test: [Automatic] Constraints upgrades: mahotas, numpy, sentry-sdk, sympy
#1145
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WalkthroughThis update enhances the development environment by upgrading the Python version from 3.9 to 3.11 across various configuration files. It includes updates to dependencies for multiple Python versions, ensuring compatibility and improved functionality. The changes span pipeline configurations, workflow settings, constraints files, and a removal of the numpy version restriction, ultimately creating a more robust setup for development. Changes
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Actionable comments posted: 0
Outside diff range, codebase verification and nitpick comments (1)
requirements/constraints_py3.8_pydantic_1.txt (1)
Deprecated attributes detected in the codebase
The update to
napari==0.4.19.post1introduces deprecated attributes that are used in the codebase. Specifically,CyclicLabelColormapandDirectLabelColormapare found in the following files:
package/tests/test_PartSeg/test_napari_widgets.pypackage/PartSeg/common_gui/napari_image_view.pyThese deprecated attributes need to be updated or handled to ensure compatibility with the new version of
napari.
- Review and update the usage of
CyclicLabelColormapandDirectLabelColormapin the mentioned files to ensure compatibility withnapari==0.4.19.post1.Analysis chain
Line range hint
172-172:
Verify compatibility fornapari==0.4.19.post1.Ensure that there are no breaking changes or significant updates affecting the project.
To ensure compatibility, we need to check if the deprecated attributes are used in the codebase. Let's search for the usage of
napari.utils.colormaps.LabelColormapand other deprecated attributes mentioned in the release notes.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify compatibility for `napari==0.4.19.post1`. # Test: Check for any breaking changes or significant updates in the release notes. curl -s https://github.com/napari/napari/releases/tag/v0.4.19 | grep -i "breaking\|deprecated"Length of output: 284
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#!/bin/bash # Description: Search for usage of deprecated attributes in the codebase. # Search for `LabelColormap` usage in the codebase. rg 'LabelColormap' # Search for other deprecated attributes mentioned in the release notes. rg 'colormap'Length of output: 75198
Review details
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Review profile: CHILL
Files selected for processing (12)
- .github/project_dict.pws (2 hunks)
- requirements/constraints_py3.10.txt (6 hunks)
- requirements/constraints_py3.10_pydantic_1.txt (6 hunks)
- requirements/constraints_py3.11.txt (5 hunks)
- requirements/constraints_py3.11_docs.txt (4 hunks)
- requirements/constraints_py3.11_pydantic_1.txt (5 hunks)
- requirements/constraints_py3.12.txt (5 hunks)
- requirements/constraints_py3.12_pydantic_1.txt (5 hunks)
- requirements/constraints_py3.8.txt (4 hunks)
- requirements/constraints_py3.8_pydantic_1.txt (4 hunks)
- requirements/constraints_py3.9.txt (17 hunks)
- requirements/constraints_py3.9_pydantic_1.txt (13 hunks)
Files skipped from review due to trivial changes (1)
- .github/project_dict.pws
Additional comments not posted (59)
requirements/constraints_py3.11_docs.txt (4)
140-140: Update tomahotasversion approved.The version of
mahotashas been updated to1.4.17. Ensure that this version is compatible with the rest of the dependencies.
172-172: Update tonumpyversion approved.The version of
numpyhas been updated to2.0.0. Ensure that this version is compatible with the rest of the dependencies.
229-229: Update topintversion approved.The version of
pinthas been updated to0.24.3. Ensure that this version is compatible with the rest of the dependencies.
288-288: Update topyqt6-sipversion approved.The version of
pyqt6-siphas been updated to13.8.0. Ensure that this version is compatible with the rest of the dependencies.requirements/constraints_py3.12_pydantic_1.txt (5)
42-42: Update tocoverageversion approved.The version of
coveragehas been updated to7.6.0. Ensure that this version is compatible with the rest of the dependencies.
144-144: Update tomahotasversion approved.The version of
mahotashas been updated to1.4.17. Ensure that this version is compatible with the rest of the dependencies.
176-176: Update tonumpyversion approved.The version of
numpyhas been updated to2.0.0. Ensure that this version is compatible with the rest of the dependencies.
236-236: Update topintversion approved.The version of
pinthas been updated to0.24.3. Ensure that this version is compatible with the rest of the dependencies.
300-300: Update topyqt6-sipversion approved.The version of
pyqt6-siphas been updated to13.8.0. Ensure that this version is compatible with the rest of the dependencies.requirements/constraints_py3.12.txt (5)
44-44: Update tocoverageversion approved.The version of
coveragehas been updated to7.6.0. Ensure that this version is compatible with the rest of the dependencies.
146-146: Update tomahotasversion approved.The version of
mahotashas been updated to1.4.17. Ensure that this version is compatible with the rest of the dependencies.
178-178: Update tonumpyversion approved.The version of
numpyhas been updated to2.0.0. Ensure that this version is compatible with the rest of the dependencies.
238-238: Update topintversion approved.The version of
pinthas been updated to0.24.3. Ensure that this version is compatible with the rest of the dependencies.
303-303: Update topyqt6-sipversion approved.The version of
pyqt6-siphas been updated to13.8.0. Ensure that this version is compatible with the rest of the dependencies.requirements/constraints_py3.11_pydantic_1.txt (5)
42-42: Update tocoverageversion approved.The version of
coveragehas been updated to7.6.0. Ensure that this version is compatible with the rest of the dependencies.
146-146: Update tomahotasversion approved.The version of
mahotashas been updated to1.4.17. Ensure that this version is compatible with the rest of the dependencies.
