Add unit tests for arcade collection output tasks (#79)

* Add docstrings and unit tests for convert model units task

* Add docstrings and unit tests for extract tick json task

* Add docstrings and unit tests for get location voxels task

* Move contours task to convert submodule

* Remove merge parsed results task

* Add ruff linter

* Fix linting issues in input module

* Update docstrings and unit tests for parse growth file task

* Add docstrings and unit tests for parse locations file task

* Add docstrings and unit tests for parse cells file task

* Apply ruff linting

* Apply more ruff linting

pyproject.toml

@@ -20,7 +20,7 @@ matplotlib = "^3.7.2"
 [tool.poetry.group.dev.dependencies]
 black = "^24.3.0"
 isort = "^5.12.0"
-mypy = "^1.3.0"
+mypy = "^1.10.0"
 pylint = "^2.16.2"
 pytest = "^7.3.0"
 pytest-cov = "^4.0.0"
@@ -30,6 +30,7 @@ furo = "^2023.5.20"
 myst-parser = "^2.0.0"
 sphinx-copybutton = "^0.5.2"
 tox = "^4.5.1"
+ruff = "^0.6.3"
 
 [tool.isort]
 profile = "black"
@@ -42,7 +43,7 @@ build-backend = "poetry.core.masonry.api"
 disable = [
     "missing-module-docstring",
 ]
-good-names = ["i", "j", "k", "x", "y", "z", "ds", "dt", "ax"]
+good-names = ["i", "j", "k", "x", "y", "z", "u", "v", "w", "ds", "dt", "ax"]
 
 [tool.pylint.design]
 max-args = 10 # maximum number of arguments for function / method
@@ -59,11 +60,49 @@ namespace_packages = true
 module = [
     "matplotlib.*",
     "pandas.*",
+    "ruamel.*",
     "simulariumio.*",
     "skimage.*",
 ]
 ignore_missing_imports = true
 
+[tool.ruff]
+line-length = 100
+target-version = "py39"
+
+[tool.ruff.lint]
+select = ["ALL"]
+ignore = [
+    "COM812", # missing-trailing-comma
+    "D100",   # undocumented-public-module
+    "D105",   # undocumented-magic-method
+    "D107",   # undocumented-public-init
+    "D202",   # no-blank-line-after-function
+    "D203",   # one-blank-line-before-class
+    "D212",   # multi-line-summary-first-line
+    "D413",   # blank-line-after-last-section
+    "D416",   # section-name-ends-in-colon
+]
+
+[tool.ruff.lint.pylint]
+max-args = 10
+
+[tool.ruff.lint.per-file-ignores]
+"tests/*.py" = [
+    "D",      # pydocstyle
+    "PT009",  # pytest-unittest-assertion
+    "PT027",  # pytest-unittest-raises-assertion
+    "INP001", # implicit-namespace-package
+    "ANN201", # missing-return-type-undocumented-public-function
+    "S311",   # suspicious-non-cryptographic-random-usage
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "if TYPE_CHECKING:",
+]
+
 [tool.tox]
 legacy_tox_ini = """
 [tox]
@@ -84,6 +123,7 @@ commands =
 [testenv:lint]
 commands =
     poetry run pylint --ignore-patterns=test.*?py src/ tests/ --fail-under=9.0
+    poetry run ruff check src/ tests/
 
 [testenv:typecheck]
 commands =

src/arcade_collection/convert/__init__.py

@@ -3,6 +3,7 @@
 from prefect import task
 
 from .convert_to_colorizer import convert_to_colorizer
+from .convert_to_contours import convert_to_contours
 from .convert_to_images import convert_to_images
 from .convert_to_meshes import convert_to_meshes
 from .convert_to_projection import convert_to_projection
@@ -11,6 +12,7 @@
 from .convert_to_simularium_shapes import convert_to_simularium_shapes
 
 convert_to_colorizer = task(convert_to_colorizer)
+convert_to_contours = task(convert_to_contours)
 convert_to_images = task(convert_to_images)
 convert_to_meshes = task(convert_to_meshes)
 convert_to_projection = task(convert_to_projection)

src/arcade_collection/output/get_voxel_contours.py → src/arcade_collection/convert/convert_to_contours.py

