refactor: hpc.env_vars() is now a function; skip exporting sing cache - #222
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kelly-sovacool wants to merge 8 commits into
Open
refactor: hpc.env_vars() is now a function; skip exporting sing cache#222kelly-sovacool wants to merge 8 commits into
kelly-sovacool wants to merge 8 commits into
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #222 +/- ##
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+ Coverage 73.42% 73.51% +0.08%
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Files 28 28
Lines 1938 1948 +10
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+ Hits 1423 1432 +9
- Misses 515 516 +1 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Pull request overview
Adds runtime environment-variable forwarding for Nextflow execution while removing the default Singularity cache export.
Changes:
- Converts HPC environment exports into methods.
- Adds environment-variable support and tests for local/SLURM runs.
- Updates Python metadata, lockfile, and GSEA CLI program names.
Reviewed changes
Copilot reviewed 7 out of 9 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
tests/test_pipeline_hpc.py |
Updates HPC environment assertions. |
tests/test_nextflow.py |
Tests environment-variable forwarding. |
src/ccbr_tools/pyproject.toml |
Updates Python and development dependencies. |
src/ccbr_tools/pipeline/nextflow.py |
Adds Nextflow environment-variable support. |
src/ccbr_tools/pipeline/hpc.py |
Refactors cluster environment exports. |
src/ccbr_tools/GSEA/multitext2excel.py |
Sets the CLI program name. |
src/ccbr_tools/GSEA/deg2gs.py |
Sets the CLI program name. |
pixi.lock |
Refreshes locked development dependencies. |
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| elif mode == "local": | ||
| if hpc: | ||
| nextflow_command = f'bash -c "module load {hpc_modules} && {hpc.env_vars} && {nextflow_command}"' | ||
| nextflow_command = f'bash -c "module load {hpc_modules} && {hpc.env_vars()} && {" && ".join(env_vars)} && {nextflow_command}"' |
Comment on lines
+137
to
+139
| nextflow_command = f'bash -c "module load {hpc_modules} && {hpc.env_vars()} && {" && ".join(env_vars)} && {nextflow_command}"' | ||
| elif env_vars: | ||
| nextflow_command = " && ".join((*env_vars, nextflow_command)) |
| pipeline_name=None, | ||
| nextflow_args=None, | ||
| debug=False, | ||
| env_vars=None, |
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Changes
do not export a singularity cachedir by default. it gets overridden by the nextflow config anyway, making troubleshooting more confusing than it needs to be.
Issues
resolves #212
PR Checklist
(
Strikethroughany points that are not applicable.)CHANGELOG.mdwith a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/