Merge branch 'add-nest-3.5rc1' of...

Merge branch 'add-nest-3.5rc1' of ebrains:technical-coordination/project-internal/devops/platform/ebrains-spack-builds into add-nest-3.5rc1

packages/nest/package.py

@@ -26,7 +26,7 @@ class Nest(CMakePackage):
     git      = "https://github.com/nest/nest-simulator.git"
 
     version('master', branch='master')
-    version('3.5-rc1',sha256='0ccc520ff642be4a30c0606150a397e6137362a2acf76ea03a8ee2aa48803a3e')
+    version('3.5_rc1',sha256='0ccc520ff642be4a30c0606150a397e6137362a2acf76ea03a8ee2aa48803a3e')
     version('3.4',    sha256='c56699111f899045ba48e55e87d14eca8763b48ebbb3648beee701a36aa3af20')
     version('3.3',    sha256='179462b966cc61f5785d2fee770bc36f86745598ace9cd97dd620622b62043ed')
     version('3.2',    sha256='583d5725882ad5e8fd4fc7ffab425da97cbbb91fadbc327e940c184e8892b958')
@@ -107,7 +107,7 @@ class Nest(CMakePackage):
 
     depends_on('mpi',               when='+mpi')
     depends_on('py-mpi4py',         when='+python+mpi', type=('run', 'test'))
-    depends_on('doxygen',           type='build')
+    # depends_on('doxygen',           type='build')
     depends_on('gsl',               when='+gsl')
     depends_on('readline',          type=('build', 'run', 'test'))
     depends_on('ncurses',          type=('build', 'run', 'test'))

packages/py-fairgraph/package.py

@@ -15,6 +15,7 @@ class PyFairgraph(PythonPackage):
 
     maintainers = ["apdavison"]
 
+    version("0.11.0", sha256="ae87acf0d9f7e0c296a889056855e759705132f2fb88f77b08c708528f9823bb")
     version("0.10.0", sha256="4ad387549a12886323f149867c0940d2e3855f2fd9b3fb44af2ba312cc4975b7")
     version("0.9.0", sha256="8ed3dd3bc274d9c25408a2e971f317d4e3aa4400636e9f4b89716ad92b721d78")
     version("0.8.2", sha256="2788acacfcab4bb2c256ddd46ca961c94bd2ca15163f1e03dcd16adbbc3784f7")

packages/py-neuroglancer-scripts/package.py

+from spack.package import *
+
+
+class PyNeuroglancerScripts(PythonPackage):
+    """Conversion of images to the Neuroglancer pre-computed format"""
+
+    homepage = "https://github.com/HumanBrainProject/neuroglancer-scripts"
+    pypi     = "neuroglancer-scripts/neuroglancer-scripts-1.1.0.tar.gz"
+
+    maintainers = ['Yann Leprince']
+
+    version('1.1.0',    sha256='395a3565808136950a1e3296b43eeda13a0108d2286eba2b2924b33c3b3abc70')
+    version('1.0.0',    sha256='524c0e3a3faebaf3952953f8097af347655bed3e70b3a4bc4043a6f216db7d28')
+    version('1.0.0rc3', sha256='715811702fe4fc88210d54ea913787ab84e17b0ff4b7c62d30130f302a0a8335')
+    version('0.3.0',    sha256='dd85c946f44f5211adf55eba04886e41dc36e9a94c723b966a8485c06d7ed253')
+    version('0.2.0',    sha256='98d906347acf1be6a6cb49ed8753d51776ed38034f395b60de15bcf790e9533c')
+
+    depends_on('python@3.5:',    type=('build', 'run'))
+
+    depends_on('py-nibabel',      type=('build', 'run'))
+    depends_on('py-numpy',        type=('build', 'run'))
+    depends_on('py-pillow',       type=('build', 'run'))
+    depends_on('py-requests',     type=('build', 'run'))
+    depends_on('py-scikit-image', type=('build', 'run'))
+    depends_on('py-tqdm',         type=('build', 'run'))
+
+    # Not needed for the purpose siibra-python
+    # depends_on('py-imagecodecs',  type=('build', 'run')) # TODO: had some issues

