Update hmftools-purple to 4.1_beta.1 #51290
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📝 WalkthroughWalkthroughThis pull request introduces updates to the Possibly related PRs
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🧹 Outside diff range and nitpick comments (1)
recipes/hmftools-redux/meta.yaml (1)
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15-15: Increment the build numberThe
buildnumber is currently set to 0. According to Bioconda best practices, the build number should be incremented when making changes to a recipe, especially when updating to a new version (including beta versions).Please update the build number as follows:
build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage('hmftools-redux', max_pin="x.x") }}🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
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📒 Files selected for processing (3)
- recipes/hmftools-esvee/meta.yaml (1 hunks)
- recipes/hmftools-purple/meta.yaml (1 hunks)
- recipes/hmftools-redux/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/hmftools-purple/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (13)
recipes/hmftools-redux/meta.yaml (3)
2-2: LGTM: Addition ofbeta_suffixvariableThe introduction of the
beta_suffixvariable enhances version flexibility and aligns with the PR objective of updating to a beta version. The implementation is correct and follows proper YAML syntax.
10-10: LGTM: Updated URL with beta suffixThe URL has been correctly updated to include the
beta_suffix, which is consistent with the versioning changes. The use of Jinja2 templating for dynamic URL generation is appropriate.Please run the following script to verify the URL:
✅ Verification successful
URL Verification Successful
The updated URL has been successfully verified, and the JAR file exists at the specified location.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the existence of the JAR file at the specified URL url="https://github.com/hartwigmedical/hmftools/releases/download/redux-v1.0_beta/redux_v1.0_beta.1.jar" http_code=$(curl -s -o /dev/null -w "%{http_code}" $url) if [ $http_code -eq 200 ]; then echo "URL is valid and file exists" else echo "Error: URL returned HTTP code $http_code" fiLength of output: 458
Script:
#!/bin/bash # Description: Verify the existence of the JAR file at the specified URL, following redirects url="https://github.com/hartwigmedical/hmftools/releases/download/redux-v1.0_beta/redux_v1.0_beta.1.jar" http_code=$(curl -s -o /dev/null -w "%{http_code}" -L "$url") if [ "$http_code" -eq 200 ]; then echo "URL is valid and file exists" else echo "Error: URL returned HTTP code $http_code" fiLength of output: 353
3-3: Verify the updated SHA256 checksumThe SHA256 checksum has been updated, which is necessary when the source file changes. While the new checksum appears to be a valid SHA256 hash, it's important to ensure its correctness.
Please run the following script to verify the checksum:
recipes/hmftools-esvee/meta.yaml (5)
2-2: LGTM: Addition of beta_suffix variableThe addition of the
beta_suffixvariable is a good practice for managing beta versions. It allows for easier updates and maintenance of the package version.
10-10: LGTM: Updated URL with beta suffixThe URL has been correctly updated to include the
beta_suffixvariable. This change is consistent with the addition of thebeta_suffixvariable and ensures that the correct beta version of the package is downloaded.
15-15: LGTM: Incremented build numberThe build number has been correctly incremented from 0 to 1. This is a necessary step when making changes to the package without changing the version number. It follows best practices for package management in Bioconda.
Line range hint
1-38: Summary: Updates for beta version transitionThe changes in this meta.yaml file successfully update the hmftools-esvee package to a beta version. Key modifications include:
- Addition of a
beta_suffixvariable for version management.- Update of the SHA256 checksum for the new package.
- Modification of the download URL to include the beta suffix.
- Increment of the build number.
These changes are consistent with Bioconda best practices and the PR objectives. The package should now correctly download and install the beta version of hmftools-esvee.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
3-3: LGTM: Updated SHA256 checksumThe SHA256 checksum has been updated, which is necessary when the source file changes. This ensures the integrity of the downloaded package.
To verify the checksum, you can run the following command after downloading the jar file:
recipes/hmftools-purple/meta.yaml (5)
1-2: LGTM: Version update and beta suffix introductionThe version update to "4.1_beta" and the introduction of a beta_suffix variable are appropriate for this beta release. This approach allows for easier management of beta versions in the future.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
10-10: LGTM: Source URL updated correctlyThe source URL has been properly updated to include both the new version and the beta suffix. The use of Jinja2 templating for both
versionandbeta_suffixvariables ensures consistency and ease of future updates.
15-15: LGTM: Build number incrementedThe build number has been correctly incremented from 0 to 1. This is appropriate for a new beta release and ensures that the package manager will recognize this as an update.
1-15: Summary: Beta version update looks good, consider reviewing test commandsThe changes for updating hmftools-purple to version 4.1_beta.1 are correct and consistent with Bioconda's practices. The version, checksum, source URL, and build number have all been appropriately updated.
However, since this is a beta release, it might introduce new features or changes.
Please verify if the existing test command
purple -version | grep Purpleis still sufficient for this beta version. Consider adding more comprehensive tests if new features have been introduced.To check for any changes in the command-line interface or new features, you can run:
#!/bin/bash # Description: Check for changes in the command-line interface # Download the new JAR file wget https://github.com/hartwigmedical/hmftools/releases/download/purple-v4.1_beta/purple_v4.1_beta.1.jar # Extract usage information java -jar purple_v4.1_beta.1.jar 2>&1 | grep -i "usage:" # Clean up rm purple_v4.1_beta.1.jarThis will help ensure that the package is properly tested in its Bioconda distribution.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
3-3: Verify the updated SHA256 checksumThe SHA256 checksum has been updated, which is necessary for the new version. However, it's important to ensure that this checksum is correct for the new source file.
To verify the checksum, you can use the following script:
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