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Update cpstools to 2.0.0 #51031

Merged
merged 2 commits into from
Sep 30, 2024
Merged

Update cpstools to 2.0.0 #51031

merged 2 commits into from
Sep 30, 2024

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@BiocondaBot BiocondaBot commented Sep 29, 2024

Update cpstools: 1.0.132.0.0

install with bioconda Conda

Info Link or Description
Recipe recipes/cpstools (click to view/edit other files)
Summary CPStools is a package for analyzing chloroplast genome sequences.
Home https://github.com/Xwb7533/CPStools
Releases https://pypi.org/pypi/cpstools/json
Recipe Maintainer(s) @mencian

This pull request was automatically generated (see docs).

Summary by CodeRabbit

  • New Features

    • Updated cpstools package to version 2.0.0, introducing new functionalities.
    • Added tqdm package as a runtime requirement for enhanced progress tracking.
  • Improvements

    • Lowered Python version requirement to support users with Python 3.9.

@BiocondaBot BiocondaBot added autobump Automatic Version Update new version labels Sep 29, 2024
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coderabbitai bot commented Sep 29, 2024

📝 Walkthrough
📝 Walkthrough

Walkthrough

The pull request updates the meta.yaml file for the cpstools package, increasing the version from "1.0.13" to "2.0.0" and changing the SHA256 checksum from "767f5739416f290726ed459bf82969b453ffd2c04aa9171e5dc7c842a8d6b81e" to "1c2c729d4979402d9f7835dea70e47c77d2e2ef6b1e822cfd1e6e008f3b98ba1". The Python version requirement has been lowered from ">=3.10" to ">=3.9", and the tqdm package has been added as a runtime requirement.

Changes

File Change Summary
recipes/cpstools/meta.yaml Version updated from "1.0.13" to "2.0.0"; SHA256 checksum updated from "767f5739416f290726ed459bf82969b453ffd2c04aa9171e5dc7c842a8d6b81e" to "1c2c729d4979402d9f7835dea70e47c77d2e2ef6b1e822cfd1e6e008f3b98ba1"; Python version requirement changed from ">=3.10" to ">=3.9"; added runtime requirement tqdm >=4.66.5.

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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 0add3f5 and 5c7e2f6.

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

2-2: Version update to 2.0.0 confirmed.

The version has been correctly updated to 2.0.0, which aligns with the PR objectives. This is a major version bump, which typically indicates significant changes or breaking updates.

Please verify if this major version update introduces any breaking changes that might require adjustments to the recipe or dependencies. You can check the changelog or release notes for version 2.0.0 using the following script:


Line range hint 28-31: Verify dependency compatibility with the new version.

While the dependencies remain unchanged, it's important to ensure they are still compatible with version 2.0.0 of cpstools, especially given this is a major version update.

Please check if the current dependency versions are still appropriate:

🧰 Tools
🪛 yamllint

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

(syntax)

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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 5c7e2f6 and 2bc73f6.

📒 Files selected for processing (1)
  • recipes/cpstools/meta.yaml (2 hunks)
🔇 Additional comments (4)
recipes/cpstools/meta.yaml (4)

2-2: Version update looks good.

The version has been correctly updated to 2.0.0 as per the PR objectives.


28-28: Ensure consistency with host Python version requirement.

The run Python version requirement has been updated to match the host requirement. This change is consistent with the update in the host section.


31-31: Verify the necessity of tqdm dependency.

A new runtime dependency on tqdm (>=4.66.5) has been added. Please confirm:

  1. Is tqdm necessary for the functionality of cpstools 2.0.0?
  2. Is the specific version requirement (>=4.66.5) justified by the package's needs?

Consider checking the package's changelog or release notes for information about this new dependency.

#!/bin/bash
# Description: Check for tqdm usage in the package

# Search for tqdm imports and usage
rg -i 'import.*tqdm|from.*tqdm|tqdm\(' --type py

24-24: Verify compatibility with Python 3.9.

The host Python version requirement has been lowered from ">=3.10" to ">=3.9". While this broadens compatibility, please ensure that the package doesn't rely on any features specific to Python 3.10+. Consider checking the package's documentation or release notes for any mentions of Python version requirements.

✅ Verification successful

Compatibility with Python 3.9 Verified.

No Python 3.10+ specific features were detected in the codebase. Lowering the Python version requirement to ">=3.9" is safe.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for Python 3.10+ specific features in the package

# Search for potential Python 3.10+ specific features
rg -i '(match.*case|TypeAlias|ParamSpec|Concatenate|UnionType|is.*type)' --type py

Length of output: 619


Script:

#!/bin/bash
# Description: Check for Python 3.10+ specific features in the package

# Search for potential Python 3.10+ specific features
rg -i '(match\s+case|TypeAlias|ParamSpec|Concatenate|Union\[|isinstance\(|pattern_matching)' --type py

Length of output: 193

{% set version = "1.0.13" %}
{% set sha256 = "767f5739416f290726ed459bf82969b453ffd2c04aa9171e5dc7c842a8d6b81e" %}
{% set version = "2.0.0" %}
{% set sha256 = "1c2c729d4979402d9f7835dea70e47c77d2e2ef6b1e822cfd1e6e008f3b98ba1" %}
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💡 Codebase verification

SHA256 checksum mismatch detected.

  • The meta.yaml file contains an invalid SHA256 value ('{{'), indicating a templating error.
  • The SHA256 checksum from PyPI for version 2.0.0 is correctly available.

Please update the meta.yaml with the correct SHA256 checksum from PyPI to ensure integrity.

🔗 Analysis chain

Verify the SHA256 checksum.

The SHA256 checksum has been updated. To ensure the integrity and correctness of the package, please verify that this new SHA256 checksum matches the one provided by PyPI for version 2.0.0 of cpstools.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the SHA256 checksum for cpstools 2.0.0

# Fetch the SHA256 from PyPI
PYPI_SHA256=$(curl -s https://pypi.org/pypi/cpstools/2.0.0/json | jq -r '.releases["2.0.0"][0].digests.sha256')

# Extract the SHA256 from the meta.yaml file
RECIPE_SHA256=$(grep 'sha256:' recipes/cpstools/meta.yaml | awk '{print $2}' | tr -d '"')

echo "PyPI SHA256: $PYPI_SHA256"
echo "Recipe SHA256: $RECIPE_SHA256"

if [ "$PYPI_SHA256" = "$RECIPE_SHA256" ]; then
    echo "SHA256 checksums match."
else
    echo "SHA256 checksums do not match!"
fi

Length of output: 399


Script:

#!/bin/bash
# Description: List all available versions of cpstools on PyPI

curl -s https://pypi.org/pypi/cpstools/json | jq -r '.releases | keys[]'

Length of output: 107

@mencian mencian merged commit 6bedbb5 into master Sep 30, 2024
7 checks passed
@mencian mencian deleted the bump/cpstools branch September 30, 2024 16:10
This was referenced Oct 6, 2024
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