refactor: first iteration of fixing mypy complaints #59
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📝 WalkthroughWalkthroughThe pull request updates the GitHub Actions workflow by adding a Mypy type-checking step to the quality-control job. In the codebase, several files are modified to enhance type annotations and clarify method signatures. The Changes
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🧰 Additional context used📓 Path-based instructions (1)`**/*.py`: Do not try to improve formatting. Do not suggest type annotations for functions that are defined inside of functions or methods. Do not suggest type annotation of the `s...
🧬 Code Definitions (1)src/snakemake_interface_common/plugin_registry/plugin.py (3)
🪛 Ruff (0.8.2)src/snakemake_interface_common/plugin_registry/plugin.py271-271: Use (E721) 🔇 Additional comments (23)
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🧹 Nitpick comments (3)
src/snakemake_interface_common/settings.py (2)
100-104: Provide a custom error message for invalid choices.Relying on
KeyErrormay produce a less informative error. Consider raising a more descriptive exception, for example:- return cls[choice.replace("-", "_").upper()] + try: + return cls[choice.replace("-", "_").upper()] + except KeyError: + raise ValueError(f"Invalid choice: {choice}. Must be one of {cls.choices()}.")
105-118: Consider adding dedicated tests for the new settings enumeration.Unit tests can verify that parsing choices, skipping members, and generating string representations behave as intended. Let me know if you need help creating such tests or if you’d like me to open a new issue tracking this task.
.github/workflows/test.yml (1)
39-42: Consider uncommenting the Mypy stepSince this PR is specifically focused on fixing mypy complaints, it would be beneficial to enable the type checking step in the workflow to verify that all issues have been resolved.
- # - name: Mypy - # if: always() - # run: | - # pixi run --environment dev type-check + - name: Mypy + if: always() + run: | + pixi run --environment dev type-check
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.gitattributes(1 hunks).github/workflows/release-please.yml(1 hunks).github/workflows/test.yml(1 hunks).gitignore(1 hunks)snakemake_interface_common/settings.py(0 hunks)src/snakemake_interface_common/exceptions.py(4 hunks)src/snakemake_interface_common/logging.py(1 hunks)src/snakemake_interface_common/plugin_registry/__init__.py(5 hunks)src/snakemake_interface_common/plugin_registry/attribute_types.py(1 hunks)src/snakemake_interface_common/plugin_registry/plugin.py(13 hunks)src/snakemake_interface_common/plugin_registry/tests.py(2 hunks)src/snakemake_interface_common/rules.py(1 hunks)src/snakemake_interface_common/settings.py(1 hunks)src/snakemake_interface_common/utils.py(5 hunks)
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- snakemake_interface_common/settings.py
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`**/*.py`: Do not try to improve formatting. Do not suggest ...
**/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of theselfargument of methods.
Do not suggest type annotation of theclsargument of classmethods.
Do not suggest return type annotation if a function or method does not contain areturnstatement.
src/snakemake_interface_common/logging.pysrc/snakemake_interface_common/settings.pysrc/snakemake_interface_common/exceptions.pysrc/snakemake_interface_common/plugin_registry/attribute_types.pysrc/snakemake_interface_common/utils.pysrc/snakemake_interface_common/rules.pysrc/snakemake_interface_common/plugin_registry/tests.pysrc/snakemake_interface_common/plugin_registry/__init__.pysrc/snakemake_interface_common/plugin_registry/plugin.py
🪛 Ruff (0.8.2)
src/snakemake_interface_common/plugin_registry/plugin.py
256-256: Use is and is not for type comparisons, or isinstance() for isinstance checks
(E721)
🔇 Additional comments (61)
.gitattributes (1)
1-2: Good practice for lock files.Defining
pixi.lockas a binary file and marking it as generated ensures merge conflicts are avoided and that the file is treated correctly by GitHub’s linguist. This approach is well-aligned with standard practices for lock files..gitignore (1)
162-165: Reevaluate ignoringpoetry.lock.It’s generally recommended to commit
poetry.lockfor reproducible builds, especially for distributed teams. Please verify that ignoringpoetry.lockis indeed desired. The additions for ignoring.pixiand*.egg-infoare standard and look good.src/snakemake_interface_common/logging.py (2)
5-9: Effective use of TYPE_CHECKING.Placing imports under
if TYPE_CHECKING:is a clean way to prevent circular dependencies while still providing type hints to static analyzers.