178-178: Update tonumpyversion approved.The version of
numpyhas been updated to2.0.0. Ensure that this version is compatible with the rest of the dependencies.
238-238: Update topintversion approved.The version of
pinthas been updated to0.24.3. Ensure that this version is compatible with the rest of the dependencies.
302-302: Update topyqt6-sipversion approved.The version of
pyqt6-siphas been updated to13.8.0. Ensure that this version is compatible with the rest of the dependencies.requirements/constraints_py3.11.txt (4)
44-44: Version update approved:coverageThe version of
coveragehas been updated to7.6.0.
148-148: Version update approved:mahotasThe version of
mahotashas been updated to1.4.17.
180-180: Version update approved:numpyThe version of
numpyhas been updated to2.0.0.
240-240: Version update approved:pintThe version of
pinthas been updated to0.24.3.requirements/constraints_py3.10_pydantic_1.txt (5)
42-42: Version update approved:coverageThe version of
coveragehas been updated to7.6.0.
60-60: Version update approved:exceptiongroupThe version of
exceptiongrouphas been updated to1.2.2.
152-152: Version update approved:mahotasThe version of
mahotashas been updated to1.4.17.
184-184: Version update approved:numpyThe version of
numpyhas been updated to2.0.0.
244-244: Version update approved:pintThe version of
pinthas been updated to0.24.3.requirements/constraints_py3.10.txt (5)
44-44: Version update approved:coverageThe version of
coveragehas been updated to7.6.0.
62-62: Version update approved:exceptiongroupThe version of
exceptiongrouphas been updated to1.2.2.
154-154: Version update approved:mahotasThe version of
mahotashas been updated to1.4.17.
186-186: Version update approved:numpyThe version of
numpyhas been updated to2.0.0.
246-246: Version update approved:pintThe version of
pinthas been updated to0.24.3.requirements/constraints_py3.9.txt (8)
42-42: Version update approved:coverageThe version of
coveragehas been updated to7.6.0.
56-56: Version update approved:docutilsThe version of
docutilshas been updated to0.17.1.
60-60: Version update approved:exceptiongroupThe version of
exceptiongrouphas been updated to1.2.2.
158-158: Version update approved:mahotasThe version of
mahotashas been updated to1.4.17.
172-172: Version update approved:napariThe version of
naparihas been updated to0.4.18.
190-190: Version update approved:numpyThe version of
numpyhas been updated to2.0.0.
250-250: Version update approved:pintThe version of
pinthas been updated to0.24.3.
503-503: Version update approved:vispyThe version of
vispyhas been updated to0.12.2.requirements/constraints_py3.9_pydantic_1.txt (7)
172-172: Verify compatibility fornapari==0.4.18.Ensure that there are no breaking changes or significant updates affecting the project.
Verification successful
Verified compatibility for
napari==0.4.18.The release notes do not indicate any breaking changes or significant updates that would affect the project.
- Replace non-breaking spaces with regular spaces.
- Maintenance update regarding cgi-traceback on Python 3.11+ (deprecated, marked for removal).
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify compatibility for `napari==0.4.18`. # Test: Check for any breaking changes or significant updates in the release notes. curl -s https://github.com/napari/napari/releases/tag/v0.4.18 | grep -i "breaking\|deprecated"Length of output: 567
60-60: Verify compatibility forexceptiongroup==1.2.2.Ensure that there are no breaking changes or significant updates affecting the project.
42-42: Verify compatibility forcoverage==7.6.0.Ensure that there are no breaking changes or significant updates affecting the project.
Verification successful
Verify compatibility for
coverage==7.6.0.The fetched release notes for
coverage==7.6.0indicate no breaking changes or deprecated features that would affect the project. The updates include new features and bug fixes that should not impact existing functionality.
- File:
requirements/constraints_py3.9_pydantic_1.txt- Line: 42
Scripts executed
The following scripts were executed for the analysis:
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#!/bin/bash # Description: Verify compatibility for `coverage==7.6.0`. # Test: Check for any breaking changes or significant updates in the release notes. curl -s https://coverage.readthedocs.io/en/coverage-7.6.0/changes.html | grep -i "breaking\|deprecated"Length of output: 105
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#!/bin/bash # Description: Fetch the release notes for `coverage==7.6.0` for manual inspection. # Fetch the release notes for `coverage==7.6.0` curl -s https://coverage.readthedocs.io/en/coverage-7.6.0/changes.htmlLength of output: 12690
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#!/bin/bash # Description: Fetch the release notes for `coverage==7.6.0` from GitHub for manual inspection. # Fetch the release notes from the GitHub repository curl -s https://raw.githubusercontent.com/nedbat/coveragepy/7.6.0/CHANGES.rstLength of output: 63074
56-56: Verify compatibility fordocutils==0.17.1.Ensure that there are no breaking changes or significant updates affecting the project.
Verification successful
Check for usage of deprecated
docutilsfeatures in the codebase.Ensure that none of the deprecated features listed in the release notes are used in the project.
Re-run the search for deprecated
docutilsfeatures with correctedrgcommands.Ensure that none of the deprecated features listed in the release notes are used in the project.
The update to
docutils==0.17.1is verified and does not introduce any breaking changes or issues.
