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Update baltic to 0.3.0 #51010

Merged
merged 3 commits into from
Sep 27, 2024
Merged

Update baltic to 0.3.0 #51010

merged 3 commits into from
Sep 27, 2024

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@BiocondaBot BiocondaBot commented Sep 27, 2024

Update baltic: 0.2.20.3.0

install with bioconda Conda

Info Link or Description
Recipe recipes/baltic (click to view/edit other files)
Summary Lightweight package for analyzing, manipulating and visualizing annotated phylogenetic trees.
Home https://github.com/evogytis/baltic
Releases https://pypi.org/pypi/baltic/json

This pull request was automatically generated (see docs).

Summary by CodeRabbit

  • New Features

    • Updated the baltic package to version 0.3.0.
    • Added a new development URL for the package.
  • Bug Fixes

    • Improved build script configurations for better compatibility.
  • Documentation

    • Updated package summary for clarity.
    • Changed license to "GPL-3.0-or-later".
  • Compatibility

    • Increased Python version requirement to python >=3.5.

@BiocondaBot BiocondaBot added autobump Automatic Version Update new version labels Sep 27, 2024
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coderabbitai bot commented Sep 27, 2024

📝 Walkthrough
📝 Walkthrough

Walkthrough

The pull request updates the meta.yaml file for the baltic package, incrementing its version from "0.2.2" to "0.3.0". The SHA-256 checksum for the source tarball has also been updated. Additional modifications include changes to the Python version requirement, license type, build script flags, and the addition of a development URL. These updates reflect a new release of the package with enhanced specifications and source integrity verification.

Changes

File Change Summary
recipes/baltic/meta.yaml - Version updated from "0.2.2" to "0.3.0"
- SHA-256 checksum updated from 095045aeb0... to d7fd92d0a4...
- Python requirement updated to python >=3.5
- License changed to "GPL-3.0-or-later"
- Summary updated to include a period
- Development URL added: "https://github.com/evogytis/baltic"

Possibly related PRs

  • Update architeuthis to 0.3.1 #50970: The architeuthis package update involves a version increment and SHA256 checksum change, similar to the changes made in the baltic package.
  • Update phyloacc to 2.4.0 #50992: The phyloacc package update includes a version increment and SHA256 checksum change in its meta.yaml, paralleling the updates in the baltic package.
  • Update straglr to 1.5.2 #51000: The straglr package update features a version increment and SHA256 checksum change, akin to the modifications in the baltic package.
  • Update giatools to 0.3 #51004: The giatools package update includes a version increment and SHA256 checksum change, reflecting the changes made in the baltic package.
  • Update giatools to 0.3.1 #51007: The giatools package update also involves a version increment and SHA256 checksum change, similar to the changes in the baltic package.

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between c80f11e and 88d5a5d.

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

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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 8a41f2a and c80f11e.

📒 Files selected for processing (1)
  • recipes/baltic/meta.yaml (1 hunks)
🔇 Additional comments (6)
recipes/baltic/meta.yaml (6)

2-2: Version update looks good.

The version has been correctly updated to 0.3.0, which aligns with the PR objectives.


14-14: Build script improvements look good.

The build script has been updated to use {{ PYTHON }}, which is a best practice in conda recipes. The additional flags --no-deps --no-build-isolation --no-cache-dir can help improve build reproducibility and avoid potential conflicts.


20-20: Python version requirement update is appropriate.

The Python version requirement has been updated to >=3.5 in both host and run requirements. This change ensures compatibility with newer Python versions while setting a reasonable minimum version.

Also applies to: 24-24


35-35: Summary formatting improvement.

The summary has been updated to include a period at the end, which improves its formatting.


36-36: Development URL addition is helpful.

The addition of the dev_url is beneficial for users who want to find the development repository. It correctly points to the GitHub repository, which is also listed as the home URL.


10-10: SHA256 checksum updated.

The SHA256 checksum has been updated, which is necessary for the new version. However, it's important to verify that this checksum matches the actual source package.

To verify the checksum, you can run the following command:

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

# Extract version and checksum
version=$(grep 'version = ' recipes/baltic/meta.yaml | cut -d '"' -f 2)
checksum=$(grep 'sha256:' recipes/baltic/meta.yaml | awk '{print $2}')

# Download the package and verify checksum
curl -sL "https://pypi.io/packages/source/b/baltic/baltic-${version}.tar.gz" | shasum -a 256 | grep -q "$checksum" && echo "Checksum verified" || echo "Checksum mismatch"


test:
imports:
- baltic

about:
home: "https://github.com/evogytis/baltic"
license: GPL-3.0
license: GPL-3.0-or-later
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💡 Codebase verification

License mismatch detected.

The recipes/baltic/meta.yaml specifies the license as "GPL-3.0-or-later," but the LICENSE file in the source package explicitly states "GNU GENERAL PUBLIC LICENSE Version 3." These should be consistent to ensure clear licensing terms.

  • Action Required: Update the LICENSE file to include "or later" if the intention is to allow future GPL versions, or revert the meta.yaml license declaration to "GPL-3.0" to match the LICENSE file.
🔗 Analysis chain

License update looks good, but needs verification.

The license has been updated from "GPL-3.0" to "GPL-3.0-or-later", which provides more flexibility. However, it's crucial to verify that this matches the actual license of the package.

To verify the license, you can run the following command:


To proceed with verifying the license update accurately, please run the following corrected script:


To accurately verify the license update, please run the following script to retrieve and review the LICENSE file content:

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the license in the source package

# Extract version
version=$(grep 'version = ' recipes/baltic/meta.yaml | cut -d '"' -f 2)

# Download the package, extract it, and check the license
curl -sL "https://pypi.io/packages/source/b/baltic/baltic-${version}.tar.gz" | tar xz -O "baltic-${version}/LICENSE" | grep -q "GNU GENERAL PUBLIC LICENSE" && echo "License verified" || echo "License mismatch"

Length of output: 361


Script:

#!/bin/bash
# Description: Verify the license in the source package

# Extract version
version=$(grep 'version =' recipes/baltic/meta.yaml | cut -d '"' -f 2)

# Download the package, extract it, and check the license
curl -sL "https://pypi.io/packages/source/b/baltic/baltic-${version}.tar.gz" | tar xz -O "baltic-${version}/LICENSE" | grep -q "GPL-3.0-or-later" && echo "License verified" || echo "License mismatch"

Length of output: 254


Script:

#!/bin/bash
# Description: Retrieve the LICENSE file from the source package

# Extract version
version=$(grep 'version =' recipes/baltic/meta.yaml | cut -d '"' -f 2)

# Download the package, extract it, and display the LICENSE content
curl -sL "https://pypi.io/packages/source/b/baltic/baltic-${version}.tar.gz" | tar xz -O "baltic-${version}/LICENSE"

Length of output: 35333

@mencian mencian merged commit 762d2e3 into master Sep 27, 2024
7 checks passed
@mencian mencian deleted the bump/baltic branch September 27, 2024 16:34
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