[biobb_mem] update 5.0.0 #51940
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| {% set name = "biobb_mem" %} | ||
| {% set version = "5.0.0" %} | ||
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| package: | ||
| name: '{{ name|lower }}' | ||
| version: '{{ version }}' | ||
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| source: | ||
| url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz | ||
| sha256: 9637a957e8bf41cc8474133d66fa991bf16ac674064f7283a1153df79349e819 | ||
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| build: | ||
| number: 0 | ||
| noarch: python | ||
| script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" | ||
| run_exports: | ||
| - {{ pin_subpackage(name, max_pin='x') }} | ||
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| requirements: | ||
| host: | ||
| - python >=3.9 | ||
| - setuptools | ||
| - biobb_common ==5.0.0 | ||
| - lipyphilic ==0.10.0 | ||
| - ambertools >=22.5 | ||
| - gromacs ==2018.6 | ||
| - chap | ||
| run: | ||
| - python >=3.9 | ||
| - biobb_common ==5.0.0 | ||
| - lipyphilic ==0.10.0 | ||
| - ambertools >=22.5 | ||
| - gromacs ==2018.6 | ||
| - chap | ||
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There was a problem hiding this comment. 💡 Codebase verification Update gromacs dependency to match other biobb packages The current gromacs 2018.6 version in biobb_mem is significantly outdated compared to other biobb packages in the repository:
Since biobb_mem depends on biobb_common 5.0.0 (latest), it should align with the gromacs versions used by other up-to-date biobb packages. Consider updating to gromacs >=2022.2 to maintain consistency across the biobb ecosystem. 🔗 Analysis chainConsider updating gromacs dependency. The recipe pins gromacs to version 2018.6, which is quite old (about 6 years old). Consider updating to a more recent version to benefit from bug fixes, performance improvements, and new features. Since we cannot directly check conda package versions in the sandbox environment, let me try to verify the gromacs versions through other means. 🏁 Scripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# Check available gromacs versions in conda-forge
conda search -c conda-forge gromacs --info
Length of output: 117 Script: #!/bin/bash
# Search for other gromacs version references in the repository
rg "gromacs.*[0-9]" --type yaml -A 2 -B 2
# Also check if there are any migration or update related files
fd -e yaml -e yml -e md -e txt | xargs rg -l "gromacs"
Length of output: 3251 |
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| test: | ||
| imports: | ||
| - biobb_mem | ||
| - biobb_mem.chap | ||
| - biobb_mem.lipyphilicBB | ||
| - biobb_mem.ambertools | ||
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| about: | ||
| home: https://github.com/bioexcel/biobb_mem | ||
| license: Apache Software License | ||
| license_family: APACHE | ||
| license_file: '' | ||
| summary: Biobb_mem is the Biobb module for membrane structure analysis. | ||
| description: "# biobb_mem\n\n### Introduction\nBiobb_mem is the Biobb module for membrane structure analysis.\nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate\ | ||
| \ new layer of compatibility and interoperability over popular\nbioinformatics tools.\nThe latest documentation of this package can be found in our readthedocs site:\n[latest API documentation](http://biobb_analysis.readthedocs.io/en/latest/).\n\ | ||
| \n\n### Copyright & Licensing\nThis software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\ | ||
| \n\n* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\ | ||
| Licensed under the\n\ | ||
| [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.\n\ | ||
| \n\ | ||
| ![](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png \"Bioexcel\")\n\n\n" | ||
| doc_url: '' | ||
| dev_url: '' | ||
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There was a problem hiding this comment. 🛠️ Refactor suggestion Add documentation and development URLs. The description mentions readthedocs documentation, but - doc_url: ''
- dev_url: ''
+ doc_url: 'http://biobb_analysis.readthedocs.io/en/latest/'
+ dev_url: 'https://github.com/bioexcel/biobb_mem'
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| extra: | ||
| recipe-maintainers: '' | ||
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There was a problem hiding this comment. Add recipe maintainers. The - recipe-maintainers: ''
+ recipe-maintainers:
+ - RubenChM
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Add the license file path.
The
license_filefield is empty but the package is Apache licensed. This should point to the LICENSE file in the source distribution.Also applies to: 44-44