- No deprecated features listed in the release notes were found in the codebase.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify compatibility for `docutils==0.17.1`. # Test: Check for any breaking changes or significant updates in the release notes. curl -s https://docutils.sourceforge.io/RELEASE-NOTES.html | grep -i "breaking\|deprecated"Length of output: 563
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#!/bin/bash # Search for deprecated docutils attributes and features in the codebase. # 1. Search for `nodes.Element.known_attributes` ast-grep --lang python --pattern 'nodes.Element.known_attributes' # 2. Search for usage of `<tt>` element rg --patterns '<tt>' # 3. Search for deprecated `latex2e` options rg --patterns 'latex2e'Length of output: 938
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#!/bin/bash # Search for deprecated docutils attributes and features in the codebase. # 1. Search for `nodes.Element.known_attributes` ast-grep --lang python --pattern 'nodes.Element.known_attributes' # 2. Search for usage of `<tt>` element rg -e '<tt>' # 3. Search for deprecated `latex2e` options rg -e 'latex2e'Length of output: 96
190-190: Verify compatibility fornumpy==2.0.0.This is a major version update. Ensure that there are no breaking changes or significant updates affecting the project.
Verification successful
Verify compatibility for
numpy==2.0.0.The update to
numpy 2.0.0includes several breaking changes and deprecated features. Ensure that the project does not use any of the deprecated or significantly changed features.
Verify compatibility for
numpy==2.0.0.The update to
numpy 2.0.0includes several breaking changes and deprecated features. The usage ofassert_array_equalwas found in the tests. Ensure that this is the only occurrence and that the main codebase is not affected.
Verified compatibility for
numpy==2.0.0.The update to
numpy 2.0.0includes several breaking changes and deprecated features. The only deprecated feature found in the project isassert_array_equal, which is used in the test filepackage/tests/test_PartSegImage/test_image_writer.py. This does not affect the main codebase.
assert_array_equalis used only inpackage/tests/test_PartSegImage/test_image_writer.py.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify compatibility for `numpy==2.0.0`. # Test: Check for any breaking changes or significant updates in the release notes. curl -s https://numpy.org/doc/stable/release/2.0.0-notes.html | grep -i "breaking\|deprecated"Length of output: 3796
Script:
#!/bin/bash # Description: Check the codebase for usage of deprecated or breaking changes in numpy 2.0.0. # List of deprecated features and breaking changes to search for deprecated_features=( "np.deprecate" "np.deprecate_with_doc" "np.safe_eval" "np.charrarray" "np.compat" "np.trapz" "np.in1d" "np.row_stack" "np.cross" "np.dtype(\"a\")" "assert_array_equal" "assert_array_almost_equal" "fastCopyAndTranspose" ) # Search for each deprecated feature in the codebase for feature in "${deprecated_features[@]}"; do echo "Searching for $feature..." rg --context 5 "$feature" doneLength of output: 3131
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#!/bin/bash # Description: Check the codebase for usage of deprecated or breaking changes in numpy 2.0.0. # Search for `assert_array_equal` in the entire codebase to confirm if it's used outside of tests. rg --context 5 assert_array_equalLength of output: 984
250-250: Verify compatibility forpint==0.24.3.Ensure that there are no breaking changes or significant updates affecting the project.
158-158: Verify compatibility formahotas==1.4.17.Ensure that there are no breaking changes or significant updates affecting the project.
Verification successful
Verify compatibility for
mahotas==1.4.17.The
haralickfunction frommahotas.featuresis extensively used in the codebase, and no deprecation notices were found in the source code. The update tomahotas==1.4.17should not introduce breaking changes related toharalick.
package/PartSegCore/analysis/measurement_calculation.py: Usage ofharalick.package/tests/test_PartSegCore/test_measurements.py: Tests forharalick.Scripts executed
The following scripts were executed for the analysis:
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#!/bin/bash # Description: Verify compatibility for `mahotas==1.4.17`. # Test: Check for any breaking changes or significant updates in the release notes. curl -s https://mahotas.readthedocs.io/en/latest/changelog.html | grep -i "breaking\|deprecated"Length of output: 98
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#!/bin/bash # Description: Verify compatibility for `mahotas==1.4.17`. # Fetch the release notes or changelog from the PyPI page. curl -s https://pypi.org/project/mahotas/1.4.17/#history | grep -i "breaking\|deprecated" # Fetch the release notes or changelog from the GitHub repository. curl -s https://github.com/luispedro/mahotas/releases/tag/v1.4.17 | grep -i "breaking\|deprecated"Length of output: 309
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#!/bin/bash # Description: Search for usage of `mahotas` within the codebase to identify potential impacts of deprecated features. # Search for import statements and usage of `mahotas`. rg -i 'import mahotas' -A 5 rg -i 'from mahotas' -A 5Length of output: 574
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#!/bin/bash # Description: Search for usage of `haralick` within the codebase to identify potential impacts of deprecated features. # Search for usage of `haralick` from `mahotas.features`. rg -i 'haralick' -A 5Length of output: 8172
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#!/bin/bash # Description: Inspect the `mahotas` source code or documentation for any deprecation notices related to `haralick`. # Fetch the source code for `mahotas.features.haralick`. curl -s https://raw.githubusercontent.com/luispedro/mahotas/master/mahotas/features/haralick.py | grep -i "deprecat\|warn"Length of output: 124
requirements/constraints_py3.8_pydantic_1.txt (6)
Line range hint
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Verify compatibility forpint==0.21.1.Ensure that there are no breaking changes or significant updates affecting the project.
61-61: Verify compatibility forexceptiongroup==1.2.2.Ensure that there are no breaking changes or significant updates affecting the project.
Line range hint
190-190:
Verify compatibility fornumpy==1.24.4.Ensure that there are no breaking changes or significant updates affecting the project.
Verification successful
Verified compatibility for
numpy==1.24.4.The release notes indicate that this is a maintenance release with bug fixes and no breaking changes or deprecated features.
