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

Fix: Maxit v11.200 #51356

Open
wants to merge 308 commits into
base: master
Choose a base branch
from
Open

Fix: Maxit v11.200 #51356

wants to merge 308 commits into from

Conversation

eunos-1128
Copy link
Contributor

@eunos-1128 eunos-1128 commented Oct 13, 2024

I changed to download a big binary to be downloaded from github release when starting build.

Ref: #50918 (comment)


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>.

@eunos-1128 eunos-1128 changed the title Maxit/v11.200 Fix: Maxit v11.200 Oct 13, 2024
Copy link
Contributor

coderabbitai bot commented Oct 13, 2024

📝 Walkthrough

Walkthrough

The pull request introduces several changes to the meta.yaml file for the MAXIT package. The version number remains 11.200, indicating a revision rather than a new version. A significant update is the change of the source URL from a specific server link to a GitHub repository URL, which may alter the source code distribution method. Correspondingly, the SHA256 checksum has been updated to match the new source package. Additionally, the build number has been incremented from 1 to 2, reflecting a new build iteration. The requirements section remains unchanged, preserving the existing build, host, and run dependencies. The test commands have not been modified, ensuring consistency in the testing process with prior versions. Overall, the changes focus on the source URL and checksum updates, along with an increment in the build number.

Possibly related PRs

Suggested labels

new version

Suggested reviewers

  • mencian
  • gbayarri

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
🪧 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.

@eunos-1128
Copy link
Contributor Author

@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Oct 13, 2024
Copy link
Contributor

@coderabbitai coderabbitai bot left a comment

Choose a reason for hiding this comment

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

Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (1)
recipes/maxit/meta.yaml (1)

Line range hint 1-85: Consider clarifying build process and updating package description.

The changes introduce a new source specifically for Linux x86_64 platforms while maintaining the original source. This approach might have implications:

  1. Build Process: Clarify how the build process differs for Linux x86_64 vs. other platforms. Consider adding comments in the recipe to explain the rationale behind using different sources.

  2. Cross-platform Compatibility: Ensure that using different sources for different platforms doesn't introduce unexpected variations in the final package.

  3. Package Description: Update the about section to mention the platform-specific builds, if relevant to end-users.

Consider adding a comment above the new source URL to explain why a different source is used for Linux x86_64:

  # Use pre-built binary for Linux x86_64 to [reason for using pre-built binary]
  - url: https://github.com/eunos-1128/maxit-binaries/archive/refs/tags/v11.200.tar.gz  # [linux and x86_64]
    sha256: b207c7c6e1b191efc28b1b42459fcf5622367d3d3db767e0b6c4326e8b14a94b  # [linux and x86_64]

Also, consider updating the about section to reflect these changes:

about:
  # ... existing content ...
  description: |
    MAXIT assists in the processing and curation of macromolecular structure data. MAXIT can:
      # ... existing description ...
    
    Note: For Linux x86_64 platforms, this package uses a pre-built binary to [reason for using pre-built binary].
📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between c6c23f3 and 345d2e4.

📒 Files selected for processing (1)
  • recipes/maxit/meta.yaml (1 hunks)
🧰 Additional context used
🔇 Additional comments (2)
recipes/maxit/meta.yaml (2)

24-24: LGTM: Build number increment is correct.

Incrementing the build number from 1 to 2 is the right approach when making changes to the package without altering its version. This follows Conda packaging best practices.


20-21: Approve new source, but suggest cleanup and verification.

The addition of a new source URL for Linux x86_64 platforms is good. However, to improve clarity:

  1. Consider removing or commenting out the old source URL and checksum (lines 9-10) if they are no longer needed.
  2. Ensure that the new binary from GitHub is equivalent to the one previously downloaded from sw-tools.rcsb.org.

To verify the integrity and contents of the new source, run:

Compare the output with the expected contents and checksum.

@martin-g
Copy link
Contributor

This PR has 300+ commits. It is time to rebase your local Git clone!

@eunos-1128
Copy link
Contributor Author

eunos-1128 commented Oct 14, 2024

This PR has 300+ commits. It is time to rebase your local Git clone!

I'll make new branch from next PR.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
please review & merge set to ask for merge
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants