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

14 files changed, 140 insertions, 15 deletions

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'))