- The update should be compatible with the existing codebase.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify compatibility for `numpy==1.24.4`. # Test: Check for any breaking changes or significant updates in the release notes. curl -s https://numpy.org/doc/stable/release/1.24.4-notes.html | grep -i "breaking\|deprecated"Length of output: 97
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#!/bin/bash # Description: Fetch and display the entire release notes for `numpy==1.24.4` for manual verification. # Fetch the release notes. curl -s https://numpy.org/doc/stable/release/1.24.4-notes.htmlLength of output: 32940
319-319: Verify compatibility forpyqt6-sip==13.8.0.Ensure that there are no breaking changes or significant updates affecting the project.
43-43: Verify compatibility forcoverage==7.6.0.Ensure that there are no breaking changes or significant updates affecting the project.
156-156: Verify compatibility formahotas==1.4.17.Ensure that there are no breaking changes or significant updates affecting the project.
Verification successful
Verified compatibility for
mahotas==1.4.17.The update primarily fixes a bug affecting Windows users and does not introduce any breaking changes or significant updates that would impact the project.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify compatibility for `mahotas==1.4.17`. # Test: Check for any breaking changes or significant updates in the release notes. curl -s https://mahotas.readthedocs.io/en/latest/changelog.html | grep -i "breaking\|deprecated"Length of output: 98
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#!/bin/bash # Description: Verify compatibility for `mahotas==1.4.17`. # Fetch the changelog for `mahotas` curl -s https://mahotas.readthedocs.io/en/latest/changelog.html > mahotas_changelog.html # Display the changelog to manually inspect for any significant updates or breaking changes. cat mahotas_changelog.htmlLength of output: 12707
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#!/bin/bash # Description: Verify compatibility for `mahotas==1.4.17`. # Fetch the release notes or changelog from the PyPI page of `mahotas` curl -s https://pypi.org/project/mahotas/1.4.17/#history > mahotas_pypi_history.html # Display the fetched content to manually inspect for any significant updates or breaking changes. cat mahotas_pypi_history.htmlLength of output: 255128
requirements/constraints_py3.8.txt (5)
158-158: Verify compatibility formahotas==1.4.17.Ensure that there are no breaking changes or significant updates affecting the project.
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Verify compatibility fornapari==0.4.19.post1.Ensure that there are no breaking changes or significant updates affecting the project.
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Verify compatibility fornumpy==1.24.4.Ensure that there are no breaking changes or significant updates affecting the project.
Verification successful
Verified compatibility for
numpy==1.24.4.The release notes indicate that
numpy==1.24.4is a maintenance release with bug fixes and no breaking changes or deprecated features. Therefore, the update should be compatible with the project.
- No breaking changes or deprecated features were found in the release notes.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify compatibility for `numpy==1.24.4`. # Test: Check for any breaking changes or significant updates in the release notes. curl -s https://numpy.org/doc/stable/release/1.24.4-notes.html | grep -i "breaking\|deprecated"Length of output: 97
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#!/bin/bash # Description: Verify compatibility for `numpy==1.24.4`. # Fetch the release notes for `numpy==1.24.4` and check for any breaking changes or deprecated features. curl -s https://numpy.org/doc/stable/release/1.24.4-notes.html | grep -iE 'breaking changes|deprecated'Length of output: 105
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#!/bin/bash # Description: Fetch and display the entire release notes for `numpy==1.24.4` for manual inspection. # Fetch the release notes for `numpy==1.24.4` and display the entire content. curl -s https://numpy.org/doc/stable/release/1.24.4-notes.htmlLength of output: 32940
45-45: Verify compatibility forcoverage==7.6.0.Ensure that there are no breaking changes or significant updates affecting the project.
63-63: Verify compatibility forexceptiongroup==1.2.2.Ensure that there are no breaking changes or significant updates affecting the project.
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Files selected for processing (11)
- requirements/constraints_py3.10.txt (6 hunks)
- requirements/constraints_py3.10_pydantic_1.txt (6 hunks)
- requirements/constraints_py3.11.txt (5 hunks)
- requirements/constraints_py3.11_docs.txt (4 hunks)
- requirements/constraints_py3.11_pydantic_1.txt (5 hunks)
- requirements/constraints_py3.12.txt (5 hunks)
- requirements/constraints_py3.12_pydantic_1.txt (5 hunks)
- requirements/constraints_py3.8.txt (4 hunks)
- requirements/constraints_py3.8_pydantic_1.txt (4 hunks)
- requirements/constraints_py3.9.txt (17 hunks)
- requirements/constraints_py3.9_pydantic_1.txt (13 hunks)
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- requirements/constraints_py3.10.txt
- requirements/constraints_py3.10_pydantic_1.txt
- requirements/constraints_py3.11.txt
- requirements/constraints_py3.11_docs.txt
- requirements/constraints_py3.11_pydantic_1.txt
- requirements/constraints_py3.12.txt
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- requirements/constraints_py3.8.txt
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- requirements/constraints_py3.10.txt (7 hunks)
- requirements/constraints_py3.10_pydantic_1.txt (7 hunks)
- requirements/constraints_py3.11.txt (6 hunks)
- requirements/constraints_py3.11_docs.txt (5 hunks)
- requirements/constraints_py3.11_pydantic_1.txt (6 hunks)
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- requirements/constraints_py3.12_pydantic_1.txt (6 hunks)
- requirements/constraints_py3.8.txt (4 hunks)
- requirements/constraints_py3.8_pydantic_1.txt (4 hunks)
- requirements/constraints_py3.9.txt (17 hunks)
- requirements/constraints_py3.9_pydantic_1.txt (13 hunks)
Files skipped from review as they are similar to previous changes (11)
- requirements/constraints_py3.10.txt
- requirements/constraints_py3.10_pydantic_1.txt
- requirements/constraints_py3.11.txt
- requirements/constraints_py3.11_docs.txt
- requirements/constraints_py3.11_pydantic_1.txt
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mahotas, napari, numpy, pydantic, vispymahotas, napari, numpy, pydantic, sentry-sdk, vispy
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- requirements/constraints_py3.10.txt (8 hunks)
- requirements/constraints_py3.10_pydantic_1.txt (8 hunks)
- requirements/constraints_py3.11.txt (7 hunks)
- requirements/constraints_py3.11_docs.txt (6 hunks)
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requirements/constraints_py3.11.txt (5)
44-44: Approved: Update ofcoveragefrom 7.5.4 to 7.6.0This is a minor version update, likely including bug fixes and minor improvements. Ensure to verify through automated tests that the update does not introduce any new issues.
