0.0"
 jsonpatch = ">=1.32"
+jsonschema = ">=3.2.0,<5.0.0"
 kubernetes = ">=24.2.0"
 orjson = ">=3.7"
 packaging = ">=21.3"
@@ -988,16 +981,17 @@ pydantic = ">=1.10.0"
 python-slugify = ">=5.0"
 pytz = ">=2021.1"
 pyyaml = ">=5.4.1"
-readchar = ">=3.0.6"
+readchar = ">=4.0.0"
 rich = ">=11.0"
-sqlalchemy = {version = ">=1.4.20,<1.4.33 || >1.4.33", extras = ["asyncio"]}
+sqlalchemy = {version = ">=1.4.22,<1.4.33 || >1.4.33,<2.0", extras = ["asyncio"]}
 toml = ">=0.10.0"
-typer = ">=0.4.1"
+typer = ">=0.4.2"
 typing-extensions = ">=4.1.0"
 uvicorn = ">=0.14.0"
+websockets = ">=10.4"
 
 [package.extras]
-dev = ["autoflake8", "cairosvg", "flake8", "flaky", "ipython", "jinja2", "mkdocs", "mkdocs-gen-files", "mkdocs-material", "mkdocstrings-python-legacy", "mock", "moto", "mypy", "pillow", "pre-commit", "pytest (>7)", "pytest-asyncio (>=0.18.2)", "pytest-cov", "pytest-env", "pytest-timeout", "pytest-xdist", "pytkdocs (>=0.14.2)", "pyyaml", "requests", "respx", "setuptools (!=60.9.0)", "virtualenv", "watchfiles"]
+dev = ["autoflake8", "cairosvg", "flake8", "flaky", "ipython", "jinja2", "mike", "mkdocs", "mkdocs-gen-files", "mkdocs-material", "mkdocstrings-python", "mock", "moto", "mypy", "numpy", "pillow", "pre-commit", "pytest (>7)", "pytest-asyncio (>=0.18.2)", "pytest-benchmark", "pytest-cov", "pytest-env", "pytest-timeout", "pytest-xdist", "pytkdocs (>=0.14.2)", "pyyaml", "requests", "respx", "setuptools (!=60.9.0)", "virtualenv", "watchfiles"]
 
 [[package]]
 name = "py"
@@ -1036,14 +1030,14 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "pydantic"
-version = "1.10.2"
+version = "1.10.5"
 description = "Data validation and settings management using python type hints"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 
 [package.dependencies]
-typing-extensions = ">=4.1.0"
+typing-extensions = ">=4.2.0"
 
 [package.extras]
 dotenv = ["python-dotenv (>=0.10.4)"]
@@ -1051,7 +1045,7 @@ email = ["email-validator (>=1.0.3)"]
 
 [[package]]
 name = "Pygments"
-version = "2.13.0"
+version = "2.14.0"
 description = "Pygments is a syntax highlighting package written in Python."
 category = "main"
 optional = false
@@ -1062,16 +1056,19 @@ plugins = ["importlib-metadata"]
 
 [[package]]
 name = "pylint"
-version = "2.15.4"
+version = "2.16.2"
 description = "python code static checker"
 category = "dev"
 optional = false
 python-versions = ">=3.7.2"
 
 [package.dependencies]
-astroid = ">=2.12.11,<=2.14.0-dev0"
+astroid = ">=2.14.2,<=2.16.0-dev0"
 colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
-dill = ">=0.2"
+dill = [
+    {version = ">=0.2", markers = "python_version < \"3.11\""},
+    {version = ">=0.3.6", markers = "python_version >= \"3.11\""},
+]
 isort = ">=4.2.5,<6"
 mccabe = ">=0.6,<0.8"
 platformdirs = ">=2.2.0"
@@ -1084,19 +1081,16 @@ spelling = ["pyenchant (>=3.2,<4.0)"]
 testutils = ["gitpython (>3)"]
 
 [[package]]
-name = "pyparsing"
-version = "3.0.9"
-description = "pyparsing module - Classes and methods to define and execute parsing grammars"
+name = "pyrsistent"
+version = "0.19.3"
+description = "Persistent/Functional/Immutable data structures"
 category = "main"
 optional = false
-python-versions = ">=3.6.8"
-
-[package.extras]
-diagrams = ["jinja2", "railroad-diagrams"]
+python-versions = ">=3.7"
 
 [[package]]
 name = "pytest"
-version = "7.2.0"
+version = "7.2.1"
 description = "pytest: simple powerful testing with Python"
 category = "dev"
 optional = false
@@ -1153,11 +1147,11 @@ six = ">=1.5"
 
 [[package]]
 name = "python-slugify"
-version = "6.1.2"
+version = "8.0.0"
 description = "A Python slugify application that also handles Unicode"
 category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+python-versions = ">=3.7"
 
 [package.dependencies]
 text-unidecode = ">=1.3"
@@ -1167,12 +1161,23 @@ unidecode = ["Unidecode (>=1.1.1)"]
 
 [[package]]
 name = "pytz"
-version = "2022.4"
+version = "2022.7.1"
 description = "World timezone definitions, modern and historical"
 category = "main"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "pytz-deprecation-shim"
+version = "0.1.0.post0"
+description = "Shims to make deprecation of pytz easier"
+category = "main"
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
+
+[package.dependencies]
+tzdata = {version = "*", markers = "python_version >= \"3.6\""}
+
 [[package]]
 name = "pytzdata"
 version = "2020.1"
@@ -1194,7 +1199,7 @@ numpy = ">=1.17.3"
 
 [[package]]
 name = "pywin32"
-version = "304"
+version = "305"
 description = "Python for Window Extensions"
 category = "main"
 optional = false
@@ -1219,9 +1224,17 @@ python-versions = ">=3.6"
 [package.dependencies]
 setuptools = ">=41.0"
 
+[[package]]
+name = "regex"
+version = "2022.10.31"
+description = "Alternative regular expression module, to replace re."
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
 [[package]]
 name = "requests"
-version = "2.28.1"
+version = "2.28.2"
 description = "Python HTTP for Humans."
 category = "main"
 optional = false
@@ -1229,7 +1242,7 @@ python-versions = ">=3.7, <4"
 
 [package.dependencies]
 certifi = ">=2017.4.17"
-charset-normalizer = ">=2,<3"
+charset-normalizer = ">=2,<4"
 idna = ">=2.5,<4"
 urllib3 = ">=1.21.1,<1.27"
 
@@ -1268,18 +1281,18 @@ idna2008 = ["idna"]
 
 [[package]]
 name = "rich"
-version = "12.6.0"
+version = "13.3.1"
 description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
 category = "main"
 optional = false
-python-versions = ">=3.6.3,<4.0.0"
+python-versions = ">=3.7.0"
 
 [package.dependencies]
-commonmark = ">=0.9.0,<0.10.0"
-pygments = ">=2.6.0,<3.0.0"
+markdown-it-py = ">=2.1.0,<3.0.0"
+pygments = ">=2.14.0,<3.0.0"
 
 [package.extras]
-jupyter = ["ipywidgets (>=7.5.1,<8.0.0)"]
+jupyter = ["ipywidgets (>=7.5.1,<9)"]
 
 [[package]]
 name = "rsa"
@@ -1334,20 +1347,20 @@ test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "sciki
 
 [[package]]
 name = "setuptools"
-version = "65.4.1"
+version = "67.4.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mock", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
 testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
 name = "simulariumio"
-version = "1.7.0"
+version = "1.7.1"
 description = "Python package that converts simulation outputs to the format consumed by the Simularium viewer website"
 category = "main"
 optional = false
@@ -1396,7 +1409,7 @@ python-versions = "*"
 
 [[package]]
 name = "Sphinx"
-version = "5.2.3"
+version = "5.3.0"
 description = "Python documentation generator"
 category = "dev"
 optional = false
@@ -1441,26 +1454,27 @@ pygments = ">=2.8"
 
 [[package]]
 name = "sphinx-rtd-theme"
-version = "1.0.0"
+version = "1.2.0"
 description = "Read the Docs theme for Sphinx"
 category = "dev"
 optional = false
-python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
 
 [package.dependencies]
-docutils = "<0.18"
-sphinx = ">=1.6"
+docutils = "<0.19"
+sphinx = ">=1.6,<7"
+sphinxcontrib-jquery = {version = ">=2.0.0,<3.0.0 || >3.0.0", markers = "python_version > \"3\""}
 
 [package.extras]
-dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client"]
+dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"]
 
 [[package]]
 name = "sphinxcontrib-applehelp"
-version = "1.0.2"
-description = "sphinxcontrib-applehelp is a sphinx extension which outputs Apple help books"
+version = "1.0.4"
+description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
 category = "dev"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.8"
 
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
@@ -1480,16 +1494,27 @@ test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-htmlhelp"
-version = "2.0.0"
+version = "2.0.1"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
 test = ["html5lib", "pytest"]
 
+[[package]]
+name = "sphinxcontrib.jquery"
+version = "2.0.0"
+description = "Extension to include jQuery on newer Sphinx releases"
+category = "dev"
+optional = false
+python-versions = ">=2.7"
+
+[package.dependencies]
+setuptools = "*"
+
 [[package]]
 name = "sphinxcontrib-jsmath"
 version = "1.0.1"
@@ -1527,7 +1552,7 @@ test = ["pytest"]
 
 [[package]]
 name = "SQLAlchemy"
-version = "1.4.41"
+version = "1.4.46"
 description = "Database Abstraction Library"
 category = "main"
 optional = false
@@ -1559,7 +1584,7 @@ sqlcipher = ["sqlcipher3_binary"]
 
 [[package]]
 name = "starlette"
-version = "0.20.4"
+version = "0.25.0"
 description = "The little ASGI library that shines."
 category = "main"
 optional = false
@@ -1570,7 +1595,7 @@ anyio = ">=3.4.0,<5"
 typing-extensions = {version = ">=3.10.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
-full = ["itsdangerous", "jinja2", "python-multipart", "pyyaml", "requests"]
+full = ["httpx (>=0.22.0)", "itsdangerous", "jinja2", "python-multipart", "pyyaml"]
 
 [[package]]
 name = "text-unidecode"
@@ -1612,15 +1637,15 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "tomlkit"
-version = "0.11.5"
+version = "0.11.6"
 description = "Style preserving TOML library"
 category = "dev"
 optional = false
-python-versions = ">=3.6,<4.0"
+python-versions = ">=3.6"
 
 [[package]]
 name = "tox"
-version = "3.26.0"
+version = "3.28.0"
 description = "tox is a generic virtualenv management and test command line tool"
 category = "dev"
 optional = false
@@ -1642,7 +1667,7 @@ testing = ["flaky (>=3.4.0)", "freezegun (>=0.3.11)", "pathlib2 (>=2.3.3)", "psu
 
 [[package]]
 name = "typer"
-version = "0.6.1"
+version = "0.7.0"
 description = "Typer, build great CLIs. Easy to code. Based on Python type hints."
 category = "main"
 optional = false
@@ -1654,24 +1679,48 @@ click = ">=7.1.1,<9.0.0"
 [package.extras]
 all = ["colorama (>=0.4.3,<0.5.0)", "rich (>=10.11.0,<13.0.0)", "shellingham (>=1.3.0,<2.0.0)"]
 dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "pre-commit (>=2.17.0,<3.0.0)"]
-doc = ["mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)"]
-test = ["black (>=22.3.0,<23.0.0)", "coverage (>=5.2,<6.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.910)", "pytest (>=4.4.0,<5.4.0)", "pytest-cov (>=2.10.0,<3.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "pytest-xdist (>=1.32.0,<2.0.0)", "rich (>=10.11.0,<13.0.0)", "shellingham (>=1.3.0,<2.0.0)"]
+doc = ["cairosvg (>=2.5.2,<3.0.0)", "mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "pillow (>=9.3.0,<10.0.0)"]
+test = ["black (>=22.3.0,<23.0.0)", "coverage (>=6.2,<7.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.910)", "pytest (>=4.4.0,<8.0.0)", "pytest-cov (>=2.10.0,<5.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "pytest-xdist (>=1.32.0,<4.0.0)", "rich (>=10.11.0,<13.0.0)", "shellingham (>=1.3.0,<2.0.0)"]
 
 [[package]]
 name = "typing-extensions"
-version = "4.4.0"
+version = "4.5.0"
 description = "Backported and Experimental Type Hints for Python 3.7+"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 
+[[package]]
+name = "tzdata"
+version = "2022.7"
+description = "Provider of IANA time zone data"
+category = "main"
+optional = false
+python-versions = ">=2"
+
+[[package]]
+name = "tzlocal"
+version = "4.2"
+description = "tzinfo object for the local timezone"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+pytz-deprecation-shim = "*"
+tzdata = {version = "*", markers = "platform_system == \"Windows\""}
+
+[package.extras]
+devenv = ["black", "pyroma", "pytest-cov", "zest.releaser"]
+test = ["pytest (>=4.3)", "pytest-mock (>=3.3)"]
+
 [[package]]
 name = "urllib3"
-version = "1.26.12"
+version = "1.26.14"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, <4"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 
 [package.extras]
 brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
@@ -1680,7 +1729,7 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [[package]]
 name = "uvicorn"
-version = "0.18.3"
+version = "0.20.0"
 description = "The lightning-fast ASGI server."
 category = "main"
 optional = false
@@ -1691,28 +1740,28 @@ click = ">=7.0"
 h11 = ">=0.8"
 
 [package.extras]
-standard = ["colorama (>=0.4)", "httptools (>=0.4.0)", "python-dotenv (>=0.13)", "pyyaml (>=5.1)", "uvloop (>=0.14.0,!=0.15.0,!=0.15.1)", "watchfiles (>=0.13)", "websockets (>=10.0)"]
+standard = ["colorama (>=0.4)", "httptools (>=0.5.0)", "python-dotenv (>=0.13)", "pyyaml (>=5.1)", "uvloop (>=0.14.0,!=0.15.0,!=0.15.1)", "watchfiles (>=0.13)", "websockets (>=10.4)"]
 
 [[package]]
 name = "virtualenv"
-version = "20.16.5"
+version = "20.19.0"
 description = "Virtual Python Environment builder"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
-distlib = ">=0.3.5,<1"
+distlib = ">=0.3.6,<1"
 filelock = ">=3.4.1,<4"
-platformdirs = ">=2.4,<3"
+platformdirs = ">=2.4,<4"
 
 [package.extras]
-docs = ["proselint (>=0.13)", "sphinx (>=5.1.1)", "sphinx-argparse (>=0.3.1)", "sphinx-rtd-theme (>=1)", "towncrier (>=21.9)"]
-testing = ["coverage (>=6.2)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=21.3)", "pytest (>=7.0.1)", "pytest-env (>=0.6.2)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.6.1)", "pytest-randomly (>=3.10.3)", "pytest-timeout (>=2.1)"]
+docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=22.12)"]
+test = ["covdefaults (>=2.2.2)", "coverage (>=7.1)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23)", "pytest (>=7.2.1)", "pytest-env (>=0.8.1)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.10)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)"]
 
 [[package]]
 name = "websocket-client"
-version = "1.4.1"
+version = "1.5.1"
 description = "WebSocket client for Python with low level API options"
 category = "main"
 optional = false
@@ -1723,6 +1772,14 @@ docs = ["Sphinx (>=3.4)", "sphinx-rtd-theme (>=0.5)"]
 optional = ["python-socks", "wsaccel"]
 test = ["websockets"]
 
+[[package]]
+name = "websockets"
+version = "10.4"
+description = "An implementation of the WebSocket Protocol (RFC 6455 & 7692)"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
 [[package]]
 name = "wrapt"
 version = "1.14.1"
@@ -1731,222 +1788,119 @@ category = "dev"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
 
-[[package]]
-name = "yarl"
-version = "1.8.1"
-description = "Yet another URL library"
-category = "main"
-optional = false
-python-versions = ">=3.7"
-
-[package.dependencies]
-idna = ">=2.0"
-multidict = ">=4.0"
-
 [[package]]
 name = "zipp"
-version = "3.9.0"
+version = "3.14.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
 
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.9"
-content-hash = "a2e69865a2ef49bf3e5466938f802e8b09c06e1808dbc684cbe825b2c9456d47"
+content-hash = "72b2c36c99e14c2dbab696e46690e7de070ef1940727e9d33428e4a632f981e2"
 
 [metadata.files]
-aiofiles = [
-    {file = "aiofiles-22.1.0-py3-none-any.whl", hash = "sha256:1142fa8e80dbae46bb6339573ad4c8c0841358f79c6eb50a493dceca14621bad"},
-    {file = "aiofiles-22.1.0.tar.gz", hash = "sha256:9107f1ca0b2a5553987a94a3c9959fe5b491fdf731389aa5b7b1bd0733e32de6"},
-]
-aiohttp = [
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-    {file = "yarl-1.8.1.tar.gz", hash = "sha256:af887845b8c2e060eb5605ff72b6f2dd2aab7a761379373fd89d314f4752abbf"},
-]
 zipp = [
-    {file = "zipp-3.9.0-py3-none-any.whl", hash = "sha256:972cfa31bc2fedd3fa838a51e9bc7e64b7fb725a8c00e7431554311f180e9980"},
-    {file = "zipp-3.9.0.tar.gz", hash = "sha256:3a7af91c3db40ec72dd9d154ae18e008c69efe8ca88dde4f9a731bb82fe2f9eb"},
+    {file = "zipp-3.14.0-py3-none-any.whl", hash = "sha256:188834565033387710d046e3fe96acfc9b5e86cbca7f39ff69cf21a4128198b7"},
+    {file = "zipp-3.14.0.tar.gz", hash = "sha256:9e5421e176ef5ab4c0ad896624e87a7b2f07aca746c9b2aa305952800cb8eecb"},
 ]
diff --git a/pyproject.toml b/pyproject.toml
index 0e87f3d..4141227 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,23 +10,23 @@ readme = "README.md"
 
 [tool.poetry.dependencies]
 python = "^3.9"
-prefect = "^2.6.0"
-numpy = "^1.23.4"
-pandas = "^1.5.1"
+prefect = "^2.8.2"
+numpy = "^1.24.2"
+pandas = "^1.5.3"
 scikit-image = "^0.19.3"
 simulariumio = "^1.7.0"
 
 [tool.poetry.group.dev.dependencies]
-black = "^22.8.0"
+black = "^22.12.0"
 isort = "^5.12.0"
 mypy = "^0.971"
-pylint = "^2.15.2"
+pylint = "^2.16.2"
 pytest = "^7.2.0"
 pytest-cov = "^4.0.0"
 pytest-subtests = "^0.8.0"
-Sphinx = "^5.1.1"
-sphinx-rtd-theme = "^1.0.0"
-sphinx_mdinclude = "^0.5.2"
+Sphinx = "^5.3.0"
+sphinx-rtd-theme = "^1.2.0"
+sphinx_mdinclude = "^0.5.3"
 tox = "^3.26.0"
 
 [tool.isort]

From b433aedd66d3d8722be89cb47c3c259e06822b17 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Wed, 22 Feb 2023 12:02:55 -0500
Subject: [PATCH 08/48] Release v0.6.1 (#22)

Co-authored-by: jessicasyu <15913767+jessicasyu@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4141227..8cb5f79 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "arcade-collection"
-version = "0.6.0"
+version = "0.6.1"
 description = "Collection of tasks for working with ARCADE."
 authors = [
     "Jessica S. Yu <jesyu@uw.edu>"

From 6e3ce0166a86c9127f3f28df62f41e572eb16fb6 Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Thu, 9 Mar 2023 13:08:12 -0500
Subject: [PATCH 09/48] Add check for zero regions (#23)

* Add check for zero regions in convert to images task

* Add check for zero regions in convert to meshes task
---
 src/arcade_collection/output/convert_to_images.py | 4 ++++
 src/arcade_collection/output/convert_to_meshes.py | 4 ++++
 2 files changed, 8 insertions(+)

diff --git a/src/arcade_collection/output/convert_to_images.py b/src/arcade_collection/output/convert_to_images.py
index ba34307..68655bc 100644
--- a/src/arcade_collection/output/convert_to_images.py
+++ b/src/arcade_collection/output/convert_to_images.py
@@ -34,6 +34,10 @@ def convert_to_images(
                         location, region if region != "DEFAULT" else None
                     )
                 ]
+
+                if len(voxels) == 0:
+                    continue
+
                 array[index, channel][tuple(np.transpose(voxels))] = 1 if binary else location_id
 
     return split_array_chunks(array, chunk_size)
diff --git a/src/arcade_collection/output/convert_to_meshes.py b/src/arcade_collection/output/convert_to_meshes.py
index 7926c42..5f22b11 100644
--- a/src/arcade_collection/output/convert_to_meshes.py
+++ b/src/arcade_collection/output/convert_to_meshes.py
@@ -28,6 +28,10 @@ def convert_to_meshes(
                         location, region if region != "DEFAULT" else None
                     )
                 ]
+
+                if len(voxels) == 0:
+                    continue
+
                 array = make_mesh_array(voxels)
                 mesh = make_mesh_object(array)
 

From d0f6e1fe985955b776caf9b8db97e18d018f5e9c Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Thu, 9 Mar 2023 13:13:10 -0500
Subject: [PATCH 10/48] Release v0.6.2 (#24)

Co-authored-by: jessicasyu <15913767+jessicasyu@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 8cb5f79..cc5b9da 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "arcade-collection"
-version = "0.6.1"
+version = "0.6.2"
 description = "Collection of tasks for working with ARCADE."
 authors = [
     "Jessica S. Yu <jesyu@uw.edu>"

From 505cdbb7c4f851c27254037f20ee77995dd77c82 Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Fri, 17 Mar 2023 16:34:32 -0400
Subject: [PATCH 11/48] Move prefect task decorator to init (#26)

---
 src/arcade_collection/input/__init__.py       | 19 +++++++++++----
 .../input/convert_to_cells_file.py            |  2 --
 .../input/convert_to_locations_file.py        |  2 --
 .../input/generate_setup_file.py              |  2 --
 .../input/group_template_conditions.py        |  3 ---
 .../input/merge_region_samples.py             |  2 --
 src/arcade_collection/output/__init__.py      | 23 +++++++++++--------
 .../output/convert_model_units.py             |  2 --
 .../output/convert_to_images.py               |  6 ++---
 .../output/convert_to_meshes.py               |  6 ++---
 .../output/convert_to_simularium.py           |  8 +++----
 .../output/extract_tick_json.py               |  3 ---
 .../output/get_location_voxels.py             |  3 ---
 .../output/merge_parsed_results.py            |  2 --
 .../output/parse_cells_file.py                |  2 --
 .../output/parse_locations_file.py            |  2 --
 16 files changed, 35 insertions(+), 52 deletions(-)

diff --git a/src/arcade_collection/input/__init__.py b/src/arcade_collection/input/__init__.py
index fdbda9d..ad4a0fe 100644
--- a/src/arcade_collection/input/__init__.py
+++ b/src/arcade_collection/input/__init__.py
@@ -1,5 +1,14 @@
-from .convert_to_cells_file import convert_to_cells_file
-from .convert_to_locations_file import convert_to_locations_file
-from .generate_setup_file import generate_setup_file
-from .group_template_conditions import group_template_conditions
-from .merge_region_samples import merge_region_samples
+import importlib
+import os
+import sys
+
+from prefect import task
+
+for module_file in os.listdir(os.path.dirname(__file__)):
+    if module_file == "__init__.py" or not module_file.endswith(".py"):
+        continue
+
+    module_name = module_file.replace(".py", "")
+
+    module = importlib.import_module(f".{module_name}", package=__name__)
+    setattr(sys.modules[__name__], module_name, task(getattr(module, module_name)))
diff --git a/src/arcade_collection/input/convert_to_cells_file.py b/src/arcade_collection/input/convert_to_cells_file.py
index e48cf56..b3261d3 100644
--- a/src/arcade_collection/input/convert_to_cells_file.py
+++ b/src/arcade_collection/input/convert_to_cells_file.py
@@ -1,8 +1,6 @@
 import pandas as pd
-from prefect import task
 
 
-@task
 def convert_to_cells_file(
     samples: pd.DataFrame,
     reference: pd.DataFrame,
diff --git a/src/arcade_collection/input/convert_to_locations_file.py b/src/arcade_collection/input/convert_to_locations_file.py
index c1b97e9..f31d0b9 100644
--- a/src/arcade_collection/input/convert_to_locations_file.py
+++ b/src/arcade_collection/input/convert_to_locations_file.py
@@ -1,10 +1,8 @@
 from typing import Optional
 
 import pandas as pd
-from prefect import task
 
 
-@task
 def convert_to_locations_file(samples: pd.DataFrame) -> list[dict]:
     locations: list[dict] = []
     samples_by_id = samples.groupby("id")
diff --git a/src/arcade_collection/input/generate_setup_file.py b/src/arcade_collection/input/generate_setup_file.py
index b8ad602..09153a0 100644
--- a/src/arcade_collection/input/generate_setup_file.py
+++ b/src/arcade_collection/input/generate_setup_file.py
@@ -3,10 +3,8 @@
 
 import numpy as np
 import pandas as pd
-from prefect import task
 
 
-@task
 def generate_setup_file(
     samples: pd.DataFrame, margins: tuple[int, int, int], potts_terms: list[str]
 ) -> str:
diff --git a/src/arcade_collection/input/group_template_conditions.py b/src/arcade_collection/input/group_template_conditions.py
index 465be1b..78c6219 100644
--- a/src/arcade_collection/input/group_template_conditions.py
+++ b/src/arcade_collection/input/group_template_conditions.py
@@ -1,9 +1,6 @@
 from itertools import groupby
 
-from prefect import task
 
-
-@task
 def group_template_conditions(conditions: list[dict], max_seeds: int) -> list[dict]:
     grouped_conditions = group_seed_ranges(conditions, max_seeds)
     condition_sets = group_condition_sets(grouped_conditions, max_seeds)
diff --git a/src/arcade_collection/input/merge_region_samples.py b/src/arcade_collection/input/merge_region_samples.py
index 4fc0c93..f230b0d 100644
--- a/src/arcade_collection/input/merge_region_samples.py
+++ b/src/arcade_collection/input/merge_region_samples.py
@@ -2,10 +2,8 @@
 
 import numpy as np
 import pandas as pd
-from prefect import task
 
 
-@task
 def merge_region_samples(
     samples: dict[str, pd.DataFrame], margins: tuple[int, int, int]
 ) -> pd.DataFrame:
diff --git a/src/arcade_collection/output/__init__.py b/src/arcade_collection/output/__init__.py
index a3dd5a2..ad4a0fe 100644
--- a/src/arcade_collection/output/__init__.py
+++ b/src/arcade_collection/output/__init__.py
@@ -1,9 +1,14 @@
-from .convert_model_units import convert_model_units
-from .convert_to_images import convert_to_images
-from .convert_to_meshes import convert_to_meshes
-from .convert_to_simularium import convert_to_simularium
-from .extract_tick_json import extract_tick_json
-from .get_location_voxels import get_location_voxels
-from .merge_parsed_results import merge_parsed_results
-from .parse_cells_file import parse_cells_file
-from .parse_locations_file import parse_locations_file
+import importlib
+import os
+import sys
+
+from prefect import task
+
+for module_file in os.listdir(os.path.dirname(__file__)):
+    if module_file == "__init__.py" or not module_file.endswith(".py"):
+        continue
+
+    module_name = module_file.replace(".py", "")
+
+    module = importlib.import_module(f".{module_name}", package=__name__)
+    setattr(sys.modules[__name__], module_name, task(getattr(module, module_name)))
diff --git a/src/arcade_collection/output/convert_model_units.py b/src/arcade_collection/output/convert_model_units.py
index 0d88385..c3c398b 100644
--- a/src/arcade_collection/output/convert_model_units.py
+++ b/src/arcade_collection/output/convert_model_units.py
@@ -1,10 +1,8 @@
 from typing import Optional, Union
 
 import pandas as pd
-from prefect import task
 
 
-@task
 def convert_model_units(
     data: pd.DataFrame, ds: float, dt: float, regions: Optional[Union[list[str], str]] = None
 ) -> None:
diff --git a/src/arcade_collection/output/convert_to_images.py b/src/arcade_collection/output/convert_to_images.py
index 68655bc..4d187a1 100644
--- a/src/arcade_collection/output/convert_to_images.py
+++ b/src/arcade_collection/output/convert_to_images.py
@@ -1,13 +1,11 @@
 import tarfile
 
 import numpy as np
-from prefect import task
 
 from arcade_collection.output.extract_tick_json import extract_tick_json
 from arcade_collection.output.get_location_voxels import get_location_voxels
 
 
-@task
 def convert_to_images(
     series_key: str,
     data_tar: tarfile.TarFile,
@@ -22,7 +20,7 @@ def convert_to_images(
     array = np.zeros((len(frames), len(regions), height, width, length), "uint16")
 
     for index, frame in enumerate(frames):
-        locations = extract_tick_json.fn(data_tar, series_key, frame, "LOCATIONS")
+        locations = extract_tick_json(data_tar, series_key, frame, "LOCATIONS")
 
         for location in locations:
             location_id = location["id"]
@@ -30,7 +28,7 @@ def convert_to_images(
             for channel, region in enumerate(regions):
                 voxels = [
                     (z, y, x)
-                    for x, y, z in get_location_voxels.fn(
+                    for x, y, z in get_location_voxels(
                         location, region if region != "DEFAULT" else None
                     )
                 ]
diff --git a/src/arcade_collection/output/convert_to_meshes.py b/src/arcade_collection/output/convert_to_meshes.py
index 5f22b11..f0eb4c4 100644
--- a/src/arcade_collection/output/convert_to_meshes.py
+++ b/src/arcade_collection/output/convert_to_meshes.py
@@ -1,14 +1,12 @@
 import tarfile
 
 import numpy as np
-from prefect import task
 from skimage import measure
 
 from arcade_collection.output.extract_tick_json import extract_tick_json
 from arcade_collection.output.get_location_voxels import get_location_voxels
 
 
-@task
 def convert_to_meshes(
     series_key: str, data_tar: tarfile.TarFile, frame_spec: tuple[int, int, int], regions: list[str]
 ) -> list[tuple[int, int, str, str]]:
@@ -16,7 +14,7 @@ def convert_to_meshes(
     meshes = []
 
     for frame in frames:
-        locations = extract_tick_json.fn(data_tar, series_key, frame, "LOCATIONS")
+        locations = extract_tick_json(data_tar, series_key, frame, "LOCATIONS")
 
         for location in locations:
             location_id = location["id"]
@@ -24,7 +22,7 @@ def convert_to_meshes(
             for region in regions:
                 voxels = [
                     (z, y, x)
-                    for x, y, z in get_location_voxels.fn(
+                    for x, y, z in get_location_voxels(
                         location, region if region != "DEFAULT" else None
                     )
                 ]
diff --git a/src/arcade_collection/output/convert_to_simularium.py b/src/arcade_collection/output/convert_to_simularium.py
index 13d9df8..d326e5a 100644
--- a/src/arcade_collection/output/convert_to_simularium.py
+++ b/src/arcade_collection/output/convert_to_simularium.py
@@ -1,7 +1,6 @@
 import tarfile
 
 import numpy as np
-from prefect import task
 from simulariumio import (
     DISPLAY_TYPE,
     AgentData,
@@ -18,7 +17,6 @@
 from arcade_collection.output.extract_tick_json import extract_tick_json
 
 
-@task
 def convert_to_simularium(
     series_key: str,
     cells_data_tar: tarfile.TarFile,
@@ -77,7 +75,7 @@ def get_agent_data(series_key: str, cells_tar: tarfile.TarFile, frames: list[int
 
     max_agents = 0
     for frame in frames:
-        cells = extract_tick_json.fn(cells_tar, series_key, frame, "CELLS")
+        cells = extract_tick_json(cells_tar, series_key, frame, "CELLS")
         max_agents = max(max_agents, len(cells))
 
     return AgentData.from_dimensions(DimensionData(total_frames, max_agents))
@@ -99,7 +97,7 @@ def convert_cells_tar(
     frame: int,
     index: int,
 ) -> None:
-    cells = extract_tick_json.fn(tar, series_key, frame, "CELLS")
+    cells = extract_tick_json(tar, series_key, frame, "CELLS")
     data.n_agents[index] = len(cells)
 
     for i, cell in enumerate(cells):
@@ -119,7 +117,7 @@ def convert_locations_tar(
     height: int,
     ds: float,
 ) -> None:
-    locations = extract_tick_json.fn(tar, series_key, frame, "LOCATIONS")
+    locations = extract_tick_json(tar, series_key, frame, "LOCATIONS")
 
     for i, location in enumerate(locations):
         data.positions[index][i] = np.array(
diff --git a/src/arcade_collection/output/extract_tick_json.py b/src/arcade_collection/output/extract_tick_json.py
index 5f4730d..d63acad 100644
--- a/src/arcade_collection/output/extract_tick_json.py
+++ b/src/arcade_collection/output/extract_tick_json.py
@@ -1,10 +1,7 @@
 import json
 import tarfile
 
