Enable Dependabot updates to Poetry, fix tests and docs build (#6)

* initial migration Co-Authored-By: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com> * linting and test shifting * updates for docs * updates and linting * reduce environment and other references * readd pypi stuff * add link to pypi badge * activate uncovered test * remove poe steps and dep * Enable Dependabot updates to Poetry lockfile * add missing ignored data for tests * linting for pyproject.toml file * add docs build fix --------- Co-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>
WayScience · Oct 30, 2024 · c35b06c · c35b06c
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commit c35b06c
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Showing 41 changed files with 10 additions and 2 deletions.
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -14,3 +14,12 @@ updates:
     schedule:
       # Check for updates to GitHub Actions every week
       interval: "weekly"
+
+  # Perform checks and updates for python poetry environment.
+  # See here for more information:
+  # https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file#pip-and-pip-compile
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      # Check for updates to poetry lockfile every week
+      interval: "weekly"
diff --git a/docs/src/conf.py b/docs/src/conf.py
@@ -35,7 +35,7 @@
     "sphinx.ext.napoleon",
     "sphinx.ext.viewcode",
     "sphinx_multiversion",
-    "sphinx_wagtail_theme",
+    "pydata_sphinx_theme",
 ]
 
 # Add any paths that contain templates here, relative to this directory.

diff --git a/pyproject.toml b/pyproject.toml
@@ -127,4 +127,3 @@ omit = [
 
 [tool.bandit]
 exclude_dirs = [ "tests" ]
-
diff --git a/tests/data/coSMicQC/output_data/test_identifier_outliers_output.parquet b/tests/data/coSMicQC/output_data/test_identifier_outliers_output.parquet
diff --git a/tests/data/coSMicQC/output_data/test_label_outliers_output.parquet b/tests/data/coSMicQC/output_data/test_label_outliers_output.parquet
diff --git a/tests/data/cytotable/CFRet_data/test_localhost231120090001_converted.parquet b/tests/data/cytotable/CFRet_data/test_localhost231120090001_converted.parquet
diff --git a/tests/data/cytotable/NF1_cellpainting_data/Plate_2_with_image_data.parquet b/tests/data/cytotable/NF1_cellpainting_data/Plate_2_with_image_data.parquet
diff --git a/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/B7_01_1_3_DAPI_001.tif b/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/B7_01_1_3_DAPI_001.tif
diff --git a/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/B7_01_2_3_GFP_001.tif b/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/B7_01_2_3_GFP_001.tif
diff --git a/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/B7_01_3_3_RFP_001.tif b/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/B7_01_3_3_RFP_001.tif
diff --git a/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/D6_01_1_2_DAPI_001.tif b/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/D6_01_1_2_DAPI_001.tif
diff --git a/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/D6_01_2_2_GFP_001.tif b/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/D6_01_2_2_GFP_001.tif
diff --git a/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/D6_01_3_2_RFP_001.tif b/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/D6_01_3_2_RFP_001.tif
diff --git a/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/D7_01_1_1_DAPI_001.tif b/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/D7_01_1_1_DAPI_001.tif
diff --git a/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/D7_01_2_1_GFP_001.tif b/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/D7_01_2_1_GFP_001.tif
diff --git a/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/D7_01_3_1_RFP_001.tif b/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/D7_01_3_1_RFP_001.tif
diff --git a/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/F7_01_1_2_DAPI_001.tif b/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/F7_01_1_2_DAPI_001.tif
diff --git a/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/F7_01_2_2_GFP_001.tif b/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/F7_01_2_2_GFP_001.tif
diff --git a/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/F7_01_3_2_RFP_001.tif b/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/F7_01_3_2_RFP_001.tif
