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Update tbtamr to 1.0.2 #51119

Merged
merged 3 commits into from
Oct 3, 2024
Merged

Update tbtamr to 1.0.2 #51119

merged 3 commits into from
Oct 3, 2024

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@BiocondaBot BiocondaBot commented Oct 3, 2024

Update tbtamr: 0.0.41.0.2

install with bioconda Conda

Info Link or Description
Recipe recipes/tbtamr (click to view/edit other files)
Summary A tool implementing TB-Profiler for reporting of genomic DST for M. tuberculosis in a CPHL
Home https://github.com/MDU-PHL/tbtamr
Releases https://pypi.org/pypi/tbtamr/json
Recipe Maintainer(s) @kristyhoran

This pull request was automatically generated (see docs).

@BiocondaBot BiocondaBot added autobump Automatic Version Update new version labels Oct 3, 2024
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coderabbitai bot commented Oct 3, 2024

📝 Walkthrough
📝 Walkthrough

Walkthrough

The pull request includes updates to the meta.yaml file for the tbtamr package. Key changes involve incrementing the version from "0.0.4" to "1.0.2", updating the SHA256 checksum, and modifying the build number from 1 to 0. The source URL has been adjusted to reflect the new version, while the requirements section has been updated to require Python version ">=3.10" and added several new dependencies. The build script has been modified, and a new dev_url field has been introduced for the package's GitHub repository.

Changes

File Path Change Summary
recipes/tbtamr/meta.yaml - Version updated from "0.0.4" to "1.0.2"
- SHA256 checksum updated from "72db1eb835574f02b0d7768e6b04e310bd2229d0f684100004b20a133eecd882" to "3b1e669a015ed7bb40977c104ae22f3a4e1e49f07c84b7043f0e6b21c8a0957a"
- Build number changed from 1 to 0
- Source URL updated for new version
- Python requirement updated from ">=3.8" to ">=3.10"
- New dependencies added: joblib, pydantic, pytest, tabulate, unidecode, pysam
- Dependencies psutil and csvtk removed from run requirements
- Build script modified to include flags --no-build-isolation and --no-cache-dir
- New field dev_url added in metadata

Possibly related PRs

  • Update sizemeup to 1.2.3 #51114: This PR updates the sizemeup package, which is a new dependency added in the main PR for the tbtamr package. The changes in both PRs involve version updates and modifications to the meta.yaml file.

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between d174c50 and a1b6f17.

📒 Files selected for processing (1)
  • recipes/tbtamr/meta.yaml (4 hunks)
🔇 Additional comments (5)
recipes/tbtamr/meta.yaml (5)

2-3: Version and checksum update looks good.

The package version has been updated from 0.0.4 to 1.0.2, which is a significant version bump. The SHA256 checksum has been updated accordingly. These changes are consistent with the PR objectives.


15-15: Build number reset is correct.

The build number has been reset to 0, which is the correct practice when updating to a new version of the package.


59-59: Addition of dev_url is beneficial.

The inclusion of the dev_url field pointing to the GitHub repository is a positive change. It provides users with a direct link to the development repository, which can be helpful for those who want to contribute or report issues.


Line range hint 24-45: Significant changes in package requirements.

  1. The minimum Python version has been increased from 3.8 to 3.10. This change might break compatibility with systems using Python 3.8 or 3.9.

  2. New dependencies have been added: joblib, pydantic, pytest, tabulate, unidecode, and pysam. These additions suggest new features or improvements in the package.

  3. Some dependencies (psutil, csvtk) have been removed according to the AI summary.

Please verify the following:

  1. Ensure that the increase in minimum Python version is intentional and necessary.
  2. Confirm that the removed dependencies (psutil, csvtk) are no longer needed.

You can use the following script to check for any remaining usage of removed dependencies:

#!/bin/bash
# Description: Check for usage of removed dependencies

# Test: Search for usage of psutil and csvtk in the package source
rg -i 'import\s+(psutil|csvtk)' $(fd -e py -d 3 . recipes/tbtamr)
rg -i '(psutil|csvtk)\.' $(fd -e py -d 3 . recipes/tbtamr)

# If any matches are found, they will be displayed
🧰 Tools
🪛 yamllint

[error] 46-46: trailing spaces

(trailing-spaces)


20-20: Build script update looks good, but verify its impact.

The addition of --no-build-isolation and --no-cache-dir flags to the build script can improve build reproducibility. However, it's important to ensure that these flags don't cause any unintended side effects in the build process.

To verify the impact of these flags, you can run the following script:


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Actionable comments posted: 0

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

Release 1.0.1 Not Found on GitHub

The meta.yaml specifies version 1.0.1, but no corresponding release was found on GitHub. Please verify that this release exists. If it does not, update the version number or create the necessary release to ensure dependencies and tests align correctly.

🔗 Analysis chain

Line range hint 23-62: Verify dependencies and test procedures for the new version.

While the requirements and test sections remain unchanged, it's important to ensure they are still appropriate for version 1.0.1. The significant version jump (0.0.4 to 1.0.1) might introduce new features or changes that could affect dependencies or require additional tests.

Please review the changelog or release notes for version 1.0.1 to confirm that:

  1. All required dependencies are still correctly listed and versioned.
  2. The existing test command (tbtamr --help) is sufficient to verify the functionality of the new version.
  3. No new tests need to be added to cover new features or changes.

You can use the following script to check for a CHANGELOG file or release notes:

If changes are needed, please update the meta.yaml file accordingly.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for CHANGELOG or release notes

# Check for CHANGELOG file
if fd -I -g 'CHANGELOG*' -d 1; then
    echo "CHANGELOG file found. Please review it for any dependency or testing changes."
else
    echo "No CHANGELOG file found in the root directory."
fi

# Check for release notes on GitHub
echo "Checking for release notes on GitHub..."
gh release view 1.0.1 -R https://github.com/MDU-PHL/tbtamr

Length of output: 671


Script:

#!/bin/bash
# Description: Verify release 1.0.1 and check dependencies

# Check for CHANGELOG file
if fd -I -g 'CHANGELOG*' -d 1; then
    echo "CHANGELOG file found. Please review it for any dependency or testing changes."
else
    echo "No CHANGELOG file found in the root directory."
fi

# Check for release notes on GitHub
echo "Checking for release notes on GitHub..."
gh release view 1.0.1 -R MDU-PHL/tbtamr

if [ $? -ne 0 ]; then
    echo "Release 1.0.1 not found on GitHub. Please verify its existence."
fi

Length of output: 497

🧰 Tools
🪛 yamllint

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

(syntax)

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 73b7059 and 5238e2b.

📒 Files selected for processing (1)
  • recipes/tbtamr/meta.yaml (2 hunks)
🔇 Additional comments (2)
recipes/tbtamr/meta.yaml (2)

15-15: Build number reset is appropriate.

Resetting the build number to 0 for a new version is a standard practice. This change is correct and aligns with the version update.


2-3: Version and SHA256 updates look good.

The version update from 0.0.4 to 1.0.1 is significant and aligns with the PR objectives. The SHA256 checksum has been updated accordingly.

To ensure the integrity of the package, please verify the SHA256 checksum using the following script:

@BiocondaBot BiocondaBot changed the title Update tbtamr to 1.0.1 Update tbtamr to 1.0.2 Oct 3, 2024
@mencian mencian merged commit b2c62fd into master Oct 3, 2024
7 checks passed
@mencian mencian deleted the bump/tbtamr branch October 3, 2024 16:31
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