Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

fix findPythonDeps.py script when called with an (absolute or relative) path to an easyconfig instead of a filename #4365

Merged
merged 3 commits into from
Oct 27, 2023

Conversation

Flamefire
Copy link
Contributor

@Flamefire Flamefire commented Oct 26, 2023

eb --missing returns a list with filenames. So an absolute path passed to --ec isn't matched which leads to an error stating you should install the EasyConfig that you are trying to find the dependencies of. Fix by getting the filename/basename first.

Example error:

findPythonDeps.py --ec ~/.local/EasyBuildDev/easybuild-easyconfigs/easybuild/easyconfigs/n/nf-core/nf-core-2.10-foss-2022b.eb nf-core==2.10
You need to install all modules on which ~/.local/EasyBuildDev/easybuild-easyconfigs/easybuild/easyconfigs/n/nf-core/nf-core-2.10-foss-2022b.eb depends first!
Missing:
	* nf-core/2.10-foss-2022b (nf-core-2.10-foss-2022b.eb)

`eb --missing` returns a list with filenames. So an absolute path passed
to `--ec` isn't matched which leads to an error stating you should
install the EasyConfig that you are trying to find the dependencies of.
Fix by getting the filename/basename first.
…aptured

This helps diagnosing failures for e.g. `eb --missing` (called with `capture_stderr=False`)
but which may print errors (e.g. failed parsing of some ECs) to stderr
@boegel boegel added this to the next release (4.8.2?) milestone Oct 27, 2023
@boegel boegel added the bug fix label Oct 27, 2023
@boegel boegel changed the title fix findPythonDeps when called with an absolute path to an EC fix findPythonDeps.py script when called with an absolute path to an EC Oct 27, 2023
@boegel boegel changed the title fix findPythonDeps.py script when called with an absolute path to an EC fix findPythonDeps.py script when called with an absolute path to an easyconfig Oct 27, 2023
Copy link
Member

@boegel boegel left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

lgtm

@boegel boegel merged commit 87c1453 into easybuilders:develop Oct 27, 2023
39 checks passed
@Flamefire Flamefire deleted the fix-findPythonDeps branch October 27, 2023 11:12
@Flamefire Flamefire changed the title fix findPythonDeps.py script when called with an absolute path to an easyconfig fix findPythonDeps.py script when called with an (absolute or relative) path to an easyconfig instead of a filename Oct 28, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants