medaka: add linux-aarch64 build

[martin-g]

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 modifications to the meta.yaml file of the medaka package. Key changes include an update of the package version from 1.0.0 to 2.0.1, along with a corresponding update to the SHA256 checksum. The build number has been incremented from 0 to 1. The entry points section has been reformatted for consistent indentation, and a new key, additional-platforms, has been added under the extra section to specify linux-aarch64 as a supported platform. Furthermore, the doc_url line has been corrected for proper indentation. No changes have been made to the requirements or other sections of the meta.yaml file.

Possibly related PRs

• tracs: add aarch64/arm64 builds #50103: Updates the meta.yaml file for the tracs package, adding linux-aarch64 as a supported platform.
• pgrc: add linux-aarch64 build #51009: Adds linux-aarch64 as an additional platform in the meta.yaml file for the pgrc package.
• pyslow5: add aarch64/arm64 builds #51105: Modifies the meta.yaml file for the pyslow5 package to include linux-aarch64 in the additional-platforms section.
• metacache: add linux-aarch64 build #51106: Adds linux-aarch64 as a supported platform in the meta.yaml file for the metacache package.
• gxf2bed: add aarch64/arm64 builds #51120: Updates the meta.yaml file for the gxf2bed package to include linux-aarch64 in the additional-platforms.
• phables: add aarch64/arm64 builds #51124: Introduces linux-aarch64 support in the phables package's meta.yaml.
• tidk: add aarch64/arm64 builds #51159: Updates the meta.yaml file for the tidk package to include linux-aarch64.
• r-cobrar: add aarch64/arm64 builds #51203: Adds linux-aarch64 as an additional platform in the meta.yaml file for the r-cobrar package.
• Update medaka to 2.0.1 #51323: Updates the meta.yaml file for the medaka package, including the same version and SHA256 changes.

Suggested labels

please review & merge

Suggested reviewers

• mencian
• bgruening

---

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 1c1935d and 5f0b27a.

📒 Files selected for processing (1)

• recipes/medaka/meta.yaml (2 hunks)

🧰 Additional context used

🔇 Additional comments (4)

recipes/medaka/meta.yaml (4)

Line range hint 20-24: Indentation improvement in entry_points section.

The indentation in the entry_points section has been adjusted for better readability and consistency with the rest of the file. This change does not affect functionality.

---

Line range hint 1-91: Overall, the changes look good and align with the PR objectives.

The update to medaka 2.0.1 has been properly implemented, including version update, SHA256 update, and build number increment. The addition of linux-aarch64 as a supported platform has been correctly added. The indentation improvements enhance readability.

Please ensure to:

1. Verify potential impacts on downstream dependencies due to the major version update.
2. Test the build process for the linux-aarch64 platform to ensure compatibility.

Once these verifications are complete, this PR should be ready for merge.

---

85-86: Addition of linux-aarch64 platform looks good.

The linux-aarch64 platform has been correctly added under the 'additional-platforms' section in 'extra'. This aligns with the PR objective to add a linux-aarch64 build for medaka.

To ensure the build process works correctly for the new platform, please run the following verification:

#!/bin/bash
# Description: Verify build process for linux-aarch64 platform

# Check if there are any platform-specific build instructions
echo "Checking for platform-specific build instructions:"
rg 'aarch64' recipes/medaka/

# Verify if any dependencies have aarch64-specific versions
echo "Checking dependencies for aarch64-specific versions:"
rg 'aarch64' recipes/medaka/meta.yaml

If no platform-specific instructions or dependencies are found, the build process should work as-is for linux-aarch64. However, it's recommended to test the build on an aarch64 system or using a cross-compilation setup to ensure compatibility.

---

Line range hint 2-3: LGTM! Version update and build number increment look good.

The version has been updated from 1.0.0 to 2.0.1, which is a major version change. The SHA256 checksum has been updated accordingly, and the build number has been correctly incremented to 1.

Given the major version update, it's important to verify that downstream dependencies are not affected. Run the following script to check for potential impacts:

Also applies to: 17-17

---

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.

[martin-g]

The Linux ARM64 builds due to:

 python >=3.10,<3.11.0a0  is not installable because there are no viable options
11:41:09 BIOCONDA INFO (OUT)    ├─ python [3.10.0|3.10.1|...|3.10.9] would require
11:41:09 BIOCONDA INFO (OUT)    │  └─ python_abi 3.10.* *_cp310, which conflicts with any installable versions previously reported;
11:41:09 BIOCONDA INFO (OUT)    ├─ python [3.10.0|3.10.1|3.10.2] would require
11:41:09 BIOCONDA INFO (OUT)    │  └─ openssl >=1.1.1l,<1.1.2a , which conflicts with any installable versions previously reported;
11:41:09 BIOCONDA INFO (OUT)    ├─ python 3.10.4 would require
11:41:09 BIOCONDA INFO (OUT)    │  └─ openssl >=1.1.1n,<1.1.2a , which conflicts with any installable versions previously reported;
11:41:09 BIOCONDA INFO (OUT)    ├─ python 3.10.5 would require
11:41:09 BIOCONDA INFO (OUT)    │  └─ openssl >=1.1.1o,<1.1.2a , which conflicts with any installable versions previously reported;
11:41:09 BIOCONDA INFO (OUT)    ├─ python 3.10.6 would require
11:41:09 BIOCONDA INFO (OUT)    │  └─ openssl >=1.1.1q,<1.1.2a , which conflicts with any installable versions previously reported;
11:41:09 BIOCONDA INFO (OUT)    ├─ python 3.10.15 would require
11:41:09 BIOCONDA INFO (OUT)    │  ├─ libzlib >=1.3.1,<2.0a0 , which conflicts with any installable versions previously reported;
11:41:09 BIOCONDA INFO (OUT)    │  └─ python_abi 3.10.* *_cp310, which conflicts with any installable versions previously reported;
11:41:09 BIOCONDA INFO (OUT)    └─ python [3.10.7|3.10.8] would require
11:41:09 BIOCONDA INFO (OUT)       └─ openssl >=1.1.1s,<1.1.2a , which conflicts with any installable versions previously reported.