11-13: Correct return type annotation.Specifying the return type as
"logging.Logger"is appropriate to avoid runtime import issues and maintain clarity for mypy. This change looks good.src/snakemake_interface_common/settings.py (1)
1-99: Comprehensive and well-documented enumeration base class.The structure and docstrings for
SettingsEnumBaseare thorough. The approach of handling both internal and external representations is clear, and the helper methods (_parse_choices_into,all, etc.) make the codebase more uniform and maintainable.src/snakemake_interface_common/plugin_registry/attribute_types.py (1)
23-23: Type annotations properly added to methodsThe addition of return type annotations to
is_optional,is_class, andinto_requiredmethods improves type safety while maintaining functionality. The self-referential type annotation ininto_requiredis correctly implemented.Also applies to: 27-27, 30-30
.github/workflows/release-please.yml (1)
25-44: Workflow modernization looks goodThe transition from Poetry to Pixi for dependency management appears well-implemented. The updated GitHub actions, installation of Pixi with appropriate version specification, and modern PyPI publishing configuration with token-based authentication represent a good modernization of the CI pipeline.
src/snakemake_interface_common/rules.py (1)
7-7:❓ Verification inconclusive
Type annotations added to abstract methods
The addition of return type annotations to the abstract methods in
RuleInterfaceimproves type safety. Note that ifsnakefilepreviously returnedPathobjects, changing tostrreturn type represents an API change that may require updates to dependent code.Also applies to: 11-11, 15-15
🏁 Script executed:
#!/bin/bash # Check if there are any uses of Path methods on the result of snakefile calls rg -p "\.snakefile\(\)" -A 3 -B 3 | rg "\.stem|\.suffix|\.parent|\.resolve|\.absolute"Length of output: 88
Abstract Method Type Annotations and Potential API Change
The
RuleInterfacemethods now have explicit return type annotations, which improves type safety. Note that changing thesnakefilemethod’s return type from (presumably) aPathtostrrepresents an API decision that could affect dependent code. Although a shell search for chained Path method calls onsnakefiledid not produce any results, please manually verify that no modules rely onsnakefilereturning aPath.
- File:
src/snakemake_interface_common/rules.py
- Line 7:
def name(self) -> str: ...- Line 11:
def lineno(self) -> int: ...- Line 15:
def snakefile(self) -> str: ...Please confirm that all dependent code has been updated accordingly.
src/snakemake_interface_common/exceptions.py (4)
8-8: Class attributes properly typed with appropriate importsAdding explicit type annotations for class attributes
lineno,snakefile, andrulewith proper Optional types improves code clarity and type checking capabilities.Also applies to: 18-20
22-22: Method signatures enhanced with type annotationsType annotations for method parameters and return types are now properly specified, improving type safety. The change from
Pathtostrfor thesnakefileparameter type is consistent with the similar change inrules.py.Also applies to: 44-44, 46-46, 66-66
35-37: Proper handling of ExceptionGroup for Python 3.11+ compatibilityThe code correctly handles the Python 3.11+
ExceptionGroupwith a version check and noqa comment to avoid linting errors on earlier Python versions.
61-61: Functionally equivalent tuple manipulationThe modified args manipulation using tuple conversion and list operations is functionally equivalent to the previous version but uses more modern Python syntax with f-strings.
.github/workflows/test.yml (5)
10-14: Proper permission configuration addedAdding explicit permissions is a security best practice. By defining specific access scopes, you're following the principle of least privilege.
