Overhaul pre-commit #166
Overhaul pre-commit #166
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WalkthroughThe recent changes enhance the project by adopting Changes
Assessment against linked issues
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #166 +/- ##
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+ Coverage 90.75% 90.85% +0.10%
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Files 12 12
Lines 1266 1291 +25
==========================================
+ Hits 1149 1173 +24
- Misses 117 118 +1 ☔ View full report in Codecov by Sentry. |
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Actionable comments posted: 0
Outside diff range, codebase verification and nitpick comments (7)
dev_docs/design_docs/Restructuring.md (1)
13-13: Grammar improvement suggestion.Consider revising "Other file I/O methods" to "The other file I/O methods" for grammatical consistency.
- - [**WIP**]Other file I/O methods to allow users to create `Embedding` instances from their own files + - [**WIP**]The other file I/O methods to allow users to create `Embedding` instances from their own filesTools
LanguageTool
[grammar] ~13-~13: Use the plural noun, or add a word such as ‘the’ or ‘some’ in front of ‘other’.
Context: ...stributed with the package - [WIP]Other file I/O methods to allow users to create `E...(OTHER_NN)
docs/embeddings/element.md (1)
181-181: Grammar correction suggestion.Consider revising the sentence for verb agreement: "Representation of materials by kernel mean embedding" might need a verb adjustment for proper agreement.
- [Representation of materials by kernel mean embedding](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.108.134107) + [Representations of materials by kernel mean embedding](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.108.134107)Tools
LanguageTool
[uncategorized] ~181-~181: This verb does not appear to agree with the subject. Consider using a different form.
Context: ... [Representation of materials by kernel mean embedding](https://journals.aps.org/prb...(AI_EN_LECTOR_REPLACEMENT_VERB_AGREEMENT)
src/elementembeddings/plotter.py (1)
57-58: Add test coverage forValueErrorinheatmap_plotter.The
heatmap_plotterfunction raises aValueErrorfor unrecognized metrics, but this path is not currently covered by tests intest_plotter.py. Please add a test case to ensure this error handling is verified.
- Add a test in
src/elementembeddings/tests/test_plotter.pythat callsheatmap_plotterwith an invalid metric to ensure theValueErroris raised.Analysis chain
Add test coverage for the new control flow.
The
elseclause inheatmap_plotterraises aValueErrorfor unrecognized metrics. Ensure this path is covered by tests to verify error handling.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that the new `ValueError` in `heatmap_plotter` is covered by tests. # Test: Search for test cases that raise `ValueError` in `heatmap_plotter`. rg --type python --word-regexp --fixed-strings 'raise ValueError("Unrecognised metric.")' -A 5Length of output: 127
Script:
#!/bin/bash # Description: Verify that the new `ValueError` in `heatmap_plotter` is covered by tests. # Test: Search for test cases that raise `ValueError` in `heatmap_plotter`. rg --type py --word-regexp --fixed-strings 'raise ValueError("Unrecognised metric.")' -A 5Length of output: 464
Script:
#!/bin/bash # Description: Find test files that might contain tests for `heatmap_plotter`. # Locate test files that import or test `heatmap_plotter`. rg --type py 'heatmap_plotter' --files-with-matchesLength of output: 128
Script:
#!/bin/bash # Description: Check if `test_plotter.py` contains tests for `ValueError` in `heatmap_plotter`. # Search for test cases expecting a `ValueError` in `test_plotter.py`. rg --type py 'ValueError' src/elementembeddings/tests/test_plotter.py -A 5Length of output: 472
Tools
GitHub Check: codecov/patch
[warning] 58-58: src/elementembeddings/plotter.py#L58
Added line #L58 was not covered by testssrc/elementembeddings/composition.py (4)
290-293: Add explicit test coverage for__repr__and__str__methods.The
__repr__and__str__methods inCompositionalEmbeddingdo not appear to be directly tested. Consider adding test cases that explicitly verify the output of these methods to ensure they produce the expected string representations.