@@ -13,7 +13,7 @@
 }
 
 
-def get_voxel_contours(
+def convert_to_contours(
     series_key: str,
     data_tar: tarfile.TarFile,
     frame: int,

src/arcade_collection/convert/convert_to_projection.py

@@ -4,7 +4,7 @@
 import matplotlib.pyplot as plt
 from matplotlib.patches import Rectangle
 
-from arcade_collection.output.get_voxel_contours import get_voxel_contours
+from arcade_collection.convert.convert_to_contours import convert_to_contours
 
 
 def convert_to_projection(
@@ -47,7 +47,7 @@ def convert_to_projection(
         "side1": list(range(1, width)),
         "side2": list(range(1, length)),
     }
-    contours = get_voxel_contours(series_key, data_tar, frame, regions, box, indices)
+    contours = convert_to_contours(series_key, data_tar, frame, regions, box, indices)
 
     for region in regions:
         color = colors[region]

src/arcade_collection/input/convert_to_cells_file.py

@@ -121,13 +121,13 @@ def convert_to_cell(
     height = samples.z.max() - samples.z.min()
 
     critical_volume = convert_value_distribution(
-        (reference["volume"] if "volume" in reference else volume),
+        reference.get("volume", volume),
         volume_distributions["DEFAULT"],
         critical_volume_distributions["DEFAULT"],
     )
 
     critical_height = convert_value_distribution(
-        (reference["height"] if "height" in reference else height),
+        reference.get("height", height),
         height_distributions["DEFAULT"],
         critical_height_distributions["DEFAULT"],
     )
@@ -146,7 +146,7 @@ def convert_to_cell(
         "criticals": [critical_volume, critical_height],
     }
 
-    if "region" in samples.columns and not samples["region"].isnull().all():
+    if "region" in samples.columns and not samples["region"].isna().all():
         regions = [
             convert_to_cell_region(
                 region,
@@ -210,13 +210,13 @@ def convert_to_cell_region(
     region_height = region_samples.z.max() - region_samples.z.min()
 
     region_critical_volume = convert_value_distribution(
-        (reference[f"volume.{region}"] if f"volume.{region}" in reference else region_volume),
+        reference.get(f"volume.{region}", region_volume),
         volume_distributions[region],
         critical_volume_distributions[region],
     )
 
     region_critical_height = convert_value_distribution(
-        (reference[f"height.{region}"] if f"height.{region}" in reference else region_height),
+        reference.get(f"height.{region}", region_height),
         height_distributions[region],
         critical_height_distributions[region],
     )
@@ -234,7 +234,7 @@ def get_cell_state(
     threshold_fractions: dict[str, float],
 ) -> str:
     """
-    Estimates cell state based on cell volume.
+    Estimate cell state based on cell volume.
 
     The threshold fractions dictionary defines the monotonic thresholds between
     different cell states. For a given volume v, critical volume V, and states
@@ -274,7 +274,7 @@ def convert_value_distribution(
     target_distribution: tuple[float, float],
 ) -> float:
     """
-    Estimates target value based on source value and source and target distributions.
+    Estimate target value based on source value and source and target distributions.
 
     Parameters
     ----------
@@ -294,13 +294,12 @@ def convert_value_distribution(
     source_avg, source_std = source_distribution
     target_avg, target_std = target_distribution
     z_scored_value = (value - source_avg) / source_std
-    converted_value = z_scored_value * target_std + target_avg
-    return converted_value
+    return z_scored_value * target_std + target_avg
 
 
 def filter_cell_reference(cell_id: int, reference: pd.DataFrame) -> dict:
     """
-    Filters reference data for given cell id.
+    Filter reference data for given cell id.
 
     Parameters
     ----------
@@ -316,5 +315,4 @@ def filter_cell_reference(cell_id: int, reference: pd.DataFrame) -> dict:
     """
 
     cell_reference = reference[reference["ID"] == cell_id].squeeze()
-    cell_reference = cell_reference.to_dict() if not cell_reference.empty else {}
-    return cell_reference
+    return cell_reference.to_dict() if not cell_reference.empty else {}