diff --git a/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/H12_01_1_1_DAPI_001.tif b/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/H12_01_1_1_DAPI_001.tif
diff --git a/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/H12_01_2_1_GFP_001.tif b/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/H12_01_2_1_GFP_001.tif
diff --git a/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/H12_01_3_1_RFP_001.tif b/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_images/H12_01_3_1_RFP_001.tif
diff --git a/...cytotable/NF1_cellpainting_data_shrunken/Plate_2_masks/B7_01_1_3_DAPI_001_MaskNuclei.tiff b/...cytotable/NF1_cellpainting_data_shrunken/Plate_2_masks/B7_01_1_3_DAPI_001_MaskNuclei.tiff
diff --git a/...a/cytotable/NF1_cellpainting_data_shrunken/Plate_2_masks/B7_01_3_3_RFP_001_MaskCells.tiff b/...a/cytotable/NF1_cellpainting_data_shrunken/Plate_2_masks/B7_01_3_3_RFP_001_MaskCells.tiff
diff --git a/...totable/NF1_cellpainting_data_shrunken/Plate_2_masks/B7_01_3_3_RFP_001_MaskCytoplasm.tiff b/...totable/NF1_cellpainting_data_shrunken/Plate_2_masks/B7_01_3_3_RFP_001_MaskCytoplasm.tiff
diff --git a/...cytotable/NF1_cellpainting_data_shrunken/Plate_2_masks/D6_01_1_2_DAPI_001_MaskNuclei.tiff b/...cytotable/NF1_cellpainting_data_shrunken/Plate_2_masks/D6_01_1_2_DAPI_001_MaskNuclei.tiff
diff --git a/...a/cytotable/NF1_cellpainting_data_shrunken/Plate_2_masks/D6_01_3_2_RFP_001_MaskCells.tiff b/...a/cytotable/NF1_cellpainting_data_shrunken/Plate_2_masks/D6_01_3_2_RFP_001_MaskCells.tiff
diff --git a/...totable/NF1_cellpainting_data_shrunken/Plate_2_masks/D6_01_3_2_RFP_001_MaskCytoplasm.tiff b/...totable/NF1_cellpainting_data_shrunken/Plate_2_masks/D6_01_3_2_RFP_001_MaskCytoplasm.tiff
diff --git a/...cytotable/NF1_cellpainting_data_shrunken/Plate_2_masks/D7_01_1_1_DAPI_001_MaskNuclei.tiff b/...cytotable/NF1_cellpainting_data_shrunken/Plate_2_masks/D7_01_1_1_DAPI_001_MaskNuclei.tiff
diff --git a/...a/cytotable/NF1_cellpainting_data_shrunken/Plate_2_masks/D7_01_3_1_RFP_001_MaskCells.tiff b/...a/cytotable/NF1_cellpainting_data_shrunken/Plate_2_masks/D7_01_3_1_RFP_001_MaskCells.tiff
diff --git a/...totable/NF1_cellpainting_data_shrunken/Plate_2_masks/D7_01_3_1_RFP_001_MaskCytoplasm.tiff b/...totable/NF1_cellpainting_data_shrunken/Plate_2_masks/D7_01_3_1_RFP_001_MaskCytoplasm.tiff
diff --git a/...cytotable/NF1_cellpainting_data_shrunken/Plate_2_masks/F7_01_1_2_DAPI_001_MaskNuclei.tiff b/...cytotable/NF1_cellpainting_data_shrunken/Plate_2_masks/F7_01_1_2_DAPI_001_MaskNuclei.tiff
diff --git a/...a/cytotable/NF1_cellpainting_data_shrunken/Plate_2_masks/F7_01_3_2_RFP_001_MaskCells.tiff b/...a/cytotable/NF1_cellpainting_data_shrunken/Plate_2_masks/F7_01_3_2_RFP_001_MaskCells.tiff
diff --git a/...totable/NF1_cellpainting_data_shrunken/Plate_2_masks/F7_01_3_2_RFP_001_MaskCytoplasm.tiff b/...totable/NF1_cellpainting_data_shrunken/Plate_2_masks/F7_01_3_2_RFP_001_MaskCytoplasm.tiff
diff --git a/...ytotable/NF1_cellpainting_data_shrunken/Plate_2_masks/H12_01_1_1_DAPI_001_MaskNuclei.tiff b/...ytotable/NF1_cellpainting_data_shrunken/Plate_2_masks/H12_01_1_1_DAPI_001_MaskNuclei.tiff
diff --git a/.../cytotable/NF1_cellpainting_data_shrunken/Plate_2_masks/H12_01_3_1_RFP_001_MaskCells.tiff b/.../cytotable/NF1_cellpainting_data_shrunken/Plate_2_masks/H12_01_3_1_RFP_001_MaskCells.tiff
diff --git a/...otable/NF1_cellpainting_data_shrunken/Plate_2_masks/H12_01_3_1_RFP_001_MaskCytoplasm.tiff b/...otable/NF1_cellpainting_data_shrunken/Plate_2_masks/H12_01_3_1_RFP_001_MaskCytoplasm.tiff
diff --git a/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_with_image_data_shrunken.parquet b/tests/data/cytotable/NF1_cellpainting_data_shrunken/Plate_2_with_image_data_shrunken.parquet
diff --git a/tests/data/cytotable/nuclear_speckles/images/plate1/slide1_A1_M10_CH0_Z09_illumcorrect.tiff b/tests/data/cytotable/nuclear_speckles/images/plate1/slide1_A1_M10_CH0_Z09_illumcorrect.tiff
diff --git a/...ytotable/nuclear_speckles/masks/plate1/slide1_A1_M10_CH0_Z09_illumcorrect_MaskNuclei.tiff b/...ytotable/nuclear_speckles/masks/plate1/slide1_A1_M10_CH0_Z09_illumcorrect_MaskNuclei.tiff
diff --git a/tests/data/cytotable/nuclear_speckles/test_slide1_converted.parquet b/tests/data/cytotable/nuclear_speckles/test_slide1_converted.parquet
Original file line number	Diff line number	Diff line change
Expand Up		@@ -127,4 +127,3 @@ omit = [

		[tool.bandit]
		exclude_dirs = [ "tests" ]