- Ensure tests in
src/elementembeddings/tests/test_composition.pyor similar files cover__repr__and__str__.Analysis chain
Ensure test coverage for
__repr__and__str__.The
__repr__and__str__methods should be covered by tests to ensure they return the expected string representations.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that the `__repr__` and `__str__` methods are covered by tests. # Test: Search for test cases that call `__repr__` or `__str__` on `CompositionalEmbedding`. rg --type python --word-regexp --fixed-strings 'CompositionalEmbedding(' -A 5Length of output: 110
Script:
#!/bin/bash # Description: Verify that the `__repr__` and `__str__` methods are covered by tests. # Test: Search for test cases that call `__repr__` or `__str__` on `CompositionalEmbedding`. rg --glob '*.py' --word-regexp --fixed-strings 'CompositionalEmbedding(' -A 5Length of output: 895
Script:
#!/bin/bash # Description: Check for explicit test coverage of `__repr__` and `__str__` methods in test files. # Test: Search for calls to `__repr__` and `__str__` on `CompositionalEmbedding` in test files. rg --glob 'src/elementembeddings/tests/*.py' --word-regexp --fixed-strings '__repr__' rg --glob 'src/elementembeddings/tests/*.py' --word-regexp --fixed-strings '__str__'Length of output: 170
Tools
GitHub Check: codecov/patch
[warning] 290-290: src/elementembeddings/composition.py#L290
Added line #L290 was not covered by tests
[warning] 293-293: src/elementembeddings/composition.py#L293
Added line #L293 was not covered by tests
625-628: Add test coverage for__repr__and__str__methods.The
__repr__and__str__methods of theSpeciesCompositionalEmbeddingclass do not appear to be covered by existing tests. Consider adding test cases to ensure these methods return the expected string representations.Analysis chain
Ensure test coverage for
__repr__and__str__.The
__repr__and__str__methods should be covered by tests to ensure they return the expected string representations.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that the `__repr__` and `__str__` methods are covered by tests. # Test: Search for test cases that call `__repr__` or `__str__` on `SpeciesCompositionalEmbedding`. rg --type python --word-regexp --fixed-strings 'SpeciesCompositionalEmbedding(' -A 5Length of output: 117
Script:
#!/bin/bash # Description: Verify that the `__repr__` and `__str__` methods are covered by tests. # Test: Search for test cases that call `__repr__` or `__str__` on `SpeciesCompositionalEmbedding`. rg --type py --word-regexp --fixed-strings 'SpeciesCompositionalEmbedding(' -A 5Length of output: 82
Script:
#!/bin/bash # Description: Search for test cases that might indirectly test `__repr__` or `__str__` by looking for assertions with expected string outputs. # Search for assertions in test files that involve expected string outputs related to `SpeciesCompositionalEmbedding`. rg --type py 'assert ' -A 3Length of output: 41932
Tools
GitHub Check: codecov/patch
[warning] 625-625: src/elementembeddings/composition.py#L625
Added line #L625 was not covered by tests
[warning] 628-628: src/elementembeddings/composition.py#L628
Added line #L628 was not covered by tests
381-381: Add test coverage for missing formula column incomposition_featuriser.The current test suite does not appear to include a test case that verifies the behavior of
composition_featuriserwhen the formula column is missing. Consider adding a test to ensure that aValueErroris raised in this scenario.
- File:
src/elementembeddings/tests/test_composition.pyAnalysis chain
Add test coverage for missing formula column.
Ensure that the validation logic for the presence of the formula column in
composition_featuriseris covered by tests.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that the validation logic for the presence of the formula column in `composition_featuriser` is covered by tests. # Test: Search for test cases that raise `ValueError` for missing formula column in `composition_featuriser`. rg --type python --word-regexp --fixed-strings 'raise ValueError' -A 5Length of output: 103
Script:
#!/bin/bash # Description: Verify that the validation logic for the presence of the formula column in `composition_featuriser` is covered by tests. # Test: Search for test cases that raise `ValueError` for missing formula column in `composition_featuriser`. rg --type py --word-regexp --fixed-strings 'raise ValueError' -A 5Length of output: 6409
Script:
#!/bin/bash # Description: Search for test cases related to `composition_featuriser` handling missing formula column. # Find test files or functions that might be testing `composition_featuriser`. rg --type py 'composition_featuriser' -A 5 # Additionally, search for test functions that mention 'formula_column' or similar. rg --type py 'formula_column' -A 5Length of output: 5872
Tools
GitHub Check: codecov/patch
[warning] 381-381: src/elementembeddings/composition.py#L381
Added line #L381 was not covered by tests
273-278: Add test coverage for type errors indistance.The type validation logic in the
distancemethod is not currently covered by tests. Please add tests to ensure that incorrect types forcomp_otherare handled properly.Analysis chain
Add test coverage for type errors in
distance.Ensure that the type validation logic in
distanceis covered by tests to handle incorrect types forcomp_other.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that the type validation logic in `distance` is covered by tests. # Test: Search for test cases that raise `TypeError` for incorrect types in `distance`. rg --type python --word-regexp --fixed-strings 'raise TypeError' -A 5Length of output: 102
Script:
#!/bin/bash # Description: Search for test cases that raise `TypeError` for incorrect types in the `distance` method. # Find Python test files and search for `TypeError` related to the `distance` method. rg --type py 'def test_' --files | xargs rg 'TypeError' -A 5Length of output: 2107
Script:
#!/bin/bash # Description: Search for test cases that raise `TypeError` for incorrect types in the `distance` method. # Find Python files in likely test directories and search for `TypeError` related to the `distance` method. fd --type f --extension py --search-path tests | xargs rg 'TypeError' -A 5Length of output: 2164
Script:
