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 Hsdecipher script #51057

Merged
merged 23 commits into from
Sep 30, 2024
Merged

Update Hsdecipher script #51057

merged 23 commits into from
Sep 30, 2024

Conversation

zx0223winner
Copy link
Contributor

@zx0223winner zx0223winner commented Sep 30, 2024

Describe your pull request here

update the script

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>.

Summary by CodeRabbit

  • New Features

    • Updated HSDecipher package to version 1.1.1 with a new build iteration.
  • Bug Fixes

    • Adjusted SHA256 checksum for the source archive to ensure integrity.
  • Documentation

    • Maintained metadata including home URL, summary, description, and license information.

Copy link
Contributor

coderabbitai bot commented Sep 30, 2024

📝 Walkthrough
📝 Walkthrough

Walkthrough

The pull request updates the meta.yaml file for the HSDecipher package, incrementing the version from "1.0.0" to "1.1.1". It includes an updated SHA256 checksum and a revised build number from 1 to 0. The package remains a noarch Python package with unchanged runtime requirements and test commands. Other metadata, such as the home URL and license information, remains intact.

Changes

File Change Summary
recipes/hsdecipher/meta.yaml - Version updated from "1.0.0" to "1.1.1"
- SHA256 checksum updated
- Build number updated from 1 to 0

Possibly related PRs

  • update Hsdecipher des #51023: This PR updates the meta.yaml file for the HSDecipher package, which is directly related to the changes made in the main PR that also modifies the meta.yaml for HSDecipher, including updates to the SHA256 checksum and build number.

Suggested reviewers

  • apeltzer

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 8ccd484 and f32c64c.

📒 Files selected for processing (1)
  • recipes/hsdecipher/meta.yaml (1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
  • recipes/hsdecipher/meta.yaml

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.

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: 1

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 82c0af1 and 8ccd484.

📒 Files selected for processing (1)
  • recipes/hsdecipher/meta.yaml (1 hunks)
🔇 Additional comments (3)
recipes/hsdecipher/meta.yaml (3)

13-13: Build number increment is correct.

The build number has been properly incremented from 1 to 2. This is the correct practice when updating a package, as it allows for tracking different builds of the same version.


Line range hint 1-38: Overall changes are consistent and well-implemented.

The updates to the meta.yaml file are consistent with a minor version update:

  1. Version has been incremented from 1.0.0 to 1.1.1.
  2. SHA256 checksum has been updated accordingly.
  3. Build number has been incremented.

The presence of the run_exports section is commendable, as it aligns with the PR objectives regarding dependency version management. Runtime requirements, test commands, and metadata remain unchanged, which is appropriate for a minor version update.

🧰 Tools
🪛 yamllint

[error] 1-1: syntax error: found character '%' that cannot start any token

(syntax)


2-2: Version update looks good.

The version has been correctly updated from "1.0.0" to "1.1.1", following semantic versioning principles. This is consistent with the PR objective to update the Hsdecipher script.

Please ensure that this version update is reflected in other relevant files or documentation. Run the following script to check for any inconsistencies:


package:
name: {{ name|lower }}
version: {{ version }}

source:
url: https://github.com/zx0223winner/{{name|lower}}_conda/archive/refs/tags/v{{version}}.tar.gz
sha256: 54ab84f8584c69a50db4678b49279b0a0b4b05cf0028eec9c2f2ea2205917b76
sha256: 7ac882c835b53a78e4dfe5120037a8237f5e79a5ab94d7d0edd893d5851007ba
Copy link
Contributor

Choose a reason for hiding this comment

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

💡 Codebase verification

Checksum Verification Failed

The verification script could not compute the SHA256 checksum because the sha256sum command is unavailable. Please update the script to use openssl for checksum calculation:

#!/bin/bash
# Description: Verify the SHA256 checksum of the source archive

# Extract version and checksum from meta.yaml
version=$(grep 'version = ' recipes/hsdecipher/meta.yaml | cut -d '"' -f 2)
expected_checksum=$(grep 'sha256: ' recipes/hsdecipher/meta.yaml | cut -d ' ' -f 4)

# Download the archive
curl -L "https://github.com/zx0223winner/hsdecipher_conda/archive/refs/tags/v${version}.tar.gz" -o hsdecipher.tar.gz

# Compute the checksum using openssl
computed_checksum=$(openssl dgst -sha256 hsdecipher.tar.gz | awk '{print $2}')

# Compare checksums
echo "Expected checksum: $expected_checksum"
echo "Computed checksum: $computed_checksum"
if [ "$expected_checksum" = "$computed_checksum" ]; then
    echo "Checksums match."
else
    echo "Checksums do not match!"
fi

# Clean up
rm hsdecipher.tar.gz
🔗 Analysis chain

SHA256 checksum has been updated.

The SHA256 checksum has been updated, which is necessary due to the version change. This ensures the integrity of the downloaded package.

To ensure the correctness of the new checksum, please verify it against the source archive. You can use the following script to download the archive and compute its checksum:

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the SHA256 checksum of the source archive

# Extract version and checksum from meta.yaml
version=$(grep 'version = ' recipes/hsdecipher/meta.yaml | cut -d '"' -f 2)
expected_checksum=$(grep 'sha256: ' recipes/hsdecipher/meta.yaml | cut -d ' ' -f 4)

# Download the archive
curl -L "https://github.com/zx0223winner/hsdecipher_conda/archive/refs/tags/v${version}.tar.gz" -o hsdecipher.tar.gz

# Compute the checksum
computed_checksum=$(sha256sum hsdecipher.tar.gz | cut -d ' ' -f 1)

# Compare checksums
echo "Expected checksum: $expected_checksum"
echo "Computed checksum: $computed_checksum"
if [ "$expected_checksum" = "$computed_checksum" ]; then
    echo "Checksums match."
else
    echo "Checksums do not match!"
fi

# Clean up
rm hsdecipher.tar.gz

Length of output: 1280

@zx0223winner
Copy link
Contributor Author

@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Sep 30, 2024
@mencian mencian merged commit dba5036 into bioconda:master Sep 30, 2024
7 checks passed
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.

4 participants