From 1701e929bc2d7c585aa52cfae7450f3f90e3eb75 Mon Sep 17 00:00:00 2001 From: Alex Leute <36964815+alex391@users.noreply.github.com> Date: Thu, 6 Jun 2024 17:34:11 -0400 Subject: [PATCH] py-pyseer and deps: new package (#44543) * 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 Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> --- .../packages/py-glmnet-python/package.py | 29 +++++++++++++++++ .../builtin/packages/py-pyseer/package.py | 31 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-glmnet-python/package.py create mode 100644 var/spack/repos/builtin/packages/py-pyseer/package.py diff --git a/var/spack/repos/builtin/packages/py-glmnet-python/package.py b/var/spack/repos/builtin/packages/py-glmnet-python/package.py new file mode 100644 index 00000000000..8b6e5cbfe59 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-glmnet-python/package.py @@ -0,0 +1,29 @@ +# 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")) diff --git a/var/spack/repos/builtin/packages/py-pyseer/package.py b/var/spack/repos/builtin/packages/py-pyseer/package.py new file mode 100644 index 00000000000..53c7c7fc0c7 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pyseer/package.py @@ -0,0 +1,31 @@ +# 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"))