#!/bin/bash # Description: Search for test cases that raise `TypeError` for incorrect types in the `distance` method. # Find all Python files and search for `TypeError` related to the `distance` method. fd --type f --extension py | xargs rg 'TypeError' -A 5Length of output: 2051
Tools
GitHub Check: codecov/patch
[warning] 273-273: src/elementembeddings/composition.py#L273
Added line #L273 was not covered by tests
[warning] 278-278: src/elementembeddings/composition.py#L278
Added line #L278 was not covered by tests
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files ignored due to path filters (2)
src/elementembeddings/tests/files/test_embedding.csvis excluded by!**/*.csvsrc/elementembeddings/tests/files/test_species_embedding.csvis excluded by!**/*.csv
Files selected for processing (66)
- .flake8 (1 hunks)
- .github/pull_request_template.md (1 hunks)
- .github/release.yml (1 hunks)
- .github/workflows/ci.yml (2 hunks)
- .github/workflows/combine-prs.yml (4 hunks)
- .github/workflows/latest_docs.yml (2 hunks)
- .github/workflows/python-publish.yml (1 hunks)
- .pre-commit-config.yaml (1 hunks)
- CHANGELOG.md (4 hunks)
- CITATION.cff (2 hunks)
- Publication/element_similarity/README.md (1 hunks)
- Publication/element_similarity/SI/element_similairty_SI.ipynb (1 hunks)
- Publication/element_similarity/SI/preprocessing.ipynb (1 hunks)
- Publication/element_similarity/csp/cosine_embeddings.ipynb (2 hunks)
- Publication/element_similarity/csp/data_radius_ratio_rules.ipynb (3 hunks)
- Publication/element_similarity/csp/smact_sp.ipynb (1 hunks)
- Publication/element_similarity/requirements_publication.txt (1 hunks)
- Publication/element_similarity/similarity_periodic_trends/similarity_measures.ipynb (1 hunks)
- README.md (5 hunks)
- contributing.md (1 hunks)
- dev_docs/design_docs/Restructuring.md (1 hunks)
- dev_docs/dev_notebooks/composition_statistics.ipynb (1 hunks)
- docs/.overrides/main.html (1 hunks)
- docs/about.md (3 hunks)
- docs/contribution.md (3 hunks)
- docs/embeddings/element.md (4 hunks)
- docs/embeddings/embeddings.md (1 hunks)
- docs/embeddings/species.md (1 hunks)
- docs/index.md (1 hunks)
- docs/installation.md (1 hunks)
- docs/python_api/composition.md (1 hunks)
- docs/python_api/python_api.md (1 hunks)
- docs/python_api/utils/io.md (1 hunks)
- docs/python_api/utils/math.md (1 hunks)
- docs/python_api/utils/species.md (1 hunks)
- docs/tutorial/composition.ipynb (11 hunks)
- docs/tutorial/usage.ipynb (1 hunks)
- docs/tutorials.md (3 hunks)
- examples/composition.ipynb (10 hunks)
- examples/usage.ipynb (1 hunks)
- mkdocs.yml (3 hunks)
- pyproject.toml (1 hunks)
- requirements-dev.txt (1 hunks)
- setup.py (1 hunks)
- src/elementembeddings/_base.py (13 hunks)
- src/elementembeddings/composition.py (30 hunks)
- src/elementembeddings/core.py (18 hunks)
- src/elementembeddings/data/element_data/element_group.json (1 hunks)
- src/elementembeddings/data/element_data/element_symbols.json (1 hunks)
- src/elementembeddings/data/element_data/ordered_periodic.txt (1 hunks)
- src/elementembeddings/data/element_representations/README.md (4 hunks)
- src/elementembeddings/data/element_representations/atomic.json (1 hunks)
- src/elementembeddings/data/element_representations/magpie_sc.json (1 hunks)
- src/elementembeddings/data/element_representations/megnet16.json (1 hunks)
- src/elementembeddings/data/element_representations/mod_petti.json (1 hunks)
- src/elementembeddings/plotter.py (6 hunks)
- src/elementembeddings/tests/files/test_embedding.json (1 hunks)
- src/elementembeddings/tests/mpl371_ft261.json (1 hunks)
- src/elementembeddings/tests/test_composition.py (5 hunks)
- src/elementembeddings/tests/test_core.py (10 hunks)
- src/elementembeddings/tests/test_plotter.py (5 hunks)
- src/elementembeddings/tests/test_utils.py (2 hunks)
- src/elementembeddings/utils/config.py (1 hunks)
- src/elementembeddings/utils/io.py (1 hunks)
- src/elementembeddings/utils/math.py (1 hunks)
- src/elementembeddings/utils/species.py (2 hunks)
Files skipped from review due to trivial changes (55)
- .flake8
- .github/pull_request_template.md
- .github/release.yml
- .github/workflows/ci.yml
- .github/workflows/combine-prs.yml
- .github/workflows/latest_docs.yml
- .github/workflows/python-publish.yml
- CHANGELOG.md
- CITATION.cff
- Publication/element_similarity/README.md
- Publication/element_similarity/SI/element_similairty_SI.ipynb
- Publication/element_similarity/SI/preprocessing.ipynb
- Publication/element_similarity/csp/cosine_embeddings.ipynb
- Publication/element_similarity/csp/data_radius_ratio_rules.ipynb
- Publication/element_similarity/csp/smact_sp.ipynb
- Publication/element_similarity/requirements_publication.txt
- Publication/element_similarity/similarity_periodic_trends/similarity_measures.ipynb
- README.md
- contributing.md
- dev_docs/dev_notebooks/composition_statistics.ipynb
- docs/.overrides/main.html
- docs/about.md
- docs/contribution.md
- docs/embeddings/embeddings.md
- docs/embeddings/species.md
- docs/index.md
- docs/installation.md
- docs/python_api/composition.md
- docs/python_api/python_api.md
- docs/python_api/utils/io.md
- docs/python_api/utils/math.md
- docs/python_api/utils/species.md
- docs/tutorial/composition.ipynb
- docs/tutorial/usage.ipynb
- docs/tutorials.md
- examples/composition.ipynb
- examples/usage.ipynb
- mkdocs.yml
- requirements-dev.txt
- setup.py
- src/elementembeddings/data/element_data/element_group.json
- src/elementembeddings/data/element_data/element_symbols.json
- src/elementembeddings/data/element_data/ordered_periodic.txt
- src/elementembeddings/data/element_representations/README.md
- src/elementembeddings/data/element_representations/atomic.json
- src/elementembeddings/data/element_representations/megnet16.json
- src/elementembeddings/data/element_representations/mod_petti.json
- src/elementembeddings/tests/files/test_embedding.json
- src/elementembeddings/tests/mpl371_ft261.json
- src/elementembeddings/tests/test_composition.py
- src/elementembeddings/tests/test_core.py
- src/elementembeddings/utils/config.py
- src/elementembeddings/utils/io.py
- src/elementembeddings/utils/math.py
- src/elementembeddings/utils/species.py
Additional context used
LanguageTool
dev_docs/design_docs/Restructuring.md
[grammar] ~13-~13: Use the plural noun, or add a word such as ‘the’ or ‘some’ in front of ‘other’.
