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Update blastbesties to 1.2.0 #52022

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Update blastbesties to 1.2.0 #52022

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Update blastbesties: 1.1.21.2.0

install with bioconda Conda

Info Link or Description
Recipe recipes/blastbesties (click to view/edit other files)
Summary Rapid discovery of reciprocal best blast pairs from BLAST output files.
Home https://github.com/Adamtaranto/blast-besties
Releases https://pypi.org/pypi/blastbesties/json

This pull request was automatically generated (see docs).

@BiocondaBot BiocondaBot added autobump Automatic Version Update new version labels Nov 9, 2024
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coderabbitai bot commented Nov 9, 2024

📝 Walkthrough
📝 Walkthrough

Walkthrough

The pull request involves an update to the meta.yaml file for the blastbesties package. The primary changes include an increment in the version number from 1.1.2 to 1.2.0. Additionally, the SHA256 checksum for the source tarball has been modified to reflect the new version, changing from 6dce21a9f92d8e47875a020c279e420ed5077d00ced3534844993a26e779e57d to 5d66264863667a505309e87e33bc186d40b98ff68c96c93c0273a68a8197757c. The Python version requirement has been raised from >=3.7 to >=3.8 in both the host and run sections. The dependency setuptools-scm has been replaced with hatchling, and hatch-vcs has been added as a new dependency. The installation script has also been modified to include the --no-cache-dir option. No other modifications to the structure or content of the meta.yaml file were made.

Possibly related PRs

  • Update meta.yaml for spec2vec #49857: This PR updates the meta.yaml file for the spec2vec package, including a version update and changes to the SHA256 checksum, similar to the version and checksum updates in the main PR for blastbesties.
  • Update: Metabuli 1.0.8 #51030: This PR updates the meta.yaml file for the metabuli package, including a version update and changes to the SHA256 checksum, paralleling the updates made in the main PR.
  • Update blaze2 to 2.5.0 #51034: This PR updates the meta.yaml file for the blaze2 package, which includes a version update and a SHA256 checksum change, similar to the changes in the main PR.
  • Update bactopia-py to 1.2.0 #51154: This PR updates the meta.yaml file for the bactopia-py package, including a version update and a SHA256 checksum change, reflecting the same type of modifications as in the main PR.
  • Update bactopia-py to 1.2.1 #51226: This PR updates the meta.yaml file for the bactopia-py package, with a version increment and SHA256 checksum update, consistent with the changes in the main PR.
  • version update #51524: This PR updates the meta.yaml file for the strainy package, including a version update and SHA256 checksum change, similar to the updates in the main PR.
  • Update pybiolib to 1.2.205 #51549: This PR updates the meta.yaml file for the pybiolib package, with a version increment and SHA256 checksum update, paralleling the changes in the main PR.
  • Update matchms dependencies #51552: This PR updates the meta.yaml file for the matchms package, including a version update and changes to the SHA256 checksum, similar to the updates in the main PR.
  • Update blaze2 to 2.5.1 #51646: This PR updates the meta.yaml file for the blaze2 package, which includes a version update and a SHA256 checksum change, consistent with the changes in the main PR.
  • Update pybiolib to 1.2.211 #51660: This PR updates the meta.yaml file for the pybiolib package, with a version increment and SHA256 checksum update, reflecting the same type of modifications as in the main PR.
  • Update pybiolib to 1.2.216 #51667: This PR updates the meta.yaml file for the pybiolib package, including a version update and SHA256 checksum change, similar to the updates in the main PR.
  • Update meta-neuro version 1.0.0 #51826: This PR updates the meta.yaml file for the meta-neuro package, including a version update and SHA256 checksum change, consistent with the changes in the main PR.
  • Update goldrush to 1.2.1 #51872: This PR updates the meta.yaml file for the goldrush package, which includes a version update and a SHA256 checksum change, similar to the updates in the main PR.
  • Update bioblend to 1.4.0 #51984: This PR updates the meta.yaml file for the bioblend package, including a version update and SHA256 checksum change, consistent with the changes in the main PR.

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 560833a and 008777a.

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

17-17: LGTM! Build script changes look good

The addition of --no-cache-dir is appropriate for container builds to reduce layer size.


2-2: Verify package integrity

The version bump and checksum update need verification against the official PyPI release.

#!/bin/bash
# Description: Verify the package version and checksum from PyPI
# Expected: Should match version 1.2.0 and SHA256 5d66264863667a505309e87e33bc186d40b98ff68c96c93c0273a68a8197757c

# Get package info from PyPI
curl -s https://pypi.org/pypi/blastbesties/1.2.0/json | jq -r '.urls[] | select(.packagetype=="sdist") | .digests.sha256'

Also applies to: 10-10


23-23: Verify Python version compatibility impact

The Python version requirement has been increased from >=3.7 to >=3.8. This is a potentially breaking change that needs verification.

#!/bin/bash
# Description: Check for Python version requirements in project files
# Expected: Should find evidence of Python 3.8 requirement in project metadata

# Check pyproject.toml or setup.py for Python requirement
fd -e toml -e py -x cat {} | rg -i "python.*3\.8"

# Check release notes for breaking changes
curl -s https://pypi.org/pypi/blastbesties/1.2.0/json | jq -r '.info.description'

Also applies to: 28-28


25-26: Verify build system migration

The change from setuptools-scm to hatchling + hatch-vcs represents a significant build system change.

#!/bin/bash
# Description: Verify build system requirements in upstream project
# Expected: Should find hatchling configuration in project files

# Check for build system configuration
fd pyproject.toml -x cat {} | rg -i "hatchling"

29-29: Verify new dependency requirement

The addition of argparse_tui as a runtime dependency needs verification against the upstream project requirements.

✅ Verification successful

Dependency requirement verified successfully

The argparse_tui dependency is correctly specified in the recipe as it is:

  • Listed as a required dependency in the upstream project's pyproject.toml
  • Available on PyPI (HTTP 200 status code)
  • Correctly spelled (matches the PyPI package name)
🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify argparse_tui dependency in upstream project
# Expected: Should find argparse_tui in project dependencies

# Check project dependencies
fd "pyproject.toml|setup.py|setup.cfg" -x cat {} | rg -i "argparse_tui"

# Check if the package is available in conda-forge
curl -s https://conda.anaconda.org/conda-forge/noarch/repodata.json | jq '.packages | keys[]' | rg -i "argparse_tui"

Length of output: 190


Script:

#!/bin/bash
# Let's check the upstream repository URL and requirements from the recipe
cat recipes/blastbesties/meta.yaml

# Also check if there are any Python files that might import or use argparse_tui
rg -l "argparse_tui" --type py

Length of output: 1038


Script:

#!/bin/bash
# Let's check the upstream repository's requirements by fetching from PyPI
curl -s https://pypi.org/pypi/blastbesties/json | jq -r '.info.requires_dist[]'

# Also check the GitHub repository's requirements files
curl -s https://raw.githubusercontent.com/Adamtaranto/blast-besties/main/pyproject.toml

# Check if the package exists on PyPI
curl -s -o /dev/null -w "%{http_code}" https://pypi.org/pypi/argparse_tui/json

Length of output: 1990


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