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py-pyseer and deps: new package (#44543)

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* py-pyseer: Added package py-pyseer and dependency py-glmnet-python
* py-glmnet-python: Updated homepage, and added comments
* Update copyrights

---------

Co-authored-by: Jen Herting <jen@herting.cc>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
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Alex Leute 2024-06-06 17:34:11 -04:00 committed by GitHub
parent 1bb3e04263
commit 1701e929bc
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# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class PyGlmnetPython(PythonPackage):
"""This is a python version of the popular glmnet library (beta release).
Glmnet fits the entire lasso or elastic-net regularization path for linear
regression, logistic and multinomial regression models, poisson regression
and the cox model."""
# Not to be confused with py-glmnet
homepage = "https://github.com/johnlees/glmnet_python/"
# Not availible on PyPI. Note that this is a fork of
# https://github.com/bbalasub1/glmnet_python, as required for py-pyseer
url = "https://github.com/johnlees/glmnet_python/archive/v1.0.2.zip"
version("1.0.2", sha256="cc80020dcebc5366dcc061aec59318efac69d23578066326d925bfc27a23cb27")
depends_on("py-setuptools", type="build")
depends_on("py-joblib@0.10.3:", type=("build", "run"))
# Not in setup.py, but imported and used:
depends_on("py-numpy", type=("build", "run"))
depends_on("py-scipy", type=("build", "run"))

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# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class PyPyseer(PythonPackage):
"""Sequence Elements Enrichment Analysis (SEER), python implementation"""
homepage = "https://pyseer.readthedocs.io/en/master/"
# Not availible on PyPI
url = "https://github.com/mgalardini/pyseer/releases/download/1.3.11/pyseer-1.3.11.tar.gz"
version("1.3.11", sha256="384313a3a14b92f873eaad53f77a319d90b584b9253785a7ca1dfc7d9220c91e")
depends_on("py-setuptools", type="build")
depends_on("py-numpy", type=("build", "run"))
depends_on("py-scipy", type=("build", "run"))
depends_on("py-pandas", type=("build", "run"))
depends_on("py-statsmodels@0.10.0:", type=("build", "run"))
depends_on("py-scikit-learn", type=("build", "run"))
depends_on("py-pysam", type=("build", "run"))
depends_on("py-dendropy", type=("build", "run"))
depends_on("py-matplotlib", type=("build", "run"))
depends_on("py-pybedtools", type=("build", "run"))
depends_on("py-tqdm", type=("build", "run"))
depends_on("py-glmnet-python@1.0.2", type=("build", "run"))