Context: ...stributed with the package - [WIP]Other file I/O methods to allow users to create `E...(OTHER_NN)
docs/embeddings/element.md
[uncategorized] ~181-~181: This verb does not appear to agree with the subject. Consider using a different form.
Context: ... [Representation of materials by kernel mean embedding](https://journals.aps.org/prb...(AI_EN_LECTOR_REPLACEMENT_VERB_AGREEMENT)
GitHub Check: codecov/patch
src/elementembeddings/plotter.py
[warning] 58-58: src/elementembeddings/plotter.py#L58
Added line #L58 was not covered by testssrc/elementembeddings/_base.py
[warning] 288-288: src/elementembeddings/_base.py#L288
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[warning] 291-292: src/elementembeddings/_base.py#L291-L292
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[warning] 340-340: src/elementembeddings/_base.py#L340
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[warning] 343-344: src/elementembeddings/_base.py#L343-L344
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[warning] 555-555: src/elementembeddings/core.py#L555
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[warning] 242-242: src/elementembeddings/composition.py#L242
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[warning] 273-273: src/elementembeddings/composition.py#L273
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[warning] 278-278: src/elementembeddings/composition.py#L278
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[warning] 290-290: src/elementembeddings/composition.py#L290
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[warning] 293-293: src/elementembeddings/composition.py#L293
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[warning] 297-297: src/elementembeddings/composition.py#L297
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Additional comments not posted (155)
.pre-commit-config.yaml (7)
8-14: Adoptrufffor linting and formatting.The adoption of
ruffas both a linter and formatter is a strategic move to streamline code quality processes. Ensure that all team members are aware of this change and have updated their local environments accordingly.
15-20: Add basic pre-commit hooks for YAML and whitespace checks.The inclusion of
check-yaml,end-of-file-fixer, andtrailing-whitespacehooks enhances basic code quality checks. These are essential for maintaining a clean and consistent codebase.
21-30: Customizemarkdownlintrules.The customization of
markdownlintrules indicates a tailored approach to markdown validation. Ensure these rules align with the project's documentation standards.
31-35: Updatenbstripoutconfiguration.Retaining
nbstripoutwith updated arguments helps manage notebook outputs effectively. This is crucial for collaborative environments where Jupyter notebooks are used.
36-42: Integrateprettierfor code formatting.The use of
prettierfor formatting non-Python files ensures consistency across different file types. Verify that this aligns with the team's workflow and file types in use.
43-47: Enablepyrightfor type checking.The addition of
pyrightwith error-level checks is a proactive step towards improving type safety. Ensure that the codebase is compatible with these checks to avoid unnecessary errors.
48-55: Introducecodespellfor spell checking.Adding
codespellenhances the robustness of pre-commit checks by catching common misspellings. Ensure that thepyproject.tomlconfiguration aligns with the project's vocabulary.dev_docs/design_docs/Restructuring.md (3)
10-14: Improve list formatting for clarity.The restructuring of bullet points enhances readability and visual hierarchy. This change helps in quickly scanning through the required features of the package.
Tools
LanguageTool
[grammar] ~13-~13: Use the plural noun, or add a word such as ‘the’ or ‘some’ in front of ‘other’.
Context: ...stributed with the package - [WIP]Other file I/O methods to allow users to create `E...(OTHER_NN)
19-22: Enhance consistency in module descriptions.The consistent indentation and alignment of bullet points improve the document's structure, making it easier to understand the relationships between features and modules.
25-26: Clarify plotting utilities description.The description of plotting utilities is now clearer, indicating potential implementations. This helps in planning future developments or extensions.
src/elementembeddings/tests/test_utils.py (2)
3-3: Use of__future__import for annotations.The use of
from __future__ import annotationsis a good practice for forward compatibility with Python's type hinting improvements.
17-19: Correct use ofClassVarfor class-level variables.The change to use
ClassVarfora,b, andcclarifies their role as class-level variables. This aligns with type hinting best practices in Python.pyproject.toml (5)
1-4: Set up build system requirements.The build system configuration using
setuptoolsis standard and should be compatible with most Python environments. Ensure that this aligns with the project's build requirements.
10-13: Configurerufffor linting and formatting.The
ruffconfiguration specifies the target Python version and line length, which are crucial for maintaining consistency. Ensure these settings align with the project's coding standards.
15-80: Comprehensive linting rules withruff.The extensive list of ignored rules in
ruffindicates a tailored approach to linting. Regularly review these settings to ensure they meet the project's evolving needs.
92-95: Configurepyrightfor type checking.The
pyrightsettings are minimal but effective for basic type checking. Consider expanding these settings as the project grows in complexity.
97-198: Customizecodespellfor spell checking.The
codespellconfiguration is detailed, with specific files and words to skip. Ensure this list is maintained to keep up with any new terminology or file types introduced in the project.docs/embeddings/element.md (3)
5-6: Standardize list formatting for external links.The consistent formatting of external links improves the document's readability and professionalism.
53-69: Enhance readability of property lists.The uniform formatting of the 22-dimensional embedding vector properties aids in clarity and quick reference.
107-151: Improve presentation of 44-dimensional features.The structured presentation of the 44 features enhances the document's clarity and usability.
src/elementembeddings/plotter.py (3)
17-21: Modernize type hints inheatmap_plotter.The type hints for the
embeddingandaxparameters have been updated to use the new union syntax, which improves readability and aligns with Python 3.10+ standards.
