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Update commec to 0.2 #52052

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Update commec to 0.2 #52052

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Update commec: 0.1.20.2

install with bioconda Conda

Info Link or Description
Recipe recipes/commec (click to view/edit other files)
Summary commec: a free, open-source, globally available tool for DNA sequence screening
Home https://github.com/ibbis-screening/common-mechanism
Releases https://github.com/ibbis-screening/common-mechanism/tags
Author @ibbis-screening

This pull request was automatically generated (see docs).

@BiocondaBot BiocondaBot added autobump Automatic Version Update new version labels Nov 12, 2024
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coderabbitai bot commented Nov 12, 2024

📝 Walkthrough
📝 Walkthrough

Walkthrough

This pull request modifies the meta.yaml file for the commec package. The primary changes include updating the package version from "0.1.2" to "0.2" and changing the SHA256 checksum from "33e99060dca151cb9d5481f47e02f1b5276b2cdf61804e7093f0cfc32bef1188" to "2076142f3ee4328ac23398288049d41ecbcdd7329d7ced9d1bb29fef86ee6503". Additionally, the setuptools dependency is added to the host requirements. These updates are focused solely on the metadata of the package, specifically its versioning, integrity verification aspects, and dependency management. There are no additional changes to the structure or commands within the meta.yaml file.

Possibly related PRs

  • Update gottcha2 to 2.1.8.7 #51946: This PR updates the gottcha2 package's meta.yaml file, including the addition of the setuptools dependency, which is also added in the main PR for the commec package.
  • Update cpstools to 2.0.2 #51187: This PR updates the cpstools package's version and SHA256 checksum in its meta.yaml, similar to the changes made in the main PR for the commec package.
  • Update vclean to 0.2.1 #51223: This PR updates the vclean package's version and SHA256 checksum in its meta.yaml, paralleling the updates in the main PR for the commec package.
  • Update bactopia-py to 1.2.1 #51226: This PR updates the bactopia-py package's version and SHA256 checksum in its meta.yaml, reflecting similar changes made in the main PR for the commec package.
  • update cosigt to v0.1.2 #51391: This PR updates the cosigt package's version and SHA256 checksum in its meta.yaml, akin to the changes in the main PR for the commec package.
  • Update iseq to 1.2.0 #51583: This PR updates the iseq package's version and SHA256 checksum in its meta.yaml, similar to the updates in the main PR for the commec package.
  • Update gencove to 2.23.1 #51819: This PR updates the gencove package's version and SHA256 checksum in its meta.yaml, reflecting the same type of changes made in the main PR for the commec package.
  • Update pycomo to 0.2.4 #52007: This PR updates the pycomo package's version and SHA256 checksum in its meta.yaml, similar to the changes in the main PR for the commec package.
  • Update oakvar to 2.12.2 #52031: This PR updates the oakvar package's version and SHA256 checksum in its meta.yaml, paralleling the updates in the main PR for the commec package.
  • Update reseek to 2.02 #52032: This PR updates the reseek package's version and SHA256 checksum in its meta.yaml, reflecting similar changes made in the main PR for the commec package.

Suggested reviewers

  • martin-g: Suggested reviewer for the changes made in the commec package's meta.yaml.

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 93c2176 and 18115a6.

📒 Files selected for processing (1)
  • recipes/commec/meta.yaml (2 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
  • recipes/commec/meta.yaml

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Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (2)
recipes/commec/meta.yaml (2)

Line range hint 15-20: Consider stricter version pinning for early-stage software

The comment in the file suggests using stricter version pinning. Given that commec is in early stages (pre-1.0), consider using x.x.x instead of x.x for max_pin to prevent potential breaking changes.

   run_exports:
-    - {{ pin_subpackage('commec', max_pin="x.x") }}
+    - {{ pin_subpackage('commec', max_pin="x.x.x") }}
🧰 Tools
🪛 yamllint

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

(syntax)


Update Python version requirement and review parallel package version

The verification confirms critical compatibility issues:

  • Both pandas 2.2.0 and numpy 2.0.0 require Python >=3.9, while the recipe only requires Python >=3.1
  • The specified parallel version (>=20240722) appears to be a future version, as the latest available version in conda-forge is 20220922

Required changes:

  • Update Python requirement to >=3.9 to ensure compatibility with dependencies
  • Review and adjust the parallel package version requirement to an existing version (<=20220922)
🔗 Analysis chain

Line range hint 24-41: Review Python version requirement and dependency compatibility

A few concerns about the dependencies:

  1. The Python requirement of >=3.1 seems outdated, as many of the dependencies (like pandas >=2.2) require Python 3.9+
  2. The parallel package requires a very specific recent version (>=20240722)

Consider:

  • Updating the Python requirement to match the minimum version required by the dependencies
  • Verifying if such a recent version of parallel is necessary

The verification results confirm that both pandas 2.2.0 and numpy 2.0.0 require Python >=3.9, which is incompatible with the current Python >=3.1 requirement. Let me verify the parallel package version using a different approach.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check minimum Python version requirements for key dependencies

# Check pandas Python requirement
curl -s https://pypi.org/pypi/pandas/2.2.0/json | jq -r '.info.requires_python'

# Check numpy Python requirement
curl -s https://pypi.org/pypi/numpy/2.0.0/json | jq -r '.info.requires_python'

# Check if parallel version exists in conda-forge
conda search -c conda-forge parallel=20240722

Length of output: 695


Script:

#!/bin/bash
# Check if the parallel package version exists in the conda-forge channel
curl -s "https://conda.anaconda.org/conda-forge/linux-64/repodata.json" | jq -r '.packages | to_entries[] | select(.value.name == "parallel") | .value.version'

Length of output: 465

🧰 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

Reviewing files that changed from the base of the PR and between 3f52935 and 93c2176.

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

2-3: Verify version and checksum authenticity

Let's verify that the version exists in the upstream repository and the SHA256 checksum matches the source tarball.

@BiocondaBot BiocondaBot deleted the bump/commec branch November 19, 2024 22:14
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