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.

Sign up for GitHub

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

Jump to bottom

dynamic version #230

Merged
merged 5 commits into from
Oct 17, 2022
Merged

dynamic version #230

merged 5 commits into from
Oct 17, 2022

Conversation

WangHong007
Copy link
Contributor

No description provided.

@github-actions
Copy link

github-actions bot commented Oct 15, 2022 •
edited
Loading

nf-core lint overall result: Passed ✅

Posted for pipeline commit c466e5e

+| ✅ 155 tests passed       |+
#| ❔   3 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-10-15 01:10:37

jpfeuffer
jpfeuffer reviewed Oct 15, 2022
View reviewed changes
Copy link
Collaborator

@jpfeuffer jpfeuffer left a comment

Choose a reason for hiding this comment

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

Looks good in general. Did you check the output?
I'm surprised that you can check packages with pip when they are installed with Conda.

@WangHong007
Copy link
Contributor Author

@jpfeuffer Hi Julianus!

When I run with conda use "import pyopenms; print(pyopenms.__version__)", I got the following version information:

"NFCORE_QUANTMS:QUANTMS:FILE_PREPARATION:MZMLSTATISTICS":
    pyopenms: Warning: OPENMS_DATA_PATH environment variable already exists. pyOpenMS will use it (/home/qinchunyuan/proteomicsDIA/quantms-newPR/work/conda/env-b594964cb2f9d0131205be432178f63f/share/OpenMS/) to locate data in the OpenMS share folder (e.g., the unimod database), instead of the default (/home/qinchunyuan/proteomicsDIA/quantms-newPR/work/conda/env-b594964cb2f9d0131205be432178f63f/lib/python3.10/site-packages/pyopenms/share/OpenMS).
2.8.0

To achieve the dynamic version I used pip show package and the output looks fine, here collated_versions.yml. The error in conda CI is very strange.

@jpfeuffer
Copy link
Collaborator

That warning should not happen on fresh installs and we could add a regex to parse for the version after the warning. But if pip show works for both Conda and Container, I am fine with it.

@jpfeuffer
Copy link
Collaborator

The Conda error is just a race condition of Conda/mamba trying to install multiple environments. We should try the new micromamba support in another PR.

@ypriverol
Copy link
Member

ypriverol commented Oct 17, 2022 •
edited
Loading

should we force this merge? @jpfeuffer

@jpfeuffer jpfeuffer merged commit 1ace2fb into bigbio:dev Oct 17, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@jpfeuffer jpfeuffer jpfeuffer left review comments

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@WangHong007 @jpfeuffer @ypriverol