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

Update: MultiQC - Bump to v1.22 #47904

Merged
merged 1 commit into from
May 23, 2024
Merged

Update: MultiQC - Bump to v1.22 #47904

merged 1 commit into from
May 23, 2024

Conversation

ewels
Copy link
Member

@ewels ewels commented May 15, 2024

  • Bumped to v1.22
  • Removed the uses_setuptools skip lint, hopefully no need to skip this any more since pkg_resources was removed in v1.16

Please read the guidelines for Bioconda recipes before opening a pull request (PR).

General instructions

  • If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title.
  • New recipes not directly relevant to the biological sciences need to be submitted to the conda-forge channel instead of Bioconda.
  • PRs require reviews prior to being merged. Once your PR is passing tests and ready to be merged, please issue the @BiocondaBot please add label command.
  • Please post questions on Gitter or ping @bioconda/core in a comment.

Instructions for avoiding API, ABI, and CLI breakage issues

Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify run_exports (see here for the rationale and comprehensive explanation).
Add a run_exports section like this:

build:
  run_exports:
    - ...

with ... being one of:

Case run_exports statement
semantic versioning {{ pin_subpackage("myrecipe", max_pin="x") }}
semantic versioning (0.x.x) {{ pin_subpackage("myrecipe", max_pin="x.x") }}
known breakage in minor versions {{ pin_subpackage("myrecipe", max_pin="x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
known breakage in patch versions {{ pin_subpackage("myrecipe", max_pin="x.x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
calendar versioning {{ pin_subpackage("myrecipe", max_pin=None) }}

while replacing "myrecipe" with either name if a name|lower variable is defined in your recipe or with the lowercase name of the package in quotes.

Bot commands for PR management

Please use the following BiocondaBot commands:

Everyone has access to the following BiocondaBot commands, which can be given in a comment:

@BiocondaBot please update Merge the master branch into a PR.
@BiocondaBot please add label Add the please review & merge label.
@BiocondaBot please fetch artifacts Post links to CI-built packages/containers.
You can use this to test packages locally.

Note that the @BiocondaBot please merge command is now depreciated. Please just squash and merge instead.

Also, the bot watches for comments from non-members that include @bioconda/<team> and will automatically re-post them to notify the addressed <team>.

Comment on lines 79 to 81
# click requires a unicode locale when used with Python 3
# extended-base generates en_US.UTF-8 locale and sets LC_ALL, LANG properly
extended-base: true
Copy link
Member Author

Choose a reason for hiding this comment

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

I'm not convinced that this is really needed now. Does anyone else have recent experience of bioconda packages using Click?

It would be nice to remove this and get smaller bioconda images. I also wonder if using a different image base could fix the Docker issues happening recently in GitPod: MultiQC/MultiQC#2283

Copy link
Member

Choose a reason for hiding this comment

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

not sure either - should we just try ?

Copy link
Member

Choose a reason for hiding this comment

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

I'm using rich-click and usually that's enough (dont need tqdm, pydantic, typeguard)

@ewels ewels requested review from matthdsm and apeltzer and removed request for matthdsm May 15, 2024 15:26
@ewels ewels changed the title MultiQC: Bump to v1.22 Update: MultiQC - Bump to v1.22 May 15, 2024
This was referenced May 15, 2024
@ewels
Copy link
Member Author

ewels commented May 22, 2024

Thanks @apeltzer ! Waiting on #41025 though.

@rpetit3
Copy link
Member

rpetit3 commented May 23, 2024

@ewels if you have no other changes needed feel free to squash and merge

@ewels ewels merged commit 32e2d69 into bioconda:master May 23, 2024
6 checks passed
ewels added a commit that referenced this pull request May 23, 2024
mencian pushed a commit that referenced this pull request May 23, 2024
* Update multiqc to 1.22.1

* Port updates from #47907

* Don't add back code that was removed in #47904

---------

Co-authored-by: Phil Ewels <[email protected]>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants