From 6aa3d519390105e64ad940161be0e076892b81cb Mon Sep 17 00:00:00 2001 From: Stas Sergienko Date: Thu, 22 Jun 2017 12:51:51 -0500 Subject: created py-tomopy package and fixed its dependencies (#4576) * 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 --- .../repos/builtin/packages/py-counter/package.py | 2 + .../repos/builtin/packages/py-dxchange/package.py | 22 ++++++---- .../repos/builtin/packages/py-dxfile/package.py | 4 +- .../repos/builtin/packages/py-edffile/package.py | 2 + .../builtin/packages/py-latexcodec/package.py | 2 + .../repos/builtin/packages/py-olefile/package.py | 38 ++++++++++++++++ .../repos/builtin/packages/py-oset/package.py | 2 + .../builtin/packages/py-pybtex-docutils/package.py | 2 + .../repos/builtin/packages/py-pybtex/package.py | 16 ++++++- .../builtin/packages/py-pywavelets/package.py | 2 +- .../repos/builtin/packages/py-spefile/package.py | 4 +- .../packages/py-sphinxcontrib-bibtex/package.py | 4 +- .../repos/builtin/packages/py-tifffile/package.py | 4 +- .../repos/builtin/packages/py-tomopy/package.py | 51 ++++++++++++++++++++++ 14 files changed, 140 insertions(+), 15 deletions(-) create mode 100644 var/spack/repos/builtin/packages/py-olefile/package.py create mode 100644 var/spack/repos/builtin/packages/py-tomopy/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-counter/package.py b/var/spack/repos/builtin/packages/py-counter/package.py index 61e1d51e6c..9be0edd839 100644 --- a/var/spack/repos/builtin/packages/py-counter/package.py +++ b/var/spack/repos/builtin/packages/py-counter/package.py @@ -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" diff --git a/var/spack/repos/builtin/packages/py-dxchange/package.py b/var/spack/repos/builtin/packages/py-dxchange/package.py index 7c745c348f..b981960438 100644 --- a/var/spack/repos/builtin/packages/py-dxchange/package.py +++ b/var/spack/repos/builtin/packages/py-dxchange/package.py @@ -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')) diff --git a/var/spack/repos/builtin/packages/py-dxfile/package.py b/var/spack/repos/builtin/packages/py-dxfile/package.py index c0942ddc98..ed8cc0b631 100644 --- a/var/spack/repos/builtin/packages/py-dxfile/package.py +++ b/var/spack/repos/builtin/packages/py-dxfile/package.py @@ -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')) diff --git a/var/spack/repos/builtin/packages/py-edffile/package.py b/var/spack/repos/builtin/packages/py-edffile/package.py index 02422dedff..878387a8ee 100644 --- a/var/spack/repos/builtin/packages/py-edffile/package.py +++ b/var/spack/repos/builtin/packages/py-edffile/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/py-latexcodec/package.py b/var/spack/repos/builtin/packages/py-latexcodec/package.py index d93050e821..bdc96d2c68 100644 --- a/var/spack/repos/builtin/packages/py-latexcodec/package.py +++ b/var/spack/repos/builtin/packages/py-latexcodec/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/py-olefile/package.py b/var/spack/repos/builtin/packages/py-olefile/package.py new file mode 100644 index 0000000000..fd778862b8 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-olefile/package.py @@ -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')) diff --git a/var/spack/repos/builtin/packages/py-oset/package.py b/var/spack/repos/builtin/packages/py-oset/package.py index 6ce7b392e6..54627323b5 100644 --- a/var/spack/repos/builtin/packages/py-oset/package.py +++ b/var/spack/repos/builtin/packages/py-oset/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/py-pybtex-docutils/package.py b/var/spack/repos/builtin/packages/py-pybtex-docutils/package.py index d951348a90..ee154d2748 100644 --- a/var/spack/repos/builtin/packages/py-pybtex-docutils/package.py +++ b/var/spack/repos/builtin/packages/py-pybtex-docutils/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/py-pybtex/package.py b/var/spack/repos/builtin/packages/py-pybtex/package.py index e0fd1ae5b0..99a0f5dfdc 100644 --- a/var/spack/repos/builtin/packages/py-pybtex/package.py +++ b/var/spack/repos/builtin/packages/py-pybtex/package.py @@ -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')) diff --git a/var/spack/repos/builtin/packages/py-pywavelets/package.py b/var/spack/repos/builtin/packages/py-pywavelets/package.py index eed3a465b0..8dbb597702 100644 --- a/var/spack/repos/builtin/packages/py-pywavelets/package.py +++ b/var/spack/repos/builtin/packages/py-pywavelets/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/py-spefile/package.py b/var/spack/repos/builtin/packages/py-spefile/package.py index 6279391bbd..d35cfae203 100644 --- a/var/spack/repos/builtin/packages/py-spefile/package.py +++ b/var/spack/repos/builtin/packages/py-spefile/package.py @@ -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' diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-bibtex/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-bibtex/package.py index 77fb43bde6..53011ee215 100644 --- a/var/spack/repos/builtin/packages/py-sphinxcontrib-bibtex/package.py +++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-bibtex/package.py @@ -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')) diff --git a/var/spack/repos/builtin/packages/py-tifffile/package.py b/var/spack/repos/builtin/packages/py-tifffile/package.py index 4412352db1..87383fdbfd 100644 --- a/var/spack/repos/builtin/packages/py-tifffile/package.py +++ b/var/spack/repos/builtin/packages/py-tifffile/package.py @@ -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')) diff --git a/var/spack/repos/builtin/packages/py-tomopy/package.py b/var/spack/repos/builtin/packages/py-tomopy/package.py new file mode 100644 index 0000000000..a77caa4dac --- /dev/null +++ b/var/spack/repos/builtin/packages/py-tomopy/package.py @@ -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')) -- cgit v1.2.3-70-g09d2