From 7b95e2f05043442ee2d2c1494c5cef7b1a489251 Mon Sep 17 00:00:00 2001 From: Luke Diorio-Toth Date: Sat, 16 Jul 2022 19:24:29 -0500 Subject: 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 --- .../repos/builtin/packages/py-phydms/package.py | 36 ++++++++++++++++++++++ .../repos/builtin/packages/py-pypdf2/package.py | 24 +++++++++++++++ .../repos/builtin/packages/py-pyvolve/package.py | 25 +++++++++++++++ .../repos/builtin/packages/py-weblogo/package.py | 6 ++-- 4 files changed, 89 insertions(+), 2 deletions(-) create mode 100644 var/spack/repos/builtin/packages/py-phydms/package.py create mode 100644 var/spack/repos/builtin/packages/py-pypdf2/package.py create mode 100644 var/spack/repos/builtin/packages/py-pyvolve/package.py (limited to 'var') 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')) -- cgit v1.2.3-70-g09d2