-from prefect import task
 
-
-@task
 def extract_tick_json(tar: tarfile.TarFile, key: str, tick: int, extension: str) -> list[dict]:
     member = tar.extractfile(f"{key}_{tick:06d}.{extension}.json")
     assert member is not None
diff --git a/src/arcade_collection/output/get_location_voxels.py b/src/arcade_collection/output/get_location_voxels.py
index c526af2..a7a5d2e 100644
--- a/src/arcade_collection/output/get_location_voxels.py
+++ b/src/arcade_collection/output/get_location_voxels.py
@@ -1,9 +1,6 @@
 from typing import Optional
 
-from prefect import task
 
-
-@task
 def get_location_voxels(location: dict, region: Optional[str] = None) -> list[tuple[int, int, int]]:
     voxels = [
         voxel
diff --git a/src/arcade_collection/output/merge_parsed_results.py b/src/arcade_collection/output/merge_parsed_results.py
index f324cff..0b3be5a 100644
--- a/src/arcade_collection/output/merge_parsed_results.py
+++ b/src/arcade_collection/output/merge_parsed_results.py
@@ -1,8 +1,6 @@
 import pandas as pd
-from prefect import task
 
 
-@task
 def merge_parsed_results(*results: pd.DataFrame) -> pd.DataFrame:
     for result in results:
         result.set_index(["ID", "TICK"], inplace=True)
diff --git a/src/arcade_collection/output/parse_cells_file.py b/src/arcade_collection/output/parse_cells_file.py
index b83a33e..8b81e8f 100644
--- a/src/arcade_collection/output/parse_cells_file.py
+++ b/src/arcade_collection/output/parse_cells_file.py
@@ -3,7 +3,6 @@
 from typing import Union
 
 import pandas as pd
-from prefect import task
 
 CELLS_COLUMNS = [
     "ID",
@@ -18,7 +17,6 @@
 ]
 
 
-@task
 def parse_cells_file(tar: tarfile.TarFile, regions: list[str]) -> pd.DataFrame:
     all_cells: list[list[Union[str, int]]] = []
 
diff --git a/src/arcade_collection/output/parse_locations_file.py b/src/arcade_collection/output/parse_locations_file.py
index fdd1c34..57a945d 100644
--- a/src/arcade_collection/output/parse_locations_file.py
+++ b/src/arcade_collection/output/parse_locations_file.py
@@ -4,7 +4,6 @@
 
 import numpy as np
 import pandas as pd
-from prefect import task
 
 CELLS_COLUMNS = [
     "ID",
@@ -21,7 +20,6 @@
 ]
 
 
-@task
 def parse_locations_file(tar: tarfile.TarFile, regions: list[str]) -> pd.DataFrame:
     all_locations: list[list[Union[str, int]]] = []
 

From 9dd908ae9a2afcc5352c65552372b0297eb01dd5 Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Fri, 17 Mar 2023 16:35:47 -0400
Subject: [PATCH 12/48] Add changelog and update actions (#25)

* Add CHANGELOG

* Update checkout action to v3

* Update release action to update CHANGELOG
---
 .github/workflows/build.yml         |  2 +-
 .github/workflows/documentation.yml |  2 +-
 .github/workflows/lint.yml          |  2 +-
 .github/workflows/publish.yml       |  2 +-
 .github/workflows/release.yml       | 46 +++++++++++++++++-
 CHANGELOG.md                        | 74 +++++++++++++++++++++++++++++
 6 files changed, 123 insertions(+), 5 deletions(-)
 create mode 100644 CHANGELOG.md

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 2aa50eb..2ea1dd7 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -13,7 +13,7 @@ jobs:
     steps:
 
     - name: Checkout the repo
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
index fe6a03d..792ac7f 100644
--- a/.github/workflows/documentation.yml
+++ b/.github/workflows/documentation.yml
@@ -12,7 +12,7 @@ jobs:
     steps:
 
     - name: Checkout the repo
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     - name: Set up Python 3.9
       uses: actions/setup-python@v2
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index d6deb55..7543b13 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -9,7 +9,7 @@ jobs:
     steps:
 
     - name: Checkout the repo
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     - name: Set up Python 3.9
       uses: actions/setup-python@v2
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index dc038b2..86b6196 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -16,7 +16,7 @@ jobs:
     steps:
 
     - name: Checkout the repo
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     - name: Extract version from branch name
       run: |
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 2dae32d..17573f3 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -12,7 +12,7 @@ jobs:
     steps:
 
     - name: Checkout the repo
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     - name: Extract version from branch name
       run: |
@@ -20,6 +20,50 @@ jobs:
         VERSION=${GITHUB_REF##*/}
         echo "RELEASE_VERSION=$VERSION" >> $GITHUB_ENV
 
+    - name: Get current date
+      run: |
+        echo "CURRENT_DATE=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
+
+    - name: Build changelog
+      id: build_changelog
+      uses: mikepenz/release-changelog-builder-action@v3.4.0
+      with:
+        configurationJson: |
+          {
+            "categories": [
+              {
+                "title": "### Features",
+                "labels": ["type: feature"]
+              },
+              {
+                "title": "### Bug fixes",
+                "labels": ["type: bug"]
+              },
+              {
+                "title": "### Tests",
+                "labels": ["type: test"]
+              },
+              {
+                "title": "### Documentation",
+                "labels": ["type: docs"]
+              }
+            ],
+            "template": "# [${{ env.RELEASE_VERSION }}](https://github.com/${{ github.repository }}/releases/tag/${{ env.RELEASE_VERSION }}) - ${{ env.CURRENT_DATE }}\n\n> Compare with [`#{{FROM_TAG}}`](https://github.com/${{ github.repository }}/compare/#{{FROM_TAG}}...${{ env.RELEASE_VERSION }})\n\n#{{CHANGELOG}}",
+            "pr_template": "- #{{TITLE}} by [@#{{AUTHOR}}](https://github.com/#{{AUTHOR}}) in [##{{NUMBER}}](#{{URL}})"
+          }
+        toTag: ${{ github.sha }}
+        token: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Update changelog
+      run: |
+        printf "%s%s" "${{ steps.build_changelog.outputs.changelog }}" "$(cat CHANGELOG.md)" > CHANGELOG.md
+
+    - uses: EndBug/add-and-commit@v9
+      with:
+          add: "CHANGELOG.md"
+          message: "Update CHANGELOG.md for ${{ env.RELEASE_VERSION }}"
+          push: 'origin ${{ github.event.push.ref }}'
+
     - name: Create pull request
       uses: repo-sync/pull-request@v2
       with:
diff --git a/CHANGELOG.md b/CHANGELOG.md
new file mode 100644
index 0000000..439a4c8
--- /dev/null
+++ b/CHANGELOG.md
@@ -0,0 +1,74 @@
+# [v0.6.2](https://github.com/bagherilab/arcade-collection/releases/tag/v0.6.2) - 2023-03-09
+
+> Compare with [`v0.6.1`](https://github.com/bagherilab/arcade-collection/compare/v0.6.1...v0.6.2)
+
+### Bug fixes
+
+- Add check for zero regions by [@jessicasyu](https://github.com/jessicasyu) in [#23](https://github.com/bagherilab/arcade-collection/pull/23)
+
+# [v0.6.1](https://github.com/bagherilab/arcade-collection/releases/tag/v0.6.1) - 2023-02-22
+
+> Compare with [`v0.6.0`](https://github.com/bagherilab/arcade-collection/compare/v0.6.0...v0.6.1)
+
+### Features
+
+- Upgrade prefect and update dependencies by [@jessicasyu](https://github.com/jessicasyu) in [#21](https://github.com/bagherilab/arcade-collection/pull/21)
+
+# [v0.6.0](https://github.com/bagherilab/arcade-collection/releases/tag/v0.6.0) - 2023-02-15
+
+> Compare with [`v0.5.0`](https://github.com/bagherilab/arcade-collection/compare/v0.5.0...v0.6.0)
+
+### Features
+
+- Add convert format tasks by [@jessicasyu](https://github.com/jessicasyu) in [#18](https://github.com/bagherilab/arcade-collection/pull/18)
+
+### Bug fixes
+
+- Fix type hints by [@jessicasyu](https://github.com/jessicasyu) in [#19](https://github.com/bagherilab/arcade-collection/pull/19)
+
+# [v0.5.0](https://github.com/bagherilab/arcade-collection/releases/tag/v0.5.0) - 2023-02-13
+
+> Compare with [`v0.4.0`](https://github.com/bagherilab/arcade-collection/compare/v0.4.0...v0.5.0)
+
+### Features
+
+- Add convert units task by [@jessicasyu](https://github.com/jessicasyu) in [#16](https://github.com/bagherilab/arcade-collection/pull/16)
+
+### Bug fixes
+
+- Update import sorting for all tasks by [@jessicasyu](https://github.com/jessicasyu) in [#15](https://github.com/bagherilab/arcade-collection/pull/15)
+
+# [v0.4.0](https://github.com/bagherilab/arcade-collection/releases/tag/v0.4.0) - 2022-11-17
+
+> Compare with [`v0.3.0`](https://github.com/bagherilab/arcade-collection/compare/v0.3.0...v0.4.0)
+
+### Features
+
+- Add extract tick json task by [@jessicasyu](https://github.com/jessicasyu) in [#7](https://github.com/bagherilab/arcade-collection/pull/7)
+- Add get location voxels task by [@jessicasyu](https://github.com/jessicasyu) in [#8](https://github.com/bagherilab/arcade-collection/pull/8)
+
+### Documentation
+
+- Add types to group template conditions task by [@jessicasyu](https://github.com/jessicasyu) in [#9](https://github.com/bagherilab/arcade-collection/pull/9)
+
+# [v0.3.0](https://github.com/bagherilab/arcade-collection/releases/tag/v0.3.0) - 2022-11-02
+
+> Compare with [`v0.2.0`](https://github.com/bagherilab/arcade-collection/compare/v0.2.0...v0.3.0)
+
+### Features
+
+- Add initialization tasks by [@jessicasyu](https://github.com/jessicasyu) in [#5](https://github.com/bagherilab/arcade-collection/pull/5)
+
+# [v0.2.0](https://github.com/bagherilab/arcade-collection/releases/tag/v0.2.0) - 2022-10-24
+
+> Compare with [`v0.1.0`](https://github.com/bagherilab/arcade-collection/compare/v0.1.0...v0.2.0)
+
+### Features
+
+- Add parse cells and locations file tasks by [@jessicasyu](https://github.com/jessicasyu) in [#3](https://github.com/bagherilab/arcade-collection/pull/3)
+
+# [v0.1.0](https://github.com/bagherilab/arcade-collection/releases/tag/v0.1.0) - 2022-10-24
+
+### Features
+
+- Add group template conditions task by [@jessicasyu](https://github.com/jessicasyu) in [#1](https://github.com/bagherilab/arcade-collection/pull/1)

From d7ed8c808a4ed79350a946f638b8135f7f52d80b Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Fri, 17 Mar 2023 16:52:36 -0400
Subject: [PATCH 13/48] Update action versions (#27)

* Update action versions

* Add admin category to actions
---
 .github/workflows/build.yml         | 6 +++---
 .github/workflows/documentation.yml | 4 ++--
 .github/workflows/lint.yml          | 4 ++--
 .github/workflows/publish.yml       | 6 +++++-
 .github/workflows/release.yml       | 4 ++++
 5 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 2ea1dd7..83635bb 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -16,7 +16,7 @@ jobs:
       uses: actions/checkout@v3
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -28,7 +28,7 @@ jobs:
 
     - name: Load cached venv
       id: cached-poetry-dependencies
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: .venv
         key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
@@ -48,7 +48,7 @@ jobs:
         pytest --cov-report xml --cov=src/ tests/
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v3
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
index 792ac7f..85ed062 100644
--- a/.github/workflows/documentation.yml
+++ b/.github/workflows/documentation.yml
@@ -15,7 +15,7 @@ jobs:
       uses: actions/checkout@v3
 
     - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: 3.9
 
@@ -30,7 +30,7 @@ jobs:
         touch docs/_build/html/.nojekyll
 
     - name: Publish docs
-      uses: JamesIves/github-pages-deploy-action@4.1.4
+      uses: JamesIves/github-pages-deploy-action@v4
       with:
         branch: gh-pages
         folder: docs/_build/html/
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 7543b13..16aa2e5 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -12,7 +12,7 @@ jobs:
       uses: actions/checkout@v3
 
     - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: 3.9
 
@@ -24,7 +24,7 @@ jobs:
 
     - name: Load cached venv
       id: cached-poetry-dependencies
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: .venv
         key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 86b6196..3c75bc8 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -46,6 +46,10 @@ jobs:
               {
                 "title": "## 📓 Documentation",
                 "labels": ["type: docs"]
+              },
+              {
+                "title": "## 📁 Admin",
+                "labels": ["type: admin"]
               }
             ],
             "template": "#{{CHANGELOG}}---\n\n**Full Changelog**: https://github.com/${{ github.repository }}/compare/#{{FROM_TAG}}...${{ env.RELEASE_VERSION }}\n",
@@ -64,7 +68,7 @@ jobs:
         token: ${{ secrets.GITHUB_TOKEN }}
 
     - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: 3.9
 
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 17573f3..11eb024 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -46,6 +46,10 @@ jobs:
               {
                 "title": "### Documentation",
                 "labels": ["type: docs"]
+              },
+              {
+                "title": "### Admin",
+                "labels": ["type: admin"]
               }
             ],
             "template": "# [${{ env.RELEASE_VERSION }}](https://github.com/${{ github.repository }}/releases/tag/${{ env.RELEASE_VERSION }}) - ${{ env.CURRENT_DATE }}\n\n> Compare with [`#{{FROM_TAG}}`](https://github.com/${{ github.repository }}/compare/#{{FROM_TAG}}...${{ env.RELEASE_VERSION }})\n\n#{{CHANGELOG}}",

From 5e7df3054dfed76e1e43517f43f1dc216b1630a7 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Fri, 17 Mar 2023 17:39:14 -0400
Subject: [PATCH 14/48] Release v0.7.0 (#28)

Co-authored-by: jessicasyu <15913767+jessicasyu@users.noreply.github.com>
---
 .github/workflows/publish.yml |  2 +-
 .github/workflows/release.yml | 20 ++++++++++++++++++--
 CHANGELOG.md                  | 27 ++++++++++++++++++++-------
 pyproject.toml                |  2 +-
 4 files changed, 40 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 3c75bc8..de3d3c9 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -8,7 +8,7 @@ on:
       - closed
 
 jobs:
-  release:
+  publish:
     if: ${{ (startsWith(github.event.pull_request.head.ref, 'release/')) && (github.event.pull_request.merged == true) }}
 
     runs-on: ubuntu-latest
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 11eb024..df2c024 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -6,7 +6,23 @@ on:
       - 'release/*'
 
 jobs:
+  check:
+    outputs:
+      status: ${{ steps.current_pr.outputs.pr_found }}
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - name: Get current PR
+      uses: 8BitJonny/gh-get-current-pr@2.2.0
+      id: current_pr
+
   release:
+    needs: check
+
+    if: needs.check.outputs.status == 'false'
+
     runs-on: ubuntu-latest
 
     steps:
@@ -52,7 +68,7 @@ jobs:
                 "labels": ["type: admin"]
               }
             ],
-            "template": "# [${{ env.RELEASE_VERSION }}](https://github.com/${{ github.repository }}/releases/tag/${{ env.RELEASE_VERSION }}) - ${{ env.CURRENT_DATE }}\n\n> Compare with [`#{{FROM_TAG}}`](https://github.com/${{ github.repository }}/compare/#{{FROM_TAG}}...${{ env.RELEASE_VERSION }})\n\n#{{CHANGELOG}}",
+            "template": "# [${{ env.RELEASE_VERSION }}](https://github.com/${{ github.repository }}/releases/tag/${{ env.RELEASE_VERSION }}) - ${{ env.CURRENT_DATE }}\n\n> Compare with [#{{FROM_TAG}}](https://github.com/${{ github.repository }}/compare/#{{FROM_TAG}}...${{ env.RELEASE_VERSION }})\n\n#{{CHANGELOG}}",
             "pr_template": "- #{{TITLE}} by [@#{{AUTHOR}}](https://github.com/#{{AUTHOR}}) in [##{{NUMBER}}](#{{URL}})"
           }
         toTag: ${{ github.sha }}
@@ -60,7 +76,7 @@ jobs:
 
     - name: Update changelog
       run: |
-        printf "%s%s" "${{ steps.build_changelog.outputs.changelog }}" "$(cat CHANGELOG.md)" > CHANGELOG.md
+        printf "%s%s\n" "${{ steps.build_changelog.outputs.changelog }}" "$(cat CHANGELOG.md)" > CHANGELOG.md
 
     - uses: EndBug/add-and-commit@v9
       with:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 439a4c8..92fb676 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,19 @@
+# [v0.7.0](https://github.com/bagherilab/arcade-collection/releases/tag/v0.7.0) - 2023-03-17
+
+> Compare with [v0.6.2](https://github.com/bagherilab/arcade-collection/compare/v0.6.2...v0.7.0)
+
+### Features
+
+- Move prefect task decorator to init by [@jessicasyu](https://github.com/jessicasyu) in [#26](https://github.com/bagherilab/arcade-collection/pull/26)
+
+### Admin
+
+- Add changelog and update actions by [@jessicasyu](https://github.com/jessicasyu) in [#25](https://github.com/bagherilab/arcade-collection/pull/25)
+- Update action versions by [@jessicasyu](https://github.com/jessicasyu) in [#27](https://github.com/bagherilab/arcade-collection/pull/27)
+
 # [v0.6.2](https://github.com/bagherilab/arcade-collection/releases/tag/v0.6.2) - 2023-03-09
 
-> Compare with [`v0.6.1`](https://github.com/bagherilab/arcade-collection/compare/v0.6.1...v0.6.2)
+> Compare with [v0.6.1](https://github.com/bagherilab/arcade-collection/compare/v0.6.1...v0.6.2)
 
 ### Bug fixes
 
@@ -8,7 +21,7 @@
 
 # [v0.6.1](https://github.com/bagherilab/arcade-collection/releases/tag/v0.6.1) - 2023-02-22
 
-> Compare with [`v0.6.0`](https://github.com/bagherilab/arcade-collection/compare/v0.6.0...v0.6.1)
+> Compare with [v0.6.0](https://github.com/bagherilab/arcade-collection/compare/v0.6.0...v0.6.1)
 
 ### Features
 
@@ -16,7 +29,7 @@
 
 # [v0.6.0](https://github.com/bagherilab/arcade-collection/releases/tag/v0.6.0) - 2023-02-15
 
-> Compare with [`v0.5.0`](https://github.com/bagherilab/arcade-collection/compare/v0.5.0...v0.6.0)
+> Compare with [v0.5.0](https://github.com/bagherilab/arcade-collection/compare/v0.5.0...v0.6.0)
 
 ### Features
 
@@ -28,7 +41,7 @@
 
 # [v0.5.0](https://github.com/bagherilab/arcade-collection/releases/tag/v0.5.0) - 2023-02-13
 
-> Compare with [`v0.4.0`](https://github.com/bagherilab/arcade-collection/compare/v0.4.0...v0.5.0)
+> Compare with [v0.4.0](https://github.com/bagherilab/arcade-collection/compare/v0.4.0...v0.5.0)
 
 ### Features
 
@@ -40,7 +53,7 @@
 
 # [v0.4.0](https://github.com/bagherilab/arcade-collection/releases/tag/v0.4.0) - 2022-11-17
 
-> Compare with [`v0.3.0`](https://github.com/bagherilab/arcade-collection/compare/v0.3.0...v0.4.0)
+> Compare with [v0.3.0](https://github.com/bagherilab/arcade-collection/compare/v0.3.0...v0.4.0)
 
 ### Features
 
@@ -53,7 +66,7 @@
 
 # [v0.3.0](https://github.com/bagherilab/arcade-collection/releases/tag/v0.3.0) - 2022-11-02
 
-> Compare with [`v0.2.0`](https://github.com/bagherilab/arcade-collection/compare/v0.2.0...v0.3.0)
+> Compare with [v0.2.0](https://github.com/bagherilab/arcade-collection/compare/v0.2.0...v0.3.0)
 
 ### Features
 
@@ -61,7 +74,7 @@
 
 # [v0.2.0](https://github.com/bagherilab/arcade-collection/releases/tag/v0.2.0) - 2022-10-24
 
-> Compare with [`v0.1.0`](https://github.com/bagherilab/arcade-collection/compare/v0.1.0...v0.2.0)
+> Compare with [v0.1.0](https://github.com/bagherilab/arcade-collection/compare/v0.1.0...v0.2.0)
 
 ### Features
 
diff --git a/pyproject.toml b/pyproject.toml
index cc5b9da..a79f676 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "arcade-collection"
-version = "0.6.2"
+version = "0.7.0"
 description = "Collection of tasks for working with ARCADE."
 authors = [
     "Jessica S. Yu <jesyu@uw.edu>"

From d365722081e6494622568f4348112a121bf2b81e Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Mon, 20 Mar 2023 14:34:09 -0400
Subject: [PATCH 15/48] Fix init import to exclude all double underscore files
 (#29)

---
 CHANGELOG.md                             | 5 +----
 src/arcade_collection/input/__init__.py  | 2 +-
 src/arcade_collection/output/__init__.py | 2 +-
 3 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 92fb676..9600858 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,12 +2,9 @@
 
 > Compare with [v0.6.2](https://github.com/bagherilab/arcade-collection/compare/v0.6.2...v0.7.0)
 
-### Features
-
-- Move prefect task decorator to init by [@jessicasyu](https://github.com/jessicasyu) in [#26](https://github.com/bagherilab/arcade-collection/pull/26)
-
 ### Admin
 
+- Move prefect task decorator to init by [@jessicasyu](https://github.com/jessicasyu) in [#26](https://github.com/bagherilab/arcade-collection/pull/26)
 - Add changelog and update actions by [@jessicasyu](https://github.com/jessicasyu) in [#25](https://github.com/bagherilab/arcade-collection/pull/25)
 - Update action versions by [@jessicasyu](https://github.com/jessicasyu) in [#27](https://github.com/bagherilab/arcade-collection/pull/27)
 
diff --git a/src/arcade_collection/input/__init__.py b/src/arcade_collection/input/__init__.py
index ad4a0fe..ff5dead 100644
--- a/src/arcade_collection/input/__init__.py
+++ b/src/arcade_collection/input/__init__.py
@@ -5,7 +5,7 @@
 from prefect import task
 
 for module_file in os.listdir(os.path.dirname(__file__)):
-    if module_file == "__init__.py" or not module_file.endswith(".py"):
+    if "__" in module_file or not module_file.endswith(".py"):
         continue
 
     module_name = module_file.replace(".py", "")
diff --git a/src/arcade_collection/output/__init__.py b/src/arcade_collection/output/__init__.py
index ad4a0fe..ff5dead 100644
--- a/src/arcade_collection/output/__init__.py
+++ b/src/arcade_collection/output/__init__.py
@@ -5,7 +5,7 @@
 from prefect import task
 
 for module_file in os.listdir(os.path.dirname(__file__)):
-    if module_file == "__init__.py" or not module_file.endswith(".py"):
+    if "__" in module_file or not module_file.endswith(".py"):
         continue
 
     module_name = module_file.replace(".py", "")

From 60515e1583f011071ea20a596971480180fab753 Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Tue, 28 Mar 2023 16:46:07 -0400
Subject: [PATCH 16/48] Update adding task decorator to init imports (#30)

---
 src/arcade_collection/input/__init__.py  | 23 ++++++++++++------
 src/arcade_collection/output/__init__.py | 31 ++++++++++++++++++------
 2 files changed, 40 insertions(+), 14 deletions(-)

diff --git a/src/arcade_collection/input/__init__.py b/src/arcade_collection/input/__init__.py
index ff5dead..29a4c36 100644
--- a/src/arcade_collection/input/__init__.py
+++ b/src/arcade_collection/input/__init__.py
@@ -1,14 +1,23 @@
 import importlib
-import os
 import sys
 
 from prefect import task
 
-for module_file in os.listdir(os.path.dirname(__file__)):
-    if "__" in module_file or not module_file.endswith(".py"):
-        continue
+from .convert_to_cells_file import convert_to_cells_file
+from .convert_to_locations_file import convert_to_locations_file
+from .generate_setup_file import generate_setup_file
+from .group_template_conditions import group_template_conditions
+from .merge_region_samples import merge_region_samples
 
-    module_name = module_file.replace(".py", "")
+TASK_MODULES = [
+    convert_to_cells_file,
+    convert_to_locations_file,
+    generate_setup_file,
+    group_template_conditions,
+    merge_region_samples,
+]
 
-    module = importlib.import_module(f".{module_name}", package=__name__)
-    setattr(sys.modules[__name__], module_name, task(getattr(module, module_name)))
+for task_module in TASK_MODULES:
+    MODULE_NAME = task_module.__name__
+    module = importlib.import_module(f".{MODULE_NAME}", package=__name__)
+    setattr(sys.modules[__name__], MODULE_NAME, task(getattr(module, MODULE_NAME)))
diff --git a/src/arcade_collection/output/__init__.py b/src/arcade_collection/output/__init__.py
index ff5dead..ce4f376 100644
--- a/src/arcade_collection/output/__init__.py
+++ b/src/arcade_collection/output/__init__.py
@@ -1,14 +1,31 @@
 import importlib
-import os
 import sys
 
 from prefect import task
 
-for module_file in os.listdir(os.path.dirname(__file__)):
-    if "__" in module_file or not module_file.endswith(".py"):
-        continue
+from .convert_model_units import convert_model_units
+from .convert_to_images import convert_to_images
+from .convert_to_meshes import convert_to_meshes
+from .convert_to_simularium import convert_to_simularium
+from .extract_tick_json import extract_tick_json
+from .get_location_voxels import get_location_voxels
+from .merge_parsed_results import merge_parsed_results
+from .parse_cells_file import parse_cells_file
+from .parse_locations_file import parse_locations_file
 
-    module_name = module_file.replace(".py", "")
+TASK_MODULES = [
+    convert_model_units,
+    convert_to_images,
+    convert_to_meshes,
+    convert_to_simularium,
+    extract_tick_json,
+    get_location_voxels,
+    merge_parsed_results,
+    parse_cells_file,
+    parse_locations_file,
+]
 
-    module = importlib.import_module(f".{module_name}", package=__name__)
-    setattr(sys.modules[__name__], module_name, task(getattr(module, module_name)))
+for task_module in TASK_MODULES:
+    MODULE_NAME = task_module.__name__
+    module = importlib.import_module(f".{MODULE_NAME}", package=__name__)
+    setattr(sys.modules[__name__], MODULE_NAME, task(getattr(module, MODULE_NAME)))

From 6181c2281570756da2c3ddabdc53a15552b92462 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Tue, 28 Mar 2023 16:50:50 -0400
Subject: [PATCH 17/48] Release v0.7.1 (#31)

Co-authored-by: jessicasyu <15913767+jessicasyu@users.noreply.github.com>
---
 CHANGELOG.md   | 12 ++++++++++++
 pyproject.toml |  2 +-
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9600858..ed69dfb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,15 @@
+# [v0.7.1](https://github.com/bagherilab/arcade-collection/releases/tag/v0.7.1) - 2023-03-28
+
+> Compare with [v0.7.0](https://github.com/bagherilab/arcade-collection/compare/v0.7.0...v0.7.1)
+
+### Bug fixes
+
+- Fix init import to exclude all double underscore files by [@jessicasyu](https://github.com/jessicasyu) in [#29](https://github.com/bagherilab/arcade-collection/pull/29)
+
+### Admin
+
+- Update adding task decorator to init imports by [@jessicasyu](https://github.com/jessicasyu) in [#30](https://github.com/bagherilab/arcade-collection/pull/30)
+
 # [v0.7.0](https://github.com/bagherilab/arcade-collection/releases/tag/v0.7.0) - 2023-03-17
 
 > Compare with [v0.6.2](https://github.com/bagherilab/arcade-collection/compare/v0.6.2...v0.7.0)
diff --git a/pyproject.toml b/pyproject.toml
index a79f676..7a7025c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "arcade-collection"
-version = "0.7.0"
+version = "0.7.1"
 description = "Collection of tasks for working with ARCADE."
 authors = [
     "Jessica S. Yu <jesyu@uw.edu>"

From 23d29096b907045270910d1c93db4476ce0c3441 Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Wed, 29 Mar 2023 18:17:42 -0400
Subject: [PATCH 18/48] Add task decorator to init imports (#32)

---
 src/arcade_collection/input/__init__.py  | 20 +++++------------
 src/arcade_collection/output/__init__.py | 28 ++++++++----------------
 2 files changed, 14 insertions(+), 34 deletions(-)

diff --git a/src/arcade_collection/input/__init__.py b/src/arcade_collection/input/__init__.py
index 29a4c36..e588637 100644
--- a/src/arcade_collection/input/__init__.py
+++ b/src/arcade_collection/input/__init__.py
@@ -1,6 +1,3 @@
-import importlib
-import sys
-
 from prefect import task
 
 from .convert_to_cells_file import convert_to_cells_file
@@ -9,15 +6,8 @@
 from .group_template_conditions import group_template_conditions
 from .merge_region_samples import merge_region_samples
 
-TASK_MODULES = [
-    convert_to_cells_file,
-    convert_to_locations_file,
-    generate_setup_file,
-    group_template_conditions,
-    merge_region_samples,
-]
-
-for task_module in TASK_MODULES:
-    MODULE_NAME = task_module.__name__
-    module = importlib.import_module(f".{MODULE_NAME}", package=__name__)
-    setattr(sys.modules[__name__], MODULE_NAME, task(getattr(module, MODULE_NAME)))
+convert_to_cells_file = task(convert_to_cells_file)
+convert_to_locations_file = task(convert_to_locations_file)
+generate_setup_file = task(generate_setup_file)
+group_template_conditions = task(group_template_conditions)
+merge_region_samples = task(merge_region_samples)
diff --git a/src/arcade_collection/output/__init__.py b/src/arcade_collection/output/__init__.py
index ce4f376..3b969fd 100644
--- a/src/arcade_collection/output/__init__.py
+++ b/src/arcade_collection/output/__init__.py
@@ -1,6 +1,3 @@
-import importlib
-import sys
-
 from prefect import task
 
 from .convert_model_units import convert_model_units
@@ -13,19 +10,12 @@
 from .parse_cells_file import parse_cells_file
 from .parse_locations_file import parse_locations_file
 
-TASK_MODULES = [
-    convert_model_units,
-    convert_to_images,
-    convert_to_meshes,
-    convert_to_simularium,
-    extract_tick_json,
-    get_location_voxels,
-    merge_parsed_results,
-    parse_cells_file,
-    parse_locations_file,
-]
-
-for task_module in TASK_MODULES:
-    MODULE_NAME = task_module.__name__
-    module = importlib.import_module(f".{MODULE_NAME}", package=__name__)
-    setattr(sys.modules[__name__], MODULE_NAME, task(getattr(module, MODULE_NAME)))
+convert_model_units = task(convert_model_units)
+convert_to_images = task(convert_to_images)
+convert_to_meshes = task(convert_to_meshes)
+convert_to_simularium = task(convert_to_simularium)
+extract_tick_json = task(extract_tick_json)
+get_location_voxels = task(get_location_voxels)
+merge_parsed_results = task(merge_parsed_results)
+parse_cells_file = task(parse_cells_file)
+parse_locations_file = task(parse_locations_file)

From dd2e9d5010c06f91f1e498cab96cee1e80822e30 Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Wed, 29 Mar 2023 18:46:28 -0400
Subject: [PATCH 19/48] Update pyproject.toml and dependencies (#33)

* Move dev configs into pyproject.toml file

* Update build and lint actions

* Update mypy version
---
 .github/workflows/build.yml |  2 +-
 .github/workflows/lint.yml  |  2 +-
 .pylintrc                   | 17 -----------
 mypy.ini                    | 13 --------
 poetry.lock                 | 60 +++++++++++++++++++++----------------
 pyproject.toml              | 53 +++++++++++++++++++++++++++++++-
 tox.ini                     | 19 ------------
 7 files changed, 88 insertions(+), 78 deletions(-)
 delete mode 100644 .pylintrc
 delete mode 100644 mypy.ini
 delete mode 100644 tox.ini

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 83635bb..ecdf5e7 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -8,7 +8,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.9", "3.10"]
 
     steps:
 
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 16aa2e5..ae397cc 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -52,4 +52,4 @@ jobs:
     - name: Check with mypy
       run: |
         source .venv/bin/activate
-        mypy --config-file mypy.ini src
+        mypy src
diff --git a/.pylintrc b/.pylintrc
deleted file mode 100644
index 97718afd..0000000
--- a/.pylintrc
+++ /dev/null
@@ -1,17 +0,0 @@
-[MESSAGES CONTROL]
-
-# Disable specific messages
-disable=missing-module-docstring
-
-# Set good names.
-good-names=i,j,x,y,z,ds,dt
-
-[DESIGN]
-
-# Maximum number of arguments for function / method
-max-args=10
-
-[SIMILARITIES]
-
-# Minimum lines number of a similarity.
-min-similarity-lines=7
diff --git a/mypy.ini b/mypy.ini
deleted file mode 100644
index 60276d5..0000000
--- a/mypy.ini
+++ /dev/null
@@ -1,13 +0,0 @@
-[mypy]
-mypy_path = src
-explicit_package_bases = True
-namespace_packages = True
-
-[mypy-pandas.*]
-ignore_missing_imports = True
-
-[mypy-simulariumio.*]
-ignore_missing_imports = True
-
-[mypy-skimage.*]
-ignore_missing_imports = True
diff --git a/poetry.lock b/poetry.lock
index 5abc82b..539ef70 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -773,11 +773,11 @@ python-versions = "*"
 