packages/py-siibra/package.py

+from spack.package import *
+
+
+class PySiibra(PythonPackage):
+    """Software interfaces for interacting with brain atlases"""
+
+    homepage = "https://github.com/FZJ-INM1-BDA/siibra-python"
+    pypi     = "siibra/siibra-0.4a57.tar.gz"
+
+    maintainers = ['x.gui@fz-juelich.de', 's.koehnen@fz-juelich.de', 't.dickscheid@fz-juelich.de']
+
+    version("0.4a57", sha256="53983c4baab84abe5dd6928c320ce87433cab02b5ed992995f0a17661c93dbff")
+    version("0.4a56", sha256="4c03d8a94c73a233e216103fa7090d057db03b1806027fabde38e8f83b852d78")
+    version("0.4a54", sha256="114765afe906383c7e6b930f1df7e26ddc15a6f295e2eab83a861eaba6d8f57f")
+    version("0.4a51", sha256="5aacd53b9b59a98a061c6b95421ab588d35ea7f6f27753c634a42ea7324cf9fe")
+    version("0.4a47", sha256="661b68cd82d4ffbf3f815fb961543cc8c42b695ee601d5856ce90bfc7ccb968a")
+    version("0.4a46", sha256="ddf17cd25c8249111d9f8c0c1088fabcc0fa8796734dc1784506155df6d57568")
+    version("0.4a35", sha256="106a61824c6e3260ee65241add88bbb2d6be4a48756c1e3173860406722a0dc0")
+    version("0.4a33", sha256="d67ba51547cb7fbc792bd14e93d083cabeac978b9a3ee4bfd5cf9aa0c95c5c94")
+    version("0.4a32", sha256="bfeca6c56cc33630a8e046f0ba8a4d9e1168916e64ffe730b4ed08b8ad06bb4c")
+    version("0.4a31", sha256="e49a1583b0b60403d799bca031c05208acd57bf5d3a605cefb3e9439bc36410d")
+    
+    depends_on('python@3.7:',             type=('build', 'run'))
+
+    depends_on('py-anytree',              type=('build', 'run'))
+    depends_on('py-nibabel',              type=('build', 'run'))
+    depends_on('py-appdirs',              type=('build', 'run'))
+    depends_on('py-scikit-image',         type=('build', 'run'))
+    depends_on('py-requests',             type=('build', 'run'))
+    depends_on('py-neuroglancer-scripts', type=('build', 'run'))
+    depends_on('py-nilearn',              type=('build', 'run'))
+    depends_on('py-typing-extensions',    type=('build', 'run'), when='^python@:3.7')
+    depends_on('py-filelock',             type=('build', 'run'))
+
+    depends_on('py-pytest',               type=('test'))
+
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def install_test(self): 
+        pytest = which("pytest")
+        pytest("-rx")
+