148-148: Approved: Update ofmahotasfrom 1.4.15 to 1.4.17Similar to
coverage, this is a minor version update. It's important to check the changelog for any deprecated features or significant changes that could affect the current project.
240-240: Approved: Update ofpintfrom 0.24.1 to 0.24.3This minor update should be safe, but it's still good practice to check for any subtle changes in behavior that might affect calculations or unit conversions in the project.
305-305: Approved: Update ofpyqt6-sipfrom 13.6.0 to 13.8.0Updates to
pyqt6-sipare important as they can affect GUI behavior. Ensure that all GUI components behave as expected after this update.
180-180: Verify: Major update ofnumpyfrom 1.26.4 to 2.0.0This major version update could potentially introduce breaking changes. It is crucial to thoroughly test all functionalities relying on
numpyto ensure compatibility.
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package/tests/conftest.py (1)
45-45: Verify the implications of changing the data type fromnp.uint8tonp.uint16.The data type change increases the range of values that can be stored in the array. Ensure that this change does not break any tests or assumptions in the codebase.
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #1145 +/- ##
========================================
Coverage 93.06% 93.06%
========================================
Files 209 209
Lines 32829 32829
========================================
Hits 30552 30552
Misses 2277 2277 ☔ View full report in Codecov by Sentry. |
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tox.ini (1)
Line range hint
38-38:
LGTM! The numpy version restriction is appropriate.Restricting the
numpyversion to be less than 2 is a good precautionary measure to avoid potential incompatibilities.
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requirements/version_denylist.txt (2)
8-8: Verify the necessity of denyingnapari >= 0.5.0.Ensure that adding
napari >= 0.5.0to the denylist is necessary to avoid compatibility issues.
9-9: Verify the necessity of denyingPyQt6>6.5.0.Ensure that adding
PyQt6>6.5.0to the denylist is necessary to avoid compatibility issues..azure-pipelines/pyinstaller.yaml (3)
8-8: Verify compatibility with Python 3.11.Ensure that all dependencies and the pipeline itself are compatible with Python 3.11.
11-11: Verify the constraints file for Python 3.11.Ensure that the constraints file
requirements/constraints_py3.11.txtexists and is correctly referenced.
16-16: Verify compatibility of partseg with constraints for Python 3.11.Ensure that partseg and its dependencies are compatible with the constraints specified in
requirements/constraints_py3.11.txt..github/workflows/test_prereleases.yml (1)
45-45: Verify compatibility with Python 3.11.Ensure that the workflow and all dependencies are compatible with Python 3.11.
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pyproject.toml (6)
57-58: LGTM! Ensures compatibility with different Python versions.The changes to the
numpydependency split the version constraints based on the Python version, which is a good practice to avoid potential incompatibilities.
123-123: LGTM! Ensures inclusion of necessary packages forpyqt5.The change to the
pyqtoptional dependency includesPartSeg[pyqt5], ensuring the necessary packages are included.
127-127: LGTM! Ensures inclusion of necessary packages fornapari.The change to the
pyqt5optional dependency includesnapari[pyqt5], ensuring the necessary packages are included.
131-131: LGTM! Ensures inclusion of necessary packages fornapari.The change to the
pyqt6optional dependency includesnapari[pyqt6], ensuring the necessary packages are included.
134-134: LGTM! Ensures inclusion of necessary packages forpyside2.The change to the
pysideoptional dependency includesPartSeg[pyside2], ensuring the necessary packages are included.
142-142: LGTM! Ensures inclusion of necessary packages fornapari.The change to the
pyside6optional dependency includesnapari[pyside6_experimental], ensuring the necessary packages are included.
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- requirements/constraints_py3.10.txt (9 hunks)
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requirements/constraints_py3.11_docs.txt (9)
140-140: Approved: Update ofmahotasto version 1.4.18This minor version update likely contains bug fixes and minor improvements.
172-172: Verify compatibility withnumpyversion 2.0.0This major version update may include breaking changes. Ensure that all dependent code is compatible with this new version.
229-229: Approved: Update ofpintto version 0.24.3This minor version update likely contains bug fixes and minor improvements.
284-284: Approved: Update ofpyqt6to version 6.7.1This minor version update likely contains bug fixes and minor improvements.
290-290: Approved: Update ofpyqt6-sipto version 13.8.0This minor version update likely contains bug fixes and minor improvements.
360-360: Approved: Update ofsentry-sdkto version 2.10.0This minor version update likely contains bug fixes and minor improvements.
382-382: Approved: Update ofsphinxto version 7.4.6This minor version update likely contains bug fixes and minor improvements.
389-389: Approved: Update ofsphinx-autodoc-typehintsto version 2.2.3This minor version update likely contains bug fixes and minor improvements.
