-
Notifications
You must be signed in to change notification settings - Fork 999
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
pysam-0.8.4+gx1.tar.gz breaks on TravisCI #2575
Comments
Thanks for submitting this. I was aware of it but haven't had a chance to fix it yet - typically it does not come up since pip should prefer our wheels over our sdists. I'll fix the sdist ASAP. Your Travis builds aren't using Galaxy pip, which is why it isn't downloading the wheels. I am not sure why - I know this was already fixed once. If you remove |
I'm intending to update my TravisCI setup to more closely follow the IUC setup, so problem may go away for me... |
Failing TravisCI was using this:
Just switched to this which I was already using with TravisCI on another repository:
Thanks! I'll leave this issue open for the underlying problem with the pysam not building. |
Pysam source builds (even for the older versions) should be fixed now. It should be less of an issue going forward because we'll be using an unmodified upstream pysam. That said, unless I keep making modified source tarballs as described in galaxyproject/starforge#180 and uploading them to wheels.galaxyproject.org for whatever releases we pin, local builds will fail if you do not have Cython installed. At least, that will be the case until pip with PEP 518 pyproject.toml support: pypa/pip#4144 is released, and pysam is updated to use pyproject.toml. But, I'm closing this, as the issue is fixed for now. |
Filing here as per @natefoo on Twitter: https://twitter.com/natefoo/status/748182338006319105
See https://travis-ci.org/peterjc/galaxy_blast/jobs/141112142 which downloads https://wheels.galaxyproject.org/packages/pysam-0.8.4+gx1.tar.gz and tries to install it, but fails with what looks like pysam-developers/pysam#79 suggesting the Galaxy wheel fo pysam is missing some headers?
The text was updated successfully, but these errors were encountered: