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created py-tomopy package and fixed its dependencies (#4576)

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* added py-tomopy package

* fixed dependencies and added import_modules

* edited deps for tomopy with import_modules and added py-olefile pkg

* changed module name

* changed dependency to python because it will not build with setuptools

* fixed dependency list for py-tomopy and py-dxchange

* added py-nose dependency

* fixed tests

* commented out dependency py-counter

* fixed dependency py-pybtex-docutils

* removed nose as a dependency

* fixed flake8 errors

* fixed import_modules

* fixed import_modules indent

* fixed various issues in tomopy and deps files
This commit is contained in:
Stas Sergienko 2017-06-22 12:51:51 -05:00 committed by Adam J. Stewart
parent 3c8e65f3d8
commit 6aa3d51939
14 changed files with 140 additions and 15 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
var/spack/repos/builtin/packages/py-counter/package.py
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@ -29,6 +29,8 @@ class PyCounter(PythonPackage):
"""Counter package defines the "counter.Counter" class similar to
bags or multisets in other languages."""
import_modules = ['counter']
homepage = "https://github.com/KelSolaar/Counter"
url = "https://pypi.io/packages/source/C/Counter/Counter-1.0.0.tar.gz"

22
var/spack/repos/builtin/packages/py-dxchange/package.py
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@ -33,15 +33,19 @@ class PyDxchange(PythonPackage):
homepage = "https://github.com/data-exchange/dxchange"
url = "https://github.com/data-exchange/dxchange/archive/v0.1.2.tar.gz"
import_modules = ['dxchange']
version('0.1.2', '36633bb67a1e7d1fb60c2300adbcbab3')
depends_on('py-setuptools', type='build')
depends_on('py-numpy', type='run')
depends_on('py-scipy', type='run')
depends_on('py-h5py', type='run')
depends_on('py-six', type='run')
depends_on('py-netcdf4', type='run')
depends_on('py-spefile', type='run')
depends_on('py-edffile', type='run')
depends_on('py-tifffile', type='run')
depends_on('py-dxfile', type='run')
depends_on('py-numpy', type=('build', 'run'))
depends_on('py-scipy', type=('build', 'run'))
depends_on('py-h5py', type=('build', 'run'))
depends_on('py-six', type=('build', 'run'))
depends_on('py-netcdf4', type=('build', 'run'))
depends_on('py-spefile', type=('build', 'run'))
depends_on('py-edffile', type=('build', 'run'))
depends_on('py-tifffile', type=('build', 'run'))
depends_on('py-dxfile', type=('build', 'run'))
depends_on('py-olefile', type=('build', 'run'))
depends_on('py-astropy', type=('build', 'run'))

4
var/spack/repos/builtin/packages/py-dxfile/package.py
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@ -32,7 +32,9 @@ class PyDxfile(PythonPackage):
homepage = "https://github.com/data-exchange/dxfile"
url = "https://github.com/data-exchange/dxfile/archive/v0.4.tar.gz"
import_modules = ['dxfile']
version('0.4', '0402cd38aefdfd5ce92feb43dda18947')
depends_on('py-setuptools', type='build')
depends_on('py-h5py', type='run')
depends_on('py-h5py', type=('build', 'run'))

2
var/spack/repos/builtin/packages/py-edffile/package.py
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@ -31,6 +31,8 @@ class PyEdffile(PythonPackage):
homepage = "https://github.com/vasole/pymca/blob/master/PyMca5/PyMcaIO/EdfFile.py"
url = "https://github.com/conda-forge/edffile-feedstock.git"
import_modules = ['EdfFile']
version('5.0.0', git='https://github.com/conda-forge/edffile-feedstock.git',
commit='be5ab4199db9f8209c59e31874934b8536b52301')

2
var/spack/repos/builtin/packages/py-latexcodec/package.py
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@ -31,6 +31,8 @@ class PyLatexcodec(PythonPackage):
homepage = "http://latexcodec.readthedocs.io"
url = "https://pypi.io/packages/source/l/latexcodec/latexcodec-1.0.4.tar.gz"
import_modules = ['latexcodec']
version('1.0.4', '72010ec2a55227a5802239cff6fd32d6')
depends_on('py-setuptools', type='build')

38
var/spack/repos/builtin/packages/py-olefile/package.py Normal file
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@ -0,0 +1,38 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class PyOlefile(PythonPackage):
"""Python package to parse, read and write Microsoft OLE2 files"""
homepage = "https://www.decalage.info/python/olefileio"
url = "https://pypi.io/packages/source/o/olefile/olefile-0.44.zip"
import_modules = ['olefile']
version('0.44', 'fc625554e4e7f0c2ddcd00baa3c74ff5')
depends_on('python@2.6:', type=('build', 'run'))

2
var/spack/repos/builtin/packages/py-oset/package.py
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@ -31,6 +31,8 @@ class PyOset(PythonPackage):
homepage = "https://pypi.python.org/pypi/oset"
url = "https://pypi.io/packages/source/o/oset/oset-0.1.3.tar.gz"
import_modules = ['oset']
version('0.1.3', 'f23e5a545d2c77df3916398d2d39a3ab')
depends_on('py-setuptools', type='build')

2
var/spack/repos/builtin/packages/py-pybtex-docutils/package.py
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@ -31,6 +31,8 @@ class PyPybtexDocutils(PythonPackage):
homepage = "https://pypi.python.org/pypi/pybtex-docutils/"
url = "https://pypi.io/packages/source/p/pybtex-docutils/pybtex-docutils-0.2.1.tar.gz"
import_modules = ['pybtex_docutils']
version('0.2.1', '7ae4b00562bd8881f582edf95009cc62')
depends_on('py-setuptools', type='build')