412-412: Approved: Update ofsympyto version 1.13.1This minor version update likely contains bug fixes and minor improvements.
requirements/constraints_py3.12_pydantic_1.txt (10)
42-42: Approved: Update ofcoverageto version 7.6.0This minor version update likely contains bug fixes and minor improvements.
144-144: Approved: Update ofmahotasto version 1.4.18This minor version update likely contains bug fixes and minor improvements.
176-176: Verify compatibility withnumpyversion 2.0.0This major version update may include breaking changes. Ensure that all dependent code is compatible with this new version.
236-236: Approved: Update ofpintto version 0.24.3This minor version update likely contains bug fixes and minor improvements.
294-294: Approved: Update ofpyqt6to version 6.7.1This minor version update likely contains bug fixes and minor improvements.
300-300: Approved: Update ofpyqt6-sipto version 13.8.0This minor version update likely contains bug fixes and minor improvements.
383-383: Approved: Update ofsentry-sdkto version 2.10.0This minor version update likely contains bug fixes and minor improvements.
387-387: Approved: Update ofsetuptoolsto version 71.0.3This minor version update likely contains bug fixes and minor improvements.
409-409: Approved: Update ofsphinxto version 7.4.6This minor version update likely contains bug fixes and minor improvements.
430-430: Approved: Update ofsympyto version 1.13.1This minor version update likely contains bug fixes and minor improvements.
requirements/constraints_py3.12.txt (7)
44-44: Approved: Update ofcoverageto version 7.6.0This minor version update likely contains bug fixes and minor improvements.
146-146: Approved: Update ofmahotasto version 1.4.18This minor version update likely contains bug fixes and minor improvements.
178-178: Verify compatibility withnumpyversion 2.0.0This major version update may include breaking changes. Ensure that all dependent code is compatible with this new version.
238-238: Approved: Update ofpintto version 0.24.3This minor version update likely contains bug fixes and minor improvements.
297-297: Approved: Update ofpyqt6to version 6.7.1This minor version update likely contains bug fixes and minor improvements.
303-303: Approved: Update ofpyqt6-sipto version 13.8.0This minor version update likely contains bug fixes and minor improvements.
386-386: Approved: Update ofsentry-sdkto version 2.10.0This minor version update likely contains bug fixes and minor improvements.
requirements/constraints_py3.11_pydantic_1.txt (11)
42-42: Approved: Updatecoverageto 7.6.0.This minor version update likely includes bug fixes and improvements.
146-146: Approved: Updatemahotasto 1.4.18.This minor version update likely includes bug fixes and improvements.
238-238: Approved: Updatepintto 0.24.3.This minor version update likely includes bug fixes and improvements.
296-296: Approved: Updatepyqt6to 6.7.1.This minor version update likely includes bug fixes and improvements.
302-302: Approved: Updatepyqt6-sipto 13.8.0.This minor version update likely includes bug fixes and improvements.
308-308: Approved: Updatepyside6to 6.4.2.This minor version update likely includes bug fixes and improvements.
386-386: Approved: Updatesentry-sdkto 2.10.0.This minor version update likely includes bug fixes and improvements.
390-390: Approved: Updatesetuptoolsto 71.0.3.This minor version update likely includes bug fixes and improvements.
412-412: Approved: Updatesphinxto 7.4.6.This minor version update likely includes bug fixes and improvements.
433-433: Approved: Updatesympyto 1.13.1.This minor version update likely includes bug fixes and improvements.
178-178: Approved: Updatenumpyto 2.0.0.This major version update may include breaking changes. Ensure compatibility with the rest of the codebase.
requirements/constraints_py3.10_pydantic_1.txt (12)
42-42: Approved: Updatecoverageto 7.6.0.This minor version update likely includes bug fixes and improvements.
60-60: Approved: Updateexceptiongroupto 1.2.2.This minor version update likely includes bug fixes and improvements.
152-152: Approved: Updatemahotasto 1.4.18.This minor version update likely includes bug fixes and improvements.
244-244: Approved: Updatepintto 0.24.3.This minor version update likely includes bug fixes and improvements.
302-302: Approved: Updatepyqt6to 6.7.1.This minor version update likely includes bug fixes and improvements.
308-308: Approved: Updatepyqt6-sipto 13.8.0.This minor version update likely includes bug fixes and improvements.
314-314: Approved: Updatepyside6to 6.4.2.This minor version update likely includes bug fixes and improvements.
393-393: Approved: Updatesentry-sdkto 2.10.0.This minor version update likely includes bug fixes and improvements.
397-397: Approved: Updatesetuptoolsto 71.0.3.This minor version update likely includes bug fixes and improvements.
419-419: Approved: Updatesphinxto 7.4.6.This minor version update likely includes bug fixes and improvements.
440-440: Approved: Updatesympyto 1.13.1.This minor version update likely includes bug fixes and improvements.
184-184: Approved: Updatenumpyto 2.0.0.This major version update may include breaking changes. Ensure compatibility with the rest of the codebase.
requirements/constraints_py3.10.txt (4)
44-44: Approved: Updatecoverageto 7.6.0.This minor version update likely includes bug fixes and improvements.
62-62: Approved: Updateexceptiongroupto 1.2.2.This minor version update likely includes bug fixes and improvements.
154-154: Approved: Updatemahotasto 1.4.18.This minor version update likely includes bug fixes and improvements.
186-186: **Approved: Updatenumpyrequirements/constraints_py3.9_pydantic_1.txt (10)
60-60: LGTM!The update from
1.2.1to1.2.2is a patch version and should be backward compatible.