 [[package]]
 name = "mypy"
-version = "0.971"
+version = "0.991"
 description = "Optional static typing for Python"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
 mypy-extensions = ">=0.4.3"
@@ -786,6 +786,7 @@ typing-extensions = ">=3.10"
 
 [package.extras]
 dmypy = ["psutil (>=4.0)"]
+install-types = ["pip"]
 python2 = ["typed-ast (>=1.4.0,<2)"]
 reports = ["lxml"]
 
@@ -1803,7 +1804,7 @@ testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools"
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.9"
-content-hash = "72b2c36c99e14c2dbab696e46690e7de070ef1940727e9d33428e4a632f981e2"
+content-hash = "b473b858673f97389893714b9f7b21ad8bab1eb63ff704635ca21c4bc76bcf00"
 
 [metadata.files]
 aiosqlite = [
@@ -2445,29 +2446,36 @@ mistune = [
     {file = "mistune-2.0.5.tar.gz", hash = "sha256:0246113cb2492db875c6be56974a7c893333bf26cd92891c85f63151cee09d34"},
 ]
 mypy = [
-    {file = "mypy-0.971-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:f2899a3cbd394da157194f913a931edfd4be5f274a88041c9dc2d9cdcb1c315c"},
-    {file = "mypy-0.971-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:98e02d56ebe93981c41211c05adb630d1d26c14195d04d95e49cd97dbc046dc5"},
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+    {file = "mypy-0.991.tar.gz", hash = "sha256:3c0165ba8f354a6d9881809ef29f1a9318a236a6d81c690094c5df32107bde06"},
 ]
 mypy-extensions = [
     {file = "mypy_extensions-1.0.0-py3-none-any.whl", hash = "sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d"},
diff --git a/pyproject.toml b/pyproject.toml
index 7a7025c..18a828d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,7 +19,7 @@ simulariumio = "^1.7.0"
 [tool.poetry.group.dev.dependencies]
 black = "^22.12.0"
 isort = "^5.12.0"
-mypy = "^0.971"
+mypy = "^0.991"
 pylint = "^2.16.2"
 pytest = "^7.2.0"
 pytest-cov = "^4.0.0"
@@ -35,3 +35,54 @@ profile = "black"
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
+
+[tool.pylint.messages_control]
+disable = [
+    "missing-module-docstring",
+]
+good-names = ["i", "j", "k", "x", "y", "z", "ds", "dt"]
+
+[tool.pylint.design]
+max-args = 10 # maximum number of arguments for function / method
+
+[tool.pylint.similarities]
+min-similarity-lines = 10 # minimum lines number of a similarity
+
+[tool.mypy]
+mypy_path = "src"
+explicit_package_bases = true
+namespace_packages = true
+
+[[tool.mypy.overrides]]
+module = [
+    "pandas",
+    "simulariumio",
+    "skimage",
+]
+ignore_missing_imports = true
+
+[tool.tox]
+legacy_tox_ini = """
+[tox]
+isolated_build = True
+envlist = py{39,310}, format, lint, typecheck
+skipsdist=True
+
+[testenv]
+allowlist_externals = poetry
+commands =
+    poetry run pytest --cov-report html --cov=src/ tests/
+
+[testenv:format]
+commands =
+    poetry run black -l 100 src/ tests/
+    poetry run isort -l 100 src/ tests/
+
+[testenv:lint]
+commands =
+    poetry run pylint --ignore-patterns=test.*?py src/ tests/ --fail-under=9.0
+
+[testenv:typecheck]
+commands =
+    poetry run mypy --disallow-untyped-calls --disallow-untyped-defs --disallow-incomplete-defs src
+"""
diff --git a/tox.ini b/tox.ini
deleted file mode 100644
index eacdfcb..0000000
--- a/tox.ini
+++ /dev/null
@@ -1,19 +0,0 @@
-[tox]
-isolated_build = True
-envlist = py{39}, linter, mypy
-skipsdist=True
-
-[testenv]
-allowlist_externals = poetry
-commands =
-    poetry run pytest --cov-report html --cov=src/ tests/
-
-[testenv:linter]
-commands =
-    poetry run black -l 100 src/ tests/
-    poetry run isort -l 100 src/ tests/
-    poetry run pylint --ignore-patterns=test.*?py src/ tests/
-
-[testenv:mypy]
-commands =
-    poetry run mypy --config-file mypy.ini --disallow-untyped-calls --disallow-untyped-defs --disallow-incomplete-defs src

From fa1f8910a09fb811d1109ab576f37c45b99c0c89 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Wed, 29 Mar 2023 18:51:33 -0400
Subject: [PATCH 20/48] Release v0.7.2 (#34)

Co-authored-by: jessicasyu <15913767+jessicasyu@users.noreply.github.com>
---
 CHANGELOG.md   | 9 +++++++++
 pyproject.toml | 2 +-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ed69dfb..4dae7ba 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,12 @@
+# [v0.7.2](https://github.com/bagherilab/arcade-collection/releases/tag/v0.7.2) - 2023-03-29
+
+> Compare with [v0.7.1](https://github.com/bagherilab/arcade-collection/compare/v0.7.1...v0.7.2)
+
+### Admin
+
+- Add task decorator to init imports by [@jessicasyu](https://github.com/jessicasyu) in [#32](https://github.com/bagherilab/arcade-collection/pull/32)
+- Update pyproject.toml and dependencies by [@jessicasyu](https://github.com/jessicasyu) in [#33](https://github.com/bagherilab/arcade-collection/pull/33)
+
 # [v0.7.1](https://github.com/bagherilab/arcade-collection/releases/tag/v0.7.1) - 2023-03-28
 
 > Compare with [v0.7.0](https://github.com/bagherilab/arcade-collection/compare/v0.7.0...v0.7.1)
diff --git a/pyproject.toml b/pyproject.toml
index 18a828d..1a160f1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "arcade-collection"
-version = "0.7.1"
+version = "0.7.2"
 description = "Collection of tasks for working with ARCADE."
 authors = [
     "Jessica S. Yu <jesyu@uw.edu>"

From 441435672d58c3b1524bf7e392d8f378e6e9186c Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Tue, 4 Apr 2023 17:31:48 -0400
Subject: [PATCH 21/48] Add separate option to convert to images task (#35)

---
 pyproject.toml                                  |  6 +++---
 .../output/convert_to_images.py                 | 17 ++++++++++++++---
 2 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 1a160f1..051958e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -55,9 +55,9 @@ namespace_packages = true
 
 [[tool.mypy.overrides]]
 module = [
-    "pandas",
-    "simulariumio",
-    "skimage",
+    "pandas.*",
+    "simulariumio.*",
+    "skimage.*",
 ]
 ignore_missing_imports = true
 
diff --git a/src/arcade_collection/output/convert_to_images.py b/src/arcade_collection/output/convert_to_images.py
index 4d187a1..8140bc1 100644
--- a/src/arcade_collection/output/convert_to_images.py
+++ b/src/arcade_collection/output/convert_to_images.py
@@ -1,4 +1,5 @@
 import tarfile
+from typing import Optional
 
 import numpy as np
 
@@ -14,7 +15,8 @@ def convert_to_images(
     box: tuple[int, int, int],
     chunk_size: int,
     binary: bool,
-) -> list[tuple[int, int, np.ndarray]]:
+    separate: bool,
+) -> list[tuple[int, int, np.ndarray, Optional[int]]]:
     length, width, height = box
     frames = list(np.arange(*frame_spec))
     array = np.zeros((len(frames), len(regions), height, width, length), "uint16")
@@ -38,7 +40,16 @@ def convert_to_images(
 
                 array[index, channel][tuple(np.transpose(voxels))] = 1 if binary else location_id
 
-    return split_array_chunks(array, chunk_size)
+    if separate:
+        chunks = [
+            (i, j, chunk, frame)
+            for index, frame in enumerate(frames)
+            for i, j, chunk in split_array_chunks(array[[index], :, :, :, :], chunk_size)
+        ]
+    else:
+        chunks = [(i, j, chunk, None) for i, j, chunk in split_array_chunks(array, chunk_size)]
+
+    return chunks
 
 
 def split_array_chunks(array: np.ndarray, chunk_size: int) -> list[tuple[int, int, np.ndarray]]:
@@ -66,7 +77,7 @@ def split_array_chunks(array: np.ndarray, chunk_size: int) -> list[tuple[int, in
             width_end = width_splits[j + 1]
 
             # Extract chunk from full contents.
-            chunk = array[:, :, :, length_start:length_end, width_start:width_end]
+            chunk = np.copy(array[:, :, :, length_start:length_end, width_start:width_end])
 
             if np.sum(chunk) != 0:
                 chunks.append((i, j, chunk))

From 0eaddd8bfc4bc16221ab17f456ea98af84376fb6 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Tue, 4 Apr 2023 17:37:39 -0400
Subject: [PATCH 22/48] Release v0.8.0 (#36)

Co-authored-by: jessicasyu <15913767+jessicasyu@users.noreply.github.com>
---
 CHANGELOG.md   | 8 ++++++++
 pyproject.toml | 2 +-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4dae7ba..7a21eec 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,11 @@
+# [v0.8.0](https://github.com/bagherilab/arcade-collection/releases/tag/v0.8.0) - 2023-04-04
+
+> Compare with [v0.7.2](https://github.com/bagherilab/arcade-collection/compare/v0.7.2...v0.8.0)
+
+### Features
+
+- Add separate option to convert to images task by [@jessicasyu](https://github.com/jessicasyu) in [#35](https://github.com/bagherilab/arcade-collection/pull/35)
+
 # [v0.7.2](https://github.com/bagherilab/arcade-collection/releases/tag/v0.7.2) - 2023-03-29
 
 > Compare with [v0.7.1](https://github.com/bagherilab/arcade-collection/compare/v0.7.1...v0.7.2)
diff --git a/pyproject.toml b/pyproject.toml
index 051958e..6546ddd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "arcade-collection"
-version = "0.7.2"
+version = "0.8.0"
 description = "Collection of tasks for working with ARCADE."
 authors = [
     "Jessica S. Yu <jesyu@uw.edu>"

From 053823ca7e3b76eb6fd56c76fcc9e32adf37fb52 Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Tue, 23 May 2023 10:27:39 -0400
Subject: [PATCH 23/48] Update lock file version (#37)

---
 poetry.lock | 3508 ++++++++++++++++++++++++---------------------------
 1 file changed, 1678 insertions(+), 1830 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 539ef70..dbc906e 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,26 +1,37 @@
+# This file is automatically @generated by Poetry 1.5.0 and should not be changed by hand.
+
 [[package]]
 name = "aiosqlite"
 version = "0.18.0"
 description = "asyncio bridge to the standard sqlite3 module"
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
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+]
 
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 name = "alabaster"
 version = "0.7.13"
 description = "A configurable sidebar-enabled Sphinx theme"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
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+]
 
 [[package]]
 name = "alembic"
 version = "1.9.4"
 description = "A database migration tool for SQLAlchemy."
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
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+    {file = "alembic-1.9.4.tar.gz", hash = "sha256:4d3bd32ecdbb7bbfb48a9fe9e6d6fd6a831a1b59d03e26e292210237373e7db5"},
+]
 
 [package.dependencies]
 Mako = "*"
@@ -33,9 +44,12 @@ tz = ["python-dateutil"]
 name = "anyio"
 version = "3.6.2"
 description = "High level compatibility layer for multiple asynchronous event loop implementations"
-category = "main"
 optional = false
 python-versions = ">=3.6.2"
+files = [
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+    {file = "anyio-3.6.2.tar.gz", hash = "sha256:25ea0d673ae30af41a0c442f81cf3b38c7e79fdc7b60335a4c14e05eb0947421"},
+]
 
 [package.dependencies]
 idna = ">=2.8"
@@ -50,9 +64,12 @@ trio = ["trio (>=0.16,<0.22)"]
 name = "apprise"
 version = "1.2.1"
 description = "Push Notifications that work with just about every platform!"
-category = "main"
 optional = false
 python-versions = ">=3.6"
+files = [
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+    {file = "apprise-1.2.1.tar.gz", hash = "sha256:67e0c227eecee260000980dbbf8ba1e5eebdbe494f4730808297c9e645c03579"},
+]
 
 [package.dependencies]
 certifi = "*"
@@ -66,9 +83,12 @@ requests-oauthlib = "*"
 name = "asgi-lifespan"
 version = "2.0.0"
 description = "Programmatic startup/shutdown of ASGI apps."
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
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+]
 
 [package.dependencies]
 sniffio = "*"
@@ -77,9 +97,12 @@ sniffio = "*"
 name = "astroid"
 version = "2.14.2"
 description = "An abstract syntax tree for Python with inference support."
-category = "dev"
 optional = false
 python-versions = ">=3.7.2"
+files = [
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+]
 
 [package.dependencies]
 lazy-object-proxy = ">=1.4.0"
@@ -93,9 +116,46 @@ wrapt = [
 name = "asyncpg"
 version = "0.27.0"
 description = "An asyncio PostgreSQL driver"
-category = "main"
 optional = false
 python-versions = ">=3.7.0"
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+    {file = "asyncpg-0.27.0-cp39-cp39-win_amd64.whl", hash = "sha256:1b6499de06fe035cf2fa932ec5617ed3f37d4ebbf663b655922e105a484a6af9"},
+    {file = "asyncpg-0.27.0.tar.gz", hash = "sha256:720986d9a4705dd8a40fdf172036f5ae787225036a7eb46e704c45aa8f62c054"},
+]
 
 [package.extras]
 dev = ["Cython (>=0.29.24,<0.30.0)", "Sphinx (>=4.1.2,<4.2.0)", "flake8 (>=5.0.4,<5.1.0)", "pytest (>=6.0)", "sphinx-rtd-theme (>=0.5.2,<0.6.0)", "sphinxcontrib-asyncio (>=0.3.0,<0.4.0)", "uvloop (>=0.15.3)"]
@@ -106,25 +166,30 @@ test = ["flake8 (>=5.0.4,<5.1.0)", "uvloop (>=0.15.3)"]
 name = "attrs"
 version = "22.2.0"
 description = "Classes Without Boilerplate"
-category = "main"
 optional = false
 python-versions = ">=3.6"
+files = [
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+    {file = "attrs-22.2.0.tar.gz", hash = "sha256:c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99"},
+]
 
 [package.extras]
 cov = ["attrs[tests]", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"]
 dev = ["attrs[docs,tests]"]
 docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope.interface"]
 tests = ["attrs[tests-no-zope]", "zope.interface"]
-tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=0.971,<0.990)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
-tests_no_zope = ["cloudpickle", "hypothesis", "mypy (>=0.971,<0.990)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy (>=0.971,<0.990)", "mypy (>=0.971,<0.990)", "pympler", "pympler", "pytest (>=4.3.0)", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-mypy-plugins", "pytest-xdist[psutil]", "pytest-xdist[psutil]"]
 
 [[package]]
 name = "Babel"
 version = "2.11.0"
 description = "Internationalization utilities"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
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+    {file = "Babel-2.11.0.tar.gz", hash = "sha256:5ef4b3226b0180dedded4229651c8b0e1a3a6a2837d45a073272f313e4cf97f6"},
+]
 
 [package.dependencies]
 pytz = ">=2015.7"
@@ -133,9 +198,22 @@ pytz = ">=2015.7"
 name = "black"
 version = "22.12.0"
 description = "The uncompromising code formatter."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
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+]
 
 [package.dependencies]
 click = ">=8.0.0"
@@ -155,25 +233,96 @@ uvloop = ["uvloop (>=0.15.2)"]
 name = "cachetools"
 version = "5.3.0"
 description = "Extensible memoizing collections and decorators"
-category = "main"
 optional = false
 python-versions = "~=3.7"
+files = [
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+]
 
 [[package]]
 name = "certifi"
 version = "2022.12.7"
 description = "Python package for providing Mozilla's CA Bundle."
-category = "main"
 optional = false
 python-versions = ">=3.6"
+files = [
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+]
 
 [[package]]
 name = "cffi"
 version = "1.15.1"
 description = "Foreign Function Interface for Python calling C code."
-category = "main"
 optional = false
 python-versions = "*"
+files = [
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 [package.dependencies]
 pycparser = "*"
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 name = "charset-normalizer"
 version = "3.0.1"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
-category = "main"
 optional = false
 python-versions = "*"
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 version = "8.1.3"
 description = "Composable command line interface toolkit"
-category = "main"
 optional = false
 python-versions = ">=3.7"
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 [package.dependencies]
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 python-versions = "*"
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 python-versions = ">=3.7"
-
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-
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+]
+
+[package.dependencies]
+tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""}
+
+[package.extras]
+toml = ["tomli"]
 
 [[package]]
 name = "croniter"
 version = "1.3.8"
 description = "croniter provides iteration for datetime object with cron like format"
-category = "main"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
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+]
 
 [package.dependencies]
 python-dateutil = "*"
@@ -250,9 +555,33 @@ python-dateutil = "*"
 name = "cryptography"
 version = "39.0.1"
 description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
-category = "main"
 optional = false
 python-versions = ">=3.6"
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+    {file = "cryptography-39.0.1-pp39-pypy39_pp73-manylinux_2_28_aarch64.whl", hash = "sha256:ef8b72fa70b348724ff1218267e7f7375b8de4e8194d1636ee60510aae104cd0"},
+    {file = "cryptography-39.0.1-pp39-pypy39_pp73-manylinux_2_28_x86_64.whl", hash = "sha256:aec5a6c9864be7df2240c382740fcf3b96928c46604eaa7f3091f58b878c0bb6"},
+    {file = "cryptography-39.0.1-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:fdd188c8a6ef8769f148f88f859884507b954cc64db6b52f66ef199bb9ad660a"},
+    {file = "cryptography-39.0.1.tar.gz", hash = "sha256:d1f6198ee6d9148405e49887803907fe8962a23e6c6f83ea7d98f1c0de375695"},
+]
 
 [package.dependencies]
 cffi = ">=1.12"
@@ -271,9 +600,12 @@ tox = ["tox"]
 name = "dateparser"
 version = "1.1.7"
 description = "Date parsing library designed to parse dates from HTML pages"
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "dateparser-1.1.7-py2.py3-none-any.whl", hash = "sha256:fbed8b738a24c9cd7f47c4f2089527926566fe539e1a06125eddba75917b1eef"},
+    {file = "dateparser-1.1.7.tar.gz", hash = "sha256:ff047d9cffad4d3113ead8ec0faf8a7fc43bab7d853ac8715e071312b53c465a"},
+]
 
 [package.dependencies]
 python-dateutil = "*"
@@ -290,9 +622,12 @@ langdetect = ["langdetect"]
 name = "dill"
 version = "0.3.6"
 description = "serialize all of python"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "dill-0.3.6-py3-none-any.whl", hash = "sha256:a07ffd2351b8c678dfc4a856a3005f8067aea51d6ba6c700796a4d9e280f39f0"},
+    {file = "dill-0.3.6.tar.gz", hash = "sha256:e5db55f3687856d8fbdab002ed78544e1c4559a130302693d839dfe8f93f2373"},
+]
 
 [package.extras]
 graph = ["objgraph (>=1.7.2)"]
@@ -301,17 +636,23 @@ graph = ["objgraph (>=1.7.2)"]
 name = "distlib"
 version = "0.3.6"
 description = "Distribution utilities"
-category = "dev"
 optional = false
 python-versions = "*"
+files = [
+    {file = "distlib-0.3.6-py2.py3-none-any.whl", hash = "sha256:f35c4b692542ca110de7ef0bea44d73981caeb34ca0b9b6b2e6d7790dda8f80e"},
+    {file = "distlib-0.3.6.tar.gz", hash = "sha256:14bad2d9b04d3a36127ac97f30b12a19268f211063d8f8ee4f47108896e11b46"},
+]
 
 [[package]]
 name = "docker"
 version = "6.0.1"
 description = "A Python library for the Docker Engine API."
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "docker-6.0.1-py3-none-any.whl", hash = "sha256:dbcb3bd2fa80dca0788ed908218bf43972772009b881ed1e20dfc29a65e49782"},
+    {file = "docker-6.0.1.tar.gz", hash = "sha256:896c4282e5c7af5c45e8b683b0b0c33932974fe6e50fc6906a0a83616ab3da97"},
+]
 
 [package.dependencies]
 packaging = ">=14.0"
@@ -327,17 +668,23 @@ ssh = ["paramiko (>=2.4.3)"]
 name = "docutils"
 version = "0.18.1"
 description = "Docutils -- Python Documentation Utilities"
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+files = [
+    {file = "docutils-0.18.1-py2.py3-none-any.whl", hash = "sha256:23010f129180089fbcd3bc08cfefccb3b890b0050e1ca00c867036e9d161b98c"},
+    {file = "docutils-0.18.1.tar.gz", hash = "sha256:679987caf361a7539d76e584cbeddc311e3aee937877c87346f31debc63e9d06"},
+]
 
 [[package]]
 name = "exceptiongroup"
 version = "1.1.0"
 description = "Backport of PEP 654 (exception groups)"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "exceptiongroup-1.1.0-py3-none-any.whl", hash = "sha256:327cbda3da756e2de031a3107b81ab7b3770a602c4d16ca618298c526f4bec1e"},
+    {file = "exceptiongroup-1.1.0.tar.gz", hash = "sha256:bcb67d800a4497e1b404c2dd44fca47d3b7a5e5433dbab67f96c1a685cdfdf23"},
+]
 
 [package.extras]
 test = ["pytest (>=6)"]
@@ -346,9 +693,12 @@ test = ["pytest (>=6)"]
 name = "fastapi"
 version = "0.92.0"
 description = "FastAPI framework, high performance, easy to learn, fast to code, ready for production"
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "fastapi-0.92.0-py3-none-any.whl", hash = "sha256:ae7b97c778e2f2ec3fb3cb4fb14162129411d99907fb71920f6d69a524340ebf"},
+    {file = "fastapi-0.92.0.tar.gz", hash = "sha256:023a0f5bd2c8b2609014d3bba1e14a1d7df96c6abea0a73070621c9862b9a4de"},
+]
 
 [package.dependencies]
 pydantic = ">=1.6.2,<1.7 || >1.7,<1.7.1 || >1.7.1,<1.7.2 || >1.7.2,<1.7.3 || >1.7.3,<1.8 || >1.8,<1.8.1 || >1.8.1,<2.0.0"
@@ -364,9 +714,12 @@ test = ["anyio[trio] (>=3.2.1,<4.0.0)", "black (==22.10.0)", "coverage[toml] (>=
 name = "filelock"
 version = "3.9.0"
 description = "A platform independent file lock."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "filelock-3.9.0-py3-none-any.whl", hash = "sha256:f58d535af89bb9ad5cd4df046f741f8553a418c01a7856bf0d173bbc9f6bd16d"},
+    {file = "filelock-3.9.0.tar.gz", hash = "sha256:7b319f24340b51f55a2bf7a12ac0755a9b03e718311dac567a0f4f7fabd2f5de"},
+]
 
 [package.extras]
 docs = ["furo (>=2022.12.7)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.5)"]
@@ -376,9 +729,12 @@ testing = ["covdefaults (>=2.2.2)", "coverage (>=7.0.1)", "pytest (>=7.2)", "pyt
 name = "fsspec"
 version = "2023.1.0"
 description = "File-system specification"
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "fsspec-2023.1.0-py3-none-any.whl", hash = "sha256:b833e2e541e9e8cde0ab549414187871243177feb3d344f9d27b25a93f5d8139"},
+    {file = "fsspec-2023.1.0.tar.gz", hash = "sha256:fbae7f20ff801eb5f7d0bedf81f25c787c0dfac5e982d98fa3884a9cde2b5411"},
+]
 
 [package.extras]
 abfs = ["adlfs"]
@@ -407,9 +763,12 @@ tqdm = ["tqdm"]
 name = "google-auth"
 version = "2.16.1"
 description = "Google Authentication Library"
-category = "main"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*"
+files = [
+    {file = "google-auth-2.16.1.tar.gz", hash = "sha256:5fd170986bce6bfd7bb5c845c4b8362edb1e0cba901e062196e83f8bb5d5d32c"},
+    {file = "google_auth-2.16.1-py2.py3-none-any.whl", hash = "sha256:75d76ea857df65938e1f71dcbcd7d0cd48e3f80b34b8870ba229c9292081f7ef"},
+]
 
 [package.dependencies]
 cachetools = ">=2.0.0,<6.0"
@@ -419,7 +778,7 @@ six = ">=1.9.0"
 
 [package.extras]
 aiohttp = ["aiohttp (>=3.6.2,<4.0.0dev)", "requests (>=2.20.0,<3.0.0dev)"]
-enterprise_cert = ["cryptography (==36.0.2)", "pyopenssl (==22.0.0)"]
+enterprise-cert = ["cryptography (==36.0.2)", "pyopenssl (==22.0.0)"]
 pyopenssl = ["cryptography (>=38.0.3)", "pyopenssl (>=20.0.0)"]
 reauth = ["pyu2f (>=0.1.5)"]
 requests = ["requests (>=2.20.0,<3.0.0dev)"]
@@ -428,9 +787,70 @@ requests = ["requests (>=2.20.0,<3.0.0dev)"]
 name = "greenlet"
 version = "2.0.2"
 description = "Lightweight in-process concurrent programming"
-category = "main"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
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+]
 
 [package.extras]
 docs = ["Sphinx", "docutils (<0.18)"]
@@ -440,9 +860,12 @@ test = ["objgraph", "psutil"]
 name = "griffe"
 version = "0.25.5"
 description = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API."
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
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+    {file = "griffe-0.25.5.tar.gz", hash = "sha256:11ea3403ef0560a1cbcf7f302eb5d21cf4c1d8ed3f8a16a75aa9f6f458caf3f1"},
+]
 
 [package.dependencies]
 colorama = ">=0.4"
@@ -454,17 +877,23 @@ async = ["aiofiles (>=0.7,<1.0)"]
 name = "h11"
 version = "0.14.0"
 description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1"
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
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+    {file = "h11-0.14.0.tar.gz", hash = "sha256:8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d"},
+]
 
 [[package]]
 name = "h2"
 version = "4.1.0"
 description = "HTTP/2 State-Machine based protocol implementation"
-category = "main"
 optional = false
 python-versions = ">=3.6.1"
+files = [
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+    {file = "h2-4.1.0.tar.gz", hash = "sha256:a83aca08fbe7aacb79fec788c9c0bac936343560ed9ec18b82a13a12c28d2abb"},
+]
 
 [package.dependencies]
 hpack = ">=4.0,<5"
@@ -474,35 +903,44 @@ hyperframe = ">=6.0,<7"
 name = "hpack"
 version = "4.0.0"
 description = "Pure-Python HPACK header compression"
-category = "main"
 optional = false
 python-versions = ">=3.6.1"
+files = [
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+    {file = "hpack-4.0.0.tar.gz", hash = "sha256:fc41de0c63e687ebffde81187a948221294896f6bdc0ae2312708df339430095"},
+]
 
 [[package]]
 name = "httpcore"
 version = "0.16.3"
 description = "A minimal low-level HTTP client."
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
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+    {file = "httpcore-0.16.3.tar.gz", hash = "sha256:c5d6f04e2fc530f39e0c077e6a30caa53f1451096120f1f38b954afd0b17c0cb"},
+]
 
 [package.dependencies]
 anyio = ">=3.0,<5.0"
 certifi = "*"
 h11 = ">=0.13,<0.15"
-sniffio = ">=1.0.0,<2.0.0"
+sniffio = "==1.*"
 
 [package.extras]
 http2 = ["h2 (>=3,<5)"]
-socks = ["socksio (>=1.0.0,<2.0.0)"]
+socks = ["socksio (==1.*)"]
 
 [[package]]
 name = "httpx"
 version = "0.23.3"
 description = "The next generation HTTP client."
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
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+    {file = "httpx-0.23.3.tar.gz", hash = "sha256:9818458eb565bb54898ccb9b8b251a28785dd4a55afbc23d0eb410754fe7d0f9"},
+]
 
 [package.dependencies]
 certifi = "*"
@@ -513,33 +951,42 @@ sniffio = "*"
 
 [package.extras]
 brotli = ["brotli", "brotlicffi"]
-cli = ["click (>=8.0.0,<9.0.0)", "pygments (>=2.0.0,<3.0.0)", "rich (>=10,<13)"]
+cli = ["click (==8.*)", "pygments (==2.*)", "rich (>=10,<13)"]
 http2 = ["h2 (>=3,<5)"]
-socks = ["socksio (>=1.0.0,<2.0.0)"]
+socks = ["socksio (==1.*)"]
 
 [[package]]
 name = "hyperframe"
 version = "6.0.1"
 description = "HTTP/2 framing layer for Python"
-category = "main"
 optional = false
 python-versions = ">=3.6.1"
+files = [
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+    {file = "hyperframe-6.0.1.tar.gz", hash = "sha256:ae510046231dc8e9ecb1a6586f63d2347bf4c8905914aa84ba585ae85f28a914"},
+]
 
 [[package]]
 name = "idna"
 version = "3.4"
 description = "Internationalized Domain Names in Applications (IDNA)"
-category = "main"
 optional = false
 python-versions = ">=3.5"
+files = [
+    {file = "idna-3.4-py3-none-any.whl", hash = "sha256:90b77e79eaa3eba6de819a0c442c0b4ceefc341a7a2ab77d7562bf49f425c5c2"},
+    {file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"},
+]
 
 [[package]]
 name = "imageio"
 version = "2.25.1"
 description = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats."
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "imageio-2.25.1-py3-none-any.whl", hash = "sha256:5bce7f88eef7ee4e9aac798d3b218fea2e98cbbaa59a3e37b730a7aa5784eeac"},
+    {file = "imageio-2.25.1.tar.gz", hash = "sha256:6021d42debd2187e9c781e494a49a30eba002fbac1eef43f491bbc731e7a6d2b"},
+]
 
 [package.dependencies]
 numpy = "*"
@@ -566,17 +1013,23 @@ tifffile = ["tifffile"]
 name = "imagesize"
 version = "1.4.1"
 description = "Getting image size from png/jpeg/jpeg2000/gif file"
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
+    {file = "imagesize-1.4.1-py2.py3-none-any.whl", hash = "sha256:0d8d18d08f840c19d0ee7ca1fd82490fdc3729b7ac93f49870406ddde8ef8d8b"},
+    {file = "imagesize-1.4.1.tar.gz", hash = "sha256:69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a"},
+]
 
 [[package]]
 name = "importlib-metadata"
 version = "6.0.0"
 description = "Read metadata from Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "importlib_metadata-6.0.0-py3-none-any.whl", hash = "sha256:7efb448ec9a5e313a57655d35aa54cd3e01b7e1fbcf72dce1bf06119420f5bad"},
+    {file = "importlib_metadata-6.0.0.tar.gz", hash = "sha256:e354bedeb60efa6affdcc8ae121b73544a7aa74156d047311948f6d711cd378d"},
+]
 
 [package.dependencies]
 zipp = ">=0.5"
@@ -590,17 +1043,23 @@ testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packag
 name = "iniconfig"
 version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"},
+    {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
+]
 
 [[package]]
 name = "isort"
 version = "5.12.0"
 description = "A Python utility / library to sort Python imports."
-category = "dev"
 optional = false
 python-versions = ">=3.8.0"
+files = [
+    {file = "isort-5.12.0-py3-none-any.whl", hash = "sha256:f84c2818376e66cf843d497486ea8fed8700b340f308f076c6fb1229dff318b6"},
+    {file = "isort-5.12.0.tar.gz", hash = "sha256:8bef7dde241278824a6d83f44a544709b065191b95b6e50894bdc722fcba0504"},
+]
 
 [package.extras]
 colors = ["colorama (>=0.4.3)"]
@@ -612,9 +1071,12 @@ requirements-deprecated-finder = ["pip-api", "pipreqs"]
 name = "Jinja2"
 version = "3.1.2"
 description = "A very fast and expressive template engine."
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "Jinja2-3.1.2-py3-none-any.whl", hash = "sha256:6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61"},
+    {file = "Jinja2-3.1.2.tar.gz", hash = "sha256:31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852"},
+]
 
 [package.dependencies]
 MarkupSafe = ">=2.0"
@@ -626,9 +1088,12 @@ i18n = ["Babel (>=2.7)"]
 name = "jsonpatch"
 version = "1.32"
 description = "Apply JSON-Patches (RFC 6902)"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+files = [
+    {file = "jsonpatch-1.32-py2.py3-none-any.whl", hash = "sha256:26ac385719ac9f54df8a2f0827bb8253aa3ea8ab7b3368457bcdb8c14595a397"},
+    {file = "jsonpatch-1.32.tar.gz", hash = "sha256:b6ddfe6c3db30d81a96aaeceb6baf916094ffa23d7dd5fa2c13e13f8b6e600c2"},
+]
 
