py-phydms, py-pypdf2, and py-pyvolve: new packages (#31540)

* py-panaroo: new package

* moving panaroo to branch

* py-phydms: new package

* added dependencies and new packages

* fixed py-pypdf2 dependencies

4 files changed, 89 insertions, 2 deletions

diff --git a/var/spack/repos/builtin/packages/py-phydms/package.py b/var/spack/repos/builtin/packages/py-phydms/package.py
new file mode 100644
index 0000000000..9930683a86
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-phydms/package.py
@@ -0,0 +1,36 @@
+# Copyright 2013-2022 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 PyPhydms(PythonPackage):
+    """phydms enables phylogenetic analyses using deep mutational scanning data
+       to inform the substitution models. It implements Experimentally informed
+       codon models (ExpCM) for phylogenetic inference and the detection of
+       biologically interesting selection."""
+
+    homepage = "http://jbloomlab.github.io/phydms"
+    pypi     = "phydms/phydms-2.4.1.tar.gz"
+
+    version('2.4.1', sha256='04eb50bdb07907214050d19214d9bc8cf2002e24ca30fbe6e0f23f013d584d5c')
+
+    depends_on('python@3.5:',   type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
+
+    depends_on('py-biopython@1.67:',   type=('build', 'run'))
+    depends_on('py-cython@0.28:',      type=('build', 'run'))
+    depends_on('py-numpy@1.16.5:',     type=('build', 'run'))
+    depends_on('py-scipy@0.18:',       type=('build', 'run'))
+    depends_on('py-matplotlib@2.0.2:', type=('build', 'run'))
+    depends_on('py-natsort@5.0.1:',    type=('build', 'run'))
+    depends_on('py-sympy@1.0:',        type=('build', 'run'))
+    depends_on('py-six@1.10:',         type=('build', 'run'))
+    depends_on('py-pandas@0.20.2:',    type=('build', 'run'))
+    depends_on('py-pyvolve@1.0.3:',    type=('build', 'run'))
+    depends_on('py-statsmodels@0.8:',  type=('build', 'run'))
+    depends_on('py-weblogo@3.4:3.5',   type=('build', 'run'))
+    depends_on('py-pypdf2@1.26:',      type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pypdf2/package.py b/var/spack/repos/builtin/packages/py-pypdf2/package.py
new file mode 100644
index 0000000000..f13e87a93f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pypdf2/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2022 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 PyPypdf2(PythonPackage):
+    """PyPDF2 is a free and open source pure-python PDF library capable of
+       splitting, merging, cropping, and transforming the pages of PDF files.
+       It can also add custom data, viewing options, and passwords to PDF files.
+       PyPDF2 can retrieve text and metadata from PDFs as well."""
+
+    homepage = "https://pypdf2.readthedocs.io/en/latest/"
+    pypi     = "PyPDF2/PyPDF2-2.5.0.tar.gz"
+
+    version('2.5.0',  sha256='5802b1f40fa79be1b5ab9edc95a4e7f7e73399589db4f0e66ca831f449e7a2cd')
+    version('1.26.0', sha256='e28f902f2f0a1603ea95ebe21dff311ef09be3d0f0ef29a3e44a932729564385')
+
+    depends_on('python@3.6:',          type=('build', 'run'), when='@2.0.0:')
+    depends_on('py-setuptools',        type='build')
+    depends_on('py-typing-extensions', type=('build', 'run'), when='@2.0.0:^python@:3.9')
diff --git a/var/spack/repos/builtin/packages/py-pyvolve/package.py b/var/spack/repos/builtin/packages/py-pyvolve/package.py
new file mode 100644
index 0000000000..fc9c7e7db5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pyvolve/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2022 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 PyPyvolve(PythonPackage):
+    """Pyvolve is an open-source Python module for simulating sequences
+       along a phylogenetic tree according to continuous-time Markov models
+       of sequence evolution"""
+
+    homepage = "https://github.com/sjspielman/pyvolve"
+    pypi     = "Pyvolve/Pyvolve-1.1.0.tar.gz"
+
+    version('1.1.0', sha256='850aae6213a95c3f8c438ef7cdab33f4dafe8ef305b6fa85bbea1a9e7484c787')
+    version('1.0.3', sha256='725d5851f24b3b4564970a999bad8e2e90782cf81a07c3a3370c492a956d9d51')
+
+    depends_on('py-setuptools',    type='build')
+    depends_on('py-biopython',     type=('build', 'run'))
+    depends_on('py-numpy@1.20.0:', type=('build', 'run'), when='@1.1.0:')
+    depends_on('py-numpy@1.7:',    type=('build', 'run'), when='@1.0.3:')
+    depends_on('py-scipy',         type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-weblogo/package.py b/var/spack/repos/builtin/packages/py-weblogo/package.py
index 4a67047fa6..6089e35914 100644
--- a/var/spack/repos/builtin/packages/py-weblogo/package.py
+++ b/var/spack/repos/builtin/packages/py-weblogo/package.py
@@ -11,9 +11,11 @@ class PyWeblogo(PythonPackage):
     sequence logos as easy and painless as possible."""
 
     homepage = "http://weblogo.threeplusone.com"
-    pypi = "weblogo/weblogo-3.6.0.tar.gz"
+    pypi     = "weblogo/weblogo-3.6.0.tar.gz"
 
-    version('3.6.0', sha256='af5a9f065581f18d71bd7c22b160c1e443932f22cab992d439d3dc8757c80a85')
+    version('3.6.0',  sha256='af5a9f065581f18d71bd7c22b160c1e443932f22cab992d439d3dc8757c80a85')
+    version('3.5.0',  sha256='84e39ee7c4f70efea55d6a92b3efdc4d2602b3d32a793f98865bca35e6bd1133')
+    version('3.4',    sha256='1fb661df47252064dd6d59d3c340b24d87bebe9048ca9ada904ac1e95669e08f')
 
     depends_on('py-setuptools', type='build')
     depends_on('ghostscript', type=('build', 'run'))