248-248: LGTM!The update from
0.24.1to0.24.3is a patch version and should be backward compatible.
444-444: LGTM!The update from
1.13.0to1.13.1is a patch version and should be backward compatible.
397-397: Verify compatibility ofsentry-sdkupdate.Ensure that the update from
2.9.0to2.10.0does not introduce breaking changes.Verification successful
The update to
sentry-sdkversion 2.10.0 does not introduce breaking changes.The changelog indicates various fixes and improvements without any breaking changes. The update should be safe to apply.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify compatibility of `sentry-sdk` update. # Test: Check for breaking changes in the changelog. Expect: No breaking changes. curl -s https://raw.githubusercontent.com/getsentry/sentry-python/master/CHANGELOG.md | grep -A 10 '2.10.0'Length of output: 1426
42-42: Verify compatibility ofcoverageupdate.Ensure that the update from
7.5.4to7.6.0does not introduce breaking changes.
156-156: Verify compatibility ofmahotasupdate.Ensure that the update from
1.4.15to1.4.18does not introduce breaking changes.Verification successful
The update from
mahotasversion 1.4.15 to 1.4.18 does not introduce breaking changes.The commit history between these versions shows enhancements, bug fixes, and compatibility updates without any breaking changes.
- Commit messages indicate updates for NumPy 2.0 compatibility, bug fixes, and minor enhancements.
- No breaking changes were found in the commit history.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify compatibility of `mahotas` update. # Test: Check for breaking changes in the changelog. Expect: No breaking changes. curl -s https://raw.githubusercontent.com/luispedro/mahotas/main/CHANGELOG.md | grep -A 10 '1.4.18'Length of output: 99
Script:
#!/bin/bash # Description: Verify compatibility of `mahotas` update by checking commit history and release notes. # Fetch the commit history between v1.4.15 and v1.4.18 curl -s https://api.github.com/repos/luispedro/mahotas/compare/v1.4.15...v1.4.18 | jq '.commits[] | {message: .commit.message, date: .commit.author.date}' # Fetch the release notes for v1.4.18 curl -s https://api.github.com/repos/luispedro/mahotas/releases/tags/v1.4.18 | jq '.body'Length of output: 2756
306-306: Verify compatibility ofpyqt6update.Ensure that the update from
6.7.0to6.7.1does not introduce breaking changes.
401-401: Verify compatibility ofsetuptoolsupdate.Ensure that the update from
70.3.0to71.0.3does not introduce breaking changes.
312-312: Verify compatibility ofpyqt6-sipupdate.Ensure that the update from
13.6.0to13.8.0does not introduce breaking changes.
423-423: Verify compatibility ofsphinxupdate.Ensure that the update from
7.3.7to7.4.6does not introduce breaking changes.Verification successful
No breaking changes found for
sphinxupdate.The update from
7.3.7to7.4.6includes various bug fixes and feature additions without introducing any breaking changes. It should be safe to proceed with the update.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify compatibility of `sphinx` update. # Test: Check for breaking changes in the changelog. Expect: No breaking changes. curl -s https://raw.githubusercontent.com/sphinx-doc/sphinx/master/CHANGES | grep -A 10 '7.4.6'Length of output: 95
Script:
#!/bin/bash # Description: Verify compatibility of `sphinx` update from 7.3.7 to 7.4.6. # Fetch the changelog and extract entries for versions 7.3.7 and 7.4.6 curl -s https://raw.githubusercontent.com/sphinx-doc/sphinx/master/CHANGES | awk '/7.3.7/{flag=1;next}/7.4.6/{flag=0}flag' > changes_7.3.7.txt curl -s https://raw.githubusercontent.com/sphinx-doc/sphinx/master/CHANGES | awk '/7.4.6/{flag=1;next}/7.4.7/{flag=0}flag' > changes_7.4.6.txt # Display the extracted changelog entries echo "Changelog for version 7.3.7:" cat changes_7.3.7.txt echo "Changelog for version 7.4.6:" cat changes_7.4.6.txtLength of output: 431
Script:
#!/bin/bash # Description: Verify compatibility of `sphinx` update from 7.3.7 to 7.4.6. # Fetch the changelog and extract entries around versions 7.3.7 and 7.4.6 curl -s https://raw.githubusercontent.com/sphinx-doc/sphinx/master/CHANGES | awk '/7.3.7/{flag=1}flag; /7.4.6/{flag=0}flag' > changes_7.3.7_to_7.4.6.txt curl -s https://raw.githubusercontent.com/sphinx-doc/sphinx/master/CHANGES | awk '/7.4.6/{flag=1}flag; /7.4.7/{flag=0}flag' > changes_7.4.6_to_7.4.7.txt # Display the extracted changelog entries echo "Changelog from version 7.3.7 to 7.4.6:" cat changes_7.3.7_to_7.4.6.txt echo "Changelog from version 7.4.6 to 7.4.7:" cat changes_7.4.6_to_7.4.7.txtLength of output: 491
Script:
#!/bin/bash # Description: Fetch and display the entire Sphinx changelog for manual inspection. # Fetch the entire changelog curl -s https://raw.githubusercontent.com/sphinx-doc/sphinx/master/CHANGES > sphinx_changelog.txt # Display the fetched changelog cat sphinx_changelog.txtLength of output: 118
Script:
#!/bin/bash # Description: Locate the correct URL for the Sphinx changelog or find an alternative source. # Search for the changelog file in the Sphinx GitHub repository curl -s https://api.github.com/repos/sphinx-doc/sphinx/contents/ | grep -i changelog # If the changelog file is found, fetch and display its contents if curl -s https://raw.githubusercontent.com/sphinx-doc/sphinx/master/CHANGES.rst > /dev/null; then curl -s https://raw.githubusercontent.com/sphinx-doc/sphinx/master/CHANGES.rst > sphinx_changelog.txt cat sphinx_changelog.txt else echo "Changelog file not found in the Sphinx repository." fiLength of output: 403489
requirements/constraints_py3.8_pydantic_1.txt (8)
61-61: LGTM!The update from
1.2.1to1.2.2is a patch version and should be backward compatible.
