new tool: orthodb #51959
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| #!/bin/bash | ||
| $PYTHON -m pip install . --no-deps --ignore-installed -vv |
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| @@ -0,0 +1,51 @@ | ||
| {% set name = "orthodb" %} | ||
| {% set version = "0.9.0" %} | ||
| {% set sha256 = "b1c776e5521c809245696c0c6388f3301d10966707774fc7fecaa4cd40481bd3" %} | ||
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| package: | ||
| name: {{ name }} | ||
| version: {{ version }} | ||
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| build: | ||
| number: 0 | ||
| noarch: python | ||
| run_exports: | ||
| - {{ pin_subpackage('orthodb', max_pin="x") }} | ||
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| source: | ||
| url: https://gitlab.com/ezlab/orthodb_py/-/archive/{{ version }}/orthodb_py-{{ version }}.tar.gz | ||
| sha256: {{ sha256 }} | ||
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| requirements: | ||
| build: | ||
| - python >=3.9 | ||
| - bash >=4.1 | ||
| host: | ||
| - python >=3.9 | ||
| - pip | ||
| - bash >=4.1 | ||
| run: | ||
| - python >=3.9 | ||
| - bash >=4.1 | ||
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There was a problem hiding this comment. 💡 Codebase verification Remove unnecessary Bash dependency requirements The package only uses Bash in the build script with a simple pip install command that doesn't require any Bash-specific features. The
Please remove the Bash requirements from all sections and fix the trailing whitespace on line 30. 🔗 Analysis chainVerify Bash dependency requirement. The inclusion of Bash >=4.1 as a requirement in all sections (build, host, run) is unusual for a Python package. Please verify if this is actually needed for the package functionality. Also, there's a trailing whitespace on line 30 that should be removed. Let me generate additional scripts to check for bash script usage specifically in the orthodb package. 🏁 Scripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# Check if the package actually uses bash in its code
rg -l 'subprocess.*bash|os.system.*bash' || echo "No direct bash usage found"
# Check if there are any shell scripts in the package
ast-grep --pattern 'from subprocess import|import subprocess'
Length of output: 11022 Script: #!/bin/bash
# Check for shell scripts in the orthodb package directory
fd -e sh . recipes/orthodb/
# Check for bash shebang in any files
rg '^#!.*bash' recipes/orthodb/
# Check build.sh and any other scripts for bash-specific features
cat recipes/orthodb/build.sh || echo "No build.sh found"
Length of output: 226 🧰 Tools🪛 yamllint[error] 30-30: trailing spaces (trailing-spaces) |
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| test: | ||
| commands: | ||
| - python -c 'import orthodb; api=orthodb.OdbAPI();' | ||
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| about: | ||
| home: https://www.ezlab.org/orthodb_v12_userguide.html | ||
| license: GPL3 | ||
| license_family: GPL3 | ||
| license_file: LICENSE | ||
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There was a problem hiding this comment. Add license file to the files section The Add this section after the source section: files:
- LICENSE |
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| summary: Interface to OrthoDB REST API. | ||
| description: Python interface to OrthoDB REST API with some additional functionality. | ||
| dev_url: https://gitlab.com/ezlab/orthodb_py | ||
| doc_url: https://www.ezlab.org/orthodb_v12_userguide.html#api | ||
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| extra: | ||
| identifiers: | ||
| - biotools:orthodb | ||
| - doi:10.1093/nar/gkac996 | ||
| - PMID:36350662 | ||
| recipe-maintainers: | ||
| - ftegenfe | ||
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🛠️ Refactor suggestion
Remove unnecessary run_exports configuration
The
run_exportssection is typically used for compiled libraries where ABI compatibility matters. For a pure Python package, this configuration is unnecessary and could potentially constrain downstream packages unnecessarily.📝 Committable suggestion