spack.yaml

 spack:
   specs:
     # Notebook
-    - r-irkernel
-    - py-ipython
+    - py-ipycanvas
     - py-ipykernel
+    - py-ipython
     - py-notebook
-    - py-ipycanvas
+    - r-irkernel
     # "collab"-specific constraint to match ("jupyterlab_widgets") in the base image
     - py-ipywidgets@:7.7
     # Collab utils
     - clb-nb-utils@0.1.0
     # EBRAINS tools
-    - nest@3.5-rc1 +sonata
+    - apbs@3.4.0
     - arbor@0.8.1 +python +mpi
-    - neuron@8.2.2 +mpi
-    - py-pynn@0.11.0 +mpi
-    - py-brian2@2.5.0.2
-    - py-tvb-data@2.7
-    - py-tvb-gdist@2.2
-    - py-tvb-library@2.8.1
-    - py-tvb-storage@2.8.1
-    - py-tvb-framework@2.8.1.1
-    - pynn-brainscales@5.0-rc1
-    - hxtorch@5.0-rc1
-    - py-nestml@5.2.0
-    - py-neo@0.12.0
-    - py-hdmf@3.4.6
-    - py-pynwb@2.1.0
-    - py-nixio@1.5.3
-    - py-cerebrus@1.3.4
-    - py-sciunit@0.2.5.1
-    - py-quantities@0.14.1
-    - py-quantities-scidash@0.12.4.3
-    - py-ebrains-kg-core@0.9.14
-    - py-ebrains-drive@0.5.1
-    - py-fairgraph@0.10.0
-    - py-nameparser@1.1.1
-    - py-lazyarray@0.5.2
-    - py-hbp-archive@1.1.1
-    - py-viziphant@0.3.0
-    - py-hippounit@1.3.6
-    - py-efel@4.0.4
-    - py-hbp-neuromorphic-platform@0.10.1
-    - py-hbp-validation-client@0.8.2
-    - py-lfpy@2.3
-    - py-elephant@0.12.0
-    - py-frites@0.4.2
-    - py-snudda@1.4.0
-    - py-pyunicore@0.14.1
-    - py-neuror@1.4.2
     - biobb-analysis@4.0.1
     - biobb-chemistry@4.0.0
     - biobb-common@4.0.0
@@ -57,22 +21,58 @@ spack:
     - biobb-model@4.0.0
     - biobb-structure-checking@3.12.1
     - biobb-structure-utils@4.0.0
+    - hxtorch@5.0-rc1
+    - nest@3.5_rc1 +sonata
+    - neuron@8.2.2 +mpi
     - nglview@3.0.4
-    - simpletraj@0.3
-    - apbs@3.4.0
+    - py-brian2@2.5.0.2
+    - py-cerebrus@1.3.4
+    - py-ebrains-drive@0.5.1
+    - py-ebrains-kg-core@0.9.14
+    - py-efel@4.0.4
+    - py-elephant@0.12.0
+    - py-fairgraph@0.11.0
+    - py-frites@0.4.2
+    - py-hbp-archive@1.1.1
+    - py-hbp-neuromorphic-platform@0.10.1
+    - py-hbp-validation-client@0.8.2
+    - py-hdmf@3.4.6
+    - py-hippounit@1.3.6
+    - py-lazyarray@0.5.2
+    - py-lfpy@2.3
+    - py-nameparser@1.1.1
+    - py-neo@0.12.0
+    - py-nestml@5.2.0
+    - py-neuror@1.4.2
+    - py-neurom@3.2.2
+    - py-nixio@1.5.3
     - py-pdb2pqr@3.5.2
-    - sda@7.3.3d
-    - r-uqsa@2.2
+    - py-pynn@0.11.0 +mpi
+    - py-pynwb@2.1.0
+    - py-pyunicore@0.14.1
+    - py-quantities-scidash@0.12.4.3
+    - py-quantities@0.14.1
+    - py-sciunit@0.2.5.1
+    - py-siibra@0.4a57
+    - py-snudda@1.4.0
+    - py-tvb-data@2.7
+    - py-tvb-framework@2.8.1.1
+    - py-tvb-gdist@2.2
+    - py-tvb-library@2.8.1
+    - py-tvb-storage@2.8.1
+    - py-viziphant@0.3.0
+    - pynn-brainscales@5.0-rc1
     - r-rgsl@0.1
     - r-sbtabvfgen@0.1
-    #- py-version-query
-    #- py-cerebstats
-    #- py-cerebunit
-    #- py-morphounit@1.0.4
-    #- py-neurom@1.4.10
-    #- py-morphio@3.1.1
+    - r-uqsa@2.2
+    - sda@7.3.3d
+    - simpletraj@0.3
     # Workflows (meta-packages)
     - wf-uq-akar4@0.1
     - wf-multi-area-model@0.1
+    #- py-cerebstats
+    #- py-cerebunit
+    #- py-morphounit@1.0.4
+    #- py-version-query
   concretizer:
     unify: true