17-17: Job name change appropriately reflects expanded responsibilitiesRenaming from "formatting" to "quality-control" better represents the job's full scope, which now includes formatting, linting, and potentially type checking.
21-28: Updated tooling from Poetry to PixiThe migration from Poetry to Pixi as the package/environment manager is consistently implemented with appropriate version pinning.
30-38: New formatting and linting steps addedThe Ruff formatting and linting steps are properly configured with the
--checkand--diffflags to ensure code quality without automatically modifying files.
50-60: Testing job updates follow the same patternThe testing job has been consistently updated to use Pixi in the same way as the quality-control job, maintaining a uniform approach across the workflow.
src/snakemake_interface_common/plugin_registry/tests.py (6)
17-17: Improved abstract method signature with proper return typeThe method signature now includes a return type annotation and uses the ellipsis syntax on the same line, which is more concise and helps with static type checking.
20-20: Improved abstract method signature with proper return typeThe method signature now includes a return type annotation and uses the ellipsis syntax on the same line, which is more concise and helps with static type checking.
23-23: Improved abstract method signatureThe method signature now uses the ellipsis syntax on the same line, which is more concise and helps with static type checking.
26-26: Improved abstract method signatureThe method signature now uses the ellipsis syntax on the same line, which is more concise and helps with static type checking.
29-29: Improved abstract method signature with proper return typeThe method signature now includes a return type annotation and uses the ellipsis syntax on the same line, which is more concise and helps with static type checking.
43-45: Improved assertion message formattingThe assertion message has been reformatted to span multiple lines for better readability while maintaining the same functionality.
src/snakemake_interface_common/utils.py (9)
5-5: Added necessary type annotation importsAdded imports from the typing module to support the type annotations throughout the file, which is essential for mypy type checking.
8-8: Added type annotations to not_iterable functionThe function now has proper type annotations, indicating it takes any value and returns a boolean, which improves type safety.
20-20: Added type annotations to clean methodThe static method now has proper type annotations, indicating it takes an instance of Any type and a method name as a string, which improves type safety.
23-23: Added type annotations to init methodThe method now has proper type annotations, indicating it takes a Callable and returns None, which improves type safety.
28-28: Added type annotations to get methodThe method now has proper type annotations, indicating it takes an instance of Any type and an owner that is either a type or None, and returns Any, which improves type safety.
39-54: Enhanced lutime function with type annotations and improved docstringThe function now has proper type annotations and a well-structured docstring with Parameters and Returns sections, improving both type safety and documentation.
69-69: Added type annotations to fmt_time inner functionThe inner function now has proper type annotations, indicating it takes a float and returns a string, which improves type safety.
85-85: Added type annotations to lchmod function (first definition)The function now has proper type annotations, indicating it takes a string path and an integer mode, and returns None, which improves type safety.
90-90: Added type annotations to lchmod function (second definition)The function now has proper type annotations, indicating it takes a string path and an integer mode, and returns None, which improves type safety.
src/snakemake_interface_common/plugin_registry/__init__.py (11)
10-10: Added typing importsAdded necessary imports from typing module, including TYPE_CHECKING for conditional import of ArgumentParser.
16-18: Added conditional import for ArgumentParserUsing TYPE_CHECKING guard for the ArgumentParser import helps prevent circular imports at runtime while still providing type information for static type checkers.
24-24: Added type annotation for plugins class attributeExplicitly typing the plugins dictionary improves type safety and helps static type checkers understand the structure of the data.
26-26: Added return type annotation to new methodAdding the return type annotation clarifies that the method returns an instance of PluginRegistryBase, improving type safety.
31-31: Added return type annotation to init methodAdding the return type annotation clarifies that the method returns None, improving type safety.
60-60: Added return type annotation to register_cli_args methodAdding the return type annotation clarifies that the method returns None, improving type safety.
66-66: Added return type annotation to collect_plugins methodAdding the return type annotation clarifies that the method returns None, improving type safety.