96-103: Modernize type hints indimension_plotter.The type hints for the
embedding,reducer_params,scatter_params, andinclude_speciesparameters have been updated to use the new union syntax, which improves readability and aligns with Python 3.10+ standards.
Line range hint
135-140: Verify exception handling in tests.The use of
pytest.raisesfor exception handling in tests is a modern approach. Ensure that all edge cases for invalid parameters indimension_plotterare covered.Verification successful
Exception handling in
dimension_plottertests is verified. The tests insrc/elementembeddings/tests/test_plotter.pyappropriately usepytest.raises(ValueError)to handle invalid parameters, such as incorrect reducer names and component numbers. This indicates that the edge cases are adequately covered.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that all edge cases for invalid parameters in `dimension_plotter` are covered by tests. # Test: Search for test cases using `pytest.raises` with `ValueError` in `dimension_plotter`. rg --type python --word-regexp --fixed-strings 'pytest.raises(ValueError)' -A 5Length of output: 112
Script:
#!/bin/bash # Description: Verify that all edge cases for invalid parameters in `dimension_plotter` are covered by tests. # Test: Search for test cases using `pytest.raises` with `ValueError` in `dimension_plotter`. rg --glob '*.py' --word-regexp --fixed-strings 'pytest.raises(ValueError)' -A 5Length of output: 3452
src/elementembeddings/tests/test_plotter.py (4)
3-3: Addannotationsimport for future compatibility.The import of
annotationsfrom__future__enhances type hinting capabilities and ensures compatibility with future Python versions.
51-51: Improve readability with single-line instantiation.The instantiation of
test_speciesusing a single line improves readability and reduces visual clutter.
135-140: Usepytest.raisesfor exception handling.Switching to
pytest.raisesfor exception handling is a modern and consistent approach. Ensure all invalid parameter cases are tested.
154-160: Usepytest.raisesfor testing exceptions.The use of
pytest.raisesenhances readability and consistency in testing exception cases for invalid dimensions.src/elementembeddings/_base.py (4)
37-38: Modernize type hints inEmbeddingBase.__init__.The type hints for
embedding_nameandfeature_labelshave been updated to use the new union syntax, enhancing readability and aligning with Python 3.10+ standards.
107-107: Modernize type hints infrom_json.The type hint for
embedding_namehas been updated to use the new union syntax, improving readability and aligning with Python 3.10+ standards.
340-344: Add test coverage for species validation.The validation logic for checking if species are in the embedding should be covered by tests to ensure error handling is robust.
Verification successful
Test coverage for species validation exists.
The
compute_distance_metricmethod is tested for scenarios that raiseValueError, indicating that the species validation logic is covered by the tests insrc/elementembeddings/tests/test_core.py.
src/elementembeddings/tests/test_core.py: Contains tests usingpytest.raises(ValueError)to cover error handling.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that the species validation logic in `compute_distance_metric` is covered by tests. # Test: Search for test cases that raise `ValueError` for missing species in `compute_distance_metric`. rg --type python --word-regexp --fixed-strings 'raise ValueError' -A 5Length of output: 103
Script:
#!/bin/bash # Description: Verify that the species validation logic in `compute_distance_metric` is covered by tests. # Test: Search for test cases that raise `ValueError` for missing species in `compute_distance_metric`. rg --type py --word-regexp --fixed-strings 'raise ValueError' -A 5 --glob '*test*.py'Length of output: 87
Script:
#!/bin/bash # Description: Search for test functions or methods that might be testing `compute_distance_metric`. # Find occurrences of `compute_distance_metric` in test files to check for indirect test coverage. rg 'compute_distance_metric' --glob '*test*.py' -A 5Length of output: 2178
Tools
GitHub Check: codecov/patch
[warning] 340-340: src/elementembeddings/_base.py#L340
Added line #L340 was not covered by tests
[warning] 343-344: src/elementembeddings/_base.py#L343-L344
Added lines #L343 - L344 were not covered by tests
288-292: Add test coverage for element validation.The validation logic for checking if elements are in the embedding should be covered by tests to ensure error handling is robust.
Tools
GitHub Check: codecov/patch
[warning] 288-288: src/elementembeddings/_base.py#L288
Added line #L288 was not covered by tests
[warning] 291-292: src/elementembeddings/_base.py#L291-L292
Added lines #L291 - L292 were not covered by testssrc/elementembeddings/core.py (7)
44-44: Modernize type hints inEmbedding.load_data.The type hint for
embedding_namehas been updated to use the new union syntax, enhancing readability and aligning with Python 3.10+ standards.
106-106: Modernize type hints infrom_json.The type hint for
embedding_namehas been updated to use the new union syntax, improving readability and aligning with Python 3.10+ standards.
120-120: Modernize type hints infrom_csv.The type hint for
embedding_namehas been updated to use the new union syntax, enhancing readability and aligning with Python 3.10+ standards.
172-172: Modernize type hints into.The type hint for
filenamehas been updated to use the new union syntax, improving readability and aligning with Python 3.10+ standards.
215-215: Modernize type hints inremove_elements.The type hint for
elementshas been updated to use the new union syntax, enhancing readability and aligning with Python 3.10+ standards.
269-269: Modernize type hints inelement_groups_dict.The return type hint has been updated to use the new dictionary syntax, improving readability and aligning with Python 3.10+ standards.
555-555: Ensure test coverage fortomethod.The
tomethod should be covered by tests to ensure that all file output paths are correctly handled.Tools
GitHub Check: codecov/patch
[warning] 555-555: src/elementembeddings/core.py#L555
Added line #L555 was not covered by testssrc/elementembeddings/composition.py (20)
28-28: Modernize type hints informula_parser.The return type hint has been updated to use the new dictionary syntax, enhancing readability and aligning with Python 3.10+ standards.
63-63: Modernize type hints in_get_sym_dict.The return type hint has been updated to use the new dictionary syntax, improving readability and aligning with Python 3.10+ standards.
82-82: Modernize type hints in_get_fractional_composition.The return type hint has been updated to use the new dictionary syntax, enhancing readability and aligning with Python 3.10+ standards.
104-104: Modernize type hints inCompositionalEmbedding.__init__.The type hint for
embeddinghas been updated to use the new union syntax, improving readability and aligning with Python 3.10+ standards.
203-203: UseClassVarfor_stats_functions_dict.The use of
ClassVarindicates that_stats_functions_dictis a class-level variable, which clarifies its intended scope and improves code clarity.
214-214: Modernize type hints infeature_vector.The type hint for
statshas been updated to use the new union syntax, improving readability and aligning with Python 3.10+ standards.
255-255: Modernize type hints indistance.The type hint for
statshas been updated to use the new union syntax, improving readability and aligning with Python 3.10+ standards.
309-313: Modernize type hints in_composition_distance.The type hints for
comp1,comp2,embedding, andstatshave been updated to use the new union syntax, improving readability and aligning with Python 3.10+ standards.
345-348: Modernize type hints incomposition_featuriser.The type hints for
data,embedding, andstatshave been updated to use the new union syntax, improving readability and aligning with Python 3.10+ standards.
416-416: Modernize type hints inSpeciesCompositionalEmbedding.__init__.The type hint for
embeddinghas been updated to use the new union syntax, improving readability and aligning with Python 3.10+ standards.
536-536: UseClassVarfor_stats_functions_dict.The use of
ClassVarindicates that_stats_functions_dictis a class-level variable, which clarifies its intended scope and improves code clarity.
547-547: Modernize type hints infeature_vector.The type hint for
statshas been updated to use the new union syntax, improving readability and aligning with Python 3.10+ standards.
588-588: Modernize type hints indistance.The type hint for
statshas been updated to use the new union syntax, improving readability and aligning with Python 3.10+ standards.
648-652: Modernize type hints in_species_composition_distance.The type hints for
comp1,comp2,embedding, andstatshave been updated to use the new union syntax, improving readability and aligning with Python 3.10+ standards.
684-688: Modernize type hints inspecies_composition_featuriser.The type hints for
data,embedding, andstatshave been updated to use the new union syntax, improving readability and aligning with Python 3.10+ standards.
716-720: Add test coverage for invalid data types.Ensure that the type validation logic in
species_composition_featuriseris covered by tests to handle incorrect data types.Tools
GitHub Check: codecov/patch
[warning] 716-716: src/elementembeddings/composition.py#L716
Added line #L716 was not covered by tests
[warning] 720-720: src/elementembeddings/composition.py#L720
Added line #L720 was not covered by tests
242-242: Add test coverage for invalid stats.Ensure that the validation logic for invalid statistics in
feature_vectoris covered by tests.Tools
GitHub Check: codecov/patch
[warning] 242-242: src/elementembeddings/composition.py#L242
Added line #L242 was not covered by tests
575-575: Add test coverage for invalid stats.Ensure that the validation logic for invalid statistics in
feature_vectoris covered by tests.Tools
GitHub Check: codecov/patch
[warning] 575-575: src/elementembeddings/composition.py#L575
Added line #L575 was not covered by tests
399-400: Add test coverage for invalid data types.Ensure that the type validation logic in
composition_featuriseris covered by tests to handle incorrect data types.Verification successful
Let's correct the command to search for
TypeErrorexceptions in Python files and re-run the script.
Let's search for test files in the repository and check if there are any tests for invalid data types in
composition_featuriser.
Let's inspect
test_composition.pyfor test cases that involvecomposition_featuriserand handle invalid data types.
Add test coverage for invalid data types in
composition_featuriser.The current test suite in
test_composition.pyforcomposition_featuriseronly covers valid input scenarios. Please add tests to handle invalid data types that would raise aTypeError.
- Consider adding tests that pass invalid data types to
composition_featuriserto ensure robust type validation.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that the type validation logic in `composition_featuriser` is covered by tests. # Test: Search for test cases that raise `TypeError` for incorrect data types in `composition_featuriser`. rg --type python --word-regexp --fixed-strings 'raise TypeError' -A 5Length of output: 102
Script:
#!/bin/bash # Description: Verify that the type validation logic in `composition_featuriser` is covered by tests. # Test: Search for test cases that raise `TypeError` for incorrect data types in `composition_featuriser`. rg --type py 'raise TypeError' -A 5Length of output: 2034
Script:
#!/bin/bash # Find all test files in the repository fd --type f --extension py --exec grep -l 'composition_featuriser' {} # Search for tests that might handle TypeError or invalid data types rg 'TypeError' --type py -A 5Length of output: 2187
Script:
#!/bin/bash # Search for test cases involving composition_featuriser in test_composition.py rg 'composition_featuriser' src/elementembeddings/tests/test_composition.py -A 5Length of output: 1429
Tools
GitHub Check: codecov/patch
[warning] 399-400: src/elementembeddings/composition.py#L399-L400
Added lines #L399 - L400 were not covered by tests
607-607: Add test coverage for type errors indistance.Ensure that the type validation logic in
distanceis covered by tests to handle incorrect types forcomp_other.Tools
GitHub Check: codecov/patch
[warning] 607-607: src/elementembeddings/composition.py#L607
Added line #L607 was not covered by testssrc/elementembeddings/data/element_representations/magpie_sc.json (97)
2-10: Data for "H" looks consistent.The numerical array for element "H" appears to be well-structured and consistent.
