possvm: new package @1.2 (#42516)

* possvm: new package @1.2

* black!

* appeasing flake8

* Updating commit ID

* Adding graphing dep

* Update var/spack/repos/builtin/packages/py-markov-clustering/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update package.py

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

var/spack/repos/builtin/packages/possvm/package.py

@@ -0,0 +1,47 @@
+# 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)
+
+import os
+
+from spack.package import *
+
+
+class Possvm(Package):
+    """Possvm (Phylogenetic Ortholog Sorting with Species oVerlap and MCL)
+    is a python tool to analyse pre-computed gene trees and identify pairs
+    and clusters of orthologous genes. It takes advantage of the species
+    overlap algorithm implemented in the ETE toolkit to parse the phylogeny
+    and identify orthologous gene pairs, and MCL clustering for orthogroup
+    identification."""
+
+    homepage = "https://github.com/xgrau/possvm-orthology"
+    git = "https://github.com/xgrau/possvm-orthology.git"
+
+    license("GPL-3.0-only", checked_by="A-N-Other")
+
+    # version number is taken from -v/--version argparse info in possvm.py
+    version("1.2", commit="3158757423edafc29aa29bf3ae0cc63a93a56df9")
+
+    depends_on("python@3.10:", type="run")
+
+    # dependencies from GitHub README.md
+    depends_on("py-ete3@3.1.2", type="run")
+    depends_on("py-markov-clustering@0.0.6.dev0", type="run")
+    depends_on("py-matplotlib@3.7.1", type="run")
+    depends_on("py-networkx@3.0", type="run")
+    depends_on("py-scipy@1.10.0", type="run")
+    depends_on("py-numpy@1.23.5", type="run")
+    depends_on("py-pandas@1.5.3", type="run")
+
+    def install(self, spec, prefix):
+        # This package has no setup.py ...
+        # Add shebangs, ensure +x, and move the scripts to prefix.bin
+        mkdirp(prefix.bin)
+        sed = Executable("sed")
+        targets = ("possvm.py", join_path("scripts", "possvm_reconstruction.py"))
+        for script in targets:
+            sed("-i", rf'1 i\#! {self.spec["python"].command.path}\n', script)
+            os.chmod(script, 0o755)
+            install(script, prefix.bin)

var/spack/repos/builtin/packages/py-markov-clustering/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 PyMarkovClustering(PythonPackage):
+    """Implementation of the Markov clustering (MCL) algorithm in python"""
+
+    homepage = "https://github.com/GuyAllard/markov_clustering"
+    pypi = "markov_clustering/markov_clustering-0.0.6.dev0.tar.gz"
+
+    license("MIT", checked_by="A-N-Other")
+
+    version(
+        "0.0.6.dev0", sha256="8f72eee0ee5d9bfbab1b28bbfa95eaa020b2bba64b528ce45030b8b4300ecf33"
+    )
+
+    variant("drawing", default=False, description="Include graphing capabilities")
+
+    depends_on("python@3", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-scipy@0.19.0:", type=("build", "run"))
+    depends_on("py-scikit-learn", type=("build", "run"))
+
+    depends_on("py-networkx", type=("build", "run"), when="+drawing")
+    depends_on("py-matplotlib", type=("build", "run"), when="+drawing")

var/spack/repos/builtin/packages/py-networkx/package.py

@@ -17,6 +17,7 @@ class PyNetworkx(PythonPackage):
     license("BSD-3-Clause")
 
     version("3.1", sha256="de346335408f84de0eada6ff9fafafff9bcda11f0a0dfaa931133debb146ab61")
+    version("3.0", sha256="9a9992345353618ae98339c2b63d8201c381c2944f38a2ab49cb45a4c667e412")
     version("2.8.6", sha256="bd2b7730300860cbd2dafe8e5af89ff5c9a65c3975b352799d87a6238b4301a6")
     version("2.7.1", sha256="d1194ba753e5eed07cdecd1d23c5cd7a3c772099bd8dbd2fea366788cf4de7ba")
     version("2.6.3", sha256="c0946ed31d71f1b732b5aaa6da5a0388a345019af232ce2f49c766e2d6795c51")