Update GoldRush to 1.2.0 #51131
Update GoldRush to 1.2.0 #51131
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🧹 Outside diff range and nitpick comments (1)
recipes/goldrush/meta.yaml (1)
43-43: Fix indentation for snakemake dependencyThe addition of
snakemakeas a runtime dependency is appropriate. However, the indentation is incorrect. Please align it with the other dependencies in therunsection.Apply this diff to fix the indentation:
- snakemake + - snakemake
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- recipes/goldrush/meta.yaml (3 hunks)
🔇 Additional comments (3)
recipes/goldrush/meta.yaml (3)
2-2: LGTM: Version update to 1.2.0The version update from 1.1.2 to 1.2.0 is consistent with the PR objectives and title.
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1-58: Document API and CLI changes, if anyThe update adheres to Bioconda guidelines, and the
run_exportssection helps prevent ABI breakage. However, there's no explicit mention of API or CLI changes in the recipe.If there are any API or CLI changes in GoldRush 1.2.0, please consider:
- Documenting them in the recipe (e.g., in the
aboutsection).- Updating the test commands if necessary to cover new or changed functionality.
To check for potential CLI changes, let's compare the help output between versions:
33-33: Verify runtime dependency for intervaltreeThe addition of
intervaltreeto thehostsection is appropriate for build-time dependencies. However, please verify if this package is also required at runtime. If so, consider adding it to therunsection as well.To check if
intervaltreeis imported in the package code:✅ Verification successful
intervaltree Added as a Build-Time Dependency
The
intervaltreepackage is not used in the runtime codebase based on the current imports. Adding it to thehostsection is appropriate, and there's no need to include it in therunsection.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check if intervaltree is imported in the package code # Test: Search for import statements of intervaltree rg --type python 'import\s+intervaltree|from\s+intervaltree\s+import'Length of output: 102
Script:
#!/bin/bash # Description: Check if intervaltree is imported in Python files by specifying the .py extension # Test: Search for import statements of intervaltree in .py files rg -g '*.py' 'import\s+intervaltree|from\s+intervaltree\s+import'Length of output: 67
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Package(s) built are ready for inspection:
Docker image(s) built:
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Updated GoldRush meta.yaml with new dependencies from 1.2.0
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
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...being one of:{{ pin_subpackage("myrecipe", max_pin="x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin="x.x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin=None) }}while replacing
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intervaltreeandsnakemake..tar.xzto.tar.gz.