fix: add missing @conda annotations#3298
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📝 WalkthroughWalkthroughThis pull request augments the test suite by adding six new test functions to Changes
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🤖 I have created a release *beep* *boop* --- ## [8.29.0](v8.28.0...v8.29.0) (2025-02-27) ### Features * provide mechanism to link between report items (snakemake.report_href, see docs) ([#3224](#3224)) ([a024e60](a024e60)) * toggles for binary labels in report ([#3296](#3296)) ([7690998](7690998)) ### Bug Fixes * add missing [@conda](https://github.com/conda) annotations ([#3298](#3298)) ([0b541cc](0b541cc)) * properly handle remote storage when waiting for pipes ([#3317](#3317)) ([9f7e092](9f7e092)) * provide proper error messages if output file preparation (pipe, mkdir) fails ([#3309](#3309)) ([77ef176](77ef176)) * record file extension (e.g. .tsv) in between workflow cache records in order to avoid that files of the wrong format are erroneously returned by the cache. This will lead to some cache misses. But avoiding errors induced by the previous behavior of ignoring file extensions when seeking for cache records is more important. ([#3314](#3314)) ([4912f00](4912f00)) * sort results lexicographically by labels in their order of appearance ([#3293](#3293)) ([a19a0ac](a19a0ac)) ### Documentation * update best practices ([7270eb3](7270eb3)) --- 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>
The snakemake tests use the decorator `@conda` to check whether the `conda` executable is in the user `$PATH` and otherwise skips them. However, some annotations are missing and hence failing instead of being skipped without `conda`: ``` tests/tests.py::test_conda_create_envs_only tests/tests.py::test_get_log_none tests/tests.py::test_get_log_both tests/tests.py::test_get_log_stderr tests/tests.py::test_get_log_stdout tests/tests.py::test_get_log_complex tests/tests.py::test_issue1046 tests/tests.py::test_containerize ``` This patch adds the missing decorator to those tests. ### QC <!-- Make sure that you can tick the boxes below. --> * [x] The PR contains a test case for the changes or the changes are already covered by an existing test case. * [x] The documentation (`docs/`) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake). <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Tests** - Expanded automated test coverage to verify environment setup processes. - Added validations for logging behavior across multiple scenarios, ensuring robust handling of different output conditions. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
🤖 I have created a release *beep* *boop* --- ## [8.29.0](snakemake/snakemake@v8.28.0...v8.29.0) (2025-02-27) ### Features * provide mechanism to link between report items (snakemake.report_href, see docs) ([snakemake#3224](snakemake#3224)) ([a024e60](snakemake@a024e60)) * toggles for binary labels in report ([snakemake#3296](snakemake#3296)) ([7690998](snakemake@7690998)) ### Bug Fixes * add missing [@conda](https://github.com/conda) annotations ([snakemake#3298](snakemake#3298)) ([0b541cc](snakemake@0b541cc)) * properly handle remote storage when waiting for pipes ([snakemake#3317](snakemake#3317)) ([9f7e092](snakemake@9f7e092)) * provide proper error messages if output file preparation (pipe, mkdir) fails ([snakemake#3309](snakemake#3309)) ([77ef176](snakemake@77ef176)) * record file extension (e.g. .tsv) in between workflow cache records in order to avoid that files of the wrong format are erroneously returned by the cache. This will lead to some cache misses. But avoiding errors induced by the previous behavior of ignoring file extensions when seeking for cache records is more important. ([snakemake#3314](snakemake#3314)) ([4912f00](snakemake@4912f00)) * sort results lexicographically by labels in their order of appearance ([snakemake#3293](snakemake#3293)) ([a19a0ac](snakemake@a19a0ac)) ### Documentation * update best practices ([7270eb3](snakemake@7270eb3)) --- 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>
The snakemake tests use the decorator
@condato check whether thecondaexecutable is in the user$PATHand otherwise skips them.However, some annotations are missing and hence failing instead of being skipped without
conda:This patch adds the missing decorator to those tests.
QC
docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).Summary by CodeRabbit