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

feat: update to gfastats 1.3.7 #50820

Merged
merged 4 commits into from
Sep 25, 2024
Merged

Conversation

Smeds
Copy link
Contributor

@Smeds Smeds commented Sep 19, 2024

update gfastats to version 1.3.7

changed from using a tar.gz to the actually git repositories since the software contains a submodule that needs to be fetched.


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>.

@Smeds
Copy link
Contributor Author

Smeds commented Sep 19, 2024

@bgruening what should I do about the linting errors?

ERROR: recipes/gfastats/meta.yaml:9: uses_vcs_url: The recipe downloads source from a VCS ERROR: recipes/gfastats/meta.yaml:10: missing_hash: The recipe is missing a checksum for a source file

I don't download a file and will therefor not be able to create a sha256 sum

@Smeds Smeds closed this Sep 19, 2024
@Smeds Smeds reopened this Sep 19, 2024
@Smeds
Copy link
Contributor Author

Smeds commented Sep 20, 2024

The developer of gfastats will upload update tar.gz file which make it possible to revert to downloading compressed files instead of fetching the actual repo.

@martin-g
Copy link
Contributor

@BiocondaBot please fetch artifacts

@BiocondaBot
Copy link
Collaborator

Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
linux-64 gfastats-1.3.7-hdcf5f25_0.tar.bz2 LinuxArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
osx-64 gfastats-1.3.7-h447d7a5_0.tar.bz2 OSXArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the OSXArtifacts directory: conda install -c ./packages <package name>

Docker image(s) built:

Package Tag CI Install with docker
gfastats 1.3.7--hdcf5f25_0 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/gfastats:1.3.7--hdcf5f25_0.tar.gz | docker load

@martin-g martin-g closed this Sep 24, 2024
@martin-g martin-g reopened this Sep 24, 2024
@martin-g
Copy link
Contributor

Closed+reopened to trigger the ARM64 CI checks

Smeds and others added 3 commits September 24, 2024 14:57
changed from using a tar.gz to the actually git repositories since the
software contains a submodule that needs to be fetched.
…ason for this PR

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
@martin-g martin-g mentioned this pull request Sep 24, 2024
@martin-g martin-g merged commit 0b12ea2 into bioconda:master Sep 25, 2024
5 checks passed
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.

4 participants