11-20: Data for "He" looks consistent.The numerical array for element "He" appears to be well-structured and consistent.
21-29: Data for "Li" looks consistent.The numerical array for element "Li" appears to be well-structured and consistent.
30-39: Data for "Be" looks consistent.The numerical array for element "Be" appears to be well-structured and consistent.
40-49: Data for "B" looks consistent.The numerical array for element "B" appears to be well-structured and consistent.
50-59: Data for "C" looks consistent.The numerical array for element "C" appears to be well-structured and consistent.
60-68: Data for "N" looks consistent.The numerical array for element "N" appears to be well-structured and consistent.
69-77: Data for "O" looks consistent.The numerical array for element "O" appears to be well-structured and consistent.
78-87: Data for "F" looks consistent.The numerical array for element "F" appears to be well-structured and consistent.
88-97: Data for "Ne" looks consistent.The numerical array for element "Ne" appears to be well-structured and consistent.
98-107: Data for "Na" looks consistent.The numerical array for element "Na" appears to be well-structured and consistent.
108-117: Data for "Mg" looks consistent.The numerical array for element "Mg" appears to be well-structured and consistent.
118-127: Data for "Al" looks consistent.The numerical array for element "Al" appears to be well-structured and consistent.
128-136: Data for "Si" looks consistent.The numerical array for element "Si" appears to be well-structured and consistent.
137-145: Data for "P" looks consistent.The numerical array for element "P" appears to be well-structured and consistent.
146-155: Data for "S" looks consistent.The numerical array for element "S" appears to be well-structured and consistent.
156-165: Data for "Cl" looks consistent.The numerical array for element "Cl" appears to be well-structured and consistent.
166-175: Data for "Ar" looks consistent.The numerical array for element "Ar" appears to be well-structured and consistent.
176-185: Data for "K" looks consistent.The numerical array for element "K" appears to be well-structured and consistent.
186-195: Data for "Ca" looks consistent.The numerical array for element "Ca" appears to be well-structured and consistent.
196-204: Data for "Sc" looks consistent.The numerical array for element "Sc" appears to be well-structured and consistent.
205-214: Data for "Ti" looks consistent.The numerical array for element "Ti" appears to be well-structured and consistent.
215-224: Data for "V" looks consistent.The numerical array for element "V" appears to be well-structured and consistent.
225-233: Data for "Cr" looks consistent.The numerical array for element "Cr" appears to be well-structured and consistent.
234-243: Data for "Mn" looks consistent.The numerical array for element "Mn" appears to be well-structured and consistent.
244-253: Data for "Fe" looks consistent.The numerical array for element "Fe" appears to be well-structured and consistent.
254-263: Data for "Co" looks consistent.The numerical array for element "Co" appears to be well-structured and consistent.
264-272: Data for "Ni" looks consistent.The numerical array for element "Ni" appears to be well-structured and consistent.
273-281: Data for "Cu" looks consistent.The numerical array for element "Cu" appears to be well-structured and consistent.
282-291: Data for "Zn" looks consistent.The numerical array for element "Zn" appears to be well-structured and consistent.
292-301: Data for "Ga" looks consistent.The numerical array for element "Ga" appears to be well-structured and consistent.
302-311: Data for "Ge" looks consistent.The numerical array for element "Ge" appears to be well-structured and consistent.
312-321: Data for "As" looks consistent.The numerical array for element "As" appears to be well-structured and consistent.
322-331: Data for "Se" looks consistent.The numerical array for element "Se" appears to be well-structured and consistent.
332-340: Data for "Br" looks consistent.The numerical array for element "Br" appears to be well-structured and consistent.
341-350: Data for "Kr" looks consistent.The numerical array for element "Kr" appears to be well-structured and consistent.
351-359: Data for "Rb" looks consistent.The numerical array for element "Rb" appears to be well-structured and consistent.
360-369: Data for "Sr" looks consistent.The numerical array for element "Sr" appears to be well-structured and consistent.
370-379: Data for "Y" looks consistent.The numerical array for element "Y" appears to be well-structured and consistent.
380-389: Data for "Zr" looks consistent.The numerical array for element "Zr" appears to be well-structured and consistent.
390-398: Data for "Nb" looks consistent.The numerical array for element "Nb" appears to be well-structured and consistent.
399-407: Data for "Mo" looks consistent.The numerical array for element "Mo" appears to be well-structured and consistent.
408-417: Data for "Tc" looks consistent.The numerical array for element "Tc" appears to be well-structured and consistent.
418-426: Data for "Ru" looks consistent.The numerical array for element "Ru" appears to be well-structured and consistent.
427-435: Data for "Rh" looks consistent.The numerical array for element "Rh" appears to be well-structured and consistent.
436-445: Data for "Pd" looks consistent.The numerical array for element "Pd" appears to be well-structured and consistent.
446-454: Data for "Ag" looks consistent.The numerical array for element "Ag" appears to be well-structured and consistent.
455-464: Data for "Cd" looks consistent.The numerical array for element "Cd" appears to be well-structured and consistent.
465-473: Data for "In" looks consistent.The numerical array for element "In" appears to be well-structured and consistent.
474-483: Data for "Sn" looks consistent.The numerical array for element "Sn" appears to be well-structured and consistent.
484-493: Data for "Sb" looks consistent.The numerical array for element "Sb" appears to be well-structured and consistent.