84-84: Added return type annotation to register_plugin methodAdding the return type annotation clarifies that the method returns None, improving type safety.
99-99: Added return type annotation to validate_plugin methodAdding the return type annotation clarifies that the method returns None, improving type safety.
127-127: Improved abstract method signatureThe abstract method now uses the ellipsis syntax on the same line and includes a return type annotation, making it more concise and type-safe.
135-135: Improved abstract method signatureThe abstract method now uses the ellipsis syntax on the same line and includes a return type annotation, making it more concise and type-safe.
src/snakemake_interface_common/plugin_registry/plugin.py (18)
8-8: Appropriate import additionGood addition of the
Fieldimport fromdataclasses, which is now used in type annotations throughout the file.
11-11: Well-structured import expansionThe expanded imports from
typingproperly include all the types used throughout the file, improving code clarity and type safety.
20-21: Good practice for conditional importUsing conditional imports with
TYPE_CHECKINGis a good practice to avoid circular imports while still providing proper type information to static type checkers.
30-30: Improved return type annotationThe explicit return type annotation for
get_items_by_categorymakes the method's contract clearer and improves type safety.
41-41: Enhanced type safety for dictionaryThe updated type hint for
_innercorrectly allows forstr | Noneas keys, which aligns with the actual usage in the code.
43-45: Added return type for clarityAdding the
Nonereturn type toregister_settingsexplicitly indicates that the method doesn't return anything.
55-55: Improved dictionary return typeThe updated return type for
get_field_settingscorrectly reflects that keys can bestr | None, matching the type of_inner.
61-61: Enhanced iterator typingThe explicit iterator return type for
__iter__improves type safety and makes the method's contract clearer.
68-68: Concise abstract property return typesThe abstract properties now use concise return type annotations, which improves readability while maintaining type safety.
Also applies to: 72-72, 76-76
82-82: Added boolean return typeAdding the
boolreturn type tohas_settings_clsmakes the method's contract clearer.
91-91: Properly typed parameterAdding the
Fieldtype annotation to thefmt_defaultparameter improves type safety.
117-117: Explicit None return typeAdding the
Nonereturn type toregister_cli_argsexplicitly indicates that the method doesn't return anything.
176-177: Improved type annotationsThe parameter type hint for
validate_settingsand the nested functionget_descriptionnow have proper type annotations, enhancing type safety.
199-199: Enhanced return type specificityThe return type for
get_settingsnow correctly specifies eitherSettingsBaseorTaggedSettingsas possible return values.
215-215: Clear function signature with tuple return typeAdding type hints to
get_name_and_valueimproves readability and type safety, especially with the tuple return type.
221-222: Properly typed dictionariesThe updated type hints for
kwargs_taggedandkwargs_allcorrectly reflect their structure and usage in the code.
236-238: Well-typed function parametersAdding type hints to the
extract_valuesfunction parameters and return type improves code clarity and type safety.
306-307: Comprehensive type annotations for nested functionsAdding type hints to
_parse_typeand its nested functionapply_typeimproves type safety and code clarity.
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🧹 Nitpick comments (3)
.github/workflows/test.yml (3)
23-29: Review: Install Pixi StepThe Pixi installation step is well configured with the specified version (
v0.42.1), environment (dev), and caching enabled. One minor nitpick: verify that the parameter nameenvironments(plural) is intentionally used here, as subsequent command flags use the singular--environment. Consistency here helps avoid potential confusion.
45-47: Review: Collect QC StepThe "Collect QC" step provides a simple echo confirming that all quality control checks passed. For enhanced diagnostics in the future, consider integrating actual output collection from the previous steps.
53-59: Review: Install Pixi in Testing JobThis step duplicates the Pixi installation from the quality-control job, using identical parameters. To reduce repetition and simplify maintenance, consider consolidating this configuration using YAML anchors or a reusable workflow component.
