Add PySCENIC #50445
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| {% set name = "pyscenic" %} | ||
| {% set version = "0.12.1" %} | ||
| {% set sha256 = "ae8fafa707d2578ffe08f9eed85f14a4cd9e1b53d57217420e2e956f0a8ddba2" %} | ||
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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: "{{ sha256 }}" | ||
| - path: dill_patch.patch | ||
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| build: | ||
| number: 0 | ||
| noarch: python | ||
| run_exports: | ||
| - "{{ pin_subpackage(name, max_pin='x.x') }}" | ||
| script: "{{ PYTHON }} -m pip install . -vv" | ||
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| requirements: | ||
| build: | ||
| - python >=3.10,<3.11 | ||
| - pip | ||
| - setuptools | ||
| - wheel | ||
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| host: | ||
| - python >=3.10,<3.11 | ||
| - pip | ||
| - setuptools | ||
| - wheel | ||
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| run: | ||
| - python >=3.10,<3.11 | ||
| - aiohttp | ||
| - arboreto | ||
| - attrs | ||
| - boltons | ||
| - cloudpickle | ||
| - cytoolz | ||
| - dill | ||
| - dask >=2023.4.1 | ||
| - distributed >=2023.4.1,<2023.5.0 | ||
| - frozendict | ||
| - fsspec | ||
| - llvmlite | ||
| - loompy | ||
| - networkx | ||
| - numba >=0.51.2 | ||
| - numexpr | ||
| - pandas >=1.3.5 | ||
| - pyyaml | ||
| - requests | ||
| - scikit-learn | ||
| - scipy | ||
| - tqdm | ||
| - umap-learn | ||
| - numpy ==1.23.5 | ||
| - pyarrow | ||
| - interlap | ||
| - ctxcore | ||
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There was a problem hiding this comment. Review and update dependency specifications. The requirements section is well-structured, but there are some points to consider:
Consider the following changes: - python >=3.10,<3.11
+ python >=3.10
- numpy ==1.23.5
+ numpy >=1.23.5
- distributed >=2023.4.1,<2023.5.0
+ distributed >=2023.4.1Regarding
Would you like assistance in implementing these changes or investigating alternatives for
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| test: | ||
| imports: | ||
| - pyscenic | ||
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| about: | ||
| home: https://github.com/aertslab/pySCENIC | ||
| summary: 'pySCENIC is a python implementation of the SCENIC pipeline' | ||
| license: MIT | ||
| license_family: MIT | ||
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Review and update dependency specifications.
The
multiprocessing_on_dillpackage is missing from the dependencies. As discussed in the past comments, this package has licensing issues. Consider one of the following options:a. Work with the upstream authors to resolve the licensing issue and add it to conda-forge.
b. Include it as a pip-installed dependency in the build script, although this is not preferred by the Bioconda team.
c. Find an alternative solution that doesn't require this package.
The numpy version is pinned to a specific version (1.23.5), which might be too restrictive. Consider allowing a range of compatible versions instead.
Some other dependencies might benefit from more flexible version constraints. Review each dependency and consider if strict version pinning is necessary.
Suggested changes:
Please choose the most appropriate solution for handling the
multiprocessing_on_dilldependency based on the options provided above.There was a problem hiding this comment.
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@coderabbitai Item 1, the multiprocessing_on_dill import is replaced by multiprocessing in the patch,
dill_patch.patch. multiprocessing_on_dill should not need to be in the dependencies.There was a problem hiding this comment.
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@aliciaaevans Thank you for the clarification. You're right, since
multiprocessing_on_dillhas been replaced withmultiprocessingin the patchdill_patch.patch, there's no need to includemultiprocessing_on_dillin the dependencies. I'll note this for future reviews.(_/)
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