 [package.dependencies]
 jsonpointer = ">=1.9"
@@ -637,17 +1102,23 @@ jsonpointer = ">=1.9"
 name = "jsonpointer"
 version = "2.3"
 description = "Identify specific nodes in a JSON document (RFC 6901)"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
+    {file = "jsonpointer-2.3-py2.py3-none-any.whl", hash = "sha256:51801e558539b4e9cd268638c078c6c5746c9ac96bc38152d443400e4f3793e9"},
+    {file = "jsonpointer-2.3.tar.gz", hash = "sha256:97cba51526c829282218feb99dab1b1e6bdf8efd1c43dc9d57be093c0d69c99a"},
+]
 
 [[package]]
 name = "jsonschema"
 version = "4.17.3"
 description = "An implementation of JSON Schema validation for Python"
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "jsonschema-4.17.3-py3-none-any.whl", hash = "sha256:a870ad254da1a8ca84b6a2905cac29d265f805acc57af304784962a2aa6508f6"},
+    {file = "jsonschema-4.17.3.tar.gz", hash = "sha256:0f864437ab8b6076ba6707453ef8f98a6a0d512a80e93f8abdb676f737ecb60d"},
+]
 
 [package.dependencies]
 attrs = ">=17.4.0"
@@ -661,9 +1132,12 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 name = "kubernetes"
 version = "26.1.0"
 description = "Kubernetes python client"
-category = "main"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "kubernetes-26.1.0-py2.py3-none-any.whl", hash = "sha256:e3db6800abf7e36c38d2629b5cb6b74d10988ee0cba6fba45595a7cbe60c0042"},
+    {file = "kubernetes-26.1.0.tar.gz", hash = "sha256:5854b0c508e8d217ca205591384ab58389abdae608576f9c9afc35a3c76a366c"},
+]
 
 [package.dependencies]
 certifi = ">=14.05.14"
@@ -675,7 +1149,7 @@ requests-oauthlib = "*"
 setuptools = ">=21.0.0"
 six = ">=1.9.0"
 urllib3 = ">=1.24.2"
-websocket-client = ">=0.32.0,<0.40.0 || >0.40.0,<0.41.0 || >=0.43.0"
+websocket-client = ">=0.32.0,<0.40.0 || >0.40.0,<0.41.dev0 || >=0.43.dev0"
 
 [package.extras]
 adal = ["adal (>=1.0.2)"]
@@ -684,37 +1158,80 @@ adal = ["adal (>=1.0.2)"]
 name = "lazy-object-proxy"
 version = "1.9.0"
 description = "A fast and thorough lazy object proxy."
-category = "dev"
-optional = false
-python-versions = ">=3.7"
-
-[[package]]
-name = "Mako"
-version = "1.2.4"
-description = "A super-fast templating language that borrows the best ideas from the existing templating languages."
-category = "main"
-optional = false
-python-versions = ">=3.7"
-
-[package.dependencies]
-MarkupSafe = ">=0.9.2"
-
-[package.extras]
-babel = ["Babel"]
-lingua = ["lingua"]
-testing = ["pytest"]
-
-[[package]]
-name = "Markdown"
-version = "3.4.1"
-description = "Python implementation of Markdown."
-category = "main"
 optional = false
 python-versions = ">=3.7"
-
-[package.dependencies]
-importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
-
+files = [
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+
+[[package]]
+name = "Mako"
+version = "1.2.4"
+description = "A super-fast templating language that borrows the best ideas from the existing templating languages."
+optional = false
+python-versions = ">=3.7"
+files = [
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+    {file = "Mako-1.2.4.tar.gz", hash = "sha256:d60a3903dc3bb01a18ad6a89cdbe2e4eadc69c0bc8ef1e3773ba53d44c3f7a34"},
+]
+
+[package.dependencies]
+MarkupSafe = ">=0.9.2"
+
+[package.extras]
+babel = ["Babel"]
+lingua = ["lingua"]
+testing = ["pytest"]
+
+[[package]]
+name = "Markdown"
+version = "3.4.1"
+description = "Python implementation of Markdown."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "Markdown-3.4.1-py3-none-any.whl", hash = "sha256:08fb8465cffd03d10b9dd34a5c3fea908e20391a2a90b88d66362cb05beed186"},
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+
+[package.dependencies]
+importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
+
 [package.extras]
 testing = ["coverage", "pyyaml"]
 
@@ -722,16 +1239,19 @@ testing = ["coverage", "pyyaml"]
 name = "markdown-it-py"
 version = "2.2.0"
 description = "Python port of markdown-it. Markdown parsing, done right!"
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
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+    {file = "markdown_it_py-2.2.0-py3-none-any.whl", hash = "sha256:5a35f8d1870171d9acc47b99612dc146129b631baf04970128b568f190d0cc30"},
+]
 
 [package.dependencies]
 mdurl = ">=0.1,<1.0"
 
 [package.extras]
 benchmarking = ["psutil", "pytest", "pytest-benchmark"]
-code_style = ["pre-commit (>=3.0,<4.0)"]
+code-style = ["pre-commit (>=3.0,<4.0)"]
 compare = ["commonmark (>=0.9,<1.0)", "markdown (>=3.4,<4.0)", "mistletoe (>=1.0,<2.0)", "mistune (>=2.0,<3.0)", "panflute (>=2.3,<3.0)"]
 linkify = ["linkify-it-py (>=1,<3)"]
 plugins = ["mdit-py-plugins"]
@@ -743,41 +1263,132 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 name = "MarkupSafe"
 version = "2.1.2"
 description = "Safely add untrusted strings to HTML/XML markup."
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
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+    {version = ">=1.23.2", markers = "python_version >= \"3.11\""},
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 pytz = ">=2020.1"
 
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 version = "0.11.0"
 description = "Utility library for gitignore style pattern matching of file paths."
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 optional = false
 python-versions = ">=3.7"
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+]
 
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 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
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@@ -906,9 +1734,12 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa
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 version = "0.20.1"
 description = "Physical quantities module"
-category = "main"
 optional = false
 python-versions = ">=3.8"
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 [package.extras]
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@@ -923,9 +1754,12 @@ xarray = ["xarray"]
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 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
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 [package.dependencies]
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@@ -1048,9 +1937,12 @@ email = ["email-validator (>=1.0.3)"]
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 version = "2.14.0"
 description = "Pygments is a syntax highlighting package written in Python."
-category = "main"
 optional = false
 python-versions = ">=3.6"
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 description = "python code static checker"
-category = "dev"
 optional = false
 python-versions = ">=3.7.2"
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 version = "4.0.3"
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 name = "regex"
 version = "2022.10.31"
 description = "Alternative regular expression module, to replace re."
-category = "main"
 optional = false
 python-versions = ">=3.6"
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 name = "requests"
 version = "2.28.2"
 description = "Python HTTP for Humans."
-category = "main"
 optional = false
 python-versions = ">=3.7, <4"
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+]
 
 [package.dependencies]
 certifi = ">=2017.4.17"
@@ -1249,15 +2373,18 @@ urllib3 = ">=1.21.1,<1.27"
 
 [package.extras]
 socks = ["PySocks (>=1.5.6,!=1.5.7)"]
-use_chardet_on_py3 = ["chardet (>=3.0.2,<6)"]
+use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "requests-oauthlib"
 version = "1.3.1"
 description = "OAuthlib authentication support for Requests."
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
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+]
 
 [package.dependencies]
 oauthlib = ">=3.0.0"
@@ -1270,9 +2397,12 @@ rsa = ["oauthlib[signedtoken] (>=3.0.0)"]
 name = "rfc3986"
 version = "1.5.0"
 description = "Validating URI References per RFC 3986"
-category = "main"
 optional = false
 python-versions = "*"
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+]
 
 [package.dependencies]
 idna = {version = "*", optional = true, markers = "extra == \"idna2008\""}
@@ -1284,9 +2414,12 @@ idna2008 = ["idna"]
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 version = "13.3.1"
 description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
-category = "main"
 optional = false
 python-versions = ">=3.7.0"
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 [package.dependencies]
 markdown-it-py = ">=2.1.0,<3.0.0"
@@ -1299,9 +2432,12 @@ jupyter = ["ipywidgets (>=7.5.1,<9)"]
 name = "rsa"
 version = "4.9"
 description = "Pure-Python RSA implementation"
-category = "main"
 optional = false
 python-versions = ">=3.6,<4"
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+]
 
 [package.dependencies]
 pyasn1 = ">=0.1.3"
@@ -1310,9 +2446,36 @@ pyasn1 = ">=0.1.3"
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 version = "0.19.3"
 description = "Image processing in Python"
-category = "main"
 optional = false
 python-versions = ">=3.7"
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 imageio = ">=2.4.1"
@@ -1334,9 +2497,31 @@ test = ["asv", "codecov", "flake8", "matplotlib (>=3.0.3)", "pooch (>=1.3.0)", "
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 version = "1.9.3"
 description = "Fundamental algorithms for scientific computing in Python"
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 python-versions = ">=3.8"
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+    {file = "scipy-1.9.3-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:4db5b30849606a95dcf519763dd3ab6fe9bd91df49eba517359e450a7d80ce2e"},
+    {file = "scipy-1.9.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c68db6b290cbd4049012990d7fe71a2abd9ffbe82c0056ebe0f01df8be5436b0"},
+    {file = "scipy-1.9.3-cp39-cp39-win_amd64.whl", hash = "sha256:5b88e6d91ad9d59478fafe92a7c757d00c59e3bdc3331be8ada76a4f8d683f58"},
+    {file = "scipy-1.9.3.tar.gz", hash = "sha256:fbc5c05c85c1a02be77b1ff591087c83bc44579c6d2bd9fb798bb64ea5e1a027"},
+]
 
 [package.dependencies]
 numpy = ">=1.18.5,<1.26.0"
@@ -1350,9 +2535,12 @@ test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "sciki
 name = "setuptools"
 version = "67.4.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "setuptools-67.4.0-py3-none-any.whl", hash = "sha256:f106dee1b506dee5102cc3f3e9e68137bbad6d47b616be7991714b0c62204251"},
+    {file = "setuptools-67.4.0.tar.gz", hash = "sha256:e5fd0a713141a4a105412233c63dc4e17ba0090c8e8334594ac790ec97792330"},
+]
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
@@ -1363,9 +2551,12 @@ testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (
 name = "simulariumio"
 version = "1.7.1"
 description = "Python package that converts simulation outputs to the format consumed by the Simularium viewer website"
-category = "main"
 optional = false
 python-versions = ">=3.8"
+files = [
+    {file = "simulariumio-1.7.1-py3-none-any.whl", hash = "sha256:be156694194a9a287af08c11ebed80ccfb19d00f1e617f826c7a559ce90e6e64"},
+    {file = "simulariumio-1.7.1.tar.gz", hash = "sha256:273f906161614b68d7c98a15130522027b1d993cf5bebec94f190d3fef967c55"},
+]
 
 [package.dependencies]
 numpy = ">=1.19.0"
@@ -1388,33 +2579,45 @@ tutorial = ["MDAnalysis (>=2.0.0)", "MDAnalysisTests (>=2.0.0)", "jupyter", "sci
 name = "six"
 version = "1.16.0"
 description = "Python 2 and 3 compatibility utilities"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
+files = [
+    {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
+    {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
+]
 
 [[package]]
 name = "sniffio"
 version = "1.3.0"
 description = "Sniff out which async library your code is running under"
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "sniffio-1.3.0-py3-none-any.whl", hash = "sha256:eecefdce1e5bbfb7ad2eeaabf7c1eeb404d7757c379bd1f7e5cce9d8bf425384"},
+    {file = "sniffio-1.3.0.tar.gz", hash = "sha256:e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101"},
+]
 
 [[package]]
 name = "snowballstemmer"
 version = "2.2.0"
 description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
-category = "dev"
 optional = false
 python-versions = "*"
+files = [
+    {file = "snowballstemmer-2.2.0-py2.py3-none-any.whl", hash = "sha256:c8e1716e83cc398ae16824e5572ae04e0d9fc2c6b985fb0f900f5f0c96ecba1a"},
+    {file = "snowballstemmer-2.2.0.tar.gz", hash = "sha256:09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1"},
+]
 
 [[package]]
 name = "Sphinx"
 version = "5.3.0"
 description = "Python documentation generator"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "Sphinx-5.3.0.tar.gz", hash = "sha256:51026de0a9ff9fc13c05d74913ad66047e104f56a129ff73e174eb5c3ee794b5"},
+    {file = "sphinx-5.3.0-py3-none-any.whl", hash = "sha256:060ca5c9f7ba57a08a1219e547b269fadf125ae25b06b9fa7f66768efb652d6d"},
+]
 
 [package.dependencies]
 alabaster = ">=0.7,<0.8"
@@ -1444,11 +2647,14 @@ test = ["cython", "html5lib", "pytest (>=4.6)", "typed_ast"]
 name = "sphinx_mdinclude"
 version = "0.5.3"
 description = "Markdown extension for Sphinx"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
-
-[package.dependencies]
+files = [
+    {file = "sphinx_mdinclude-0.5.3-py3-none-any.whl", hash = "sha256:02afadf4597aecf8255a702956eff5b8c5cb9658ea995c3d361722d2ed78cca9"},
+    {file = "sphinx_mdinclude-0.5.3.tar.gz", hash = "sha256:2998e3d18b3022c9983d1b72191fe37e25ffccd54165cbe3acb22cceedd91af4"},
+]
+
+[package.dependencies]
 docutils = ">=0.16,<1.0"
 mistune = ">=2.0,<3.0"
 pygments = ">=2.8"
@@ -1457,9 +2663,12 @@ pygments = ">=2.8"
 name = "sphinx-rtd-theme"
 version = "1.2.0"
 description = "Read the Docs theme for Sphinx"
-category = "dev"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
+files = [
+    {file = "sphinx_rtd_theme-1.2.0-py2.py3-none-any.whl", hash = "sha256:f823f7e71890abe0ac6aaa6013361ea2696fc8d3e1fa798f463e82bdb77eeff2"},
+    {file = "sphinx_rtd_theme-1.2.0.tar.gz", hash = "sha256:a0d8bd1a2ed52e0b338cbe19c4b2eef3c5e7a048769753dac6a9f059c7b641b8"},
+]
 
 [package.dependencies]
 docutils = "<0.19"
@@ -1473,9 +2682,12 @@ dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"]
 name = "sphinxcontrib-applehelp"
 version = "1.0.4"
 description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
+files = [
+    {file = "sphinxcontrib-applehelp-1.0.4.tar.gz", hash = "sha256:828f867945bbe39817c210a1abfd1bc4895c8b73fcaade56d45357a348a07d7e"},
+    {file = "sphinxcontrib_applehelp-1.0.4-py3-none-any.whl", hash = "sha256:29d341f67fb0f6f586b23ad80e072c8e6ad0b48417db2bde114a4c9746feb228"},
+]
 
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
@@ -1485,9 +2697,12 @@ test = ["pytest"]
 name = "sphinxcontrib-devhelp"
 version = "1.0.2"
 description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document."
-category = "dev"
 optional = false
 python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-devhelp-1.0.2.tar.gz", hash = "sha256:ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4"},
+    {file = "sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl", hash = "sha256:8165223f9a335cc1af7ffe1ed31d2871f325254c0423bc0c4c7cd1c1e4734a2e"},
+]
 
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
@@ -1497,9 +2712,12 @@ test = ["pytest"]
 name = "sphinxcontrib-htmlhelp"
 version = "2.0.1"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
+files = [
+    {file = "sphinxcontrib-htmlhelp-2.0.1.tar.gz", hash = "sha256:0cbdd302815330058422b98a113195c9249825d681e18f11e8b1f78a2f11efff"},
+    {file = "sphinxcontrib_htmlhelp-2.0.1-py3-none-any.whl", hash = "sha256:c38cb46dccf316c79de6e5515e1770414b797162b23cd3d06e67020e1d2a6903"},
+]
 
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
@@ -1509,1666 +2727,67 @@ test = ["html5lib", "pytest"]
 name = "sphinxcontrib.jquery"
 version = "2.0.0"
 description = "Extension to include jQuery on newer Sphinx releases"
-category = "dev"
 optional = false
 python-versions = ">=2.7"
+files = [
+    {file = "sphinxcontrib-jquery-2.0.0.tar.gz", hash = "sha256:8fb65f6dba84bf7bcd1aea1f02ab3955ac34611d838bcc95d4983b805b234daa"},
+    {file = "sphinxcontrib_jquery-2.0.0-py3-none-any.whl", hash = "sha256:ed47fa425c338ffebe3c37e1cdb56e30eb806116b85f01055b158c7057fdb995"},
+]
 
 [package.dependencies]
 setuptools = "*"
-
-[[package]]
-name = "sphinxcontrib-jsmath"
-version = "1.0.1"
-description = "A sphinx extension which renders display math in HTML via JavaScript"
-category = "dev"
-optional = false
-python-versions = ">=3.5"
-
-[package.extras]
-test = ["flake8", "mypy", "pytest"]
-
-[[package]]
-name = "sphinxcontrib-qthelp"
-version = "1.0.3"
-description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document."
-category = "dev"
-optional = false
-python-versions = ">=3.5"
-
-[package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
-test = ["pytest"]
-
-[[package]]
-name = "sphinxcontrib-serializinghtml"
-version = "1.1.5"
-description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)."
-category = "dev"
-optional = false
-python-versions = ">=3.5"
-
-[package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
-test = ["pytest"]
-
-[[package]]
-name = "SQLAlchemy"
-version = "1.4.46"
-description = "Database Abstraction Library"
-category = "main"
-optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
-
-[package.dependencies]
-greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"}
-
-[package.extras]
-aiomysql = ["aiomysql", "greenlet (!=0.4.17)"]
-aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing_extensions (!=3.10.0.1)"]
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-mysql = ["mysqlclient (>=1.4.0)", "mysqlclient (>=1.4.0,<2)"]
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-oracle = ["cx_oracle (>=7)", "cx_oracle (>=7,<8)"]
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-postgresql_asyncpg = ["asyncpg", "greenlet (!=0.4.17)"]
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-postgresql_psycopg2binary = ["psycopg2-binary"]
-postgresql_psycopg2cffi = ["psycopg2cffi"]
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-sqlcipher = ["sqlcipher3_binary"]
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-python-versions = ">=3.7"
-
-[package.dependencies]
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-
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-
-[package.dependencies]
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-[package.extras]
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+
+[[package]]
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@@ -3211,67 +2830,273 @@ SQLAlchemy = [
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+
+[package.extras]
+docs = ["Sphinx (>=3.4)", "sphinx-rtd-theme (>=0.5)"]
+optional = ["python-socks", "wsaccel"]
+test = ["websockets"]
+
+[[package]]
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+optional = false
+python-versions = ">=3.7"
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@@ -3342,7 +3167,14 @@ websockets = [
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 ]
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+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
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@@ -3408,7 +3240,23 @@ wrapt = [
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 ]
-zipp = [
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+[[package]]
+name = "zipp"
+version = "3.14.0"
+description = "Backport of pathlib-compatible object wrapper for zip files"
+optional = false
+python-versions = ">=3.7"
+files = [
     {file = "zipp-3.14.0-py3-none-any.whl", hash = "sha256:188834565033387710d046e3fe96acfc9b5e86cbca7f39ff69cf21a4128198b7"},
     {file = "zipp-3.14.0.tar.gz", hash = "sha256:9e5421e176ef5ab4c0ad896624e87a7b2f07aca746c9b2aa305952800cb8eecb"},
 ]
+
+[package.extras]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
+
+[metadata]
+lock-version = "2.0"
+python-versions = "^3.9"
+content-hash = "b473b858673f97389893714b9f7b21ad8bab1eb63ff704635ca21c4bc76bcf00"

From db3e5f26f09e61b0ca0872bb09740936b73a0739 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 24 May 2023 14:22:29 -0400
Subject: [PATCH 24/48] Bump starlette from 0.25.0 to 0.27.0 (#39)

Co-authored-by: jessicasyu <15913767+jessicasyu@users.noreply.github.com>
---
 poetry.lock | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index dbc906e..d6a4602 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -691,24 +691,24 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "fastapi"
-version = "0.92.0"
+version = "0.95.2"
 description = "FastAPI framework, high performance, easy to learn, fast to code, ready for production"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "fastapi-0.92.0-py3-none-any.whl", hash = "sha256:ae7b97c778e2f2ec3fb3cb4fb14162129411d99907fb71920f6d69a524340ebf"},
-    {file = "fastapi-0.92.0.tar.gz", hash = "sha256:023a0f5bd2c8b2609014d3bba1e14a1d7df96c6abea0a73070621c9862b9a4de"},
+    {file = "fastapi-0.95.2-py3-none-any.whl", hash = "sha256:d374dbc4ef2ad9b803899bd3360d34c534adc574546e25314ab72c0c4411749f"},
+    {file = "fastapi-0.95.2.tar.gz", hash = "sha256:4d9d3e8c71c73f11874bcf5e33626258d143252e329a01002f767306c64fb982"},
 ]
 
 [package.dependencies]
 pydantic = ">=1.6.2,<1.7 || >1.7,<1.7.1 || >1.7.1,<1.7.2 || >1.7.2,<1.7.3 || >1.7.3,<1.8 || >1.8,<1.8.1 || >1.8.1,<2.0.0"
-starlette = ">=0.25.0,<0.26.0"
+starlette = ">=0.27.0,<0.28.0"
 
 [package.extras]
 all = ["email-validator (>=1.1.1)", "httpx (>=0.23.0)", "itsdangerous (>=1.1.0)", "jinja2 (>=2.11.2)", "orjson (>=3.2.1)", "python-multipart (>=0.0.5)", "pyyaml (>=5.3.1)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0)", "uvicorn[standard] (>=0.12.0)"]
 dev = ["pre-commit (>=2.17.0,<3.0.0)", "ruff (==0.0.138)", "uvicorn[standard] (>=0.12.0,<0.21.0)"]
-doc = ["mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-markdownextradata-plugin (>=0.1.7,<0.3.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "pyyaml (>=5.3.1,<7.0.0)", "typer[all] (>=0.6.1,<0.8.0)"]
-test = ["anyio[trio] (>=3.2.1,<4.0.0)", "black (==22.10.0)", "coverage[toml] (>=6.5.0,<8.0)", "databases[sqlite] (>=0.3.2,<0.7.0)", "email-validator (>=1.1.1,<2.0.0)", "flask (>=1.1.2,<3.0.0)", "httpx (>=0.23.0,<0.24.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.982)", "orjson (>=3.2.1,<4.0.0)", "passlib[bcrypt] (>=1.7.2,<2.0.0)", "peewee (>=3.13.3,<4.0.0)", "pytest (>=7.1.3,<8.0.0)", "python-jose[cryptography] (>=3.3.0,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "pyyaml (>=5.3.1,<7.0.0)", "ruff (==0.0.138)", "sqlalchemy (>=1.3.18,<1.4.43)", "types-orjson (==3.6.2)", "types-ujson (==5.6.0.0)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)"]
+doc = ["mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-markdownextradata-plugin (>=0.1.7,<0.3.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "pyyaml (>=5.3.1,<7.0.0)", "typer-cli (>=0.0.13,<0.0.14)", "typer[all] (>=0.6.1,<0.8.0)"]
+test = ["anyio[trio] (>=3.2.1,<4.0.0)", "black (==23.1.0)", "coverage[toml] (>=6.5.0,<8.0)", "databases[sqlite] (>=0.3.2,<0.7.0)", "email-validator (>=1.1.1,<2.0.0)", "flask (>=1.1.2,<3.0.0)", "httpx (>=0.23.0,<0.24.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.982)", "orjson (>=3.2.1,<4.0.0)", "passlib[bcrypt] (>=1.7.2,<2.0.0)", "peewee (>=3.13.3,<4.0.0)", "pytest (>=7.1.3,<8.0.0)", "python-jose[cryptography] (>=3.3.0,<4.0.0)", "python-multipart (>=0.0.5,<0.0.7)", "pyyaml (>=5.3.1,<7.0.0)", "ruff (==0.0.138)", "sqlalchemy (>=1.3.18,<1.4.43)", "types-orjson (==3.6.2)", "types-ujson (==5.7.0.1)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)"]
 
 [[package]]
 name = "filelock"
@@ -2857,13 +2857,13 @@ sqlcipher = ["sqlcipher3-binary"]
 
 [[package]]
 name = "starlette"
-version = "0.25.0"
+version = "0.27.0"
 description = "The little ASGI library that shines."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "starlette-0.25.0-py3-none-any.whl", hash = "sha256:774f1df1983fd594b9b6fb3ded39c2aa1979d10ac45caac0f4255cbe2acb8628"},
-    {file = "starlette-0.25.0.tar.gz", hash = "sha256:854c71e73736c429c2bdb07801f2c76c9cba497e7c3cf4988fde5e95fe4cdb3c"},
+    {file = "starlette-0.27.0-py3-none-any.whl", hash = "sha256:918416370e846586541235ccd38a474c08b80443ed31c578a418e2209b3eef91"},
+    {file = "starlette-0.27.0.tar.gz", hash = "sha256:6a6b0d042acb8d469a01eba54e9cda6cbd24ac602c4cd016723117d6a7e73b75"},
 ]
 
 [package.dependencies]

From a01b402dc2d9b25dfa47a383d5dee1d93d6b213f Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 24 May 2023 14:30:49 -0400
Subject: [PATCH 25/48] Bump requests from 2.28.2 to 2.31.0 (#38)

Co-authored-by: jessicasyu <15913767+jessicasyu@users.noreply.github.com>
---
 poetry.lock | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index d6a4602..83a3986 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2356,20 +2356,20 @@ files = [
 
 [[package]]
 name = "requests"
-version = "2.28.2"
+version = "2.31.0"
 description = "Python HTTP for Humans."
 optional = false
-python-versions = ">=3.7, <4"
+python-versions = ">=3.7"
 files = [
-    {file = "requests-2.28.2-py3-none-any.whl", hash = "sha256:64299f4909223da747622c030b781c0d7811e359c37124b4bd368fb8c6518baa"},
-    {file = "requests-2.28.2.tar.gz", hash = "sha256:98b1b2782e3c6c4904938b84c0eb932721069dfdb9134313beff7c83c2df24bf"},
+    {file = "requests-2.31.0-py3-none-any.whl", hash = "sha256:58cd2187c01e70e6e26505bca751777aa9f2ee0b7f4300988b709f44e013003f"},
+    {file = "requests-2.31.0.tar.gz", hash = "sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1"},
 ]
 
 [package.dependencies]
 certifi = ">=2017.4.17"
 charset-normalizer = ">=2,<4"
 idna = ">=2.5,<4"
-urllib3 = ">=1.21.1,<1.27"
+urllib3 = ">=1.21.1,<3"
 
 [package.extras]
 socks = ["PySocks (>=1.5.6,!=1.5.7)"]

From e8480255a056db38487912c7f4580513b26c6383 Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Wed, 24 May 2023 15:58:05 -0400
Subject: [PATCH 26/48] Update dev dependencies (#40)

---
 poetry.lock    | 330 +++++++++++++++++++++----------------------------
 pyproject.toml |  10 +-
 2 files changed, 148 insertions(+), 192 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 83a3986..37fe720 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -327,6 +327,17 @@ files = [
 [package.dependencies]
 pycparser = "*"
 
+[[package]]
+name = "chardet"
+version = "5.1.0"
+description = "Universal encoding detector for Python 3"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "chardet-5.1.0-py3-none-any.whl", hash = "sha256:362777fb014af596ad31334fde1e8c327dfdb076e1960d1694662d46a6917ab9"},
+    {file = "chardet-5.1.0.tar.gz", hash = "sha256:0d62712b956bc154f85fb0a266e2a3c5913c2967e00348701b32411d6def31e5"},
+]
+
 [[package]]
 name = "charset-normalizer"
 version = "3.0.1"
@@ -712,18 +723,18 @@ test = ["anyio[trio] (>=3.2.1,<4.0.0)", "black (==23.1.0)", "coverage[toml] (>=6
 
 [[package]]
 name = "filelock"
-version = "3.9.0"
+version = "3.12.0"
 description = "A platform independent file lock."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "filelock-3.9.0-py3-none-any.whl", hash = "sha256:f58d535af89bb9ad5cd4df046f741f8553a418c01a7856bf0d173bbc9f6bd16d"},
-    {file = "filelock-3.9.0.tar.gz", hash = "sha256:7b319f24340b51f55a2bf7a12ac0755a9b03e718311dac567a0f4f7fabd2f5de"},
+    {file = "filelock-3.12.0-py3-none-any.whl", hash = "sha256:ad98852315c2ab702aeb628412cbf7e95b7ce8c3bf9565670b4eaecf1db370a9"},
+    {file = "filelock-3.12.0.tar.gz", hash = "sha256:fc03ae43288c013d2ea83c8597001b1129db351aad9c57fe2409327916b8e718"},
 ]
 
 [package.extras]
-docs = ["furo (>=2022.12.7)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.5)"]
-testing = ["covdefaults (>=2.2.2)", "coverage (>=7.0.1)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-timeout (>=2.1)"]
+docs = ["furo (>=2023.3.27)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.23,!=1.23.4)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.2.3)", "diff-cover (>=7.5)", "pytest (>=7.3.1)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest-timeout (>=2.1)"]
 
 [[package]]
 name = "fsspec"
@@ -1353,45 +1364,41 @@ files = [
 
 [[package]]
 name = "mypy"
-version = "0.991"
+version = "1.3.0"
 description = "Optional static typing for Python"
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "mypy-1.3.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:1c4c42c60a8103ead4c1c060ac3cdd3ff01e18fddce6f1016e08939647a0e703"},
+    {file = "mypy-1.3.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:e86c2c6852f62f8f2b24cb7a613ebe8e0c7dc1402c61d36a609174f63e0ff017"},
+    {file = "mypy-1.3.0-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:f9dca1e257d4cc129517779226753dbefb4f2266c4eaad610fc15c6a7e14283e"},
+    {file = "mypy-1.3.0-cp39-cp39-win_amd64.whl", hash = "sha256:95d8d31a7713510685b05fbb18d6ac287a56c8f6554d88c19e73f724a445448a"},
+    {file = "mypy-1.3.0-py3-none-any.whl", hash = "sha256:a8763e72d5d9574d45ce5881962bc8e9046bf7b375b0abf031f3e6811732a897"},
+    {file = "mypy-1.3.0.tar.gz", hash = "sha256:e1f4d16e296f5135624b34e8fb741eb0eadedca90862405b1f1fde2040b9bd11"},
+]
+
+[package.dependencies]
+mypy-extensions = ">=1.0.0"
 tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
 typing-extensions = ">=3.10"
 
@@ -1538,13 +1545,13 @@ files = [
 
 [[package]]
 name = "packaging"
-version = "23.0"
+version = "23.1"
 description = "Core utilities for Python packages"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "packaging-23.0-py3-none-any.whl", hash = "sha256:714ac14496c3e68c99c29b00845f7a2b85f3bb6f1078fd9f72fd20f0570002b2"},
-    {file = "packaging-23.0.tar.gz", hash = "sha256:b6ad297f8907de0fa2fe1ccbd26fdaf387f5f47c7275fedf8cce89f99446cf97"},
+    {file = "packaging-23.1-py3-none-any.whl", hash = "sha256:994793af429502c4ea2ebf6bf664629d07c1a9fe974af92966e4b8d2df7edc61"},
+    {file = "packaging-23.1.tar.gz", hash = "sha256:a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f"},
 ]
 
 [[package]]
@@ -1752,18 +1759,18 @@ xarray = ["xarray"]
 
 [[package]]
 name = "platformdirs"
-version = "3.0.0"
+version = "3.5.1"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "platformdirs-3.0.0-py3-none-any.whl", hash = "sha256:b1d5eb14f221506f50d6604a561f4c5786d9e80355219694a1b244bcd96f4567"},
-    {file = "platformdirs-3.0.0.tar.gz", hash = "sha256:8a1228abb1ef82d788f74139988b137e78692984ec7b08eaa6c65f1723af28f9"},
+    {file = "platformdirs-3.5.1-py3-none-any.whl", hash = "sha256:e2378146f1964972c03c085bb5662ae80b2b8c06226c54b2ff4aa9483e8a13a5"},
+    {file = "platformdirs-3.5.1.tar.gz", hash = "sha256:412dae91f52a6f84830f39a8078cecd0e866cb72294a5c66808e74d5e88d251f"},
 ]
 
 [package.extras]
-docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.22,!=1.23.4)"]
-test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest (>=7.2.1)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"]
+docs = ["furo (>=2023.3.27)", "proselint (>=0.13)", "sphinx (>=6.2.1)", "sphinx-autodoc-typehints (>=1.23,!=1.23.4)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.3.1)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"]
 
 [[package]]
 name = "pluggy"
@@ -1834,17 +1841,6 @@ websockets = ">=10.4"
 [package.extras]
 dev = ["autoflake8", "cairosvg", "flake8", "flaky", "ipython", "jinja2", "mike", "mkdocs", "mkdocs-gen-files", "mkdocs-material", "mkdocstrings-python", "mock", "moto", "mypy", "numpy", "pillow", "pre-commit", "pytest (>7)", "pytest-asyncio (>=0.18.2)", "pytest-benchmark", "pytest-cov", "pytest-env", "pytest-timeout", "pytest-xdist", "pytkdocs (>=0.14.2)", "pyyaml", "requests", "respx", "setuptools (!=60.9.0)", "virtualenv", "watchfiles"]
 