16
var/spack/repos/builtin/packages/py-pybtex/package.py
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@ -33,9 +33,23 @@ class PyPybtex(PythonPackage):
homepage = "https://pybtex.org"
url = "https://pypi.io/packages/source/P/Pybtex/pybtex-0.21.tar.gz"
import_modules = [
'custom_fixers', 'pybtex', 'pybtex.style', 'pybtex.tests',
'pybtex.database', 'pybtex.backends', 'pybtex.bibtex',
'pybtex.charwidths', 'pybtex.markup', 'pybtex.plugin',
'pybtex.style.sorting', 'pybtex.style.names',
'pybtex.style.labels', 'pybtex.style.formatting',
'pybtex.tests.database_test', 'pybtex.tests.bst_parser_test',
'pybtex.tests.data', 'pybtex.database.output',
'pybtex.database.input', 'pybtex.database.format',
'pybtex.database.convert'
]
version('0.21', 'e7b320b2bcb34c664c4385533a2ea831')
depends_on('py-setuptools', type='build')
depends_on('py-latexcodec@1.0.4:', type=('build', 'run'))
depends_on('py-pyyaml@3.01:', type=('build', 'run'))
depends_on('py-counter@1:', when='^python@:2.6', type=('build', 'run'))
# This dependency breaks concretization
# See https://github.com/LLNL/spack/issues/2793
# depends_on('py-counter@1:', when='^python@:2.6', type=('build', 'run'))

2
var/spack/repos/builtin/packages/py-pywavelets/package.py
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@ -35,7 +35,7 @@ class PyPywavelets(PythonPackage):
version('0.5.2', 'aedda732f064cf9395f03d37f1003d1a')
import_modules = ['pywt']
import_modules = ['pywt', 'pywt.data']
depends_on('py-setuptools', type='build')
depends_on('py-cython', type='build')

4
var/spack/repos/builtin/packages/py-spefile/package.py
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@ -32,10 +32,12 @@ class PySpefile(PythonPackage):
homepage = "https://github.com/conda-forge/spefile-feedstock"
url = "https://github.com/conda-forge/spefile-feedstock.git"
import_modules = ['spefile']
version('1.6', git='https://github.com/conda-forge/spefile-feedstock.git',
commit='24394e066da8dee5e7608f556ca0203c9db217f9')
depends_on('py-setuptools', type='build')
depends_on('py-numpy', type='run')
depends_on('py-numpy', type=('build', 'run'))
build_directory = 'recipe/src'

4
var/spack/repos/builtin/packages/py-sphinxcontrib-bibtex/package.py
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@ -31,12 +31,14 @@ class PySphinxcontribBibtex(PythonPackage):
homepage = "https://pypi.python.org/pypi/sphinxcontrib-bibtex"
url = "https://pypi.io/packages/source/s/sphinxcontrib-bibtex/sphinxcontrib-bibtex-0.3.5.tar.gz"
import_modules = ['sphinxcontrib', 'sphinxcontrib.bibtex']
version('0.3.5', 'd3c86836e2f6227b55a5ca9108590b1c')
depends_on('py-setuptools', type='build')
depends_on('py-latexcodec@0.3.0:', type=('build', 'run'))
depends_on('py-pybtex@0.17:', type=('build', 'run'))
depends_on('pybtex-docutils@0.2.0:', type=('build', 'run'))
depends_on('py-pybtex-docutils@0.2.0:', type=('build', 'run'))
depends_on('py-six@1.4.1:', type=('build', 'run'))
depends_on('py-sphinx@1.0:', type=('build', 'run'))
depends_on('py-oset@0.1.3:', type=('build', 'run'))

4
var/spack/repos/builtin/packages/py-tifffile/package.py
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@ -31,7 +31,9 @@ class PyTifffile(PythonPackage):
homepage = "https://github.com/blink1073/tifffile"
url = "https://pypi.io/packages/source/t/tifffile/tifffile-0.12.1.tar.gz"
import_modules = ['tifffile']
version('0.12.1', '8a8afa74dd0df7915ac376a6cd7eeffc')
depends_on('py-setuptools', type='build')
depends_on('py-numpy@1.8.2:', type=('build', 'run'))
depends_on('py-numpy@1.8.2:', type=('build', 'run'))

51
var/spack/repos/builtin/packages/py-tomopy/package.py Normal file
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@ -0,0 +1,51 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class PyTomopy(PythonPackage):
"""TomoPy is an open-source Python package for tomographic data
processing and image reconstruction."""
homepage = "http://tomopy.readthedocs.io/en/latest/index.html"
url = "https://github.com/tomopy/tomopy/archive/1.0.0.tar.gz"
import_modules = [
'tomopy', 'doc', 'tomopy.util', 'tomopy.sim', 'tomopy.recon',
'tomopy.prep', 'tomopy.misc', 'tomopy.io', 'doc.demo'
]
version('1.0.0', '986ac2c85a4af9ada0403b4c746d2cd4')
depends_on('py-setuptools', type='build')
depends_on('py-numpy', type=('build', 'run'))
depends_on('py-h5py', type=('build', 'run'))
depends_on('py-scipy', type=('build', 'run'))
depends_on('py-six', type=('build', 'run'))
depends_on('py-scikit-image', type=('build', 'run'))
depends_on('py-pywavelets', type=('build', 'run'))
depends_on('py-pyfftw', type=('build', 'run'))
depends_on('py-dxchange', type=('build', 'run'))