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 <jen@herting.cc>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>

2 files changed, 60 insertions, 0 deletions

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 0000000000..8b6e5cbfe5
--- /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 0000000000..53c7c7fc0c
--- /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"))