-[[package]]
-name = "py"
-version = "1.11.0"
-description = "library with cross-python path, ini-parsing, io, code, log facilities"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-files = [
-    {file = "py-1.11.0-py2.py3-none-any.whl", hash = "sha256:607c53218732647dff4acdfcd50cb62615cedf612e72d1724fb1a0cc6405b378"},
-    {file = "py-1.11.0.tar.gz", hash = "sha256:51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719"},
-]
-
 [[package]]
 name = "pyasn1"
 version = "0.4.8"
@@ -1976,6 +1972,25 @@ typing-extensions = {version = ">=3.10.0", markers = "python_version < \"3.10\""
 spelling = ["pyenchant (>=3.2,<4.0)"]
 testutils = ["gitpython (>3)"]
 
+[[package]]
+name = "pyproject-api"
+version = "1.5.1"
+description = "API to interact with the python pyproject.toml based projects"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "pyproject_api-1.5.1-py3-none-any.whl", hash = "sha256:4698a3777c2e0f6b624f8a4599131e2a25376d90fe8d146d7ac74c67c6f97c43"},
+    {file = "pyproject_api-1.5.1.tar.gz", hash = "sha256:435f46547a9ff22cf4208ee274fca3e2869aeb062a4834adfc99a4dd64af3cf9"},
+]
+
+[package.dependencies]
+packaging = ">=23"
+tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""}
+
+[package.extras]
+docs = ["furo (>=2022.12.7)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.22,!=1.23.4)"]
+testing = ["covdefaults (>=2.2.2)", "importlib-metadata (>=6)", "pytest (>=7.2.1)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "virtualenv (>=20.17.1)", "wheel (>=0.38.4)"]
+
 [[package]]
 name = "pyrsistent"
 version = "0.19.3"
@@ -2014,17 +2029,16 @@ files = [
 
 [[package]]
 name = "pytest"
-version = "7.2.1"
+version = "7.3.1"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pytest-7.2.1-py3-none-any.whl", hash = "sha256:c7c6ca206e93355074ae32f7403e8ea12163b1163c976fee7d4d84027c162be5"},
-    {file = "pytest-7.2.1.tar.gz", hash = "sha256:d45e0952f3727241918b8fd0f376f5ff6b301cc0777c6f9a556935c92d8a7d42"},
+    {file = "pytest-7.3.1-py3-none-any.whl", hash = "sha256:3799fa815351fea3a5e96ac7e503a96fa51cc9942c3753cda7651b93c1cfa362"},
+    {file = "pytest-7.3.1.tar.gz", hash = "sha256:434afafd78b1d78ed0addf160ad2b77a30d35d4bdf8af234fe621919d9ed15e3"},
 ]
 
 [package.dependencies]
-attrs = ">=19.2.0"
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
 exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
 iniconfig = "*"
@@ -2033,7 +2047,7 @@ pluggy = ">=0.12,<2.0"
 tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 
 [package.extras]
-testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"]
+testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"]
 
 [[package]]
 name = "pytest-cov"
@@ -2055,16 +2069,17 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtuale
 
 [[package]]
 name = "pytest-subtests"
-version = "0.8.0"
+version = "0.11.0"
 description = "unittest subTest() support and subtests fixture"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "pytest-subtests-0.8.0.tar.gz", hash = "sha256:46eb376022e926950816ccc23502de3277adcc1396652ddb3328ce0289052c4d"},
-    {file = "pytest_subtests-0.8.0-py3-none-any.whl", hash = "sha256:4e28ca52cf7a46645c1ded7933745b69334cdc97a412ed4431f7be7cef9a0994"},
+    {file = "pytest-subtests-0.11.0.tar.gz", hash = "sha256:51865c88457545f51fb72011942f0a3c6901ee9e24cbfb6d1b9dc1348bafbe37"},
+    {file = "pytest_subtests-0.11.0-py3-none-any.whl", hash = "sha256:453389984952eec85ab0ce0c4f026337153df79587048271c7fd0f49119c07e4"},
 ]
 
 [package.dependencies]
+attrs = ">=19.2.0"
 pytest = ">=7.0"
 
 [[package]]
@@ -2609,39 +2624,34 @@ files = [
 ]
 
 [[package]]
-name = "Sphinx"
-version = "5.3.0"
+name = "sphinx"
+version = "1.8.5"
 description = "Python documentation generator"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
-    {file = "Sphinx-5.3.0.tar.gz", hash = "sha256:51026de0a9ff9fc13c05d74913ad66047e104f56a129ff73e174eb5c3ee794b5"},
-    {file = "sphinx-5.3.0-py3-none-any.whl", hash = "sha256:060ca5c9f7ba57a08a1219e547b269fadf125ae25b06b9fa7f66768efb652d6d"},
+    {file = "Sphinx-1.8.5-py2.py3-none-any.whl", hash = "sha256:9f3e17c64b34afc653d7c5ec95766e03043cc6d80b0de224f59b6b6e19d37c3c"},
+    {file = "Sphinx-1.8.5.tar.gz", hash = "sha256:c7658aab75c920288a8cf6f09f244c6cfdae30d82d803ac1634d9f223a80ca08"},
 ]
 
 [package.dependencies]
 alabaster = ">=0.7,<0.8"
-babel = ">=2.9"
-colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
-docutils = ">=0.14,<0.20"
-imagesize = ">=1.3"
-importlib-metadata = {version = ">=4.8", markers = "python_version < \"3.10\""}
-Jinja2 = ">=3.0"
-packaging = ">=21.0"
-Pygments = ">=2.12"
-requests = ">=2.5.0"
-snowballstemmer = ">=2.0"
-sphinxcontrib-applehelp = "*"
-sphinxcontrib-devhelp = "*"
-sphinxcontrib-htmlhelp = ">=2.0.0"
-sphinxcontrib-jsmath = "*"
-sphinxcontrib-qthelp = "*"
-sphinxcontrib-serializinghtml = ">=1.1.5"
-
-[package.extras]
-docs = ["sphinxcontrib-websupport"]
-lint = ["docutils-stubs", "flake8 (>=3.5.0)", "flake8-bugbear", "flake8-comprehensions", "flake8-simplify", "isort", "mypy (>=0.981)", "sphinx-lint", "types-requests", "types-typed-ast"]
-test = ["cython", "html5lib", "pytest (>=4.6)", "typed_ast"]
+babel = ">=1.3,<2.0 || >2.0"
+colorama = {version = ">=0.3.5", markers = "sys_platform == \"win32\""}
+docutils = ">=0.11"
+imagesize = "*"
+Jinja2 = ">=2.3"
+packaging = "*"
+Pygments = ">=2.0"
+requests = ">=2.0.0"
+setuptools = "*"
+six = ">=1.5"
+snowballstemmer = ">=1.1"
+sphinxcontrib-websupport = "*"
+
+[package.extras]
+test = ["enum34", "flake8 (>=3.5.0)", "flake8-import-order", "html5lib", "mock", "mypy", "pytest", "pytest-cov", "typed-ast"]
+websupport = ["sqlalchemy (>=0.9)", "whoosh (>=2.0)"]
 
 [[package]]
 name = "sphinx_mdinclude"
@@ -2678,51 +2688,6 @@ sphinxcontrib-jquery = {version = ">=2.0.0,<3.0.0 || >3.0.0", markers = "python_
 [package.extras]
 dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"]
 
-[[package]]
-name = "sphinxcontrib-applehelp"
-version = "1.0.4"
-description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "sphinxcontrib-applehelp-1.0.4.tar.gz", hash = "sha256:828f867945bbe39817c210a1abfd1bc4895c8b73fcaade56d45357a348a07d7e"},
-    {file = "sphinxcontrib_applehelp-1.0.4-py3-none-any.whl", hash = "sha256:29d341f67fb0f6f586b23ad80e072c8e6ad0b48417db2bde114a4c9746feb228"},
-]
-
-[package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
-test = ["pytest"]
-
-[[package]]
-name = "sphinxcontrib-devhelp"
-version = "1.0.2"
-description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document."
-optional = false
-python-versions = ">=3.5"
-files = [
-    {file = "sphinxcontrib-devhelp-1.0.2.tar.gz", hash = "sha256:ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4"},
-    {file = "sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl", hash = "sha256:8165223f9a335cc1af7ffe1ed31d2871f325254c0423bc0c4c7cd1c1e4734a2e"},
-]
-
-[package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
-test = ["pytest"]
-
-[[package]]
-name = "sphinxcontrib-htmlhelp"
-version = "2.0.1"
-description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "sphinxcontrib-htmlhelp-2.0.1.tar.gz", hash = "sha256:0cbdd302815330058422b98a113195c9249825d681e18f11e8b1f78a2f11efff"},
-    {file = "sphinxcontrib_htmlhelp-2.0.1-py3-none-any.whl", hash = "sha256:c38cb46dccf316c79de6e5515e1770414b797162b23cd3d06e67020e1d2a6903"},
-]
-
-[package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
-test = ["html5lib", "pytest"]
-
 [[package]]
 name = "sphinxcontrib.jquery"
 version = "2.0.0"
@@ -2738,28 +2703,14 @@ files = [
 setuptools = "*"
 
 [[package]]
-name = "sphinxcontrib-jsmath"
-version = "1.0.1"
-description = "A sphinx extension which renders display math in HTML via JavaScript"
-optional = false
-python-versions = ">=3.5"
-files = [
-    {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"},
-    {file = "sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl", hash = "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178"},
-]
-
-[package.extras]
-test = ["flake8", "mypy", "pytest"]
-
-[[package]]
-name = "sphinxcontrib-qthelp"
-version = "1.0.3"
-description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document."
+name = "sphinxcontrib-serializinghtml"
+version = "1.1.5"
+description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)."
 optional = false
 python-versions = ">=3.5"
 files = [
-    {file = "sphinxcontrib-qthelp-1.0.3.tar.gz", hash = "sha256:4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72"},
-    {file = "sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl", hash = "sha256:bd9fc24bcb748a8d51fd4ecaade681350aa63009a347a8c14e637895444dfab6"},
+    {file = "sphinxcontrib-serializinghtml-1.1.5.tar.gz", hash = "sha256:aa5f6de5dfdf809ef505c4895e51ef5c9eac17d0f287933eb49ec495280b6952"},
+    {file = "sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl", hash = "sha256:352a9a00ae864471d3a7ead8d7d79f5fc0b57e8b3f95e9867eb9eb28999b92fd"},
 ]
 
 [package.extras]
@@ -2767,19 +2718,22 @@ lint = ["docutils-stubs", "flake8", "mypy"]
 test = ["pytest"]
 
 [[package]]
-name = "sphinxcontrib-serializinghtml"
-version = "1.1.5"
-description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)."
+name = "sphinxcontrib-websupport"
+version = "1.2.4"
+description = "Sphinx API for Web Apps"
 optional = false
 python-versions = ">=3.5"
 files = [
-    {file = "sphinxcontrib-serializinghtml-1.1.5.tar.gz", hash = "sha256:aa5f6de5dfdf809ef505c4895e51ef5c9eac17d0f287933eb49ec495280b6952"},
-    {file = "sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl", hash = "sha256:352a9a00ae864471d3a7ead8d7d79f5fc0b57e8b3f95e9867eb9eb28999b92fd"},
+    {file = "sphinxcontrib-websupport-1.2.4.tar.gz", hash = "sha256:4edf0223a0685a7c485ae5a156b6f529ba1ee481a1417817935b20bde1956232"},
+    {file = "sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl", hash = "sha256:6fc9287dfc823fe9aa432463edd6cea47fa9ebbf488d7f289b322ffcfca075c7"},
 ]
 
+[package.dependencies]
+sphinxcontrib-serializinghtml = "*"
+
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
-test = ["pytest"]
+lint = ["flake8"]
+test = ["Sphinx", "pytest", "sqlalchemy", "whoosh"]
 
 [[package]]
 name = "SQLAlchemy"
@@ -2936,28 +2890,30 @@ files = [
 
 [[package]]
 name = "tox"
-version = "3.28.0"
+version = "4.5.1"
 description = "tox is a generic virtualenv management and test command line tool"
 optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+python-versions = ">=3.7"
 files = [
-    {file = "tox-3.28.0-py2.py3-none-any.whl", hash = "sha256:57b5ab7e8bb3074edc3c0c0b4b192a4f3799d3723b2c5b76f1fa9f2d40316eea"},
-    {file = "tox-3.28.0.tar.gz", hash = "sha256:d0d28f3fe6d6d7195c27f8b054c3e99d5451952b54abdae673b71609a581f640"},
+    {file = "tox-4.5.1-py3-none-any.whl", hash = "sha256:d25a2e6cb261adc489604fafd76cd689efeadfa79709965e965668d6d3f63046"},
+    {file = "tox-4.5.1.tar.gz", hash = "sha256:5a2eac5fb816779dfdf5cb00fecbc27eb0524e4626626bb1de84747b24cacc56"},
 ]
 
 [package.dependencies]
-colorama = {version = ">=0.4.1", markers = "platform_system == \"Windows\""}
-filelock = ">=3.0.0"
-packaging = ">=14"
-pluggy = ">=0.12.0"
-py = ">=1.4.17"
-six = ">=1.14.0"
-tomli = {version = ">=2.0.1", markers = "python_version >= \"3.7\" and python_version < \"3.11\""}
-virtualenv = ">=16.0.0,<20.0.0 || >20.0.0,<20.0.1 || >20.0.1,<20.0.2 || >20.0.2,<20.0.3 || >20.0.3,<20.0.4 || >20.0.4,<20.0.5 || >20.0.5,<20.0.6 || >20.0.6,<20.0.7 || >20.0.7"
+cachetools = ">=5.3"
+chardet = ">=5.1"
+colorama = ">=0.4.6"
+filelock = ">=3.11"
+packaging = ">=23.1"
+platformdirs = ">=3.2"
+pluggy = ">=1"
+pyproject-api = ">=1.5.1"
+tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""}
+virtualenv = ">=20.21"
 
 [package.extras]
-docs = ["pygments-github-lexers (>=0.0.5)", "sphinx (>=2.0.0)", "sphinxcontrib-autoprogram (>=0.1.5)", "towncrier (>=18.5.0)"]
-testing = ["flaky (>=3.4.0)", "freezegun (>=0.3.11)", "pathlib2 (>=2.3.3)", "psutil (>=5.6.1)", "pytest (>=4.0.0)", "pytest-cov (>=2.5.1)", "pytest-mock (>=1.10.0)", "pytest-randomly (>=1.0.0)"]
+docs = ["furo (>=2023.3.27)", "sphinx (>=6.1.3)", "sphinx-argparse-cli (>=1.11)", "sphinx-autodoc-typehints (>=1.23,!=1.23.4)", "sphinx-copybutton (>=0.5.2)", "sphinx-inline-tabs (>=2022.1.2b11)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=22.12)"]
+testing = ["build[virtualenv] (>=0.10)", "covdefaults (>=2.3)", "devpi-process (>=0.3)", "diff-cover (>=7.5)", "distlib (>=0.3.6)", "flaky (>=3.7)", "hatch-vcs (>=0.3)", "hatchling (>=1.14)", "psutil (>=5.9.4)", "pytest (>=7.3.1)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest-xdist (>=3.2.1)", "re-assert (>=1.1)", "time-machine (>=2.9)", "wheel (>=0.40)"]
 
 [[package]]
 name = "typer"
@@ -3056,23 +3012,23 @@ standard = ["colorama (>=0.4)", "httptools (>=0.5.0)", "python-dotenv (>=0.13)",
 
 [[package]]
 name = "virtualenv"
-version = "20.19.0"
+version = "20.23.0"
 description = "Virtual Python Environment builder"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "virtualenv-20.19.0-py3-none-any.whl", hash = "sha256:54eb59e7352b573aa04d53f80fc9736ed0ad5143af445a1e539aada6eb947dd1"},
-    {file = "virtualenv-20.19.0.tar.gz", hash = "sha256:37a640ba82ed40b226599c522d411e4be5edb339a0c0de030c0dc7b646d61590"},
+    {file = "virtualenv-20.23.0-py3-none-any.whl", hash = "sha256:6abec7670e5802a528357fdc75b26b9f57d5d92f29c5462ba0fbe45feacc685e"},
+    {file = "virtualenv-20.23.0.tar.gz", hash = "sha256:a85caa554ced0c0afbd0d638e7e2d7b5f92d23478d05d17a76daeac8f279f924"},
 ]
 
 [package.dependencies]
 distlib = ">=0.3.6,<1"
-filelock = ">=3.4.1,<4"
-platformdirs = ">=2.4,<4"
+filelock = ">=3.11,<4"
+platformdirs = ">=3.2,<4"
 
 [package.extras]
-docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=22.12)"]
-test = ["covdefaults (>=2.2.2)", "coverage (>=7.1)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23)", "pytest (>=7.2.1)", "pytest-env (>=0.8.1)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.10)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)"]
+docs = ["furo (>=2023.3.27)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=22.12)"]
+test = ["covdefaults (>=2.3)", "coverage (>=7.2.3)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.3.1)", "pytest-env (>=0.8.1)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.10)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=67.7.1)", "time-machine (>=2.9)"]
 
 [[package]]
 name = "websocket-client"
@@ -3259,4 +3215,4 @@ testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools"
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "b473b858673f97389893714b9f7b21ad8bab1eb63ff704635ca21c4bc76bcf00"
+content-hash = "12309d0970389ab5b71eaf0a6ee92693e4a9041344db40acd4014488befddde3"
diff --git a/pyproject.toml b/pyproject.toml
index 6546ddd..e8963d9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,15 +19,15 @@ simulariumio = "^1.7.0"
 [tool.poetry.group.dev.dependencies]
 black = "^22.12.0"
 isort = "^5.12.0"
-mypy = "^0.991"
+mypy = "^1.3.0"
 pylint = "^2.16.2"
-pytest = "^7.2.0"
+pytest = "^7.3.0"
 pytest-cov = "^4.0.0"
-pytest-subtests = "^0.8.0"
-Sphinx = "^5.3.0"
+pytest-subtests = "^0.11.0"
+sphinx = "^1.6.0"
 sphinx-rtd-theme = "^1.2.0"
 sphinx_mdinclude = "^0.5.3"
-tox = "^3.26.0"
+tox = "^4.5.1"
 
 [tool.isort]
 profile = "black"

From 628d3576ad2ddc4bcd01b4526e6c30233b262f10 Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Tue, 27 Jun 2023 15:33:09 -0400
Subject: [PATCH 27/48] Update autogenerated documentation (#41)

* Update docs dependencies

* Update LICENSE

* Add custom module template and filters

* Add changelog to docs

* Update README and docs index

* Update custom doc templates
---
 LICENSE                            |   2 +-
 Makefile                           |   1 -
 README.md                          |  66 ++++++
 docs/_templates/custom_module.rst  |  49 ++++
 docs/_templates/custom_summary.rst |  64 ++++++
 docs/changelog.rst                 |   6 +
 docs/conf.py                       |  64 ++++--
 docs/index.rst                     |  35 ++-
 poetry.lock                        | 347 +++++++++++++++++++----------
 pyproject.toml                     |   7 +-
 10 files changed, 493 insertions(+), 148 deletions(-)
 create mode 100644 docs/_templates/custom_module.rst
 create mode 100644 docs/_templates/custom_summary.rst
 create mode 100644 docs/changelog.rst

diff --git a/LICENSE b/LICENSE
index 7f7e207..ddb26e4 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2022, Bagheri Lab
+Copyright (c) 2023, Bagheri Lab
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
diff --git a/Makefile b/Makefile
index 4ea9a84..ec62ee4 100644
--- a/Makefile
+++ b/Makefile
@@ -21,7 +21,6 @@ build: # run tox tests and lint
 	tox
 
 docs: # generates documentation
-	sphinx-apidoc -o docs/ -f -M -e src/* **/tests/
 	make -C docs html
 
 release:
diff --git a/README.md b/README.md
index 24f5bca..498a410 100644
--- a/README.md
+++ b/README.md
@@ -3,3 +3,69 @@
 [![Lint Status](https://github.com/bagherilab/arcade-collection/workflows/lint/badge.svg)](https://github.com/bagherilab/arcade-collection/actions?query=workflow%3Alint)
 [![Documentation](https://github.com/bagherilab/arcade-collection/workflows/documentation/badge.svg)](https://bagherilab.github.io/arcade-collection/)
 [![Code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+Collection of tasks for working with ARCADE.
+Designed to be used both in [Prefect](https://docs.prefect.io/latest/) workflows and as modular, useful pieces of code.
+
+# Installation
+
+The collection can be installed using:
+
+```bash
+pip install arcade-collection
+```
+
+We recommend using [Poetry](https://python-poetry.org/) to manage and install dependencies.
+To install into your Poetry project, use:
+
+```bash
+poetry add arcade-collection
+```
+
+# Usage
+
+## Prefect workflows
+
+All tasks in this collection are wrapped in a Prefect `@task` decorator, and can be used directly in a Prefect `@flow`.
+Running tasks within a [Prefect](https://docs.prefect.io/latest/) flow enables you to take advantage of features such as automatically retrying failed tasks, monitoring workflow states, running tasks concurrently, deploying and scheduling flows, and more.
+
+```python
+from prefect import flow
+from arcade_collection.<module_name> import <task_name>
+
+@flow
+def run_flow():
+    <task_name>()
+
+if __name__ == "__main__":
+    run_flow()
+```
+
+See [cell-abm-pipeline](https://github.com/allen-cell-animated/cell-abm-pipeline) for examples of using tasks from different collections to build a pipeline for simulating and analyzing agent-based model data.
+
+## Individual tasks
+
+Not all use cases require a full workflow.
+Tasks in this collection can be used without the Prefect `@task` decorator by simply importing directly from the module:
+
+```python
+from arcade_collection.<module_name>.<task_name> import <task_name>
+
+def main():
+    <task_name>()
+
+if __name__ == "__main__":
+    main()
+```
+
+or using the `.fn()` method:
+
+```python
+from arcade_collection.<module_name> import <task_name>
+
+def main():
+    <task_name>.fn()
+
+if __name__ == "__main__":
+    main()
+```
diff --git a/docs/_templates/custom_module.rst b/docs/_templates/custom_module.rst
new file mode 100644
index 0000000..9eb45c5
--- /dev/null
+++ b/docs/_templates/custom_module.rst
@@ -0,0 +1,49 @@
+{{ objname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+    :members:
+    :undoc-members:
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Module Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
diff --git a/docs/_templates/custom_summary.rst b/docs/_templates/custom_summary.rst
new file mode 100644
index 0000000..6689efc
--- /dev/null
+++ b/docs/_templates/custom_summary.rst
@@ -0,0 +1,64 @@
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+    :members:
+    :undoc-members:
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Module Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+{% block modules %}
+{% if modules %}
+
+.. currentmodule:: {{module | custom_module }}
+
+.. autosummary::
+   :toctree:
+   :template: custom_module.rst
+   :recursive:
+{% for item in modules %}
+   {{ item | custom_fullname }}
+{%- endfor %}
+{% endif %}
+{% endblock %}
diff --git a/docs/changelog.rst b/docs/changelog.rst
new file mode 100644
index 0000000..8ffa703
--- /dev/null
+++ b/docs/changelog.rst
@@ -0,0 +1,6 @@
+---------
+Changelog
+---------
+
+.. include:: ../CHANGELOG.md
+   :parser: myst_parser.sphinx_
diff --git a/docs/conf.py b/docs/conf.py
index 877d7c9..53432fd 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -10,20 +10,21 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 
+import importlib.metadata
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../src'))
+from datetime import datetime
 
-import sphinx_rtd_theme
+from sphinx.ext.autosummary.generate import AutosummaryRenderer
 
-# -- Project information -----------------------------------------------------
+sys.path.insert(0, os.path.abspath("../src"))
 
-project = 'Container collection'
-copyright = 'YYYY, AUTHOR_NAME'
-author = 'AUTHOR_NAME'
+# -- Project information -----------------------------------------------------
 
-# The full version, including alpha/beta/rc tags
-release = 'VERSION NUMBER X.X.X'
+project = "ARCADE Collection"
+author = importlib.metadata.metadata("arcade-collection")["Author"]
+copyright = f"{datetime.now().year}, {author}, Bagheri Lab"
+release = importlib.metadata.version("arcade-collection")
 
 # -- General configuration ---------------------------------------------------
 
@@ -32,39 +33,62 @@
 # ones.
 extensions = [
     "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
     "sphinx.ext.viewcode",
     "sphinx.ext.napoleon",
-    "sphinx_rtd_theme",
-    "sphinx_mdinclude",
+    "myst_parser",
+    "sphinx_copybutton",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # Decides whether module names are prepended to all object names.
 add_module_names = False
 
 # Default options for autodoc directives.
 autodoc_default_options = {
-    'member-order': 'bysource',
-    'undoc-members': True,
+    "member-order": "bysource",
+    "undoc-members": True,
 }
 
-# List of modules to be mocked up. Useful when some external dependencies are not met at build time and break the building process.
+# List of modules to be mocked up. Useful when some external dependencies are
+# not met at build time and break the building process.
 autodoc_mock_imports = []
 
+# Controls how to represent typehints.
+autodoc_typehints = "description"
+
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'sphinx_rtd_theme'
+html_theme = "furo"
+
+# The name for this set of Sphinx documents.
+html_title = f"<strong>{project}</strong> <br />{release}"
+
+# -- Patch custom template filters -------------------------------------------
+
+
+def custom_fullname_filter(fullname):
+    return ".".join(fullname.split(".")[1:])
+
+
+def custom_module_filter(module):
+    return module.split(".")[0]
+
+
+def patch_init(self, app):
+    AutosummaryRenderer.__original_init__(self, app)
+    self.env.filters["custom_fullname"] = custom_fullname_filter
+    self.env.filters["custom_module"] = custom_module_filter
+
 
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+AutosummaryRenderer.__original_init__ = AutosummaryRenderer.__init__
+AutosummaryRenderer.__init__ = patch_init
diff --git a/docs/index.rst b/docs/index.rst
index d1b3737..e6039b7 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -1,16 +1,29 @@
+|
+
+.. include:: ../README.md
+   :parser: myst_parser.sphinx_
+
+Module reference
+================
+
+.. autosummary::
+   :toctree: _summary
+   :caption: Module reference
+   :template: custom_summary.rst
+   :recursive:
+
+   arcade_collection.input
+   arcade_collection.output
+
 .. toctree::
    :hidden:
-   :maxdepth: 1
-   :caption: Contents:
-
-   Overview <self>
-   Package modules <modules>
+   :caption: Development
 
-.. mdinclude:: ../README.md
+   Changelog <changelog>
 
-Indices and tables
-==================
+.. toctree::
+   :hidden:
+   :caption: Project links
 
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+   GitHub <https://github.com/bagherilab/arcade-collection>
+   PyPI <https://pypi.org/project/arcade-collection/>
diff --git a/poetry.lock b/poetry.lock
index 37fe720..aa88ed4 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -194,6 +194,24 @@ files = [
 [package.dependencies]
 pytz = ">=2015.7"
 
+[[package]]
+name = "beautifulsoup4"
+version = "4.12.2"
+description = "Screen-scraping library"
+optional = false
+python-versions = ">=3.6.0"
+files = [
+    {file = "beautifulsoup4-4.12.2-py3-none-any.whl", hash = "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"},
+    {file = "beautifulsoup4-4.12.2.tar.gz", hash = "sha256:492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da"},
+]
+
+[package.dependencies]
+soupsieve = ">1.2"
+
+[package.extras]
+html5lib = ["html5lib"]
+lxml = ["lxml"]
+
 [[package]]
 name = "black"
 version = "22.12.0"
@@ -564,34 +582,30 @@ python-dateutil = "*"
 
 [[package]]
 name = "cryptography"
-version = "39.0.1"
+version = "41.0.1"
 description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "cryptography-39.0.1-cp36-abi3-macosx_10_12_universal2.whl", hash = "sha256:6687ef6d0a6497e2b58e7c5b852b53f62142cfa7cd1555795758934da363a965"},
-    {file = "cryptography-39.0.1-cp36-abi3-macosx_10_12_x86_64.whl", hash = "sha256:706843b48f9a3f9b9911979761c91541e3d90db1ca905fd63fee540a217698bc"},
-    {file = "cryptography-39.0.1-cp36-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.manylinux_2_24_aarch64.whl", hash = "sha256:5d2d8b87a490bfcd407ed9d49093793d0f75198a35e6eb1a923ce1ee86c62b41"},
-    {file = "cryptography-39.0.1-cp36-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:83e17b26de248c33f3acffb922748151d71827d6021d98c70e6c1a25ddd78505"},
-    {file = "cryptography-39.0.1-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:e124352fd3db36a9d4a21c1aa27fd5d051e621845cb87fb851c08f4f75ce8be6"},
-    {file = "cryptography-39.0.1-cp36-abi3-manylinux_2_24_x86_64.whl", hash = "sha256:5aa67414fcdfa22cf052e640cb5ddc461924a045cacf325cd164e65312d99502"},
-    {file = "cryptography-39.0.1-cp36-abi3-manylinux_2_28_aarch64.whl", hash = "sha256:35f7c7d015d474f4011e859e93e789c87d21f6f4880ebdc29896a60403328f1f"},
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 ]
 
 [package.dependencies]
@@ -600,12 +614,12 @@ cffi = ">=1.12"
 [package.extras]
 docs = ["sphinx (>=5.3.0)", "sphinx-rtd-theme (>=1.1.1)"]
 docstest = ["pyenchant (>=1.6.11)", "sphinxcontrib-spelling (>=4.0.1)", "twine (>=1.12.0)"]
-pep8test = ["black", "check-manifest", "mypy", "ruff", "types-pytz", "types-requests"]
-sdist = ["setuptools-rust (>=0.11.4)"]
+nox = ["nox"]
+pep8test = ["black", "check-sdist", "mypy", "ruff"]
+sdist = ["build"]
 ssh = ["bcrypt (>=3.1.5)"]
-test = ["hypothesis (>=1.11.4,!=3.79.2)", "iso8601", "pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-shard (>=0.1.2)", "pytest-subtests", "pytest-xdist", "pytz"]
+test = ["pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-xdist"]
 test-randomorder = ["pytest-randomly"]
-tox = ["tox"]
 
 [[package]]
 name = "dateparser"
@@ -770,6 +784,23 @@ smb = ["smbprotocol"]
 ssh = ["paramiko"]
 tqdm = ["tqdm"]
 
+[[package]]
+name = "furo"
+version = "2023.5.20"
+description = "A clean customisable Sphinx documentation theme."
+optional = false
+python-versions = ">=3.7"
+files = [
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+    {file = "furo-2023.5.20.tar.gz", hash = "sha256:40e09fa17c6f4b22419d122e933089226dcdb59747b5b6c79363089827dea16f"},
+]
+
+[package.dependencies]
+beautifulsoup4 = "*"
+pygments = ">=2.7"
+sphinx = ">=6.0,<8.0"
+sphinx-basic-ng = "*"
+
 [[package]]
 name = "google-auth"
 version = "2.16.1"
@@ -1248,13 +1279,13 @@ testing = ["coverage", "pyyaml"]
 
 [[package]]
 name = "markdown-it-py"
-version = "2.2.0"
+version = "3.0.0"
 description = "Python port of markdown-it. Markdown parsing, done right!"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "markdown-it-py-3.0.0.tar.gz", hash = "sha256:e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb"},
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 ]
 
 [package.dependencies]
@@ -1267,7 +1298,7 @@ compare = ["commonmark (>=0.9,<1.0)", "markdown (>=3.4,<4.0)", "mistletoe (>=1.0
 linkify = ["linkify-it-py (>=1,<3)"]
 plugins = ["mdit-py-plugins"]
 profiling = ["gprof2dot"]
-rtd = ["attrs", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
+rtd = ["jupyter_sphinx", "mdit-py-plugins", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
 testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
 [[package]]
@@ -1340,6 +1371,25 @@ files = [
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 ]
 
+[[package]]
+name = "mdit-py-plugins"
+version = "0.4.0"
+description = "Collection of plugins for markdown-it-py"
+optional = false
+python-versions = ">=3.8"
+files = [
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+]
+
+[package.dependencies]
+markdown-it-py = ">=1.0.0,<4.0.0"
+
+[package.extras]
+code-style = ["pre-commit"]
+rtd = ["myst-parser", "sphinx-book-theme"]
+testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
+
 [[package]]
 name = "mdurl"
 version = "0.1.2"
@@ -1351,17 +1401,6 @@ files = [
     {file = "mdurl-0.1.2.tar.gz", hash = "sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba"},
 ]
 
-[[package]]
-name = "mistune"
-version = "2.0.5"
-description = "A sane Markdown parser with useful plugins and renderers"
-optional = false
-python-versions = "*"
-files = [
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-]
-
 [[package]]
 name = "mypy"
 version = "1.3.0"
@@ -1419,6 +1458,32 @@ files = [
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 ]
 