494-503: Data for "Te" looks consistent.The numerical array for element "Te" appears to be well-structured and consistent.
504-513: Data for "I" looks consistent.The numerical array for element "I" appears to be well-structured and consistent.
514-523: Data for "Xe" looks consistent.The numerical array for element "Xe" appears to be well-structured and consistent.
524-532: Data for "Cs" looks consistent.The numerical array for element "Cs" appears to be well-structured and consistent.
533-541: Data for "Ba" looks consistent.The numerical array for element "Ba" appears to be well-structured and consistent.
542-551: Data for "La" looks consistent.The numerical array for element "La" appears to be well-structured and consistent.
552-561: Data for "Ce" looks consistent.The numerical array for element "Ce" appears to be well-structured and consistent.
562-571: Data for "Pr" looks consistent.The numerical array for element "Pr" appears to be well-structured and consistent.
572-581: Data for "Nd" looks consistent.The numerical array for element "Nd" appears to be well-structured and consistent.
582-591: Data for "Pm" looks consistent.The numerical array for element "Pm" appears to be well-structured and consistent.
592-601: Data for "Sm" looks consistent.The numerical array for element "Sm" appears to be well-structured and consistent.
602-610: Data for "Eu" looks consistent.The numerical array for element "Eu" appears to be well-structured and consistent.
611-620: Data for "Gd" looks consistent.The numerical array for element "Gd" appears to be well-structured and consistent.
621-630: Data for "Tb" looks consistent.The numerical array for element "Tb" appears to be well-structured and consistent.
631-640: Data for "Dy" looks consistent.The numerical array for element "Dy" appears to be well-structured and consistent.
641-650: Data for "Ho" looks consistent.The numerical array for element "Ho" appears to be well-structured and consistent.
651-660: Data for "Er" looks consistent.The numerical array for element "Er" appears to be well-structured and consistent.
661-670: Data for "Tm" looks consistent.The numerical array for element "Tm" appears to be well-structured and consistent.
671-679: Data for "Yb" looks consistent.The numerical array for element "Yb" appears to be well-structured and consistent.
680-689: Data for "Lu" looks consistent.The numerical array for element "Lu" appears to be well-structured and consistent.
690-699: Data for "Hf" looks consistent.The numerical array for element "Hf" appears to be well-structured and consistent.
700-709: Data for "Ta" looks consistent.The numerical array for element "Ta" appears to be well-structured and consistent.
710-719: Data for "W" looks consistent.The numerical array for element "W" appears to be well-structured and consistent.
720-729: Data for "Re" looks consistent.The numerical array for element "Re" appears to be well-structured and consistent.
730-739: Data for "Os" looks consistent.The numerical array for element "Os" appears to be well-structured and consistent.
740-748: Data for "Ir" looks consistent.The numerical array for element "Ir" appears to be well-structured and consistent.
749-757: Data for "Pt" looks consistent.The numerical array for element "Pt" appears to be well-structured and consistent.
758-766: Data for "Au" looks consistent.The numerical array for element "Au" appears to be well-structured and consistent.
767-776: Data for "Hg" looks consistent.The numerical array for element "Hg" appears to be well-structured and consistent.
777-786: Data for "Tl" looks consistent.The numerical array for element "Tl" appears to be well-structured and consistent.
787-796: Data for "Pb" looks consistent.The numerical array for element "Pb" appears to be well-structured and consistent.
797-806: Data for "Bi" looks consistent.The numerical array for element "Bi" appears to be well-structured and consistent.
807-815: Data for "Po" looks consistent.The numerical array for element "Po" appears to be well-structured and consistent.
816-825: Data for "At" looks consistent.The numerical array for element "At" appears to be well-structured and consistent.
826-835: Data for "Rn" looks consistent.The numerical array for element "Rn" appears to be well-structured and consistent.
836-844: Data for "Fr" looks consistent.The numerical array for element "Fr" appears to be well-structured and consistent.
845-854: Data for "Ra" looks consistent.The numerical array for element "Ra" appears to be well-structured and consistent.
855-864: Data for "Ac" looks consistent.The numerical array for element "Ac" appears to be well-structured and consistent.
865-874: Data for "Th" looks consistent.The numerical array for element "Th" appears to be well-structured and consistent.
875-883: Data for "Pa" looks consistent.The numerical array for element "Pa" appears to be well-structured and consistent.
884-893: Data for "U" looks consistent.The numerical array for element "U" appears to be well-structured and consistent.
894-903: Data for "Np" looks consistent.The numerical array for element "Np" appears to be well-structured and consistent.
904-913: Data for "Pu" looks consistent.The numerical array for element "Pu" appears to be well-structured and consistent.
914-923: Data for "Am" looks consistent.The numerical array for element "Am" appears to be well-structured and consistent.
924-933: Data for "Cm" looks consistent.The numerical array for element "Cm" appears to be well-structured and consistent.
934-943: Data for "Bk" looks consistent.The numerical array for element "Bk" appears to be well-structured and consistent.
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Actionable comments posted: 0
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (1)
- src/elementembeddings/tests/test_composition.py (8 hunks)
Files skipped from review as they are similar to previous changes (1)
- src/elementembeddings/tests/test_composition.py
Linting and formatting overhaul
Description
Closes #165
Type of change
Please delete options that are not relevant.
How Has This Been Tested?
Test Configuration:
Reviewers
N/A
Checklist:
Summary by CodeRabbit
New Features
CompositionalEmbeddingclass, improving test coverage.Bug Fixes
Documentation
Refactor
Chores