feat: allow skipping apptainer and conda tests if not available by veprbl · Pull Request #3074 · snakemake/snakemake

veprbl · 2024-09-05T23:30:09Z

There is no point to attempt testing apptainer and/or conda if they are not in the environment. This also marks few tests with @connected.

Summary by CodeRabbit

New Features
- Introduced conditional test execution based on the availability of Apptainer and Conda environments.
- Added new pytest markers to enhance test suite flexibility.
Bug Fixes
- Improved robustness of the testing framework by ensuring tests can be skipped if required tools are not present.
Documentation
- Updated test functions to reflect their association with specific deployment methods for better clarity.

coderabbitai · 2024-09-05T23:30:21Z

Walkthrough

The changes introduce two functions, has_apptainer() and has_conda(), to check for the availability of Apptainer and Conda executables. New pytest markers, apptainer and conda, are defined to conditionally skip tests based on the presence of these tools. Various test functions in tests/tests.py are updated with these markers, allowing tests to be executed in specific environments managed by Conda and Apptainer.

Changes

Files	Change Summary
`tests/common.py`	Added functions `has_apptainer()` and `has_conda()` to check for Apptainer and Conda executables. Introduced new pytest markers `apptainer` and `conda`.
`tests/tests.py`	Updated numerous test functions with `@conda` and `@apptainer` decorators to associate tests with specific deployment methods. Added `@connected` to some tests.

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coderabbitai

Actionable comments posted: 0

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 2ec61f4 and 02d9726.

Files selected for processing (2)

tests/common.py (2 hunks)
tests/tests.py (33 hunks)

Additional context used

Path-based instructions (2)

tests/common.py (1)

Pattern **/*.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 self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

tests/tests.py (1)

Pattern **/*.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 self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

Additional comments not posted (4)

tests/common.py (4)

72-76: Function has_apptainer is correctly implemented.

The function uses shutil.which() to check for the presence of "apptainer" or "singularity" executables, which is a standard and effective method for this purpose.

79-80: Function has_conda is correctly implemented.

The function uses shutil.which() to check for the presence of the "conda" executable, which is a standard and effective method for this purpose.

101-105: Pytest marker apptainer is correctly defined.

The marker uses the has_apptainer() function to conditionally skip tests if Apptainer or Singularity is not available. The reason for skipping is clearly and appropriately stated.

107-111: Pytest marker conda is correctly defined.

The marker uses the has_conda() function to conditionally skip tests if Conda is not available. The reason for skipping is clearly and appropriately stated.

sonarqubecloud · 2024-09-06T15:39:45Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

coderabbitai

Actionable comments posted: 0

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 02d9726 and a20ec26.

Files selected for processing (2)

tests/common.py (2 hunks)
tests/tests.py (33 hunks)

Files skipped from review as they are similar to previous changes (2)

tests/common.py
tests/tests.py

🤖 I have created a release *beep* *boop* --- ## [8.20.0](v8.19.3...v8.20.0) (2024-09-07) ### Features * allow skipping apptainer and conda tests if not available ([#3074](#3074)) ([c3cd4e0](c3cd4e0)) * MANIFEST.in: include tests/ in sdist ([#3073](#3073)) ([e24f3fc](e24f3fc)) ### Bug Fixes * add subfolders of report template to package data ([14a8f22](14a8f22)) * Inconsistent Linting Output Formatting ([#3064](#3064)) ([90e51ae](90e51ae)) * retry when downloading assets ([58e41b0](58e41b0)) * skip asset download if files are already present ([#3076](#3076)) ([0d3d1e1](0d3d1e1)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

veprbl requested a review from johanneskoester as a code owner September 5, 2024 23:30

coderabbitai bot reviewed Sep 5, 2024

View reviewed changes

feat: allow skipping apptainer and conda tests if not available

a20ec26

veprbl force-pushed the pr/skipif_conda_apptainer branch from 02d9726 to a20ec26 Compare September 6, 2024 15:39

coderabbitai bot reviewed Sep 6, 2024

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johanneskoester approved these changes Sep 7, 2024

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johanneskoester merged commit c3cd4e0 into snakemake:main Sep 7, 2024

coderabbitai bot mentioned this pull request Feb 17, 2025

fix: add missing @conda annotations #3298

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coderabbitai bot mentioned this pull request Feb 26, 2025

feat: make conda/apptainer/network tests skippable via env vars #3312

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feat: allow skipping apptainer and conda tests if not available#3074

feat: allow skipping apptainer and conda tests if not available#3074
johanneskoester merged 1 commit intosnakemake:mainfrom
veprbl:pr/skipif_conda_apptainer

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veprbl commented Sep 5, 2024 •

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