adding morphology stack one package at a time: part 1 (spack#721)

* Add py-quaternion

* update NeuroM

* add plotly-helper

* Add py-cut-plane

* bump pathlib 

* add morph-tool

var/spack/repos/builtin/packages/py-cut-plane/package.py

@@ -0,0 +1,27 @@
+# Copyright 2013-2020 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 PyCutPlane(PythonPackage):
+    """Python morphology manipulation toolkit"""
+
+    homepage = "https://bbpcode.epfl.ch/code/#/admin/projects/nse/cut-plane"
+    git      = "ssh://bbpcode.epfl.ch/nse/cut-plane"
+
+    version('develop', branch='master')
+    version('0.0.7', tag='cut-plane-v0.0.7')
+
+    depends_on('py-setuptools', type=('build', 'run'))
+
+    depends_on('py-neurom@mut_morphio', type='run', when='@0.1.14:')
+    depends_on('py-pyquaternion', type='run')
+    depends_on('py-entity-management', type='run')
+    depends_on('py-plotly-helper', type='run')
+
+    def patch(self):
+        filter_file(".*dash.*", "", "setup.py")

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

@@ -1,4 +1,4 @@
-# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Copyright 2013-2020 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)
@@ -10,8 +10,13 @@ class PyNeurom(PythonPackage):
     """Python library neuron morphology analysis"""
 
     homepage = "https://github.com/BlueBrain/NeuroM"
+    git = "https://github.com/BlueBrain/NeuroM.git"
     url = "https://pypi.io/packages/source/n/neurom/neurom-1.4.10.tar.gz"
 
+    version('develop', branch='master')
+    version('mut_morphio', branch='mut_morphio')
+
+    version('1.4.15', sha256='d84f04c292ed9b2fe1d34d6e754a133f69ef81a038947d836dd4f34ccd7b4607')
     version('1.4.14', sha256='e541f6c8a11826caa2b2d1cf18015a10ec7009f12813edfc2655084c7cf5021b')
     version('1.4.10', sha256='c94823133bb15b5756c22391e05948871ff77c0212e91ad375903ca437e18aeb')
 
@@ -24,6 +29,7 @@ class PyNeurom(PythonPackage):
     depends_on('py-matplotlib@1.3.1:', type='run')
     depends_on('py-numpy@1.8.0:', type='run')
     depends_on('py-plotly@3.0.0', type='run', when='+plotly')
+    depends_on('py-morphio', type='run')
     depends_on('py-pylru@1.0:', type='run')
     depends_on('py-pyyaml@3.10:', type='run')
     depends_on('py-scipy@0.17.0:', type='run')

var/spack/repos/builtin/packages/py-pathlib2/package.py

@@ -10,10 +10,11 @@ class PyPathlib2(PythonPackage):
     """Backport of pathlib from python 3.4"""
 
     homepage = "https://pypi.python.org/pypi/pathlib2"
-    url      = "https://pypi.io/packages/source/p/pathlib2/pathlib2-2.3.2.tar.gz"
+    url      = "https://pypi.io/packages/source/p/pathlib2/pathlib2-2.3.5.tar.gz"
 
     import_modules = ['pathlib2']
 
+    version('2.3.5', sha256='6cd9a47b597b37cc57de1c05e56fb1a1c9cc9fab04fe78c29acd090418529868')
     version('2.3.2', sha256='8eb170f8d0d61825e09a95b38be068299ddeda82f35e96c3301a8a5e7604cb83')
     version('2.1.0', sha256='deb3a960c1d55868dfbcac98432358b92ba89d95029cddd4040db1f27405055c')
 

var/spack/repos/builtin/packages/py-plotly-helper/package.py

@@ -0,0 +1,21 @@
+# Copyright 2013-2020 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 PyPlotlyHelper(PythonPackage):
+    """Python morphology manipulation toolkit"""
+
+    homepage = "https://bbpcode.epfl.ch/code/#/admin/projects/nse/plotly-helper"
+    git      = "ssh://bbpcode.epfl.ch/nse/plotly-helper"
+
+    version('develop', branch='master')
+    version('0.0.2', tag='plotly-helper-v0.0.2')
+
+    depends_on('py-setuptools', type=('build', 'run'))
+
+    depends_on('py-neurom@mut_morphio+plotly', type='run')

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

@@ -0,0 +1,20 @@
+# Copyright 2013-2020 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 PyPyquaternion(PythonPackage):
+    """Python morphology manipulation toolkit"""
+
+    homepage = "https://kieranwynn.github.io/pyquaternion/"
+    url      = "https://pypi.org/packages/source/p/pyquaternion/pyquaternion-0.9.5.tar.gz"
+
+    version('0.9.5', sha256='2d89d19259d62a8fbd25219eee7dacc1f6bb570becb70e1e883f622597c7d81d')
+
+    depends_on('py-setuptools', type=('build', 'run'))
+
+    depends_on('py-numpy', type='run')