From aa4d55004cdd134a9ad5d4e35032b6c4644e75a6 Mon Sep 17 00:00:00 2001
From: snehring <7978778+snehring@users.noreply.github.com>
Date: Fri, 20 Oct 2023 06:53:41 -0500
Subject: Add package py-macs3 and dependencies (#40498)

* py-cykhash: adding new package py-cykhash

* py-hmmlearn: adding new package py-hmmlearn

* py-macs3: adding new package py-macs3

* py-macs3: adding python version restriction and other changes.
---
 .../repos/builtin/packages/py-cykhash/package.py   | 20 ++++++++++++++++
 .../repos/builtin/packages/py-hmmlearn/package.py  | 28 ++++++++++++++++++++++
 .../repos/builtin/packages/py-macs3/package.py     | 26 ++++++++++++++++++++
 3 files changed, 74 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-cykhash/package.py
 create mode 100644 var/spack/repos/builtin/packages/py-hmmlearn/package.py
 create mode 100644 var/spack/repos/builtin/packages/py-macs3/package.py

diff --git a/var/spack/repos/builtin/packages/py-cykhash/package.py b/var/spack/repos/builtin/packages/py-cykhash/package.py
new file mode 100644
index 0000000000..85d67fb979
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-cykhash/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2023 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 PyCykhash(PythonPackage):
+    """Cython wrapper for khash-sets/maps, efficient implementation of isin and unique."""
+
+    homepage = "https://github.com/realead/cykhash"
+    pypi = "cykhash/cykhash-2.0.1.tar.gz"
+
+    maintainers("snehring")
+
+    version("2.0.1", sha256="b4794bc9f549114d8cf1d856d9f64e08ff5f246bf043cf369fdb414e9ceb97f7")
+
+    depends_on("py-setuptools", type="build")
+    depends_on("py-cython@0.28:", type="build")
diff --git a/var/spack/repos/builtin/packages/py-hmmlearn/package.py b/var/spack/repos/builtin/packages/py-hmmlearn/package.py
new file mode 100644
index 0000000000..16bfb20ccf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-hmmlearn/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2023 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 PyHmmlearn(PythonPackage):
+    """hmmlearn is a set of algorithms for unsupervised learning and
+    inference of Hidden Markov Models."""
+
+    homepage = "https://github.com/hmmlearn/hmmlearn"
+    pypi = "hmmlearn/hmmlearn-0.3.0.tar.gz"
+
+    maintainers("snehring")
+
+    version("0.3.0", sha256="d13a91ea3695df881465e3d36132d7eef4e84d483f4ba538a4b46e24b5ea100f")
+
+    depends_on("py-setuptools", type="build")
+    depends_on("py-setuptools-scm@3.3:", type="build")
+    depends_on("py-pybind11@2.6:", type="build")
+
+    depends_on("py-numpy@1.10:", type=("build", "run"))
+    depends_on("py-scikit-learn@0.16:", type=("build", "run"))
+    depends_on("py-scipy@0.19:", type=("build", "run"))
+
+    conflicts("py-scikit-learn@=0.22.0", msg="Not compatible with scikit-learn@0.22.0")
diff --git a/var/spack/repos/builtin/packages/py-macs3/package.py b/var/spack/repos/builtin/packages/py-macs3/package.py
new file mode 100644
index 0000000000..be94b9c290
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-macs3/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2023 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 PyMacs3(PythonPackage):
+    """MACS: Model-based Analysis for ChIP-Seq"""
+
+    homepage = "https://github.com/macs3-project/MACS/"
+    pypi = "MACS3/MACS3-3.0.0b3.tar.gz"
+
+    maintainers("snehring")
+
+    version("3.0.0b3", sha256="caa794d4cfcd7368447eae15878505315dac44c21546e8fecebb3561e9cee362")
+
+    depends_on("python@3.9:", type=("build", "run"))
+
+    depends_on("py-setuptools@60.0:", type="build")
+    depends_on("py-cython@0.29:0", type=("build", "run"))
+
+    depends_on("py-numpy@1.19:", type=("build", "run"))
+    depends_on("py-cykhash@2", type=("build", "run"))
+    depends_on("py-hmmlearn@0.3:", type=("build", "run"))
-- 
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