CI: put pysceptre's scripts/ on PYTHONPATH for the Nextflow DAG step - #3
Merged
Merged
Conversation
watteg-make-test-data imports sceptre_io, which pysceptre does not ship in its wheel, so the step failed with ModuleNotFoundError on every push since the Python switch. Fetch scripts/ at the pinned tag, as the container does. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
WattEG reads the .h5mu pysceptre's export writes, but only pixi.toml listed them, so a pip or uv install (and CI) lacked them: the Nextflow DAG step then failed with No module named 'anndata'. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
-profile standard kept the real requests, and PREPARE_SIM_INPUT's 32 GB exceeds the 15.6 GB runner, so Nextflow refused the task before running its stub. The stub profile caps resources for this, as pixi's pipeline-test does. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
2 tasks done
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
The tests workflow's Nextflow DAG step fails with
ModuleNotFoundError: No module named 'sceptre_io':watteg-make-test-dataimports pysceptre'sscripts/sceptre_io.py, which is not in pysceptre's wheel. This fetchesscripts/at the pinned tag (v0.2.0) and puts it onPYTHONPATH, as the container image does.🤖 Generated with Claude Code