+[[package]]
+name = "myst-parser"
+version = "2.0.0"
+description = "An extended [CommonMark](https://spec.commonmark.org/) compliant parser,"
+optional = false
+python-versions = ">=3.8"
+files = [
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+    {file = "myst_parser-2.0.0.tar.gz", hash = "sha256:ea929a67a6a0b1683cdbe19b8d2e724cd7643f8aa3e7bb18dd65beac3483bead"},
+]
+
+[package.dependencies]
+docutils = ">=0.16,<0.21"
+jinja2 = "*"
+markdown-it-py = ">=3.0,<4.0"
+mdit-py-plugins = ">=0.4,<1.0"
+pyyaml = "*"
+sphinx = ">=6,<8"
+
+[package.extras]
+code-style = ["pre-commit (>=3.0,<4.0)"]
+linkify = ["linkify-it-py (>=2.0,<3.0)"]
+rtd = ["ipython", "pydata-sphinx-theme (==v0.13.0rc4)", "sphinx-autodoc2 (>=0.4.2,<0.5.0)", "sphinx-book-theme (==1.0.0rc2)", "sphinx-copybutton", "sphinx-design2", "sphinx-pyscript", "sphinx-tippy (>=0.3.1)", "sphinx-togglebutton", "sphinxext-opengraph (>=0.8.2,<0.9.0)", "sphinxext-rediraffe (>=0.2.7,<0.3.0)"]
+testing = ["beautifulsoup4", "coverage[toml]", "pytest (>=7,<8)", "pytest-cov", "pytest-param-files (>=0.3.4,<0.4.0)", "pytest-regressions", "sphinx-pytest"]
+testing-docutils = ["pygments", "pytest (>=7,<8)", "pytest-param-files (>=0.3.4,<0.4.0)"]
+
 [[package]]
 name = "networkx"
 version = "3.0"
@@ -2427,18 +2492,18 @@ idna2008 = ["idna"]
 
 [[package]]
 name = "rich"
-version = "13.3.1"
+version = "13.4.2"
 description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
 optional = false
 python-versions = ">=3.7.0"
 files = [
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+    {file = "rich-13.4.2-py3-none-any.whl", hash = "sha256:8f87bc7ee54675732fa66a05ebfe489e27264caeeff3728c945d25971b6485ec"},
+    {file = "rich-13.4.2.tar.gz", hash = "sha256:d653d6bccede5844304c605d5aac802c7cf9621efd700b46c7ec2b51ea914898"},
 ]
 
 [package.dependencies]
-markdown-it-py = ">=2.1.0,<3.0.0"
-pygments = ">=2.14.0,<3.0.0"
+markdown-it-py = ">=2.2.0"
+pygments = ">=2.13.0,<3.0.0"
 
 [package.extras]
 jupyter = ["ipywidgets (>=7.5.1,<9)"]
@@ -2623,94 +2688,155 @@ files = [
     {file = "snowballstemmer-2.2.0.tar.gz", hash = "sha256:09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1"},
 ]
 
+[[package]]
+name = "soupsieve"
+version = "2.4.1"
+description = "A modern CSS selector implementation for Beautiful Soup."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "soupsieve-2.4.1-py3-none-any.whl", hash = "sha256:1c1bfee6819544a3447586c889157365a27e10d88cde3ad3da0cf0ddf646feb8"},
+    {file = "soupsieve-2.4.1.tar.gz", hash = "sha256:89d12b2d5dfcd2c9e8c22326da9d9aa9cb3dfab0a83a024f05704076ee8d35ea"},
+]
+
 [[package]]
 name = "sphinx"
-version = "1.8.5"
+version = "7.0.1"
 description = "Python documentation generator"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=3.8"
 files = [
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-    {file = "Sphinx-1.8.5.tar.gz", hash = "sha256:c7658aab75c920288a8cf6f09f244c6cfdae30d82d803ac1634d9f223a80ca08"},
+    {file = "Sphinx-7.0.1.tar.gz", hash = "sha256:61e025f788c5977d9412587e733733a289e2b9fdc2fef8868ddfbfc4ccfe881d"},
+    {file = "sphinx-7.0.1-py3-none-any.whl", hash = "sha256:60c5e04756c1709a98845ed27a2eed7a556af3993afb66e77fec48189f742616"},
 ]
 
 [package.dependencies]
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-colorama = {version = ">=0.3.5", markers = "sys_platform == \"win32\""}
-docutils = ">=0.11"
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-Jinja2 = ">=2.3"
-packaging = "*"
-Pygments = ">=2.0"
-requests = ">=2.0.0"
-setuptools = "*"
-six = ">=1.5"
-snowballstemmer = ">=1.1"
-sphinxcontrib-websupport = "*"
+babel = ">=2.9"
+colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
+docutils = ">=0.18.1,<0.21"
+imagesize = ">=1.3"
+importlib-metadata = {version = ">=4.8", markers = "python_version < \"3.10\""}
+Jinja2 = ">=3.0"
+packaging = ">=21.0"
+Pygments = ">=2.13"
+requests = ">=2.25.0"
+snowballstemmer = ">=2.0"
+sphinxcontrib-applehelp = "*"
+sphinxcontrib-devhelp = "*"
+sphinxcontrib-htmlhelp = ">=2.0.0"
+sphinxcontrib-jsmath = "*"
+sphinxcontrib-qthelp = "*"
+sphinxcontrib-serializinghtml = ">=1.1.5"
+
+[package.extras]
+docs = ["sphinxcontrib-websupport"]
+lint = ["docutils-stubs", "flake8 (>=3.5.0)", "flake8-simplify", "isort", "mypy (>=0.990)", "ruff", "sphinx-lint", "types-requests"]
+test = ["cython", "filelock", "html5lib", "pytest (>=4.6)"]
+
+[[package]]
+name = "sphinx-basic-ng"
+version = "1.0.0b1"
+description = "A modern skeleton for Sphinx themes."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "sphinx_basic_ng-1.0.0b1-py3-none-any.whl", hash = "sha256:ade597a3029c7865b24ad0eda88318766bcc2f9f4cef60df7e28126fde94db2a"},
+    {file = "sphinx_basic_ng-1.0.0b1.tar.gz", hash = "sha256:89374bd3ccd9452a301786781e28c8718e99960f2d4f411845ea75fc7bb5a9b0"},
+]
+
+[package.dependencies]
+sphinx = ">=4.0"
 
 [package.extras]
-test = ["enum34", "flake8 (>=3.5.0)", "flake8-import-order", "html5lib", "mock", "mypy", "pytest", "pytest-cov", "typed-ast"]
-websupport = ["sqlalchemy (>=0.9)", "whoosh (>=2.0)"]
+docs = ["furo", "ipython", "myst-parser", "sphinx-copybutton", "sphinx-inline-tabs"]
 
 [[package]]
-name = "sphinx_mdinclude"
-version = "0.5.3"
-description = "Markdown extension for Sphinx"
+name = "sphinx-copybutton"
+version = "0.5.2"
+description = "Add a copy button to each of your code cells."
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "sphinx_mdinclude-0.5.3-py3-none-any.whl", hash = "sha256:02afadf4597aecf8255a702956eff5b8c5cb9658ea995c3d361722d2ed78cca9"},
-    {file = "sphinx_mdinclude-0.5.3.tar.gz", hash = "sha256:2998e3d18b3022c9983d1b72191fe37e25ffccd54165cbe3acb22cceedd91af4"},
+    {file = "sphinx-copybutton-0.5.2.tar.gz", hash = "sha256:4cf17c82fb9646d1bc9ca92ac280813a3b605d8c421225fd9913154103ee1fbd"},
+    {file = "sphinx_copybutton-0.5.2-py3-none-any.whl", hash = "sha256:fb543fd386d917746c9a2c50360c7905b605726b9355cd26e9974857afeae06e"},
 ]
 
 [package.dependencies]
-docutils = ">=0.16,<1.0"
-mistune = ">=2.0,<3.0"
-pygments = ">=2.8"
+sphinx = ">=1.8"
+
+[package.extras]
+code-style = ["pre-commit (==2.12.1)"]
+rtd = ["ipython", "myst-nb", "sphinx", "sphinx-book-theme", "sphinx-examples"]
 
 [[package]]
-name = "sphinx-rtd-theme"
-version = "1.2.0"
-description = "Read the Docs theme for Sphinx"
+name = "sphinxcontrib-applehelp"
+version = "1.0.4"
+description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
 optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
+python-versions = ">=3.8"
 files = [
-    {file = "sphinx_rtd_theme-1.2.0-py2.py3-none-any.whl", hash = "sha256:f823f7e71890abe0ac6aaa6013361ea2696fc8d3e1fa798f463e82bdb77eeff2"},
-    {file = "sphinx_rtd_theme-1.2.0.tar.gz", hash = "sha256:a0d8bd1a2ed52e0b338cbe19c4b2eef3c5e7a048769753dac6a9f059c7b641b8"},
+    {file = "sphinxcontrib-applehelp-1.0.4.tar.gz", hash = "sha256:828f867945bbe39817c210a1abfd1bc4895c8b73fcaade56d45357a348a07d7e"},
+    {file = "sphinxcontrib_applehelp-1.0.4-py3-none-any.whl", hash = "sha256:29d341f67fb0f6f586b23ad80e072c8e6ad0b48417db2bde114a4c9746feb228"},
 ]
 
-[package.dependencies]
-docutils = "<0.19"
-sphinx = ">=1.6,<7"
-sphinxcontrib-jquery = {version = ">=2.0.0,<3.0.0 || >3.0.0", markers = "python_version > \"3\""}
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-devhelp"
+version = "1.0.2"
+description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document."
+optional = false
+python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-devhelp-1.0.2.tar.gz", hash = "sha256:ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4"},
+    {file = "sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl", hash = "sha256:8165223f9a335cc1af7ffe1ed31d2871f325254c0423bc0c4c7cd1c1e4734a2e"},
+]
+
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-htmlhelp"
+version = "2.0.1"
+description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "sphinxcontrib-htmlhelp-2.0.1.tar.gz", hash = "sha256:0cbdd302815330058422b98a113195c9249825d681e18f11e8b1f78a2f11efff"},
+    {file = "sphinxcontrib_htmlhelp-2.0.1-py3-none-any.whl", hash = "sha256:c38cb46dccf316c79de6e5515e1770414b797162b23cd3d06e67020e1d2a6903"},
+]
 
 [package.extras]
-dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"]
+lint = ["docutils-stubs", "flake8", "mypy"]
+test = ["html5lib", "pytest"]
 
 [[package]]
-name = "sphinxcontrib.jquery"
-version = "2.0.0"
-description = "Extension to include jQuery on newer Sphinx releases"
+name = "sphinxcontrib-jsmath"
+version = "1.0.1"
+description = "A sphinx extension which renders display math in HTML via JavaScript"
 optional = false
-python-versions = ">=2.7"
+python-versions = ">=3.5"
 files = [
-    {file = "sphinxcontrib-jquery-2.0.0.tar.gz", hash = "sha256:8fb65f6dba84bf7bcd1aea1f02ab3955ac34611d838bcc95d4983b805b234daa"},
-    {file = "sphinxcontrib_jquery-2.0.0-py3-none-any.whl", hash = "sha256:ed47fa425c338ffebe3c37e1cdb56e30eb806116b85f01055b158c7057fdb995"},
+    {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"},
+    {file = "sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl", hash = "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178"},
 ]
 
-[package.dependencies]
-setuptools = "*"
+[package.extras]
+test = ["flake8", "mypy", "pytest"]
 
 [[package]]
-name = "sphinxcontrib-serializinghtml"
-version = "1.1.5"
-description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)."
+name = "sphinxcontrib-qthelp"
+version = "1.0.3"
+description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document."
 optional = false
 python-versions = ">=3.5"
 files = [
-    {file = "sphinxcontrib-serializinghtml-1.1.5.tar.gz", hash = "sha256:aa5f6de5dfdf809ef505c4895e51ef5c9eac17d0f287933eb49ec495280b6952"},
-    {file = "sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl", hash = "sha256:352a9a00ae864471d3a7ead8d7d79f5fc0b57e8b3f95e9867eb9eb28999b92fd"},
+    {file = "sphinxcontrib-qthelp-1.0.3.tar.gz", hash = "sha256:4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72"},
+    {file = "sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl", hash = "sha256:bd9fc24bcb748a8d51fd4ecaade681350aa63009a347a8c14e637895444dfab6"},
 ]
 
 [package.extras]
@@ -2718,22 +2844,19 @@ lint = ["docutils-stubs", "flake8", "mypy"]
 test = ["pytest"]
 
 [[package]]
-name = "sphinxcontrib-websupport"
-version = "1.2.4"
-description = "Sphinx API for Web Apps"
+name = "sphinxcontrib-serializinghtml"
+version = "1.1.5"
+description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)."
 optional = false
 python-versions = ">=3.5"
 files = [
-    {file = "sphinxcontrib-websupport-1.2.4.tar.gz", hash = "sha256:4edf0223a0685a7c485ae5a156b6f529ba1ee481a1417817935b20bde1956232"},
-    {file = "sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl", hash = "sha256:6fc9287dfc823fe9aa432463edd6cea47fa9ebbf488d7f289b322ffcfca075c7"},
+    {file = "sphinxcontrib-serializinghtml-1.1.5.tar.gz", hash = "sha256:aa5f6de5dfdf809ef505c4895e51ef5c9eac17d0f287933eb49ec495280b6952"},
+    {file = "sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl", hash = "sha256:352a9a00ae864471d3a7ead8d7d79f5fc0b57e8b3f95e9867eb9eb28999b92fd"},
 ]
 
-[package.dependencies]
-sphinxcontrib-serializinghtml = "*"
-
 [package.extras]
-lint = ["flake8"]
-test = ["Sphinx", "pytest", "sqlalchemy", "whoosh"]
+lint = ["docutils-stubs", "flake8", "mypy"]
+test = ["pytest"]
 
 [[package]]
 name = "SQLAlchemy"
@@ -3215,4 +3338,4 @@ testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools"
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "12309d0970389ab5b71eaf0a6ee92693e4a9041344db40acd4014488befddde3"
+content-hash = "2d22160a42d2e0db98695e81626ab69938c7a45d7ee539e388619aece7b0186d"
diff --git a/pyproject.toml b/pyproject.toml
index e8963d9..a5fcf95 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,9 +24,10 @@ pylint = "^2.16.2"
 pytest = "^7.3.0"
 pytest-cov = "^4.0.0"
 pytest-subtests = "^0.11.0"
-sphinx = "^1.6.0"
-sphinx-rtd-theme = "^1.2.0"
-sphinx_mdinclude = "^0.5.3"
+sphinx = "^7.0.1"
+furo = "^2023.5.20"
+myst-parser = "^2.0.0"
+sphinx-copybutton = "^0.5.2"
 tox = "^4.5.1"
 
 [tool.isort]

From 3232c251ead0b734ff97626ac8ba59e1e084710c Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Tue, 27 Jun 2023 17:25:52 -0400
Subject: [PATCH 28/48] Fix documentation workflow (#42)

---
 .github/workflows/documentation.yml | 22 ++++++++++++++++++++--
 1 file changed, 20 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
index 85ed062..6967c3b 100644
--- a/.github/workflows/documentation.yml
+++ b/.github/workflows/documentation.yml
@@ -19,13 +19,31 @@ jobs:
       with:
         python-version: 3.9
 
+    - name: Install poetry
+      uses: snok/install-poetry@v1
+      with:
+        virtualenvs-create: true
+        virtualenvs-in-project: true
+
+    - name: Load cached venv
+      id: cached-poetry-dependencies
+      uses: actions/cache@v3
+      with:
+        path: .venv
+        key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+
     - name: Install dependencies
+      if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+      run: |
+        poetry install --no-interaction --no-root
+
+    - name: Install library
       run: |
-        python -m pip install --upgrade pip
-        pip install Sphinx sphinx-rtd-theme sphinx-mdinclude
+        poetry install --no-interaction
 
     - name: Generate documentation with Sphinx
       run: |
+        source .venv/bin/activate
         make docs
         touch docs/_build/html/.nojekyll
 

From 00fd2e30673c2e34eacfa9bbf56b4e4c2daa6a55 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Thu, 29 Jun 2023 17:02:01 -0400
Subject: [PATCH 29/48] Release v0.8.1 (#43)

Co-authored-by: jessicasyu <15913767+jessicasyu@users.noreply.github.com>
---
 CHANGELOG.md   | 16 ++++++++++++++++
 pyproject.toml |  2 +-
 2 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7a21eec..e07cefd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,19 @@
+# [v0.8.1](https://github.com/bagherilab/arcade-collection/releases/tag/v0.8.1) - 2023-06-29
+
+> Compare with [v0.8.0](https://github.com/bagherilab/arcade-collection/compare/v0.8.0...v0.8.1)
+
+### Documentation
+
+- Update autogenerated documentation by [@jessicasyu](https://github.com/jessicasyu) in [#41](https://github.com/bagherilab/arcade-collection/pull/41)
+
+### Admin
+
+- Update lock file version by [@jessicasyu](https://github.com/jessicasyu) in [#37](https://github.com/bagherilab/arcade-collection/pull/37)
+- Bump starlette from 0.25.0 to 0.27.0 by [@dependabot[bot]](https://github.com/dependabot[bot]) in [#39](https://github.com/bagherilab/arcade-collection/pull/39)
+- Bump requests from 2.28.2 to 2.31.0 by [@dependabot[bot]](https://github.com/dependabot[bot]) in [#38](https://github.com/bagherilab/arcade-collection/pull/38)
+- Update dev dependencies by [@jessicasyu](https://github.com/jessicasyu) in [#40](https://github.com/bagherilab/arcade-collection/pull/40)
+- Fix documentation workflow by [@jessicasyu](https://github.com/jessicasyu) in [#42](https://github.com/bagherilab/arcade-collection/pull/42)
+
 # [v0.8.0](https://github.com/bagherilab/arcade-collection/releases/tag/v0.8.0) - 2023-04-04
 
 > Compare with [v0.7.2](https://github.com/bagherilab/arcade-collection/compare/v0.7.2...v0.8.0)
diff --git a/pyproject.toml b/pyproject.toml
index a5fcf95..7833731 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "arcade-collection"
-version = "0.8.0"
+version = "0.8.1"
 description = "Collection of tasks for working with ARCADE."
 authors = [
     "Jessica S. Yu <jesyu@uw.edu>"

From d61bd083da68e3cc1d6a2d0c6d6b66800d34973c Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Thu, 6 Jul 2023 11:32:28 -0400
Subject: [PATCH 30/48] Add resolution to convert to simularium task (#44)

---
 .../output/convert_to_simularium.py           | 186 +++++++++++++-----
 1 file changed, 135 insertions(+), 51 deletions(-)

diff --git a/src/arcade_collection/output/convert_to_simularium.py b/src/arcade_collection/output/convert_to_simularium.py
index d326e5a..af024a2 100644
--- a/src/arcade_collection/output/convert_to_simularium.py
+++ b/src/arcade_collection/output/convert_to_simularium.py
@@ -1,6 +1,9 @@
+import random
 import tarfile
+from typing import Optional, Union
 
 import numpy as np
+import pandas as pd
 from simulariumio import (
     DISPLAY_TYPE,
     AgentData,
@@ -15,6 +18,7 @@
 )
 
 from arcade_collection.output.extract_tick_json import extract_tick_json
+from arcade_collection.output.get_location_voxels import get_location_voxels
 
 
 def convert_to_simularium(
@@ -26,20 +30,27 @@ def convert_to_simularium(
     ds: float,
     dt: float,
     phase_colors: dict[str, str],
+    resolution: Optional[int] = None,
 ) -> str:
     length, width, height = box
     frames = list(np.arange(*frame_spec))
 
+    data = format_tar_data(series_key, cells_data_tar, locations_data_tar, frames, resolution)
+
     meta_data = get_meta_data(series_key, length, width, height, ds)
-    agent_data = get_agent_data(series_key, cells_data_tar, frames)
-    agent_data.display_data = get_display_data(phase_colors)
+    agent_data = get_agent_data(data)
+    agent_data.display_data = get_display_data(data, phase_colors)
 
-    for index, frame in enumerate(frames):
+    for index, (frame, group) in enumerate(data.groupby("frame")):
+        n_agents = len(group)
         agent_data.times[index] = float(frame) * dt
-        convert_cells_tar(agent_data, cells_data_tar, series_key, frame, index)
-        convert_locations_tar(
-            agent_data, locations_data_tar, series_key, frame, index, length, width, height, ds
-        )
+        agent_data.n_agents[index] = n_agents
+        agent_data.unique_ids[index][:n_agents] = range(0, n_agents)
+        agent_data.types[index][:n_agents] = group["name"]
+        agent_data.radii[index][:n_agents] = group["radius"]
+        agent_data.positions[index][:n_agents, 0] = (group["x"] - length / 2.0) * ds
+        agent_data.positions[index][:n_agents, 1] = (width / 2.0 - group["y"]) * ds
+        agent_data.positions[index][:n_agents, 2] = (group["z"] - height / 2.0) * ds
 
     return TrajectoryConverter(
         TrajectoryData(
@@ -70,60 +81,133 @@ def get_meta_data(series_key: str, length: int, width: int, height: int, ds: flo
     return meta_data
 
 
-def get_agent_data(series_key: str, cells_tar: tarfile.TarFile, frames: list[int]) -> AgentData:
-    total_frames = len(frames)
-
-    max_agents = 0
-    for frame in frames:
-        cells = extract_tick_json(cells_tar, series_key, frame, "CELLS")
-        max_agents = max(max_agents, len(cells))
-
+def get_agent_data(data: pd.DataFrame) -> AgentData:
+    total_frames = len(data["frame"].unique())
+    max_agents = data.groupby("frame")["name"].count().max()
     return AgentData.from_dimensions(DimensionData(total_frames, max_agents))
 
 
-def get_display_data(phase_colors: dict[str, str]) -> DisplayData:
+def get_display_data(data: pd.DataFrame, phase_colors: dict[str, str]) -> DisplayData:
     display_data = {}
 
-    for phase, color in phase_colors.items():
-        display_data[phase] = DisplayData(name=phase, color=color, display_type=DISPLAY_TYPE.SPHERE)
+    for name in data["name"].unique():
+        _, cell_id, phase = name.split("#")
+
+        random.seed(cell_id)
+        jitter = (random.random() - 0.5) / 2
+
+        display_data[name] = DisplayData(
+            name=name,
+            display_type=DISPLAY_TYPE.SPHERE,
+            color=shade_color(phase_colors[phase], jitter),
+        )
 
     return display_data
 
 
-def convert_cells_tar(
-    data: AgentData,
-    tar: tarfile.TarFile,
+def format_tar_data(
     series_key: str,
-    frame: int,
-    index: int,
-) -> None:
-    cells = extract_tick_json(tar, series_key, frame, "CELLS")
-    data.n_agents[index] = len(cells)
+    cells_tar: tarfile.TarFile,
+    locs_tar: tarfile.TarFile,
+    frames: list[int],
+    resolution: Optional[int],
+) -> pd.DataFrame:
+    data: list[list[Union[int, str, float]]] = []
 
-    for i, cell in enumerate(cells):
-        data.unique_ids[index][i] = cell["id"]
-        data.types[index].append(cell["phase"])
-        data.radii[index][i] = (cell["voxels"] ** (1.0 / 3)) / 1.5
+    for frame in frames:
+        cells = extract_tick_json(cells_tar, series_key, frame, "CELLS")
+        locations = extract_tick_json(locs_tar, series_key, frame, "LOCATIONS")
 
+        for cell, location in zip(cells, locations):
+            regions = [loc["region"] for loc in location["location"]]
 
-def convert_locations_tar(
-    data: AgentData,
-    tar: tarfile.TarFile,
-    series_key: str,
-    frame: int,
-    index: int,
-    length: int,
-    width: int,
-    height: int,
-    ds: float,
-) -> None:
-    locations = extract_tick_json(tar, series_key, frame, "LOCATIONS")
-
-    for i, location in enumerate(locations):
-        data.positions[index][i] = np.array(
-            [
-                (location["center"][0] - length / 2) * ds,
-                (width / 2 - location["center"][1]) * ds,
-                (location["center"][2] - height / 2) * ds,
-            ]
-        )
+            for region in regions:
+                name = f"{region}#{cell['id']}#{cell['phase']}"
+
+                all_voxels = get_location_voxels(location, region if region != "DEFAULT" else None)
+                all_voxels = [(x, y, z) for x, y, z in all_voxels]
+
+                if resolution is None:
+                    radius = (len(all_voxels) ** (1.0 / 3)) / 1.5
+                    center = list(np.array(all_voxels).mean(axis=0))
+                    data = data + [[name, int(frame), radius] + center]
+                else:
+                    radius = resolution / 2
+                    center_offset = (resolution - 1) / 2
+
+                    resolution_voxels = get_resolution_voxels(all_voxels, resolution)
+                    border_voxels = filter_border_voxels(set(resolution_voxels), resolution)
+                    center_voxels = [
+                        [x + center_offset, y + center_offset, z + center_offset]
+                        for x, y, z in border_voxels
+                    ]
+
+                    data = data + [[name, int(frame), radius] + voxel for voxel in center_voxels]
+
+    return pd.DataFrame(data, columns=["name", "frame", "radius", "x", "y", "z"])
+
+
+def get_resolution_voxels(
+    voxels: list[tuple[int, int, int]], resolution: int
+) -> list[tuple[int, int, int]]:
+    df = pd.DataFrame(voxels, columns=["x", "y", "z"])
+
+    min_x, min_y, min_z = df.min()
+    max_x, max_y, max_z = df.max()
+
+    samples = [
+        (sx, sy, sz)
+        for sx in np.arange(min_x, max_x, resolution)
+        for sy in np.arange(min_y, max_y, resolution)
+        for sz in np.arange(min_z, max_z, resolution)
+    ]
+
+    offsets = [
+        (dx, dy, dz)
+        for dx in range(resolution)
+        for dy in range(resolution)
+        for dz in range(resolution)
+    ]
+
+    resolution_voxels = []
+
+    for sx, sy, sz in samples:
+        sample_voxels = [(sx + dx, sy + dy, sz + dz) for dx, dy, dz in offsets]
+
+        if len(set(sample_voxels) - set(voxels)) < len(offsets) / 2:
+            resolution_voxels.append((sx, sy, sz))
+
+    return resolution_voxels
+
+
+def filter_border_voxels(
+    voxels: set[tuple[int, int, int]], resolution: int
+) -> list[tuple[int, int, int]]:
+    offsets = [
+        (resolution, 0, 0),
+        (-resolution, 0, 0),
+        (0, resolution, 0),
+        (0, -resolution, 0),
+        (0, 0, resolution),
+        (0, 0, -resolution),
+    ]
+    filtered_voxels = []
+
+    for x, y, z in voxels:
+        neighbors = [(x + dx, y + dy, z + dz) for dx, dy, dz in offsets]
+        if len(set(neighbors) - set(voxels)) != 0:
+            filtered_voxels.append((x, y, z))
+
+    return filtered_voxels
+
+
+def shade_color(color: str, alpha: float) -> str:
+    old_color = color.replace("#", "")
+    old_red, old_green, old_blue = [int(old_color[i : i + 2], 16) for i in (0, 2, 4)]
+    layer_color = 0 if alpha < 0 else 255
+
+    new_red = round(old_red + (layer_color - old_red) * abs(alpha))
+    new_green = round(old_green + (layer_color - old_green) * abs(alpha))
+    new_blue = round(old_blue + (layer_color - old_blue) * abs(alpha))
+
+    return f"#{new_red:02x}{new_green:02x}{new_blue:02x}"

From f9096a1f447a4c5c989df4282539405cbbb30526 Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Thu, 6 Jul 2023 11:35:02 -0400
Subject: [PATCH 31/48] Add task for converting to colorizer format (#45)

---
 src/arcade_collection/output/__init__.py      |  2 +
 .../output/convert_to_colorizer.py            | 77 +++++++++++++++++++
 .../output/convert_to_images.py               | 25 +++++-
 3 files changed, 101 insertions(+), 3 deletions(-)
 create mode 100644 src/arcade_collection/output/convert_to_colorizer.py

diff --git a/src/arcade_collection/output/__init__.py b/src/arcade_collection/output/__init__.py
index 3b969fd..82b9470 100644
--- a/src/arcade_collection/output/__init__.py
+++ b/src/arcade_collection/output/__init__.py
@@ -1,6 +1,7 @@
 from prefect import task
 
 from .convert_model_units import convert_model_units
+from .convert_to_colorizer import convert_to_colorizer
 from .convert_to_images import convert_to_images
 from .convert_to_meshes import convert_to_meshes
 from .convert_to_simularium import convert_to_simularium
@@ -11,6 +12,7 @@
 from .parse_locations_file import parse_locations_file
 
 convert_model_units = task(convert_model_units)
+convert_to_colorizer = task(convert_to_colorizer)
 convert_to_images = task(convert_to_images)
 convert_to_meshes = task(convert_to_meshes)
 convert_to_simularium = task(convert_to_simularium)
diff --git a/src/arcade_collection/output/convert_to_colorizer.py b/src/arcade_collection/output/convert_to_colorizer.py
new file mode 100644
index 0000000..d5d8adb
--- /dev/null
+++ b/src/arcade_collection/output/convert_to_colorizer.py
@@ -0,0 +1,77 @@
+import numpy as np
+import pandas as pd
+
+from arcade_collection.output.convert_model_units import convert_model_units
+
+
+def convert_to_colorizer(
+    all_data: pd.DataFrame,
+    features: list[str],
+    frame_spec: tuple[int, int, int],
+    ds: float,
+    dt: float,
+    regions: list[str],
+) -> dict:
+    frames = list(np.arange(*frame_spec))
+    manifest = get_manifest_data(features, frames)
+
+    convert_model_units(all_data, ds, dt, regions)
+    frame_data = all_data[all_data["TICK"].isin(frames)]
+
+    outliers = get_outliers_from_data(frame_data)
+    tracks = get_tracks_from_data(frame_data)
+    times = get_times_from_data(frame_data)
+
+    colorizer_json = {
+        "manifest": manifest,
+        "outliers": outliers,
+        "tracks": tracks,
+        "times": times,
+    }
+
+    for feature in features:
+        colorizer_json[feature] = get_feature_from_data(frame_data, feature)
+
+    return colorizer_json
+
+
+def get_manifest_data(features: list[str], frames: list[int]) -> dict:
+    manifest = {
+        "frames": [f"frame_{i}.png" for i in range(len(frames))],
+        "features": {
+            feature: f"feature_{feature_index}.json"
+            for feature_index, feature in enumerate(features)
+        },
+        "outliers": "outliers.json",
+        "tracks": "tracks.json",
+        "times": "times.json",
+    }
+
+    return manifest
+
+
+def get_outliers_from_data(data: pd.DataFrame) -> dict:
+    outliers = [False] * len(data)
+    outliers_json = {"data": outliers, "min": False, "max": True}
+    return outliers_json
+
+
+def get_tracks_from_data(data: pd.DataFrame) -> dict:
+    tracks = data["ID"]
+    tracks_json = {"data": list(tracks)}
+    return tracks_json
+
+
+def get_times_from_data(data: pd.DataFrame) -> dict:
+    times = data["time"]
+    times_json = {"data": list(times)}
+    return times_json
+
+
+def get_feature_from_data(data: pd.DataFrame, feature: str) -> dict:
+    feature_values = data[feature]
+    feature_min = float(np.nanmin(feature_values))
+    feature_max = float(np.nanmax(feature_values))
+
+    feature_json = {"data": list(feature_values), "min": feature_min, "max": feature_max}
+    return feature_json
diff --git a/src/arcade_collection/output/convert_to_images.py b/src/arcade_collection/output/convert_to_images.py
index 8140bc1..68381d5 100644
--- a/src/arcade_collection/output/convert_to_images.py
+++ b/src/arcade_collection/output/convert_to_images.py
@@ -14,8 +14,9 @@ def convert_to_images(
     regions: list[str],
     box: tuple[int, int, int],
     chunk_size: int,
-    binary: bool,
-    separate: bool,
+    binary: bool = False,
+    separate: bool = False,
+    flatten: bool = False,
 ) -> list[tuple[int, int, np.ndarray, Optional[int]]]:
     length, width, height = box
     frames = list(np.arange(*frame_spec))
@@ -40,7 +41,13 @@ def convert_to_images(
 
                 array[index, channel][tuple(np.transpose(voxels))] = 1 if binary else location_id
 
-    if separate:
+    if separate and flatten:
+        chunks = [
+            (i, j, flatten_array_chunk(chunk), frame)
+            for index, frame in enumerate(frames)
+            for i, j, chunk in split_array_chunks(array[[index], :, :, :, :], chunk_size)
+        ]
+    elif separate:
         chunks = [
             (i, j, chunk, frame)
             for index, frame in enumerate(frames)
@@ -83,3 +90,15 @@ def split_array_chunks(array: np.ndarray, chunk_size: int) -> list[tuple[int, in
                 chunks.append((i, j, chunk))
 
     return chunks
+
+
+def flatten_array_chunk(array: np.ndarray) -> np.ndarray:
+    array_flat = array[0, 0, :, :, :].max(axis=0)
+
+    array_rgba = np.zeros((*array_flat.shape, 4), dtype=np.uint8)
+    array_rgba[:, :, 0] = (array_flat & 0x000000FF) >> 0
+    array_rgba[:, :, 1] = (array_flat & 0x0000FF00) >> 8
+    array_rgba[:, :, 2] = (array_flat & 0x00FF0000) >> 16
+    array_rgba[:, :, 3] = 255  # (array_flat & 0x00FF0000) >> 24
+
+    return array_rgba

