Feature add breathe and m2r (#10180)

* Added a package for the MDAnalysis toolkit.

* Added python packages for breathe and m2r.  Updated versions and URL
for the sphinx package.

* Fixed flake8 error

* Updated package requirements based on feedback.

* Updated with requirements from the setup.py

* Switched it back to pypi.

var/spack/repos/builtin/packages/py-breathe/package.py

+# Copyright 2013-2018 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 PyBreathe(PythonPackage):
+    """This is an extension to reStructuredText and Sphinx to be able to read
+    and render the Doxygen xml output."""
+
+    homepage = "https://github.com/michaeljones/breathe"
+    url      = "https://github.com/michaeljones/breathe/archive/v4.11.1.tar.gz"
+
+    version('4.11.1', sha256='84723eefc7cc05da6895e2dd6e7c72926c5fd88a67de57edce42d99c058c7e06')
+    version('4.11.0', sha256='8c9f900560529ca2f589f26759be94c2accad14fd83fee34d353cf6f446e09f6')
+    version('4.10.0', sha256='10e294ca2927d40c83343674186ce6fad539acfb464ffd765fd371adc1126d4d')
+    version('4.9.1',  sha256='3e1e31b879dcd1fe1ebdaf4d0b11356b8e348ac5af101cafa9e54956716a7f02')
+    version('4.9.0',  sha256='a2b4b8cd2c4ef708ae69dd174e65731b1e18c24f8670036d2f5e608558be2613')
+    version('4.8.0',  sha256='edac7732ad8702ea0425773f1f0c98e7ad5028dbba5fe6483f32a1df3afe2f31')
+    version('4.7.3',  sha256='35e2e937fad97c6d7e287db6007184325284130ab50e1154fe126cffc09a1989')
+    version('4.7.2',  sha256='982d47909d22fcd71b48bad5aef3644294340b24f612b2887cde2e3be464d960')
+    version('4.7.1',  sha256='afb1ab0084b25d3670fa8f5cf2eeaee6fe61bfc77876e3816b140eacd4949875')
+    version('4.7.0',  sha256='5629c67f5adb41f39375d36c5f0d60d34b1230be268125e535205d77f69211e4')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-sphinx @1.4:', type=('build', 'run'))
+    depends_on('py-docutils @0.5:', type=('build', 'run'))
+    depends_on('py-six@1.4:', type=('build', 'run'))
+    depends_on('doxygen @1.8.4:')

var/spack/repos/builtin/packages/py-m2r/package.py

+# Copyright 2013-2018 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 PyM2r(PythonPackage):
+    """M2R converts a markdown file including reStructuredText (rst) markups to
+    a valid rst format."""
+
+    homepage = "https://github.com/miyakogi/m2r"
+    url      = "https://github.com/miyakogi/m2r/archive/v0.2.1.tar.gz"
+
+    version('0.2.1',  sha256='9286c1a5d7548f34b0a12017444e4c441781bef4b71f321f723e314b76b6c498')
+    version('0.2.0',  sha256='e9b7476203c4a5e3b822eb0ef110011d7b427d2c0dbdc4030f9cbcd239fbd4d6')
+    version('0.1.15', sha256='4ca4c73385512f6e54db8e152ba157fc3eea84f9e942fe60a12ace5078ff83df')
+    version('0.1.14', sha256='d8f844cc6f0c954e55eb3d599e436b337e7f97559dafa7ff54412a5f06f0867c')
+    version('0.1.13', sha256='97f81a45b922f7700e0c0dfd742c79d904e337e92ec4241a11aa579713a1afa4')
+    version('0.1.12', sha256='585b5b4e30494858de49ad844cafeb752bd12764fd6c20ca8496ddd4be5e8d21')
+    version('0.1.11', sha256='a29ef03a0b67116ba8e394a4b3f8afc354211b899f89dedf9c4c0b79828e9ca7')
+    version('0.1.10', sha256='4c7a92f111ac842b9c4d3719b8d785b26cb1cf6e81ec0940f8fe0ccc078e6925')
+    version('0.1.9',  sha256='86fe3c8c54a59807e0ef8cfe5a79fc013b4aaced1f3db493878f5ec1a46bb6d5')
+    version('0.1.8',  sha256='2bfeb2f3de5f9fe9cd411aba82767a6473a43db96ca1730c03b0fe0167239b7e')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-mistune',    type=('build', 'run'))
+    depends_on('py-docutils', type=('build', 'run'))

var/spack/repos/builtin/packages/py-sphinx/package.py

@@ -21,6 +21,7 @@ class PySphinx(PythonPackage):
         'sphinx.environment.collectors', 'sphinx.environment.adapters'
     ]
 
+    version('1.8.2',   sha256='120732cbddb1b2364471c3d9f8bfd4b0c5b550862f99a65736c77f970b142aea')
     version('1.7.4', '95f3b83f521314600e5b09e99cf32c46')
     version('1.6.3', 'c5ad61f4e0974375ca2c2b58ef8d5411')
     version('1.6.1', '26cb1cdca7aa4afc8c925d926b6268e7')