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Snakemake: New Version 6.12.3 (#28252)

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* snakemake: New version
The newer versions of snakemake have a lot of new dependencies. The
optional dependencies still have to be added.

* removed comment

* some changes

* added reports variant

* deprecate older version and add me as maintainer

* Added dependency py-ratelimiter
This commit is contained in:
Marcus Boden 2022-01-05 17:53:30 +01:00 committed by GitHub
parent c226835aa5
commit 3e992aa283
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2 changed files with 52 additions and 3 deletions
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19
var/spack/repos/builtin/packages/py-ratelimiter/package.py Normal file
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@ -0,0 +1,19 @@
# Copyright 2013-2021 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 import *
class PyRatelimiter(PythonPackage):
"""Simple Python module providing rate limiting."""
homepage = 'https://github.com/RazerM/ratelimiter'
pypi = 'ratelimiter/ratelimiter-1.2.0.post0.tar.gz'
maintainers = ['marcusboden']
version('1.2.0.post0', '5c395dcabdbbde2e5178ef3f89b568a3066454a6ddc223b76473dac22f89b4f7')
depends_on('py-setuptools', type='build')

36
var/spack/repos/builtin/packages/snakemake/package.py
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@ -10,11 +10,41 @@ class Snakemake(PythonPackage):
"""Snakemake is an MIT-licensed workflow management system."""
homepage = "https://snakemake.readthedocs.io/en/stable/"
pypi = "snakemake/snakemake-3.11.2.tar.gz"
pypi = "snakemake/snakemake-6.12.3.tar.gz"
maintainers = ['marcusboden']
version('3.11.2', sha256='f7a3b586bc2195f2dce4a4817b7ec828b6d2a0cff74a04e0f7566dcd923f9761')
version('6.12.3', sha256='af86af9a540da3dceb05dad1040f1d3d733e6a695f8b3f8c30f8cf3bc6570a88')
version('3.11.2', sha256='f7a3b586bc2195f2dce4a4817b7ec828b6d2a0cff74a04e0f7566dcd923f9761', deprecated=True)
depends_on('python@3.3:3.6')
depends_on('py-requests', type=('build', 'run'))
depends_on('py-setuptools', type=('build', 'run'))
depends_on('py-wrapt', type=('build', 'run'))
depends_on('python@3.3:3.6', when='@:5')
with when('@6:'):
depends_on('python@3.5:')
depends_on('py-pyyaml', type=('build', 'run'))
depends_on('py-configargparse', type=('build', 'run'))
depends_on('py-appdirs', type=('build', 'run'))
depends_on('py-datrie', type=('build', 'run'))
depends_on('py-jsonschema', type=('build', 'run'))
depends_on('py-docutils', type=('build', 'run'))
depends_on('py-gitpython', type=('build', 'run'))
depends_on('py-psutil', type=('build', 'run'))
depends_on('py-nbformat', type=('build', 'run'))
depends_on('py-toposort', type=('build', 'run'))
depends_on('py-connectionpool@0.0.3:', type=('build', 'run'))
depends_on('py-pulp@2.0:', type=('build', 'run'))
depends_on('py-smart-open@3.0:', type=('build', 'run'))
depends_on('py-filelock', type=('build', 'run'))
depends_on('py-stopit', type=('build', 'run'))
depends_on('py-tabulate', type=('build', 'run'))
depends_on('py-ratelimiter', type=('build', 'run'))
variant('reports', default=False, description='Generate self-contained HTML reports')
with when('+reports'):
depends_on('py-jinja2', type=('build', 'run'))
depends_on('py-networkx', type=('build', 'run'))
depends_on('py-pygments', type=('build', 'run'))
depends_on('py-pygraphviz', type=('build', 'run'))