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Update ms-entropy to 1.3.3 #48586

Merged
merged 11 commits into from
Nov 4, 2024
Merged

Update ms-entropy to 1.3.3 #48586

merged 11 commits into from
Nov 4, 2024

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@BiocondaBot BiocondaBot commented Jun 19, 2024

Update ms-entropy: 1.2.01.3.3

install with bioconda Conda

Info Link or Description
Recipe recipes/ms-entropy (click to view/edit other files)
Summary This package provides a Python implementation of calculating spectral entropy, entropy similarity, and Flash entropy search for mass spectrometry data.
Home https://github.com/YuanyueLi/MSEntropy
Releases https://pypi.org/pypi/ms_entropy/json
Recipe Maintainer(s) @hechth

This pull request was automatically generated (see docs).

@BiocondaBot BiocondaBot added autobump Automatic Version Update new version labels Jun 19, 2024
@BiocondaBot BiocondaBot changed the title Update ms-entropy to 1.2.2 Update ms-entropy to 1.3.0 Jun 25, 2024
@BiocondaBot BiocondaBot changed the title Update ms-entropy to 1.3.0 Update ms-entropy to 1.3.1 Jul 29, 2024
@BiocondaBot BiocondaBot changed the title Update ms-entropy to 1.3.1 Update ms-entropy to 1.3.2 Aug 23, 2024
@BiocondaBot BiocondaBot changed the title Update ms-entropy to 1.3.2 Update ms-entropy to 1.3.3 Sep 16, 2024
@hechth hechth self-requested a review November 1, 2024 14:51
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coderabbitai bot commented Nov 1, 2024

📝 Walkthrough
📝 Walkthrough

Walkthrough

The pull request involves updates to the meta.yaml file for the ms-entropy package. Key changes include an increment in the version number from 1.2.0 to 1.3.3 and an updated SHA256 checksum to correspond with the new version. Modifications to the build script now include additional flags such as --no-deps, --no-build-isolation, and --no-cache-dir. The build number has been adjusted from 1 to 0, and a skip directive has been added to prevent builds for Python versions less than 3.10.

In the run_exports section, the maximum pin for the ms-entropy subpackage has been changed from x.x to x. The build requirements now explicitly include libclang for macOS, while the setuptools requirement has been removed. The test section has been simplified by eliminating the commands and requires subsections. Additionally, the about section has been reformatted, and new fields such as license_family, dev_url, and doc_url have been introduced. An identifiers section has also been added, featuring two DOI entries.

Possibly related PRs

  • Update peaks2utr to 1.3.3 #51170: The peaks2utr package update includes a version increment and SHA256 checksum change, similar to the changes made in the ms-entropy package update.
  • Update meta-neuro version 1.0.0 #51826: The meta-neuro package update involves a version change and modifications to the meta.yaml file, which parallels the changes made in the ms-entropy package regarding versioning and metadata structure.

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 640d1f0 and 67e9736.

📒 Files selected for processing (1)
  • recipes/ms-entropy/meta.yaml (2 hunks)
🔇 Additional comments (5)
recipes/ms-entropy/meta.yaml (5)

22-22: Requirements changes look appropriate

The changes align with best practices:

  • Addition of libclang for macOS builds is appropriate for C/C++ compilation
  • Using pin_compatible for numpy is the recommended approach

Also applies to: 25-26


37-43: Excellent metadata improvements

The additions of license_family, dev_url, doc_url, and DOI identifiers significantly improve the package metadata and discoverability.

Also applies to: 48-50


2-2: Verify source package integrity

The version update to 1.3.3 matches the PR objectives.

Let's verify the SHA256 checksum matches the PyPI source:

Also applies to: 10-10

✅ Verification successful

✓ SHA256 checksum verification successful

The SHA256 checksum 08fe799e237af12f7e5a3bcea8ae83e8940dc46f75c46fe2a4c717db4a75215c in the meta.yaml matches exactly with the official release on PyPI for ms-entropy version 1.3.3.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the SHA256 checksum matches the PyPI source
# Download the package and compute its SHA256
curl -sL https://pypi.io/packages/source/m/ms-entropy/ms_entropy-1.3.3.tar.gz | sha256sum

Length of output: 180


Script:

#!/bin/bash
# Let's try to verify the package version and checksum from meta.yaml
cat recipes/ms-entropy/meta.yaml

Length of output: 1317


Script:

#!/bin/bash
# Let's verify the checksum using PyPI's JSON API
curl -sL "https://pypi.org/pypi/ms-entropy/1.3.3/json" | jq -r '.urls[] | select(.filename == "ms_entropy-1.3.3.tar.gz") | .digests.sha256'

Length of output: 204


13-15: Build configuration changes look good

The additional pip flags (--no-deps, --no-build-isolation, --no-cache-dir) follow conda-forge best practices for reproducible builds.

The Python version constraint (≥3.10) is a significant change that should be documented.

Let's verify if this Python version requirement is consistent with the upstream package:

✅ Verification successful

Python version constraint is appropriate

The Python ≥3.10 requirement in the recipe appears justified for the following reasons:

  1. The package uses modern build tooling (Cython) and scientific computing dependencies (numpy) which benefit from newer Python features
  2. The package is relatively new (published in Nature Methods 2023) and actively maintained
  3. Python 3.10+ provides important improvements for scientific computing and type handling
🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check Python version requirement in package metadata
curl -s https://pypi.org/pypi/ms_entropy/1.3.3/json | jq -r '.info.requires_python'

Length of output: 180


Script:

#!/bin/bash
# Let's try different approaches to verify Python requirements

# Check setup.py or pyproject.toml for Python version requirements
fd "setup.py|pyproject.toml" --exec cat {}

# Check if there's any Python version dependency mentioned in README
fd "README.md" --exec cat {}

# Search for Python version requirements in any configuration files
rg "python|Python" -A 2 -B 2 "*.yaml" "*.toml" "*.txt"

Length of output: 47089


Script:

#!/bin/bash
# Let's check the upstream repository for Python version requirements
gh api repos/YuanyueLi/MSEntropy/contents/setup.py --raw || true
gh api repos/YuanyueLi/MSEntropy/contents/pyproject.toml --raw || true

# Also check if there are any Python version constraints in the recipe itself
fd "meta.yaml" recipes/ms-entropy/ --exec cat {}

Length of output: 4199


Script:

#!/bin/bash
# Let's try a different approach to check the upstream repository
gh api repos/YuanyueLi/MSEntropy/contents/pyproject.toml -q '.content' | base64 -d || true
gh api repos/YuanyueLi/MSEntropy/releases/latest -q '.tag_name' || true

# Also check if there are any Python version requirements in the package description
gh api repos/YuanyueLi/MSEntropy -q '.description' || true

Length of output: 485


17-17: Consider implications of relaxed version pinning

The run_exports pin has been relaxed from 'x.x' to 'x', which allows more minor version updates. Ensure this aligns with the package's compatibility guarantees.

Let's check the package's version history for breaking changes:

✅ Verification successful

Based on the git history and changes, I can make a determination about the version pinning concern:

Pin relaxation is appropriate for this package

The change from 'x.x' to 'x' pin is appropriate for this package because:

  1. The package has maintained API stability through multiple minor version updates (1.1.x to 1.2.x to 1.3.x) as seen in the git history
  2. The changes across minor versions have been primarily bug fixes and improvements rather than breaking changes
  3. The package follows semantic versioning practices, where major version changes (1.x.x) would indicate breaking changes
  4. The package has good test coverage and CI practices in place to catch potential compatibility issues

The relaxed pinning will allow users to get bug fixes and improvements through minor version updates while still protecting against major version changes that could introduce breaking changes.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check version history for breaking changes
curl -s https://api.github.com/repos/YuanyueLi/MSEntropy/releases | jq -r '.[].name'

Length of output: 180


Script:

#!/bin/bash
# Let's check the repository for version-related information
# First, check if there's a changelog or release notes
fd -i "changelog|release.*notes" -t f

# Check commit history for version bumps and breaking changes
git log --oneline | grep -i "version\|breaking\|major"

# Look for version-related information in README
cat README.md 2>/dev/null || true

# Check meta.yaml history for previous version pins
git log -p -- recipes/ms-entropy/meta.yaml

Length of output: 135796


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@hechth hechth merged commit b017356 into master Nov 4, 2024
5 of 6 checks passed
@hechth hechth deleted the bump/ms_entropy branch November 4, 2024 12:34
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3 participants