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

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* py-panaroo: new package

* moving panaroo to branch

* py-phydms: new package

* added dependencies and new packages

* fixed py-pypdf2 dependencies
This commit is contained in:
Luke Diorio-Toth 2022-07-16 19:24:29 -05:00 committed by GitHub
parent 03c1962252
commit 7b95e2f050
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4 changed files with 89 additions and 2 deletions
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var/spack/repos/builtin/packages/py-phydms/package.py Normal file
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# 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'))

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var/spack/repos/builtin/packages/py-pypdf2/package.py Normal file
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# 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')

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var/spack/repos/builtin/packages/py-pyvolve/package.py Normal file
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# 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'))

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var/spack/repos/builtin/packages/py-weblogo/package.py
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@ -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'))