[biobb_common] update 5.0.0

[PauAndrio]

Describe your pull request here

---

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>.

[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request introduces updates to the meta.yaml file for the biobb_common package. The version number has been incremented from 4.2.0 to 5.0.0, and the SHA256 checksum for the source tarball has been updated to reflect this new version. The minimum Python version requirement has been raised from >=3.8.0 to >=3.9.0 for both the host and run environments. Additionally, the jsonschema dependency has been added to both sections. The copyright year for the Institute for Research in Biomedicine has been updated to 2024, aligning with the Barcelona Supercomputing Center. These changes encompass version updates, dependency modifications, and copyright adjustments.

Possibly related PRs

• 2024.4 #50977: Updates the meta.yaml file for the biobb_structure_checking package, involving versioning and SHA256 checksum updates.
• Update PhyloAcc recipe #51090: Modifies the meta.yaml file for the PhyloAcc package, including updates to the build number and Python version compatibility.
• Fix pgscatalog-utils 1.4.1 #51256: Updates the pgscatalog-utils package's meta.yaml file, focusing on versioning and SHA256 checksum updates.

Suggested labels

autobump, new version

Suggested reviewers

• gbayarri

---

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 57cddcc and 016e315.

📒 Files selected for processing (1)

• recipes/biobb_common/meta.yaml (3 hunks)

🧰 Additional context used

🔇 Additional comments (5)

recipes/biobb_common/meta.yaml (5)

52-53: Copyright year update approved.

The copyright year for the Institute for Research in Biomedicine has been correctly updated to 2024, matching the Barcelona Supercomputing Center's copyright year.

This update maintains current legal protection for the software.

---

21-21: Python version requirement update approved.

The minimum Python version has been increased from 3.8.0 to 3.9.0 for both host and run environments. This change may impact users with older Python installations.

Please ensure that this change is necessary and documented. Consider the following:

1. Check if any new features from Python 3.9 are being used in the package.
2. Verify that CI systems and test environments support Python 3.9+.
3. Update documentation to reflect the new Python version requirement.

You can use the following command to check the Python versions used in the CI:

#!/bin/bash
# Check Python versions in CI configuration
grep -r "python" .github/workflows/

Also applies to: 28-28

---

10-10: SHA256 checksum update approved.

The SHA256 checksum has been updated, which is necessary due to the new version of the package.

To ensure the integrity of the package, please verify that the new checksum matches the source tarball. You can use the following command:

#!/bin/bash
# Verify the SHA256 checksum
curl -sL https://pypi.io/packages/source/b/biobb_common/biobb_common-5.0.0.tar.gz | sha256sum

Compare the output with the checksum in the meta.yaml file.

---

26-26: Addition of jsonschema dependency approved.

The jsonschema package has been added as a dependency in both host and run sections. This addition may impact the package's functionality and installation process.

Please ensure that:

1. The jsonschema dependency is necessary and used in the package.
2. Consider adding version constraints if specific versions are required.
3. Update documentation to mention this new dependency.

You can use the following command to check where jsonschema is used in the package:

#!/bin/bash
# Check usage of jsonschema in the package
rg -i 'import.*jsonschema|from.*jsonschema' --type python

Also applies to: 32-32

---

2-2: Version update to 5.0.0 approved.

The version has been correctly updated to 5.0.0, which aligns with the PR title. As this is a major version update, it likely includes significant changes or breaking changes.

Please ensure that all breaking changes are documented and that downstream dependencies are updated accordingly. You can use the following command to check for reverse dependencies:

---

Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media?

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

🪧 Tips

Chat

There are 3 ways to chat with CodeRabbit:

• Review comments: Directly reply to a review comment made by CodeRabbit. Example:
  • I pushed a fix in commit <commit_id>, please review it.
  • Generate unit testing code for this file.
  • Open a follow-up GitHub issue for this discussion.
• Files and specific lines of code (under the "Files changed" tab): Tag @coderabbitai in a new review comment at the desired location with your query. Examples:
  • @coderabbitai generate unit testing code for this file.
  • @coderabbitai modularize this function.
• PR comments: Tag @coderabbitai in a new PR comment to ask questions about the PR branch. For the best results, please provide a very specific query, as very limited context is provided in this mode. Examples:
  • @coderabbitai gather interesting stats about this repository and render them as a table. Additionally, render a pie chart showing the language distribution in the codebase.
  • @coderabbitai read src/utils.ts and generate unit testing code.
  • @coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.
  • @coderabbitai help me debug CodeRabbit configuration file.

Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments.

CodeRabbit Commands (Invoked using PR comments)

• @coderabbitai pause to pause the reviews on a PR.
• @coderabbitai resume to resume the paused reviews.
• @coderabbitai review to trigger an incremental review. This is useful when automatic reviews are disabled for the repository.
• @coderabbitai full review to do a full review from scratch and review all the files again.
• @coderabbitai summary to regenerate the summary of the PR.
• @coderabbitai resolve resolve all the CodeRabbit review comments.
• @coderabbitai configuration to show the current CodeRabbit configuration for the repository.
• @coderabbitai help to get help.

Other keywords and placeholders

• Add @coderabbitai ignore anywhere in the PR description to prevent this PR from being reviewed.
• Add @coderabbitai summary to generate the high-level summary at a specific location in the PR description.
• Add @coderabbitai anywhere in the PR title to generate the title automatically.

CodeRabbit Configuration File (.coderabbit.yaml)

• You can programmatically configure CodeRabbit by adding a .coderabbit.yaml file to the root of your repository.
• Please see the configuration documentation for more information.
• If your editor has YAML language server enabled, you can add the path at the top of this file to enable auto-completion and validation: # yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json

Documentation and Community

• Visit our Documentation for detailed information on how to use CodeRabbit.
• Join our Discord Community to get help, request features, and share feedback.
• Follow us on X/Twitter for updates and announcements.