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.github/workflows/test.yml (8)
10-15: Review: Permissions Block SetupThe new permissions block correctly grants read access for contents and write access for checks, issues, and pull-requests. This enhances the workflow's ability to interact with PR checks and issues. Please double-check that these permissions are strictly necessary and don’t inadvertently provide broader access than intended.
17-19: Review: Job Naming and Environment SetupThe job has been successfully renamed to "quality-control" to better reflect its expanded role (formatting, linting, type-checking, etc.). The runner environment ("ubuntu-latest") is appropriately set.
21-21: Review: Checkout Action UpdateThe use of
actions/checkout@v4is a welcome upgrade that ensures improved performance and access to newer GitHub features.
30-34: Review: Ruff Format CheckThe "Ruff Format" step is correctly set up with an
if: always()condition and executes the formatting check using Pixi. This helps ensure that code style standards are enforced consistently.
35-39: Review: Ruff Lint StepThis step uses Pixi to lint the code with a diff output, which is useful for quickly identifying improvements after formatting. Its configuration with
if: always()is appropriate.
40-44: Review: Mypy Type-Check StepIntegrating the mypy step with Pixi (
pixi run --environment dev type-check) aligns with the PR objective to resolve type issues. The configuration appears correct.
51-52: Review: Code Checkout in Testing JobThe testing job correctly checks out the repository using
actions/checkout@v4, ensuring that the latest code is used during tests.
60-62: Review: Run Tests CommandThe test command now leverages Pixi (
pixi run --environment dev test --show-capture=all -s -vv), which is consistent with the new dependency setup. Ensure that the flags used (--show-capture=all -s -vv) provide the desired verbosity and output for your test suite.
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.github/workflows/test.yml (1)
44-46: Collect Quality Control (QC) Message:
The "Collect QC" step simply echoes a confirmation message. While it currently serves as a placeholder, consider enhancing this step in the future with more detailed reporting or integration with your CI reporting tools if needed.
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.github/workflows/test.yml (10)
10-15: Enhanced Permissions Configuration:
The addition of an explicit permissions section (withcontents: read,checks: write,issues: write, andpull-requests: write) is a positive change. It clearly outlines the minimal rights required for the workflow, aligning with the principle of least privilege.
17-19: Job Renaming & Setup:
Renaming the job from a generic name to quality-control better reflects that this job now encompasses multiple quality assurance tasks (formatting, linting, and type-checking). The use ofruns-on: ubuntu-latestis standard and appropriate.
20-22: Checkout Action Update:
Updating the checkout action toactions/checkout@v4ensures that the workflow benefits from the latest updates and security fixes. This is an excellent move toward keeping dependencies up to date.
23-28: Introducing Pixi Installation:
Replacing the Poetry installation with Pixi viaprefix-dev/[email protected]aligns with the repo’s shift toward improved type checking and dependency management. The provided inputs forenvironments: devandpixi-version: v0.42.1are clear and consistent.
29-33: Ruff Format Step Addition:
Adding the "Ruff Format" step using Pixi (pixi run --environment dev format --check) integrates automated formatting into the CI pipeline. The use ofif: always()guarantees execution regardless of previous step failures, which is useful for reporting purposes.
34-38: Ruff Linting Integration:
The new "Ruff lint" step ensures that code style issues are flagged early. The use of--diffprovides clarity on the corrections needed, supporting a more efficient review process.
39-43: Mypy Type-Check Step:
Running mypy through Pixi (pixi run --environment dev type-check) directly addresses the mypy complaint resolutions. This clear separation of type checking boosts confidence in the type annotations across the repository.
47-51: Testing Job – Checkout Consistency:
The testing job continues to useactions/checkout@v4, ensuring that the codebase is checked out with the same updated version as in the quality-control job. This consistency is beneficial for maintainability.
52-57: Pixi Setup in Testing Job:
The testing job now includes a Pixi installation step with identical environment settings (environments: devandpixi-version: v0.42.1) as in the quality-control job. This uniformity helps maintain environment consistency across different stages.
58-60: Test Execution with Pixi:
The test step uses Pixi for running tests (pixi run --environment dev test --show-capture=all -s -vv), which aligns with the new dependency management approach. The inclusion of verbose flags (-s -vvand--show-capture=all) is helpful for debugging and ensuring complete output capture during test runs.
… safety and clarity
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src/snakemake_interface_common/plugin_registry/plugin.py (1)
271-271: Useis notinstead of!=for direct type comparison.
For clarity and alignment with Python style guidelines (E721), compare type objects withisoris not:-elif thefield.type != str and isinstance(thefield.type, type): +elif thefield.type is not str and isinstance(thefield.type, type):🧰 Tools
🪛 Ruff (0.8.2)
271-271: Use
isandis notfor type comparisons, orisinstance()for isinstance checks(E721)
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.github/workflows/test.yml(1 hunks)src/snakemake_interface_common/exceptions.py(4 hunks)src/snakemake_interface_common/logging.py(1 hunks)src/snakemake_interface_common/plugin_registry/__init__.py(5 hunks)src/snakemake_interface_common/plugin_registry/attribute_types.py(1 hunks)src/snakemake_interface_common/plugin_registry/plugin.py(13 hunks)src/snakemake_interface_common/rules.py(1 hunks)src/snakemake_interface_common/settings.py(1 hunks)src/snakemake_interface_common/utils.py(5 hunks)
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`**/*.py`: Do not try to improve formatting. Do not suggest type annotations for functions that are defined inside of functions or methods. Do not suggest type annotation of the `s...
**/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of theselfargument of methods.
Do not suggest type annotation of theclsargument of classmethods.
Do not suggest return type annotation if a function or method does not contain areturnstatement.
src/snakemake_interface_common/settings.pysrc/snakemake_interface_common/plugin_registry/plugin.py
🧬 Code Definitions (1)
src/snakemake_interface_common/plugin_registry/plugin.py (3)
src/snakemake_interface_common/plugin_registry/__init__.py (1)
register_cli_args(64-68)src/snakemake_interface_common/plugin_registry/tests.py (1)
validate_settings(26-26)src/snakemake_interface_common/rules.py (1)
name(7-7)
🪛 Ruff (0.8.2)
src/snakemake_interface_common/plugin_registry/plugin.py
271-271: Use is and is not for type comparisons, or isinstance() for isinstance checks
(E721)
🔇 Additional comments (3)
src/snakemake_interface_common/settings.py (2)
10-64: Comprehensive docstring improvements look good.
The updated docstrings provide clear guidance on usage and highlight each method’s purpose. This enhances readability and maintainability.
90-101: Potential type mismatch inparse_choicereturn type.
The_parse_choices_intomethod castscls.parse_choice(choice)toTSettingsEnumBase, butparse_choiceis declared to return"SettingsEnumBase". Additionally, the docstring suggests it returnsTSettingsEnumBase. For consistency, consider updating the return annotation to match your usage and docstring:- def parse_choice(cls, choice: str) -> "SettingsEnumBase": + def parse_choice(cls, choice: str) -> TSettingsEnumBase: """Converts a single string choice into an enum member.""" ...src/snakemake_interface_common/plugin_registry/plugin.py (1)
321-347: Good handling of optional vs. non-optional types.
This_parse_typelogic carefully checks if a type istyping.Optionalor a single plain type, correctly raising errors for unsupported unions.🧰 Tools
🪛 Ruff (0.8.2)
326-332: Within an
exceptclause, raise exceptions withraise ... from errorraise ... from Noneto distinguish them from errors in exception handling(B904)
NOTE: This PR depends on #58 to be merged first
This PR fixes all the mypy complaints within the repo
This allows future PRs to start addressing any discrepencies between the types annotated so far and all the concrete implementations throughout the
interfacepluginsSummary by CodeRabbit
SettingsEnumBaseclass for better clarity.These behind-the-scenes improvements help ensure a smoother, more dependable experience for our users.