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Add PySCENIC #50445
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clean up recipe, pin python to >=3.6
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@@ -0,0 +1,11 @@ | ||
--- pyscenic-0.12.1/src/pyscenic/prune.py 2022-11-21 10:38:05.000000000 +0000 | ||
+++ pyscenic-0.12.1/src/pyscenic/prune.py 2024-10-02 10:20:58.423708208 +0000 | ||
@@ -20,8 +20,8 @@ | ||
from dask import delayed | ||
from dask.dataframe import from_delayed | ||
from dask.distributed import Client, LocalCluster | ||
-from multiprocessing_on_dill.connection import Pipe | ||
-from multiprocessing_on_dill.context import Process | ||
+from multiprocessing import Pipe | ||
+from multiprocessing import Process | ||
|
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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 }}" | ||
patches: | ||
- dill_patch.patch | ||
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||
build: | ||
number: 0 | ||
noarch: python | ||
entry_points: | ||
- pyscenic = pyscenic.cli.pyscenic:main | ||
- db2feather = pyscenic.cli.db2feather:main | ||
- csv2loom = pyscenic.cli.csv2loom:main | ||
- invertdb = pyscenic.cli.invertdb:main | ||
- gmt2regions = pyscenic.cli.gmt2regions:main | ||
run_exports: | ||
- "{{ pin_subpackage(name, max_pin='x.x') }}" | ||
script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" | ||
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requirements: | ||
host: | ||
- python >=3.6 | ||
- pip | ||
- setuptools | ||
run: | ||
- python >=3.6 | ||
- aiohttp | ||
- arboreto | ||
- attrs | ||
- boltons | ||
- cloudpickle | ||
- cytoolz | ||
- dill | ||
- dask-core >=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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test: | ||
imports: | ||
- pyscenic | ||
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about: | ||
home: "https://github.com/aertslab/pySCENIC" | ||
summary: "Python implementation of the SCENIC pipeline for transcription factor inference from single-cell transcriptomics experiments." | ||
license: "GPL-3.0-or-later" | ||
license_family: GPL3 | ||
license_file: "LICENSE.txt" | ||
dev_url: "https://github.com/aertslab/pySCENIC" | ||
doc_url: "https://scenic.aertslab.org" | ||
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extra: | ||
identifiers: | ||
- doi:10.1038/nmeth.4463 | ||
- doi:10.1038/s41592-023-01938-4 | ||
- biotools:scenic |
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🛠️ Refactor suggestion
Enhance test coverage.
While the import check is a good start, consider adding more comprehensive tests for a package of this complexity.
Suggested additions:
These additional tests would ensure that the CLI entry points are working correctly.