From c1793c321d704a3a7cd656e92476dda56c9fad0f Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Fri, 14 Jul 2023 17:40:33 -0400
Subject: [PATCH 32/48] Add extract feature bins task (#46)

---
 src/arcade_collection/output/__init__.py      |  2 +
 .../output/extract_feature_bins.py            | 78 +++++++++++++++++++
 2 files changed, 80 insertions(+)
 create mode 100644 src/arcade_collection/output/extract_feature_bins.py

diff --git a/src/arcade_collection/output/__init__.py b/src/arcade_collection/output/__init__.py
index 82b9470..0bb5298 100644
--- a/src/arcade_collection/output/__init__.py
+++ b/src/arcade_collection/output/__init__.py
@@ -5,6 +5,7 @@
 from .convert_to_images import convert_to_images
 from .convert_to_meshes import convert_to_meshes
 from .convert_to_simularium import convert_to_simularium
+from .extract_feature_bins import extract_feature_bins
 from .extract_tick_json import extract_tick_json
 from .get_location_voxels import get_location_voxels
 from .merge_parsed_results import merge_parsed_results
@@ -16,6 +17,7 @@
 convert_to_images = task(convert_to_images)
 convert_to_meshes = task(convert_to_meshes)
 convert_to_simularium = task(convert_to_simularium)
+extract_feature_bins = task(extract_feature_bins)
 extract_tick_json = task(extract_tick_json)
 get_location_voxels = task(get_location_voxels)
 merge_parsed_results = task(merge_parsed_results)
diff --git a/src/arcade_collection/output/extract_feature_bins.py b/src/arcade_collection/output/extract_feature_bins.py
new file mode 100644
index 0000000..df37af4
--- /dev/null
+++ b/src/arcade_collection/output/extract_feature_bins.py
@@ -0,0 +1,78 @@
+import tarfile
+from math import sqrt
+
+import numpy as np
+import pandas as pd
+
+from arcade_collection.output.extract_tick_json import extract_tick_json
+from arcade_collection.output.get_location_voxels import get_location_voxels
+
+
+def extract_feature_bins(
+    data_tars: dict[str, tarfile.TarFile],
+    frame: int,
+    scale: float,
+) -> pd.DataFrame:
+    feature_data: dict[tuple[int, int], list[int]] = {}
+
+    for series_key, data_tar in data_tars.items():
+        locations = extract_tick_json(data_tar, series_key, frame, "LOCATIONS")
+
+        for location in locations:
+            voxels = get_location_voxels(location)
+            array = np.array(voxels)
+
+            volume = len(array)
+            height = np.ptp(array[:, 2]) + 1
+            positions = np.array(list({(x, y) for x, y in array[:, :2].tolist()}))
+
+            for x, y in positions:
+                key = (x, y)
+
+                if key not in feature_data:
+                    feature_data[key] = [0, 0, 0]
+
+                feature_data[key][0] += 1
+                feature_data[key][1] += volume
+                feature_data[key][2] += height
+
+    coordinates = list(feature_data.keys())
+    values = list(feature_data.values())
+
+    feature_bins = bin_to_hex(coordinates, values, scale)
+    feature_bins_dataframe = pd.DataFrame(
+        [[x, y] + list(np.array(v).mean(axis=0)) for (x, y), v in feature_bins.items()],
+        columns=["x", "y", "count", "volume", "height"],
+    )
+
+    return feature_bins_dataframe
+
+
+def bin_to_hex(
+    coordinates: list[tuple[int, int]], values: list[list[int]], scale: float = 1.0
+) -> dict[tuple[float, float], list[list[int]]]:
+    bins: dict[tuple[float, float], list[list[int]]] = {}
+
+    for (x, y), v in zip(coordinates, values):
+        sx = x / scale
+        sy = y / scale
+
+        cx1 = scale * round(sx / sqrt(3)) * sqrt(3)
+        cy1 = scale * round(sy)
+        dist1 = sqrt((x - cx1) ** 2 + (y - cy1) ** 2)
+
+        cx2 = scale * (round(sx / sqrt(3) - 0.4999) + 0.5) * sqrt(3)
+        cy2 = scale * (round(sy - 0.49999) + 0.5)
+        dist2 = sqrt((x - cx2) ** 2 + (y - cy2) ** 2)
+
+        if dist1 < dist2:
+            center = (cx1, cy1)
+        else:
+            center = (cx2, cy2)
+
+        if center not in bins:
+            bins[center] = []
+
+        bins[center].append(v)
+
+    return bins

From fbf14776a596ed3530585beccc11d3d204aa6dad Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Fri, 14 Jul 2023 17:43:46 -0400
Subject: [PATCH 33/48] Release v0.9.0 (#47)

Co-authored-by: jessicasyu <15913767+jessicasyu@users.noreply.github.com>
---
 CHANGELOG.md   | 10 ++++++++++
 pyproject.toml |  2 +-
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e07cefd..db3632b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,13 @@
+# [v0.9.0](https://github.com/bagherilab/arcade-collection/releases/tag/v0.9.0) - 2023-07-14
+
+> Compare with [v0.8.1](https://github.com/bagherilab/arcade-collection/compare/v0.8.1...v0.9.0)
+
+### Features
+
+- Add resolution to convert to simularium task by [@jessicasyu](https://github.com/jessicasyu) in [#44](https://github.com/bagherilab/arcade-collection/pull/44)
+- Add task for converting to colorizer format by [@jessicasyu](https://github.com/jessicasyu) in [#45](https://github.com/bagherilab/arcade-collection/pull/45)
+- Add extract feature bins task by [@jessicasyu](https://github.com/jessicasyu) in [#46](https://github.com/bagherilab/arcade-collection/pull/46)
+
 # [v0.8.1](https://github.com/bagherilab/arcade-collection/releases/tag/v0.8.1) - 2023-06-29
 
 > Compare with [v0.8.0](https://github.com/bagherilab/arcade-collection/compare/v0.8.0...v0.8.1)
diff --git a/pyproject.toml b/pyproject.toml
index 7833731..624fdf1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "arcade-collection"
-version = "0.8.1"
+version = "0.9.0"
 description = "Collection of tasks for working with ARCADE."
 authors = [
     "Jessica S. Yu <jesyu@uw.edu>"

From 99e765569875a7ddd0d38e7ee601666e106a7d93 Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Fri, 4 Aug 2023 16:15:47 -0400
Subject: [PATCH 34/48] Remove extract feature bins task (#48)

---
 src/arcade_collection/output/__init__.py      |  2 -
 .../output/extract_feature_bins.py            | 78 -------------------
 2 files changed, 80 deletions(-)
 delete mode 100644 src/arcade_collection/output/extract_feature_bins.py

diff --git a/src/arcade_collection/output/__init__.py b/src/arcade_collection/output/__init__.py
index 0bb5298..82b9470 100644
--- a/src/arcade_collection/output/__init__.py
+++ b/src/arcade_collection/output/__init__.py
@@ -5,7 +5,6 @@
 from .convert_to_images import convert_to_images
 from .convert_to_meshes import convert_to_meshes
 from .convert_to_simularium import convert_to_simularium
-from .extract_feature_bins import extract_feature_bins
 from .extract_tick_json import extract_tick_json
 from .get_location_voxels import get_location_voxels
 from .merge_parsed_results import merge_parsed_results
@@ -17,7 +16,6 @@
 convert_to_images = task(convert_to_images)
 convert_to_meshes = task(convert_to_meshes)
 convert_to_simularium = task(convert_to_simularium)
-extract_feature_bins = task(extract_feature_bins)
 extract_tick_json = task(extract_tick_json)
 get_location_voxels = task(get_location_voxels)
 merge_parsed_results = task(merge_parsed_results)
diff --git a/src/arcade_collection/output/extract_feature_bins.py b/src/arcade_collection/output/extract_feature_bins.py
deleted file mode 100644
index df37af4..0000000
--- a/src/arcade_collection/output/extract_feature_bins.py
+++ /dev/null
@@ -1,78 +0,0 @@
-import tarfile
-from math import sqrt
-
-import numpy as np
-import pandas as pd
-
-from arcade_collection.output.extract_tick_json import extract_tick_json
-from arcade_collection.output.get_location_voxels import get_location_voxels
-
-
-def extract_feature_bins(
-    data_tars: dict[str, tarfile.TarFile],
-    frame: int,
-    scale: float,
-) -> pd.DataFrame:
-    feature_data: dict[tuple[int, int], list[int]] = {}
-
-    for series_key, data_tar in data_tars.items():
-        locations = extract_tick_json(data_tar, series_key, frame, "LOCATIONS")
-
-        for location in locations:
-            voxels = get_location_voxels(location)
-            array = np.array(voxels)
-
-            volume = len(array)
-            height = np.ptp(array[:, 2]) + 1
-            positions = np.array(list({(x, y) for x, y in array[:, :2].tolist()}))
-
-            for x, y in positions:
-                key = (x, y)
-
-                if key not in feature_data:
-                    feature_data[key] = [0, 0, 0]
-
-                feature_data[key][0] += 1
-                feature_data[key][1] += volume
-                feature_data[key][2] += height
-
-    coordinates = list(feature_data.keys())
-    values = list(feature_data.values())
-
-    feature_bins = bin_to_hex(coordinates, values, scale)
-    feature_bins_dataframe = pd.DataFrame(
-        [[x, y] + list(np.array(v).mean(axis=0)) for (x, y), v in feature_bins.items()],
-        columns=["x", "y", "count", "volume", "height"],
-    )
-
-    return feature_bins_dataframe
-
-
-def bin_to_hex(
-    coordinates: list[tuple[int, int]], values: list[list[int]], scale: float = 1.0
-) -> dict[tuple[float, float], list[list[int]]]:
-    bins: dict[tuple[float, float], list[list[int]]] = {}
-
-    for (x, y), v in zip(coordinates, values):
-        sx = x / scale
-        sy = y / scale
-
-        cx1 = scale * round(sx / sqrt(3)) * sqrt(3)
-        cy1 = scale * round(sy)
-        dist1 = sqrt((x - cx1) ** 2 + (y - cy1) ** 2)
-
-        cx2 = scale * (round(sx / sqrt(3) - 0.4999) + 0.5) * sqrt(3)
-        cy2 = scale * (round(sy - 0.49999) + 0.5)
-        dist2 = sqrt((x - cx2) ** 2 + (y - cy2) ** 2)
-
-        if dist1 < dist2:
-            center = (cx1, cy1)
-        else:
-            center = (cx2, cy2)
-
-        if center not in bins:
-            bins[center] = []
-
-        bins[center].append(v)
-
-    return bins

From 2bd20462be7c4b5d4b92c0c729fd4963d2a7df8d Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Thu, 17 Aug 2023 11:25:40 -0400
Subject: [PATCH 35/48] Add module docstrings (#49)

* Change autodoc typehints to signature

* Add module docstrings
---
 docs/_templates/custom_module.rst        | 4 ++--
 docs/_templates/custom_summary.rst       | 4 ++--
 docs/conf.py                             | 2 +-
 src/arcade_collection/input/__init__.py  | 2 ++
 src/arcade_collection/output/__init__.py | 2 ++
 5 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/docs/_templates/custom_module.rst b/docs/_templates/custom_module.rst
index 9eb45c5..466d2a8 100644
--- a/docs/_templates/custom_module.rst
+++ b/docs/_templates/custom_module.rst
@@ -1,8 +1,8 @@
 {{ objname | escape | underline}}
 
 .. automodule:: {{ fullname }}
-    :members:
-    :undoc-members:
+   :members:
+   :undoc-members:
 
    {% block attributes %}
    {% if attributes %}
diff --git a/docs/_templates/custom_summary.rst b/docs/_templates/custom_summary.rst
index 6689efc..f579cd9 100644
--- a/docs/_templates/custom_summary.rst
+++ b/docs/_templates/custom_summary.rst
@@ -1,8 +1,8 @@
 {{ fullname | escape | underline}}
 
 .. automodule:: {{ fullname }}
-    :members:
-    :undoc-members:
+   :members:
+   :undoc-members:
 
    {% block attributes %}
    {% if attributes %}
diff --git a/docs/conf.py b/docs/conf.py
index 53432fd..47d9edc 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -62,7 +62,7 @@
 autodoc_mock_imports = []
 
 # Controls how to represent typehints.
-autodoc_typehints = "description"
+autodoc_typehints = "signature"
 
 # -- Options for HTML output -------------------------------------------------
 
diff --git a/src/arcade_collection/input/__init__.py b/src/arcade_collection/input/__init__.py
index e588637..246f5d3 100644
--- a/src/arcade_collection/input/__init__.py
+++ b/src/arcade_collection/input/__init__.py
@@ -1,3 +1,5 @@
+"""Tasks for generating input files for ARCADE."""
+
 from prefect import task
 
 from .convert_to_cells_file import convert_to_cells_file
diff --git a/src/arcade_collection/output/__init__.py b/src/arcade_collection/output/__init__.py
index 82b9470..1dff9a6 100644
--- a/src/arcade_collection/output/__init__.py
+++ b/src/arcade_collection/output/__init__.py
@@ -1,3 +1,5 @@
+"""Tasks for processing output files from ARCADE."""
+
 from prefect import task
 
 from .convert_model_units import convert_model_units

From 322a8e0d6d86be5cc667a46fa8781c13454fa341 Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Thu, 17 Aug 2023 11:34:29 -0400
Subject: [PATCH 36/48] Update publish workflow to use trusted publisher (#50)

---
 .github/workflows/publish.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index de3d3c9..90dfb1d 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -13,6 +13,9 @@ jobs:
 
     runs-on: ubuntu-latest
 
+    permissions:
+      id-token: write
+
     steps:
 
     - name: Checkout the repo
@@ -84,5 +87,3 @@ jobs:
 
     - name: Publish package
       uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        password: ${{ secrets.PYPI_TOKEN }}

From cc667db6617c926d1ae0257b9de1ae5026427e04 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Thu, 17 Aug 2023 11:43:00 -0400
Subject: [PATCH 37/48] Release v0.9.1 (#51)

Co-authored-by: jessicasyu <15913767+jessicasyu@users.noreply.github.com>
---
 CHANGELOG.md   | 16 ++++++++++++++++
 pyproject.toml |  2 +-
 2 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index db3632b..be471fa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,19 @@
+# [v0.9.1](https://github.com/bagherilab/arcade-collection/releases/tag/v0.9.1) - 2023-08-17
+
+> Compare with [v0.9.0](https://github.com/bagherilab/arcade-collection/compare/v0.9.0...v0.9.1)
+
+### Bug fixes
+
+- Remove extract feature bins task by [@jessicasyu](https://github.com/jessicasyu) in [#48](https://github.com/bagherilab/arcade-collection/pull/48)
+
+### Documentation
+
+- Add module docstrings by [@jessicasyu](https://github.com/jessicasyu) in [#49](https://github.com/bagherilab/arcade-collection/pull/49)
+
+### Admin
+
+- Update publish workflow to use trusted publisher by [@jessicasyu](https://github.com/jessicasyu) in [#50](https://github.com/bagherilab/arcade-collection/pull/50)
+
 # [v0.9.0](https://github.com/bagherilab/arcade-collection/releases/tag/v0.9.0) - 2023-07-14
 
 > Compare with [v0.8.1](https://github.com/bagherilab/arcade-collection/compare/v0.8.1...v0.9.0)
diff --git a/pyproject.toml b/pyproject.toml
index 624fdf1..27d04a2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "arcade-collection"
-version = "0.9.0"
+version = "0.9.1"
 description = "Collection of tasks for working with ARCADE."
 authors = [
     "Jessica S. Yu <jesyu@uw.edu>"

From efec58f4411dd6c9bfc4878aa88253de36b42074 Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Fri, 18 Aug 2023 15:30:08 -0400
Subject: [PATCH 38/48] Update workflow permissions and badges (#52)

* Add write permission to allow action to create release

* Add read permission to allow action to generate changelog

* Update workflows to generate and publish badges

* Update README badge links
---
 .github/workflows/build.yml         | 62 ++++++++++++++++++++++++++---
 .github/workflows/documentation.yml | 60 +++++++++++++++++++++++++++-
 .github/workflows/lint.yml          | 31 +++++++++++++++
 .github/workflows/publish.yml       | 23 ++++++++++-
 README.md                           | 12 +++---
 docs/_badges/template.svg           | 11 +++++
 6 files changed, 186 insertions(+), 13 deletions(-)
 create mode 100644 docs/_badges/template.svg

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index ecdf5e7..bfb132c 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -45,11 +45,61 @@ jobs:
     - name: Test with pytest
       run: |
         source .venv/bin/activate
-        pytest --cov-report xml --cov=src/ tests/
+        pytest --cov-report html --cov=src/ tests/
+        rm htmlcov/.gitignore
 
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
+    - name: Publish coverage report
+      if: ${{ github.ref == 'refs/heads/main' && matrix.python-version == '3.10' }}
+      uses: JamesIves/github-pages-deploy-action@v4
       with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        file: ./coverage.xml
-        verbose: true
+        branch: gh-pages
+        folder: htmlcov
+        target-folder: _coverage
+
+    - name: Extract coverage percent
+      if: ${{ github.ref == 'refs/heads/main' && matrix.python-version == '3.10' }}
+      run: |
+        echo "COVERAGE=$(grep -oP 'pc_cov">\K([0-9]+)' htmlcov/index.html)" >> $GITHUB_ENV
+
+    - name: Generate coverage badge
+      if: ${{ github.ref == 'refs/heads/main' && matrix.python-version == '3.10' }}
+      uses: knightdave/anybadge-action@v1.1.0
+      with:
+        file: docs/_badges/coverage.svg
+        label: coverage
+        value: ${{ env.COVERAGE }}
+        value_format: "%d%%"
+        anybadge_args: 50=red 60=orange 80=yellow 100=green
+        template: docs/_badges/template.svg
+        overwrite: true
+
+    - name: Generate passing badge
+      if: success()
+      uses: knightdave/anybadge-action@v1.1.0
+      with:
+        file: docs/_badges/build.svg
+        label: build
+        value: passing
+        color: green
+        template: docs/_badges/template.svg
+        overwrite: true
+
+    - name: Generate failing badge
+      if: failure()
+      uses: knightdave/anybadge-action@v1.1.0
+      with:
+        file: docs/_badges/build.svg
+        label: build
+        value: failing
+        color: red
+        template: docs/_badges/template.svg
+        overwrite: true
+
+    - name: Publish badge
+      if: success() || failure()
+      uses: JamesIves/github-pages-deploy-action@v4
+      with:
+        branch: gh-pages
+        folder: docs/_badges
+        target-folder: _badges
+        clean: false
diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
index 6967c3b..51858d7 100644
--- a/.github/workflows/documentation.yml
+++ b/.github/workflows/documentation.yml
@@ -51,4 +51,62 @@ jobs:
       uses: JamesIves/github-pages-deploy-action@v4
       with:
         branch: gh-pages
-        folder: docs/_build/html/
+        folder: docs/_build/html
+        clean-exclude: |
+          _badges
+          _coverage
+
+    - name: Generate style badge
+      uses: knightdave/anybadge-action@v1.1.0
+      with:
+        file: docs/_badges/style.svg
+        label: code style
+        value: black
+        color: black
+        template: docs/_badges/template.svg
+        overwrite: true
+
+    - name: Extract license
+      run: |
+        echo "LICENSE=$(grep -oP 'license = "\K([A-z-0-9]+)(?=")' pyproject.toml)" >> $GITHUB_ENV
+
+    - name: Generate license badge
+      uses: knightdave/anybadge-action@v1.1.0
+      with:
+        file: docs/_badges/license.svg
+        label: license
+        value: ${{ env.LICENSE }}
+        color: yellowgreen
+        template: docs/_badges/template.svg
+        overwrite: true
+
+    - name: Generate passing badge
+      if: success()
+      uses: knightdave/anybadge-action@v1.1.0
+      with:
+        file: docs/_badges/documentation.svg
+        label: documentation
+        value: passing
+        color: green
+        template: docs/_badges/template.svg
+        overwrite: true
+
+    - name: Generate failing badge
+      if: failure()
+      uses: knightdave/anybadge-action@v1.1.0
+      with:
+        file: docs/_badges/documentation.svg
+        label: documentation
+        value: failing
+        color: red
+        template: docs/_badges/template.svg
+        overwrite: true
+
+    - name: Publish badge
+      if: success() || failure()
+      uses: JamesIves/github-pages-deploy-action@v4
+      with:
+        branch: gh-pages
+        folder: docs/_badges
+        target-folder: _badges
+        clean: false
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index ae397cc..a99ae83 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -53,3 +53,34 @@ jobs:
       run: |
         source .venv/bin/activate
         mypy src
+
+    - name: Generate passing badge
+      if: success()
+      uses: knightdave/anybadge-action@v1.1.0
+      with:
+        file: docs/_badges/lint.svg
+        label: lint
+        value: passing
+        color: green
+        template: docs/_badges/template.svg
+        overwrite: true
+
+    - name: Generate failing badge
+      if: failure()
+      uses: knightdave/anybadge-action@v1.1.0
+      with:
+        file: docs/_badges/lint.svg
+        label: lint
+        value: failing
+        color: red
+        template: docs/_badges/template.svg
+        overwrite: true
+
+    - name: Publish badge
+      if: success() || failure()
+      uses: JamesIves/github-pages-deploy-action@v4
+      with:
+        branch: gh-pages
+        folder: docs/_badges
+        target-folder: _badges
+        clean: false
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 90dfb1d..17a1886 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -15,6 +15,8 @@ jobs:
 
     permissions:
       id-token: write
+      contents: write
+      pull-requests: read
 
     steps:
 
@@ -68,7 +70,6 @@ jobs:
         tag: ${{ env.RELEASE_VERSION }}
         name: ${{ env.RELEASE_VERSION }}
         body: ${{ steps.build_changelog.outputs.changelog }}
-        token: ${{ secrets.GITHUB_TOKEN }}
 
     - name: Set up Python 3.9
       uses: actions/setup-python@v4
@@ -87,3 +88,23 @@ jobs:
 
     - name: Publish package
       uses: pypa/gh-action-pypi-publish@release/v1
+
+    - name: Generate version badge
+      if: success()
+      uses: knightdave/anybadge-action@v1.1.0
+      with:
+        file: docs/_badges/version.svg
+        label: version
+        value: ${{ env.RELEASE_VERSION }}
+        color: steelblue
+        template: docs/_badges/template.svg
+        overwrite: true
+
+    - name: Publish badge
+      if: success()
+      uses: JamesIves/github-pages-deploy-action@v4
+      with:
+        branch: gh-pages
+        folder: docs/_badges
+        target-folder: _badges
+        clean: false
diff --git a/README.md b/README.md
index 498a410..735183d 100644
--- a/README.md
+++ b/README.md
@@ -1,8 +1,10 @@
-[![Build Status](https://github.com/bagherilab/arcade-collection/workflows/build/badge.svg)](https://github.com/bagherilab/arcade-collection/actions?query=workflow%3Abuild)
-[![Codecov](https://img.shields.io/codecov/c/gh/bagherilab/arcade-collection?token=OXH1XGZOCI)](https://codecov.io/gh/bagherilab/arcade-collection)
-[![Lint Status](https://github.com/bagherilab/arcade-collection/workflows/lint/badge.svg)](https://github.com/bagherilab/arcade-collection/actions?query=workflow%3Alint)
-[![Documentation](https://github.com/bagherilab/arcade-collection/workflows/documentation/badge.svg)](https://bagherilab.github.io/arcade-collection/)
-[![Code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Build Status](https://bagherilab.github.io/arcade-collection/_badges/build.svg)](https://github.com/bagherilab/arcade-collection/actions?query=workflow%3Abuild)
+[![Lint Status](https://bagherilab.github.io/arcade-collection/_badges/lint.svg)](https://github.com/bagherilab/arcade-collection/actions?query=workflow%3Alint)
+[![Documentation](https://bagherilab.github.io/arcade-collection/_badges/documentation.svg)](https://bagherilab.github.io/arcade-collection/)
+[![Coverage](https://bagherilab.github.io/arcade-collection/_badges/coverage.svg)](https://bagherilab.github.io/arcade-collection/_coverage/)
+[![Code style](https://bagherilab.github.io/arcade-collection/_badges/style.svg)](https://github.com/psf/black)
+[![Version](https://bagherilab.github.io/arcade-collection/_badges/version.svg)](https://pypi.org/project/arcade-collection/)
+[![License](https://bagherilab.github.io/arcade-collection/_badges/license.svg)](https://github.com/bagherilab/arcade-collection/blob/main/LICENSE)
 
 Collection of tasks for working with ARCADE.
 Designed to be used both in [Prefect](https://docs.prefect.io/latest/) workflows and as modular, useful pieces of code.
diff --git a/docs/_badges/template.svg b/docs/_badges/template.svg
new file mode 100644
index 0000000..a569e65
--- /dev/null
+++ b/docs/_badges/template.svg
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<svg xmlns="http://www.w3.org/2000/svg" width="{{ badge width }}" height="20">
+    <g shape-rendering="crispEdges">
+        <rect width="{{ color split x }}" height="20" fill="#555555"/>
+        <rect x="{{ color split x }}" width="{{ value width }}" height="20" fill="{{ color }}"/>
+    </g>
+    <g fill="#FFFFFF" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="{{ font size }}">
+        <text x="{{ label anchor }}" y="14" fill="#FFFFFF">{{ label }}</text>
+        <text x="{{ value anchor }}" y="14" fill="#FFFFFF">{{ value }}</text>
+    </g>
+</svg>
\ No newline at end of file

From 155e60c1d0cbedf28f2069edb723f09e0bcdec1f Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Fri, 18 Aug 2023 15:42:44 -0400
Subject: [PATCH 39/48] Release v0.9.2 (#53)

Co-authored-by: jessicasyu <15913767+jessicasyu@users.noreply.github.com>
---
 CHANGELOG.md   | 8 ++++++++
 pyproject.toml | 2 +-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index be471fa..ad5fdd2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,11 @@
+# [v0.9.2](https://github.com/bagherilab/arcade-collection/releases/tag/v0.9.2) - 2023-08-18
+
+> Compare with [v0.9.1](https://github.com/bagherilab/arcade-collection/compare/v0.9.1...v0.9.2)
+
+### Admin
+
+- Update workflow permissions and badges by [@jessicasyu](https://github.com/jessicasyu) in [#52](https://github.com/bagherilab/arcade-collection/pull/52)
+
 # [v0.9.1](https://github.com/bagherilab/arcade-collection/releases/tag/v0.9.1) - 2023-08-17
 
 > Compare with [v0.9.0](https://github.com/bagherilab/arcade-collection/compare/v0.9.0...v0.9.1)
diff --git a/pyproject.toml b/pyproject.toml
index 27d04a2..c8da844 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "arcade-collection"
-version = "0.9.1"
+version = "0.9.2"
 description = "Collection of tasks for working with ARCADE."
 authors = [
     "Jessica S. Yu <jesyu@uw.edu>"

From a267efb046b36c3c5891c940fd19a165a85abafd Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Fri, 18 Aug 2023 16:04:55 -0400
Subject: [PATCH 40/48] Fix workflow badge steps (#54)

---
 .github/workflows/documentation.yml | 4 ++--
 .github/workflows/publish.yml       | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
index 51858d7..6a9fd72 100644
--- a/.github/workflows/documentation.yml
+++ b/.github/workflows/documentation.yml
@@ -85,7 +85,7 @@ jobs:
       uses: knightdave/anybadge-action@v1.1.0
       with:
         file: docs/_badges/documentation.svg
-        label: documentation
+        label: docs
         value: passing
         color: green
         template: docs/_badges/template.svg
@@ -96,7 +96,7 @@ jobs:
       uses: knightdave/anybadge-action@v1.1.0
       with:
         file: docs/_badges/documentation.svg
-        label: documentation
+        label: docs
         value: failing
         color: red
         template: docs/_badges/template.svg
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 17a1886..3db7699 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -96,7 +96,7 @@ jobs:
         file: docs/_badges/version.svg
         label: version
         value: ${{ env.RELEASE_VERSION }}
-        color: steelblue
+        color: teal
         template: docs/_badges/template.svg
         overwrite: true
 

From a49462360d470af2cb83c1b16438954bab3c7e81 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Fri, 18 Aug 2023 16:14:33 -0400
Subject: [PATCH 41/48] Release v0.9.3 (#55)

Co-authored-by: jessicasyu <15913767+jessicasyu@users.noreply.github.com>
---
 CHANGELOG.md   | 8 ++++++++
 pyproject.toml | 2 +-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ad5fdd2..209f27e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,11 @@
+# [v0.9.3](https://github.com/bagherilab/arcade-collection/releases/tag/v0.9.3) - 2023-08-18
+
+> Compare with [v0.9.2](https://github.com/bagherilab/arcade-collection/compare/v0.9.2...v0.9.3)
+
+### Admin
+
+- Fix workflow badge steps by [@jessicasyu](https://github.com/jessicasyu) in [#54](https://github.com/bagherilab/arcade-collection/pull/54)
+
 # [v0.9.2](https://github.com/bagherilab/arcade-collection/releases/tag/v0.9.2) - 2023-08-18
 
 > Compare with [v0.9.1](https://github.com/bagherilab/arcade-collection/compare/v0.9.1...v0.9.2)
diff --git a/pyproject.toml b/pyproject.toml
index c8da844..353155d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "arcade-collection"
-version = "0.9.2"
+version = "0.9.3"
 description = "Collection of tasks for working with ARCADE."
 authors = [
     "Jessica S. Yu <jesyu@uw.edu>"

From fd11731d851d1030e418eb64c8081d6953289ed9 Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Fri, 18 Aug 2023 17:57:15 -0400
Subject: [PATCH 42/48] Update build workflow to get results across matrix
 (#56)

* Update build workflow to summarize results

* Update README

* Add missing publish coverage badge step
---
 .github/workflows/build.yml | 29 +++++++++++++++++++++++++++++
 README.md                   |  4 ++--
 2 files changed, 31 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index bfb132c..33aded2 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -73,6 +73,35 @@ jobs:
         template: docs/_badges/template.svg
         overwrite: true
 
+    - name: Publish badge
+      if: ${{ github.ref == 'refs/heads/main' && matrix.python-version == '3.10' }}
+      uses: JamesIves/github-pages-deploy-action@v4
+      with:
+        branch: gh-pages
+        folder: docs/_badges
+        target-folder: _badges
+        clean: false
+
+  result:
+    if: ${{ always() }}
+
+    runs-on: ubuntu-latest
+
+    needs: [build]
+
+    steps:
+
+    - name: Checkout the repo
+      uses: actions/checkout@v3
+
+    - name: Get build result
+      run: |
+        if [[ ${{ needs.build.result }} == "success" || ${{ needs.build.result }} == "skipped" ]]; then
+          exit 0
+        else
+          exit 1
+        fi
+
     - name: Generate passing badge
       if: success()
       uses: knightdave/anybadge-action@v1.1.0
diff --git a/README.md b/README.md
index 735183d..c5e72b7 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,5 @@
-[![Build Status](https://bagherilab.github.io/arcade-collection/_badges/build.svg)](https://github.com/bagherilab/arcade-collection/actions?query=workflow%3Abuild)
-[![Lint Status](https://bagherilab.github.io/arcade-collection/_badges/lint.svg)](https://github.com/bagherilab/arcade-collection/actions?query=workflow%3Alint)
+[![Build status](https://bagherilab.github.io/arcade-collection/_badges/build.svg)](https://github.com/bagherilab/arcade-collection/actions?query=workflow%3Abuild)
+[![Lint status](https://bagherilab.github.io/arcade-collection/_badges/lint.svg)](https://github.com/bagherilab/arcade-collection/actions?query=workflow%3Alint)
 [![Documentation](https://bagherilab.github.io/arcade-collection/_badges/documentation.svg)](https://bagherilab.github.io/arcade-collection/)
 [![Coverage](https://bagherilab.github.io/arcade-collection/_badges/coverage.svg)](https://bagherilab.github.io/arcade-collection/_coverage/)
 [![Code style](https://bagherilab.github.io/arcade-collection/_badges/style.svg)](https://github.com/psf/black)

From 81b9114c9fdc26626f5012a1af6c1deae05d3d88 Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Fri, 25 Aug 2023 11:00:45 -0400
Subject: [PATCH 43/48] Update convert to simularium task to display meshes
 (#57)

* Add center and invert options to convert to meshes

* Add mesh option to convert to simularium

* Fix y coordinate offset
---
 .../output/convert_to_meshes.py               | 55 +++++++++++--------
 .../output/convert_to_simularium.py           | 34 ++++++++----
 2 files changed, 56 insertions(+), 33 deletions(-)

diff --git a/src/arcade_collection/output/convert_to_meshes.py b/src/arcade_collection/output/convert_to_meshes.py
index f0eb4c4..99428a5 100644
--- a/src/arcade_collection/output/convert_to_meshes.py
+++ b/src/arcade_collection/output/convert_to_meshes.py
@@ -8,11 +8,18 @@
 
 
 def convert_to_meshes(
-    series_key: str, data_tar: tarfile.TarFile, frame_spec: tuple[int, int, int], regions: list[str]
+    series_key: str,
+    data_tar: tarfile.TarFile,
+    frame_spec: tuple[int, int, int],
+    regions: list[str],
+    box: tuple[int, int, int],
+    invert: bool = False,
 ) -> list[tuple[int, int, str, str]]:
     frames = list(np.arange(*frame_spec))
     meshes = []
 
