From ee9ad5873a043e78949cbe5b7b031fb857d288e7 Mon Sep 17 00:00:00 2001 From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com> Date: Mon, 15 Jul 2024 15:08:21 -0400 Subject: [PATCH] Bump dependency versions (#77) * Bump setuptools (67.4.0 -> 70.3.0) * Bump zipp (3.14.0 -> 3.19.2) * Bump prefect (2.16.1 -> 2.19.8) * Bump jinja2 (3.1.3 -> 3.1.4) * Bump idna (3.4 -> 3.7) * Bump black (22.12.0 -> 24.4.2) * Bump certifi (2024.2.2 -> 2024.7.4) * Bump pillow (10.2.0 -> 10.4.0) * Bump requests (2.31.0 -> 2.32.3) * Bump urllib3 (2.2.1 -> 2.2.2) * Bump pydantic (1.10.5 -> 2.8.2) * Fix linting errors --- poetry.lock | 604 +++++++++++------- pyproject.toml | 2 +- .../convert/convert_to_simularium_shapes.py | 2 +- .../output/parse_growth_file.py | 2 +- .../output/test_convert_model_units.py | 4 + .../output/test_parse_growth_file.py | 4 + 6 files changed, 399 insertions(+), 219 deletions(-) diff --git a/poetry.lock b/poetry.lock index 85d3241..332e6be 100644 --- a/poetry.lock +++ b/poetry.lock @@ -40,6 +40,17 @@ SQLAlchemy = ">=1.3.0" [package.extras] tz = 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Based on Python type hints." optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" files = [ - {file = "typer-0.7.0-py3-none-any.whl", hash = "sha256:b5e704f4e48ec263de1c0b3a2387cd405a13767d2f907f44c1a08cbad96f606d"}, - {file = "typer-0.7.0.tar.gz", hash = "sha256:ff797846578a9f2a201b53442aedeb543319466870fbe1c701eab66dd7681165"}, + {file = "typer-0.12.3-py3-none-any.whl", hash = "sha256:070d7ca53f785acbccba8e7d28b08dcd88f79f1fbda035ade0aecec71ca5c914"}, + {file = "typer-0.12.3.tar.gz", hash = "sha256:49e73131481d804288ef62598d97a1ceef3058905aa536a1134f90891ba35482"}, ] [package.dependencies] -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 = ["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)"] +click = ">=8.0.0" +rich = ">=10.11.0" +shellingham = ">=1.3.0" +typing-extensions = ">=3.7.4.3" [[package]] name = "typing-extensions" @@ -3655,6 +3816,17 @@ files = [ {file = "typing_extensions-4.10.0.tar.gz", hash = "sha256:b0abd7c89e8fb96f98db18d86106ff1d90ab692004eb746cf6eda2682f91b3cb"}, ] +[[package]] +name = "typing-extensions" +version = "4.12.2" +description = "Backported and Experimental Type Hints for Python 3.8+" +optional = false +python-versions = ">=3.8" +files = [ + {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"}, + {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"}, +] + [[package]] name = "tzdata" version = "2022.7" @@ -3761,13 +3933,13 @@ files = [ [[package]] name = "urllib3" -version = "2.2.1" +version = "2.2.2" description = "HTTP library with thread-safe connection pooling, file post, and more." optional = false python-versions = ">=3.8" files = [ - {file = "urllib3-2.2.1-py3-none-any.whl", hash = "sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d"}, - {file = "urllib3-2.2.1.tar.gz", hash = "sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19"}, + {file = "urllib3-2.2.2-py3-none-any.whl", hash = "sha256:a448b2f64d686155468037e1ace9f2d2199776e17f0a46610480d311f73e3472"}, + {file = "urllib3-2.2.2.tar.gz", hash = "sha256:dd505485549a7a552833da5e6063639d0d177c04f23bc3864e41e5dc5f612168"}, ] [package.extras] @@ -3983,20 +4155,20 @@ files = [ [[package]] name = "zipp" -version = "3.14.0" +version = "3.19.2" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "zipp-3.14.0-py3-none-any.whl", hash = "sha256:188834565033387710d046e3fe96acfc9b5e86cbca7f39ff69cf21a4128198b7"}, - {file = "zipp-3.14.0.tar.gz", hash = "sha256:9e5421e176ef5ab4c0ad896624e87a7b2f07aca746c9b2aa305952800cb8eecb"}, + {file = "zipp-3.19.2-py3-none-any.whl", hash = "sha256:f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c"}, + {file = "zipp-3.19.2.tar.gz", hash = "sha256:bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19"}, ] [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)"] +doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "0790541a2280953fc7f696f3ac688bc7dd87ec21c6c14fd8d143063f86e99740" +content-hash = "e5ae414f66519de1ce964f23109467fe03407141c236bf932834037751f407e8" diff --git a/pyproject.toml b/pyproject.toml index 630c6e8..7682ed5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,7 +18,7 @@ simulariumio = "^1.7.0" matplotlib = "^3.7.2" [tool.poetry.group.dev.dependencies] -black = "^22.12.0" +black = "^24.3.0" isort = "^5.12.0" mypy = "^1.3.0" pylint = "^2.16.2" diff --git a/src/arcade_collection/convert/convert_to_simularium_shapes.py b/src/arcade_collection/convert/convert_to_simularium_shapes.py index a0b3d31..9e101c1 100644 --- a/src/arcade_collection/convert/convert_to_simularium_shapes.py +++ b/src/arcade_collection/convert/convert_to_simularium_shapes.py @@ -109,7 +109,7 @@ def format_patch_for_shapes( graph_tar, series_key, frame, "GRAPH", field="graph" ) - for (from_node, to_node, edge) in graph_timepoint: + for from_node, to_node, edge in graph_timepoint: edge_type, radius, _, _, _, _, flow = edge name = f"VASCULATURE##{'UNDEFINED' if isnan(flow) else EDGE_TYPES[edge_type + 2]}" diff --git a/src/arcade_collection/output/parse_growth_file.py b/src/arcade_collection/output/parse_growth_file.py index 399c1dc..c958c4e 100644 --- a/src/arcade_collection/output/parse_growth_file.py +++ b/src/arcade_collection/output/parse_growth_file.py @@ -121,7 +121,7 @@ def parse_growth_timepoint(timepoint: dict, seed: int) -> list: parsed_data = [] time = timepoint["time"] - for (location, cells) in timepoint["cells"]: + for location, cells in timepoint["cells"]: u, v, w, z = location for cell in cells: diff --git a/tests/arcade_collection/output/test_convert_model_units.py b/tests/arcade_collection/output/test_convert_model_units.py index 465c59c..89f21fa 100644 --- a/tests/arcade_collection/output/test_convert_model_units.py +++ b/tests/arcade_collection/output/test_convert_model_units.py @@ -51,3 +51,7 @@ def test_estimate_spatial_resolution_invalid_spatiall_key(self): self.assertEqual(1, estimate_spatial_resolution(f"{ds_key}_B_C")) self.assertEqual(1, estimate_spatial_resolution(f"A_{ds_key}_C")) self.assertEqual(1, estimate_spatial_resolution(f"A_B_{ds_key}")) + + +if __name__ == "__main__": + unittest.main() diff --git a/tests/arcade_collection/output/test_parse_growth_file.py b/tests/arcade_collection/output/test_parse_growth_file.py index 6706e76..f6850ea 100644 --- a/tests/arcade_collection/output/test_parse_growth_file.py +++ b/tests/arcade_collection/output/test_parse_growth_file.py @@ -123,3 +123,7 @@ def test_parse_growth_timepoint(self): expected_df = pd.DataFrame(expected_dict) self.assertTrue(expected_df.equals(returned_df)) + + +if __name__ == "__main__": + unittest.main()