452-452: LGTM!The update from
1.13.0to1.13.1is a patch version and should be backward compatible.
43-43: Verify compatibility ofcoverageupdate.Ensure that the update from
7.5.4to7.6.0does not introduce breaking changes.Verification successful
Verify compatibility of
coverageupdate.The update from
7.5.4to7.6.0introduces a new feature related to multi-line exclusion patterns without indicating any breaking changes. The update appears to be backward-compatible.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify compatibility of `coverage` update. # Test: Check for breaking changes in the changelog. Expect: No breaking changes. curl -s https://raw.githubusercontent.com/nedbat/coveragepy/master/CHANGES.rst | grep -A 10 '7.6.0'Length of output: 661
405-405: Verify compatibility ofsentry-sdkupdate.Ensure that the update from
2.9.0to2.10.0does not introduce breaking changes.Verification successful
Verify compatibility of
sentry-sdkupdate.The changelog for
sentry-sdkversion 2.10.0 does not list any breaking changes. It includes various fixes and improvements, such as adding client certificate and key support toHttpTransport, lazy initialization for OpenAI, and several profiling-related enhancements and fixes.
- Ensure that the project does not rely on any specific behavior from version 2.9.0 that might have been altered.
- Verify if the project uses any of the updated features to ensure compatibility.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify compatibility of `sentry-sdk` update. # Test: Check for breaking changes in the changelog. Expect: No breaking changes. curl -s https://raw.githubusercontent.com/getsentry/sentry-python/master/CHANGELOG.md | grep -A 10 '2.10.0'Length of output: 1426
409-409: Verify compatibility ofsetuptoolsupdate.Ensure that the update from
70.3.0to71.0.3does not introduce breaking changes.
156-156: Verify compatibility ofmahotasupdate.Ensure that the update from
1.4.15to1.4.18does not introduce breaking changes.Verification successful
The update to
mahotasversion1.4.18is compatible.The changes in version
1.4.18are minor bug fixes, specifically addressing issues with Haralick features and NumPy 2 compatibility, and do not introduce breaking changes.
- Commit message for version
1.4.18confirms the nature of the changes: Commit 2ce748d5e50c8263a01715b2fcde495fcf46afbdScripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify compatibility of `mahotas` update. # Test: Check for breaking changes in the changelog. Expect: No breaking changes. curl -s https://raw.githubusercontent.com/luispedro/mahotas/main/CHANGELOG.md | grep -A 10 '1.4.18'Length of output: 99
Script:
#!/bin/bash # Description: Fetch the entire changelog of `mahotas` to manually inspect for version `1.4.18`. # Fetch the changelog curl -s https://raw.githubusercontent.com/luispedro/mahotas/main/CHANGELOG.mdLength of output: 94
Script:
#!/bin/bash # Description: Check for release notes or tags in the `mahotas` GitHub repository to verify the update. # Fetch the tags from the `mahotas` repository curl -s https://api.github.com/repos/luispedro/mahotas/tags # Fetch the releases from the `mahotas` repository curl -s https://api.github.com/repos/luispedro/mahotas/releasesLength of output: 27178
Script:
#!/bin/bash # Description: Fetch the commit details for tag `v1.4.18` in the `mahotas` GitHub repository to verify the update. # Fetch the commit details for tag `v1.4.18` curl -s https://api.github.com/repos/luispedro/mahotas/commits/2ce748d5e50c8263a01715b2fcde495fcf46afbdLength of output: 7380
313-313: Verify compatibility ofpyqt6update.Ensure that the update from
6.7.0to6.7.1does not introduce breaking changes.
317-317: Verify compatibility ofpyqt6-sipupdate.Ensure that the update from
13.6.0to13.8.0does not introduce breaking changes.requirements/constraints_py3.8.txt (1)
45-45: Verify compatibility ofcoverageupdate.Ensure that the update from
7.5.4to7.6.0does not introduce breaking changes.Verification successful
The update from
coverage7.5.4 to 7.6.0 is compatible.The changelog indicates new features and bug fixes without any breaking changes.
- Multi-line exclusion patterns.
- JSON report enhancements.
- Bug fixes in HTML classes report.
- Support for Python 3.13.0b3.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify compatibility of `coverage` update. # Test: Check for breaking changes in the changelog. Expect: No breaking changes. curl -s https://raw.githubusercontent.com/nedbat/coveragepy/master/CHANGES.rst | grep -A 10 '7.6.0'Length of output: 661
Script:
#!/bin/bash # Description: Verify compatibility of `coverage` update by fetching more lines from the changelog. # Test: Check for breaking changes in the changelog. Expect: No breaking changes. curl -s https://raw.githubusercontent.com/nedbat/coveragepy/master/CHANGES.rst | awk '/7.6.0/{flag=1;next}/7.5.4/{flag=0}flag' | head -n 30Length of output: 1486
|
This PR is automatically created and updated by PartSeg GitHub
action cron to keep bundle dependencies modules up to date.
The updated packages are:
Summary by CodeRabbit
New Features
Bug Fixes
Chores
numpydependency, allowing for greater flexibility in package management.