+    length, width, height = box
+
     for frame in frames:
         locations = extract_tick_json(data_tar, series_key, frame, "LOCATIONS")
 
@@ -21,7 +28,7 @@ def convert_to_meshes(
 
             for region in regions:
                 voxels = [
-                    (z, y, x)
+                    (x, width - y - 1, z)
                     for x, y, z in get_location_voxels(
                         location, region if region != "DEFAULT" else None
                     )
@@ -30,58 +37,60 @@ def convert_to_meshes(
                 if len(voxels) == 0:
                     continue
 
-                array = make_mesh_array(voxels)
-                mesh = make_mesh_object(array)
+                center = list(np.array(voxels).mean(axis=0))
+                array = make_mesh_array(voxels, length, width, height)
+                mesh = make_mesh_object(array, center, invert)
 
                 meshes.append((frame, location_id, region, mesh))
 
     return meshes
 
 
-def make_mesh_array(voxels: list[tuple[int, int, int]]) -> np.ndarray:
-    mins = np.min(voxels, axis=0)
-    maxs = np.max(voxels, axis=0)
-    height, width, length = np.subtract(maxs, mins) + 3
-    array = np.zeros((height, width, length), dtype=np.uint8)
-
-    voxels_transposed = [voxel - mins + 1 for voxel in voxels]
-    array[tuple(np.transpose(voxels_transposed))] = 7
+def make_mesh_array(
+    voxels: list[tuple[int, int, int]], length: int, width: int, height: int
+) -> np.ndarray:
+    # Create array.
+    array = np.zeros((length, width, height), dtype=np.uint8)
+    array[tuple(np.transpose(voxels))] = 7
 
     # Get set of zero neighbors for all voxels.
     offsets = [(-1, 0, 0), (1, 0, 0), (0, -1, 0), (0, 1, 0), (0, 0, -1), (0, 0, 1)]
     neighbors = {
-        (z + i, y + j, x + k)
-        for z, y, x in voxels_transposed
-        for k, j, i in offsets
-        if array[z + k, y + j, x + i] == 0
+        (x + i, y + j, z + k)
+        for x, y, z in voxels
+        for i, j, k in offsets
+        if array[x + i, y + j, z + k] == 0
     }
 
     # Remove invalid neighbors on borders.
     neighbors = {
-        (z, y, x)
-        for z, y, x in neighbors
+        (x, y, z)
+        for x, y, z in neighbors
         if x != 0 and y != 0 and z != 0 and x != length - 1 and y != width - 1 and z != height - 1
     }
 
     # Smooth array levels based on neighbor counts.
-    for z, y, x in neighbors:
-        array[z, y, x] = sum(array[z + k, y + j, x + i] == 7 for k, j, i in offsets) + 1
+    for x, y, z in neighbors:
+        array[x, y, z] = sum(array[x + i, y + j, z + k] == 7 for i, j, k in offsets) + 1
 
     return array
 
 
-def make_mesh_object(array: np.ndarray) -> str:
+def make_mesh_object(array: np.ndarray, center: list[float], invert: bool = False) -> str:
     verts, faces, normals, _ = measure.marching_cubes(array, level=3, allow_degenerate=False)
     mesh = ""
     faces = faces + 1
 
     for item in verts:
-        mesh += f"v {item[0]} {item[1]} {item[2]}\n"
+        mesh += f"v {item[0] - center[0]} {item[1] - center[1]} {item[2] - center[2]}\n"
 
     for item in normals:
         mesh += f"vn {item[0]} {item[1]} {item[2]}\n"
 
     for item in faces:
-        mesh += f"f {item[2]}//{item[2]} {item[1]}//{item[1]} {item[0]}//{item[0]}\n"
+        if invert:
+            mesh += f"f {item[0]}//{item[0]} {item[1]}//{item[1]} {item[2]}//{item[2]}\n"
+        else:
+            mesh += f"f {item[2]}//{item[2]} {item[1]}//{item[1]} {item[0]}//{item[0]}\n"
 
     return mesh
diff --git a/src/arcade_collection/output/convert_to_simularium.py b/src/arcade_collection/output/convert_to_simularium.py
index af024a2..178d7e8 100644
--- a/src/arcade_collection/output/convert_to_simularium.py
+++ b/src/arcade_collection/output/convert_to_simularium.py
@@ -31,6 +31,7 @@ def convert_to_simularium(
     dt: float,
     phase_colors: dict[str, str],
     resolution: Optional[int] = None,
+    url: Optional[str] = None,
 ) -> str:
     length, width, height = box
     frames = list(np.arange(*frame_spec))
@@ -39,7 +40,7 @@ def convert_to_simularium(
 
     meta_data = get_meta_data(series_key, length, width, height, ds)
     agent_data = get_agent_data(data)
-    agent_data.display_data = get_display_data(data, phase_colors)
+    agent_data.display_data = get_display_data(series_key, data, phase_colors, url)
 
     for index, (frame, group) in enumerate(data.groupby("frame")):
         n_agents = len(group)
@@ -87,20 +88,30 @@ def get_agent_data(data: pd.DataFrame) -> AgentData:
     return AgentData.from_dimensions(DimensionData(total_frames, max_agents))
 
 
-def get_display_data(data: pd.DataFrame, phase_colors: dict[str, str]) -> DisplayData:
+def get_display_data(
+    series_key: str, data: pd.DataFrame, phase_colors: dict[str, str], url: Optional[str] = None
+) -> DisplayData:
     display_data = {}
 
     for name in data["name"].unique():
-        _, cell_id, phase = name.split("#")
+        region, cell_id, phase, frame = name.split("#")
 
         random.seed(cell_id)
         jitter = (random.random() - 0.5) / 2
 
-        display_data[name] = DisplayData(
-            name=name,
-            display_type=DISPLAY_TYPE.SPHERE,
-            color=shade_color(phase_colors[phase], jitter),
-        )
+        if url is not None:
+            display_data[name] = DisplayData(
+                name=cell_id,
+                display_type=DISPLAY_TYPE.OBJ,
+                url=f"{url}/{series_key}_{int(frame):06d}_{int(cell_id):06d}_{region}.MESH.obj",
+                color=shade_color(phase_colors[phase], jitter),
+            )
+        else:
+            display_data[name] = DisplayData(
+                name=cell_id,
+                display_type=DISPLAY_TYPE.SPHERE,
+                color=shade_color(phase_colors[phase], jitter),
+            )
 
     return display_data
 
@@ -122,15 +133,18 @@ def format_tar_data(
             regions = [loc["region"] for loc in location["location"]]
 
             for region in regions:
-                name = f"{region}#{cell['id']}#{cell['phase']}"
+                name = f"{region}#{cell['id']}#{cell['phase']}#"
 
                 all_voxels = get_location_voxels(location, region if region != "DEFAULT" else None)
-                all_voxels = [(x, y, z) for x, y, z in all_voxels]
 
                 if resolution is None:
                     radius = (len(all_voxels) ** (1.0 / 3)) / 1.5
                     center = list(np.array(all_voxels).mean(axis=0))
                     data = data + [[name, int(frame), radius] + center]
+                elif resolution == 0:
+                    radius = 1
+                    center = list(np.array(all_voxels).mean(axis=0))
+                    data = data + [[f"{name}{frame}", int(frame), radius] + center]
                 else:
                     radius = resolution / 2
                     center_offset = (resolution - 1) / 2

From 77f66b244d97bc460db8fb007675653c06ace835 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Mon, 28 Aug 2023 14:41:52 -0400
Subject: [PATCH 44/48] Release v0.10.0 (#58)

Co-authored-by: jessicasyu <15913767+jessicasyu@users.noreply.github.com>
---
 CHANGELOG.md   | 12 ++++++++++++
 pyproject.toml |  2 +-
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 209f27e..70a9967 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,15 @@
+# [v0.10.0](https://github.com/bagherilab/arcade-collection/releases/tag/v0.10.0) - 2023-08-28
+
+> Compare with [v0.9.3](https://github.com/bagherilab/arcade-collection/compare/v0.9.3...v0.10.0)
+
+### Features
+
+- Update convert to simularium task to display meshes by [@jessicasyu](https://github.com/jessicasyu) in [#57](https://github.com/bagherilab/arcade-collection/pull/57)
+
+### Admin
+
+- Update build workflow to get results across matrix by [@jessicasyu](https://github.com/jessicasyu) in [#56](https://github.com/bagherilab/arcade-collection/pull/56)
+
 # [v0.9.3](https://github.com/bagherilab/arcade-collection/releases/tag/v0.9.3) - 2023-08-18
 
 > Compare with [v0.9.2](https://github.com/bagherilab/arcade-collection/compare/v0.9.2...v0.9.3)
diff --git a/pyproject.toml b/pyproject.toml
index 353155d..2bdd993 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "arcade-collection"
-version = "0.9.3"
+version = "0.10.0"
 description = "Collection of tasks for working with ARCADE."
 authors = [
     "Jessica S. Yu <jesyu@uw.edu>"

From 4fb9189a3da17c5ed4d3f3f019d8575b0e1b585f Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Wed, 6 Sep 2023 14:22:08 -0400
Subject: [PATCH 45/48] Add task for converting to projection format (#59)

* Add matplotlib dependency

* Add convert to projection task

* Add projection convert task to init

* Increase projection figure size
---
 poetry.lock                                   | 335 +++++++++++++++++-
 pyproject.toml                                |   4 +-
 src/arcade_collection/output/__init__.py      |   2 +
 .../output/convert_to_projection.py           | 177 +++++++++
 4 files changed, 516 insertions(+), 2 deletions(-)
 create mode 100644 src/arcade_collection/output/convert_to_projection.py

diff --git a/poetry.lock b/poetry.lock
index aa88ed4..d3226df 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -489,6 +489,64 @@ files = [
     {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
 ]
 
+[[package]]
+name = "contourpy"
+version = "1.1.0"
+description = "Python library for calculating contours of 2D quadrilateral grids"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "contourpy-1.1.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:89f06eff3ce2f4b3eb24c1055a26981bffe4e7264acd86f15b97e40530b794bc"},
+    {file = "contourpy-1.1.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:dffcc2ddec1782dd2f2ce1ef16f070861af4fb78c69862ce0aab801495dda6a3"},
+    {file = "contourpy-1.1.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:25ae46595e22f93592d39a7eac3d638cda552c3e1160255258b695f7b58e5655"},
+    {file = "contourpy-1.1.0-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:17cfaf5ec9862bc93af1ec1f302457371c34e688fbd381f4035a06cd47324f48"},
+    {file = "contourpy-1.1.0-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:18a64814ae7bce73925131381603fff0116e2df25230dfc80d6d690aa6e20b37"},
+    {file = "contourpy-1.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:90c81f22b4f572f8a2110b0b741bb64e5a6427e0a198b2cdc1fbaf85f352a3aa"},
+    {file = "contourpy-1.1.0-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:53cc3a40635abedbec7f1bde60f8c189c49e84ac180c665f2cd7c162cc454baa"},
+    {file = "contourpy-1.1.0-cp310-cp310-win_amd64.whl", hash = "sha256:1f795597073b09d631782e7245016a4323cf1cf0b4e06eef7ea6627e06a37ff2"},
+    {file = "contourpy-1.1.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:0b7b04ed0961647691cfe5d82115dd072af7ce8846d31a5fac6c142dcce8b882"},
+    {file = "contourpy-1.1.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:27bc79200c742f9746d7dd51a734ee326a292d77e7d94c8af6e08d1e6c15d545"},
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+    {file = "contourpy-1.1.0-pp38-pypy38_pp73-win_amd64.whl", hash = "sha256:a67259c2b493b00e5a4d0f7bfae51fb4b3371395e47d079a4446e9b0f4d70e76"},
+    {file = "contourpy-1.1.0-pp39-pypy39_pp73-macosx_10_9_x86_64.whl", hash = "sha256:2b836d22bd2c7bb2700348e4521b25e077255ebb6ab68e351ab5aa91ca27e027"},
+    {file = "contourpy-1.1.0-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:084eaa568400cfaf7179b847ac871582199b1b44d5699198e9602ecbbb5f6104"},
+    {file = "contourpy-1.1.0-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:911ff4fd53e26b019f898f32db0d4956c9d227d51338fb3b03ec72ff0084ee5f"},
+    {file = "contourpy-1.1.0.tar.gz", hash = "sha256:e53046c3863828d21d531cc3b53786e6580eb1ba02477e8681009b6aa0870b21"},
+]
+
+[package.dependencies]
+numpy = ">=1.16"
+
+[package.extras]
+bokeh = ["bokeh", "selenium"]
+docs = ["furo", "sphinx-copybutton"]
+mypy = ["contourpy[bokeh,docs]", "docutils-stubs", "mypy (==1.2.0)", "types-Pillow"]
+test = ["Pillow", "contourpy[test-no-images]", "matplotlib"]
+test-no-images = ["pytest", "pytest-cov", "wurlitzer"]
+
 [[package]]
 name = "coolname"
 version = "2.2.0"
@@ -621,6 +679,17 @@ ssh = ["bcrypt (>=3.1.5)"]
 test = ["pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-xdist"]
 test-randomorder = ["pytest-randomly"]
 
+[[package]]
+name = "cycler"
+version = "0.11.0"
+description = "Composable style cycles"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "cycler-0.11.0-py3-none-any.whl", hash = "sha256:3a27e95f763a428a739d2add979fa7494c912a32c17c4c38c4d5f082cad165a3"},
+    {file = "cycler-0.11.0.tar.gz", hash = "sha256:9c87405839a19696e837b3b818fed3f5f69f16f1eec1a1ad77e043dcea9c772f"},
+]
+
 [[package]]
 name = "dateparser"
 version = "1.1.7"
@@ -750,6 +819,63 @@ files = [
 docs = ["furo (>=2023.3.27)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.23,!=1.23.4)"]
 testing = ["covdefaults (>=2.3)", "coverage (>=7.2.3)", "diff-cover (>=7.5)", "pytest (>=7.3.1)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest-timeout (>=2.1)"]
 
+[[package]]
+name = "fonttools"
+version = "4.42.1"
+description = "Tools to manipulate font files"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "fonttools-4.42.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:ed1a13a27f59d1fc1920394a7f596792e9d546c9ca5a044419dca70c37815d7c"},
+    {file = "fonttools-4.42.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:c9b1ce7a45978b821a06d375b83763b27a3a5e8a2e4570b3065abad240a18760"},
+    {file = "fonttools-4.42.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:f720fa82a11c0f9042376fd509b5ed88dab7e3cd602eee63a1af08883b37342b"},
+    {file = "fonttools-4.42.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:db55cbaea02a20b49fefbd8e9d62bd481aaabe1f2301dabc575acc6b358874fa"},
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+    {file = "matplotlib-3.7.2-pp38-pypy38_pp73-win_amd64.whl", hash = "sha256:936bba394682049919dda062d33435b3be211dc3dcaa011e09634f060ec878b2"},
+    {file = "matplotlib-3.7.2-pp39-pypy39_pp73-macosx_10_12_x86_64.whl", hash = "sha256:bc221ffbc2150458b1cd71cdd9ddd5bb37962b036e41b8be258280b5b01da1dd"},
+    {file = "matplotlib-3.7.2-pp39-pypy39_pp73-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:35d74ebdb3f71f112b36c2629cf32323adfbf42679e2751252acd468f5001c07"},
+    {file = "matplotlib-3.7.2-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:717157e61b3a71d3d26ad4e1770dc85156c9af435659a25ee6407dc866cb258d"},
+    {file = "matplotlib-3.7.2-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:20f844d6be031948148ba49605c8b96dfe7d3711d1b63592830d650622458c11"},
+    {file = "matplotlib-3.7.2.tar.gz", hash = "sha256:a8cdb91dddb04436bd2f098b8fdf4b81352e68cf4d2c6756fcc414791076569b"},
+]
+
+[package.dependencies]
+contourpy = ">=1.0.1"
+cycler = ">=0.10"
+fonttools = ">=4.22.0"
+importlib-resources = {version = ">=3.2.0", markers = "python_version < \"3.10\""}
+kiwisolver = ">=1.0.1"
+numpy = ">=1.20"
+packaging = ">=20.0"
+pillow = ">=6.2.0"
+pyparsing = ">=2.3.1,<3.1"
+python-dateutil = ">=2.7"
+
 [[package]]
 name = "mccabe"
 version = "0.7.0"
@@ -2037,6 +2356,20 @@ typing-extensions = {version = ">=3.10.0", markers = "python_version < \"3.10\""
 spelling = ["pyenchant (>=3.2,<4.0)"]
 testutils = ["gitpython (>3)"]
 
+[[package]]
+name = "pyparsing"
+version = "3.0.9"
+description = "pyparsing module - Classes and methods to define and execute parsing grammars"
+optional = false
+python-versions = ">=3.6.8"
+files = [
+    {file = "pyparsing-3.0.9-py3-none-any.whl", hash = "sha256:5026bae9a10eeaefb61dab2f09052b9f4307d44aee4eda64b309723d8d206bbc"},
+    {file = "pyparsing-3.0.9.tar.gz", hash = "sha256:2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb"},
+]
+
+[package.extras]
+diagrams = ["jinja2", "railroad-diagrams"]
+
 [[package]]
 name = "pyproject-api"
 version = "1.5.1"
@@ -3338,4 +3671,4 @@ testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools"
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "2d22160a42d2e0db98695e81626ab69938c7a45d7ee539e388619aece7b0186d"
+content-hash = "3917639fa43db94996473b948403936c5903357f7f1f5ea754c70a8bf2b5ffc3"
diff --git a/pyproject.toml b/pyproject.toml
index 2bdd993..16bdf23 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,6 +15,7 @@ numpy = "^1.24.2"
 pandas = "^1.5.3"
 scikit-image = "^0.19.3"
 simulariumio = "^1.7.0"
+matplotlib = "^3.7.2"
 
 [tool.poetry.group.dev.dependencies]
 black = "^22.12.0"
@@ -41,7 +42,7 @@ build-backend = "poetry.core.masonry.api"
 disable = [
     "missing-module-docstring",
 ]
-good-names = ["i", "j", "k", "x", "y", "z", "ds", "dt"]
+good-names = ["i", "j", "k", "x", "y", "z", "ds", "dt", "ax"]
 
 [tool.pylint.design]
 max-args = 10 # maximum number of arguments for function / method
@@ -56,6 +57,7 @@ namespace_packages = true
 
 [[tool.mypy.overrides]]
 module = [
+    "matplotlib.*",
     "pandas.*",
     "simulariumio.*",
     "skimage.*",
diff --git a/src/arcade_collection/output/__init__.py b/src/arcade_collection/output/__init__.py
index 1dff9a6..240568a 100644
--- a/src/arcade_collection/output/__init__.py
+++ b/src/arcade_collection/output/__init__.py
@@ -6,6 +6,7 @@
 from .convert_to_colorizer import convert_to_colorizer
 from .convert_to_images import convert_to_images
 from .convert_to_meshes import convert_to_meshes
+from .convert_to_projection import convert_to_projection
 from .convert_to_simularium import convert_to_simularium
 from .extract_tick_json import extract_tick_json
 from .get_location_voxels import get_location_voxels
@@ -17,6 +18,7 @@
 convert_to_colorizer = task(convert_to_colorizer)
 convert_to_images = task(convert_to_images)
 convert_to_meshes = task(convert_to_meshes)
+convert_to_projection = task(convert_to_projection)
 convert_to_simularium = task(convert_to_simularium)
 extract_tick_json = task(extract_tick_json)
 get_location_voxels = task(get_location_voxels)
diff --git a/src/arcade_collection/output/convert_to_projection.py b/src/arcade_collection/output/convert_to_projection.py
new file mode 100644
index 0000000..871e622
--- /dev/null
+++ b/src/arcade_collection/output/convert_to_projection.py
@@ -0,0 +1,177 @@
+import tarfile
+from typing import Optional
+
+import matplotlib as mpl
+import matplotlib.pyplot as plt
+import numpy as np
+from matplotlib.patches import Rectangle
+
+from arcade_collection.output.extract_tick_json import extract_tick_json
+from arcade_collection.output.get_location_voxels import get_location_voxels
+
+
+def convert_to_projection(
+    series_key: str,
+    data_tar: tarfile.TarFile,
+    frame: int,
+    regions: list[str],
+    box: tuple[int, int, int],
+    ds: float,
+    dt: float,
+    scale: int,
+) -> mpl.figure.Figure:
+    fig = plt.figure(figsize=(10, 10), constrained_layout=True)
+    length, width, height = box
+
+    ax = fig.add_subplot()
+
+    ax.invert_yaxis()
+    ax.get_xaxis().set_ticks([])
+    ax.get_yaxis().set_ticks([])
+    ax.set_xlim([0, length - 1])
+    ax.set_ylim([width - 1, 0])
+    ax.set_box_aspect(1)
+
+    ax_horz = ax.inset_axes([0, 1.005, 1, height / width], sharex=ax)
+    ax_horz.set_ylim([0, height - 1])
+    ax_horz.get_yaxis().set_ticks([])
+
+    ax_vert = ax.inset_axes([1.005, 0, height / length, 1], sharey=ax)
+    ax_vert.set_xlim([0, height - 1])
+    ax_vert.get_xaxis().set_ticks([])
+
+    locations = extract_tick_json(data_tar, series_key, frame, "LOCATIONS")
+
+    if len(regions) == 1:
+        region = None if regions[0] == "DEFAULT" else regions[0]
+
+        arr_1 = create_projection_array(locations, length, width, height, region)
+        ax.imshow(arr_1, cmap="bone", interpolation="none", vmin=0, vmax=1)
+
+        arr_2 = create_projection_array(locations, length, width, height, region, (0, 2, 1))
+        ax_horz.imshow(arr_2, cmap="bone", interpolation="none", vmin=0, vmax=1)
+
+        arr_3 = create_projection_array(locations, length, width, height, region, (2, 1, 0))
+        ax_vert.imshow(arr_3, cmap="bone", interpolation="none", vmin=0, vmax=1)
+    elif len(regions) == 2:
+        region_a = None if regions[0] == "DEFAULT" else regions[0]
+        region_b = None if regions[1] == "DEFAULT" else regions[1]
+
+        arr_a1 = create_projection_array(locations, length, width, height, region_a)
+        arr_b1 = create_projection_array(locations, length, width, height, region_b)
+        arr_1 = join_projection_arrays(arr_a1, arr_b1)
+        ax.imshow(arr_1, interpolation="none")
+
+        arr_a2 = create_projection_array(locations, length, width, height, region_a, (0, 2, 1))
+        arr_b2 = create_projection_array(locations, length, width, height, region_b, (0, 2, 1))
+        arr_2 = join_projection_arrays(arr_a2, arr_b2)
+        ax_horz.imshow(arr_2, interpolation="none")
+
+        arr_a3 = create_projection_array(locations, length, width, height, region_a, (2, 1, 0))
+        arr_b3 = create_projection_array(locations, length, width, height, region_b, (2, 1, 0))
+        arr_3 = join_projection_arrays(arr_a3, arr_b3)
+        ax_vert.imshow(arr_3, interpolation="none")
+
+    add_frame_timestamp(ax, length, width, dt, frame, "#ffffff")
+    add_frame_scalebar(ax, length, width, ds, scale, "#ffffff")
+
+    return fig
+
+
+def create_projection_array(
+    locations: list,
+    length: int,
+    width: int,
+    height: int,
+    region: Optional[str] = None,
+    rotate: Optional[tuple[int, int, int]] = None,
+) -> np.ndarray:
+    array = np.zeros((length, width, height))
+
+    for location in locations:
+        voxels = get_location_voxels(location, region)
+
+        if len(voxels) == 0:
+            continue
+
+        array[tuple(np.transpose(voxels))] = location["id"]
+
+    if rotate is not None:
+        array = np.moveaxis(array, [0, 1, 2], rotate)
+        length, width, height = array.shape
+
+    borders = np.zeros((width, length))
+
+    for i in range(length):
+        for j in range(width):
+            for k in range(height):
+                target = array[i][j][k]
+
+                if target != 0:
+                    neighbors = [
+                        1
+                        for ii in [-1, 0, 1]
+                        for jj in [-1, 0, 1]
+                        if array[i + ii][j + jj][k] == target
+                    ]
+                    borders[j][i] += 9 - sum(neighbors)
+
+    normalize = borders.max()
+    borders = borders / normalize
+
+    return borders
+
+
+def join_projection_arrays(array_a: np.ndarray, array_b: np.ndarray) -> np.ndarray:
+    length, width = array_a.shape
+    array = np.zeros((length, width, 3))
+
+    array[:, :, 0] = array_a
+    array[:, :, 2] = array_a
+
+    array[:, :, 1] = array_b
+    array[:, :, 2] = np.maximum(array[:, :, 2], array_b)
+
+    return array
+
+
+def add_frame_timestamp(
+    ax: mpl.axes.Axes, length: int, width: int, dt: float, frame: int, color: str
+) -> None:
+    hours, minutes = divmod(round(frame * dt, 2), 1)
+    timestamp = f"{int(hours):02d}H:{round(minutes*60):02d}M"
+
+    ax.text(
+        0.03 * length,
+        0.96 * width,
+        timestamp,
+        fontfamily="monospace",
+        fontsize=20,
+        color=color,
+        fontweight="bold",
+    )
+
+
+def add_frame_scalebar(
+    ax: mpl.axes.Axes, length: int, width: int, ds: float, scale: int, color: str
+) -> None:
+    scalebar = scale / ds
+
+    ax.add_patch(
+        Rectangle(
+            (0.95 * length - scalebar, 0.92 * width),
+            scalebar,
+            0.01 * width,
+            snap=True,
+            color=color,
+        )
+    )
+
+    ax.text(
+        0.95 * length - scalebar / 2,
+        0.975 * width,
+        f"{scale} $\\mu$m",
+        fontsize=10,
+        color=color,
+        horizontalalignment="center",
+    )

From 7364fc2fdd4aa096469a9b9a2af40cf7ecf94149 Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Wed, 6 Sep 2023 14:28:07 -0400
Subject: [PATCH 46/48] Fix get location voxels return type (#60)

---
 src/arcade_collection/output/get_location_voxels.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/arcade_collection/output/get_location_voxels.py b/src/arcade_collection/output/get_location_voxels.py
index a7a5d2e..57696ff 100644
--- a/src/arcade_collection/output/get_location_voxels.py
+++ b/src/arcade_collection/output/get_location_voxels.py
@@ -3,9 +3,9 @@
 
 def get_location_voxels(location: dict, region: Optional[str] = None) -> list[tuple[int, int, int]]:
     voxels = [
-        voxel
+        (x, y, z)
         for loc in location["location"]
-        for voxel in loc["voxels"]
+        for x, y, z in loc["voxels"]
         if not region or loc["region"] == region
     ]
     return voxels

From 6f5f1ea7b70d40864889245cfafe69079a84f625 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Wed, 6 Sep 2023 14:45:36 -0400
Subject: [PATCH 47/48] Release v0.11.0 (#61)

Co-authored-by: jessicasyu <15913767+jessicasyu@users.noreply.github.com>
---
 CHANGELOG.md   | 12 ++++++++++++
 pyproject.toml |  2 +-
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 70a9967..eff000f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,15 @@
+# [v0.11.0](https://github.com/bagherilab/arcade-collection/releases/tag/v0.11.0) - 2023-09-06
+
+> Compare with [v0.10.0](https://github.com/bagherilab/arcade-collection/compare/v0.10.0...v0.11.0)
+
+### Features
+
+- Add task for converting to projection format by [@jessicasyu](https://github.com/jessicasyu) in [#59](https://github.com/bagherilab/arcade-collection/pull/59)
+
+### Bug fixes
+
+- Fix get location voxels return type by [@jessicasyu](https://github.com/jessicasyu) in [#60](https://github.com/bagherilab/arcade-collection/pull/60)
+
 # [v0.10.0](https://github.com/bagherilab/arcade-collection/releases/tag/v0.10.0) - 2023-08-28
 
 > Compare with [v0.9.3](https://github.com/bagherilab/arcade-collection/compare/v0.9.3...v0.10.0)
diff --git a/pyproject.toml b/pyproject.toml
index 16bdf23..c939372 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "arcade-collection"
-version = "0.10.0"
+version = "0.11.0"
 description = "Collection of tasks for working with ARCADE."
 authors = [
     "Jessica S. Yu <jesyu@uw.edu>"

From 04eaa4d559ab958afd43f5a94b02694961d51acd Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Fri, 15 Sep 2023 12:01:38 -0400
Subject: [PATCH 48/48] Move convert tasks into convert package (#62)

* Move convert tasks to dedicated package

* Update inits for convert package

* Fix init docstring
---
 src/arcade_collection/convert/__init__.py         | 15 +++++++++++++++
 .../{output => convert}/convert_to_colorizer.py   |  0
 .../{output => convert}/convert_to_images.py      |  0
 .../{output => convert}/convert_to_meshes.py      |  0
 .../{output => convert}/convert_to_projection.py  |  0
 .../{output => convert}/convert_to_simularium.py  |  0
 src/arcade_collection/output/__init__.py          | 10 ----------
 7 files changed, 15 insertions(+), 10 deletions(-)
 create mode 100644 src/arcade_collection/convert/__init__.py
 rename src/arcade_collection/{output => convert}/convert_to_colorizer.py (100%)
 rename src/arcade_collection/{output => convert}/convert_to_images.py (100%)
 rename src/arcade_collection/{output => convert}/convert_to_meshes.py (100%)
 rename src/arcade_collection/{output => convert}/convert_to_projection.py (100%)
 rename src/arcade_collection/{output => convert}/convert_to_simularium.py (100%)

diff --git a/src/arcade_collection/convert/__init__.py b/src/arcade_collection/convert/__init__.py
new file mode 100644
index 0000000..7677fbb
--- /dev/null
+++ b/src/arcade_collection/convert/__init__.py
@@ -0,0 +1,15 @@
+"""Tasks for converting ARCADE files to other formats."""
+
+from prefect import task
+
+from .convert_to_colorizer import convert_to_colorizer
+from .convert_to_images import convert_to_images
+from .convert_to_meshes import convert_to_meshes
+from .convert_to_projection import convert_to_projection
+from .convert_to_simularium import convert_to_simularium
+
+convert_to_colorizer = task(convert_to_colorizer)
+convert_to_images = task(convert_to_images)
+convert_to_meshes = task(convert_to_meshes)
+convert_to_projection = task(convert_to_projection)
+convert_to_simularium = task(convert_to_simularium)
diff --git a/src/arcade_collection/output/convert_to_colorizer.py b/src/arcade_collection/convert/convert_to_colorizer.py
similarity index 100%
rename from src/arcade_collection/output/convert_to_colorizer.py
rename to src/arcade_collection/convert/convert_to_colorizer.py
diff --git a/src/arcade_collection/output/convert_to_images.py b/src/arcade_collection/convert/convert_to_images.py
similarity index 100%
rename from src/arcade_collection/output/convert_to_images.py
rename to src/arcade_collection/convert/convert_to_images.py
diff --git a/src/arcade_collection/output/convert_to_meshes.py b/src/arcade_collection/convert/convert_to_meshes.py
similarity index 100%
rename from src/arcade_collection/output/convert_to_meshes.py
rename to src/arcade_collection/convert/convert_to_meshes.py
diff --git a/src/arcade_collection/output/convert_to_projection.py b/src/arcade_collection/convert/convert_to_projection.py
similarity index 100%
rename from src/arcade_collection/output/convert_to_projection.py
rename to src/arcade_collection/convert/convert_to_projection.py
diff --git a/src/arcade_collection/output/convert_to_simularium.py b/src/arcade_collection/convert/convert_to_simularium.py
similarity index 100%
rename from src/arcade_collection/output/convert_to_simularium.py
rename to src/arcade_collection/convert/convert_to_simularium.py
diff --git a/src/arcade_collection/output/__init__.py b/src/arcade_collection/output/__init__.py
index 240568a..438a252 100644
--- a/src/arcade_collection/output/__init__.py
+++ b/src/arcade_collection/output/__init__.py
@@ -3,11 +3,6 @@
 from prefect import task
 
 from .convert_model_units import convert_model_units
-from .convert_to_colorizer import convert_to_colorizer
-from .convert_to_images import convert_to_images
-from .convert_to_meshes import convert_to_meshes
-from .convert_to_projection import convert_to_projection
-from .convert_to_simularium import convert_to_simularium
 from .extract_tick_json import extract_tick_json
 from .get_location_voxels import get_location_voxels
 from .merge_parsed_results import merge_parsed_results
@@ -15,11 +10,6 @@
 from .parse_locations_file import parse_locations_file
 
 convert_model_units = task(convert_model_units)
-convert_to_colorizer = task(convert_to_colorizer)
-convert_to_images = task(convert_to_images)
-convert_to_meshes = task(convert_to_meshes)
-convert_to_projection = task(convert_to_projection)
-convert_to_simularium = task(convert_to_simularium)
 extract_tick_json = task(extract_tick_json)
 get_location_voxels = task(get_location_voxels)
 merge_parsed_results = task(merge_parsed_results)