diff --git a/packages/acpype/.gitkeep b/packages/acpype/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/packages/ambertools/.gitkeep b/packages/ambertools/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/packages/biobb-analysis/.gitkeep b/packages/biobb-analysis/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/packages/biobb-chemistry/.gitkeep b/packages/biobb-chemistry/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/packages/biobb-common/.gitkeep b/packages/biobb-common/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/packages/biobb-gromacs/.gitkeep b/packages/biobb-gromacs/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/packages/biobb-io/.gitkeep b/packages/biobb-io/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/packages/biobb-model/.gitkeep b/packages/biobb-model/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/packages/biobb-structure-checking/.gitkeep b/packages/biobb-structure-checking/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/packages/biobb-structure-utils/.gitkeep b/packages/biobb-structure-utils/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/packages/nest/.gitkeep b/packages/nest/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/packages/nest/package.py b/packages/nest/package.py
index fdac260819d164b1e9de3a009065a3ac660460c5..21b657780372c9c3810eb3f6008b6bbf55d02a31 100644
--- a/packages/nest/package.py
+++ b/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'))
diff --git a/packages/nglview/.gitkeep b/packages/nglview/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/packages/py-fairgraph/package.py b/packages/py-fairgraph/package.py
index 66997e6865a028fb8a486af8e1a9a691c681f227..2e0fd8e1d7a580f8a5087dfdd10b71f2ea049a63 100644
--- a/packages/py-fairgraph/package.py
+++ b/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")
diff --git a/packages/py-neuroglancer-scripts/package.py b/packages/py-neuroglancer-scripts/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..a2604f78389dc2ab78f733b913fee8046c5d6a09
--- /dev/null
+++ b/packages/py-neuroglancer-scripts/package.py
@@ -0,0 +1,28 @@
+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
diff --git a/packages/py-siibra/package.py b/packages/py-siibra/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..a64b177390a7170a7c6057c0a45dda3becc684ff
--- /dev/null
+++ b/packages/py-siibra/package.py
@@ -0,0 +1,42 @@
+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")
+
diff --git a/packages/simpletraj/.gitkeep b/packages/simpletraj/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/spack.yaml b/spack.yaml
index b0fca7377ca3c8c4deff48ba61beb7e650348054..a86f0050aa345f187f11ec985ff46cdf29a242dd 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -1,54 +1,18 @@
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