update branch

.gitignore

 __pycache__
 *.pyc
+*.err
+*.out
+.spack-env/
+spack.lock

.gitlab-ci.yml

@@ -6,6 +6,7 @@ variables:
   GITLAB_BUILD_ENV_DOCKER_IMAGE: docker-registry.ebrains.eu/tc/ebrains-spack-build-env/gitlab_runners_nfs:devel
   SPACK_VERSION: v0.20.0
   SPACK_PATH_GITLAB: /mnt/spack_v0.20.0
+  SYSTEMNAME: ebrainslab
 
 # start an OpenShift Job that will build the Spack environment
 .deploy-build-environment:
@@ -181,7 +182,6 @@ build-spack-env-on-runner:
     SPACK_USER_CONFIG_PATH: $CI_PROJECT_DIR/.spack
   script:
     - git clone --depth 1 -c advice.detachedHead=false -c feature.manyFiles=true --branch $SPACK_VERSION https://github.com/spack/spack $SPACK_DEV_PATH
-    - cp packages.yaml $SPACK_DEV_PATH/etc/spack/packages.yaml
     # SPACK PATCH: the post-build logs on install-time-test-logs.txt gets ovewritten by the post-install logs.
     # quick fix for that: (TODO: investigate more and open PR)
     - sed -i "s/self.file_like, \"w\"/self.file_like, \"a\"/g" $SPACK_DEV_PATH/lib/spack/llnl/util/tty/log.py
@@ -196,8 +196,11 @@ build-spack-env-on-runner:
     - spack load gcc@10.3.0
     - spack compiler find
     - spack repo add .
-    - spack env create $SPACK_DEV_ENV spack.yaml
+    - spack env create $SPACK_DEV_ENV
     - spack env activate $SPACK_DEV_ENV
+    - rm -rf $SPACK_ENV/site-config && cp -r site-config $SPACK_ENV
+    - spack-python site-config/ymerge.py spack.yaml site-config/$SYSTEMNAME/spack.yaml > /tmp/spack.yaml
+    - cp /tmp/spack.yaml $SPACK_ENV/
     - spack install -y -j2 --fresh --test root
   after_script:
     - mkdir spack_logs
@@ -255,8 +258,6 @@ sync-gitlab-spack-instance:
     # SPACK PATCH: the post-build logs on install-time-test-logs.txt gets ovewritten by the post-install logs.
     # quick fix for that: (TODO: investigate more and open PR)
     - sed -i "s/self.file_like, \"w\"/self.file_like, \"a\"/g" $SPACK_PATH/spack/lib/spack/llnl/util/tty/log.py
-    # copy package settings
-    - cp $CI_PROJECT_DIR/packages.yaml $SPACK_PATH/spack/etc/spack/packages.yaml
     # activate spack
     - . $SPACK_PATH/spack/share/spack/setup-env.sh
     # get latest state of EBRAINS repo
@@ -264,16 +265,20 @@ sync-gitlab-spack-instance:
     - spack repo list | grep -q ebrains-spack-builds && echo "Repository registered already" || spack repo add $SPACK_REPO_PATH
     - spack repo list
     # install compiler (if not already installed)
-    - EBRAINS_SPACK_COMPILER=$(grep 'compiler' $CI_PROJECT_DIR/packages.yaml | awk -F'[][]' '{ print $2 }')
+    - EBRAINS_SPACK_COMPILER=$(grep 'compiler' $CI_PROJECT_DIR/site-config/$SYSTEMNAME/packages.yaml | awk -F'[][]' '{ print $2 }')
     - spack compiler find
     - spack compiler list | grep -q $EBRAINS_SPACK_COMPILER || spack install $EBRAINS_SPACK_COMPILER
     - spack load $EBRAINS_SPACK_COMPILER
     - spack compiler find
     - spack compiler list
-    # activate and update environment (and create it, if it doesn't exist)
-    - spack env list | grep -q $SPACK_NFS_ENV && echo "Environment created already" || spack env create $SPACK_NFS_ENV $CI_PROJECT_DIR/spack.yaml
+    # activate environment (and create it, if it doesn't exist)
+    - spack env list | grep -q $SPACK_NFS_ENV && echo "Environment created already" || spack env create $SPACK_NFS_ENV
     - spack env activate $SPACK_NFS_ENV
-    - cp $CI_PROJECT_DIR/spack.yaml $SPACK_ROOT/var/spack/environments/$SPACK_NFS_ENV/spack.yaml
+    # update environment site-configs
+    - rm -rf $SPACK_ENV/site-config && cp -r site-config $SPACK_ENV
+    # update spack.yaml: merge top-level and site-specific spack.yaml files
+    - spack-python site-config/ymerge.py spack.yaml site-config/$SYSTEMNAME/spack.yaml > /tmp/spack.yaml
+    - cp /tmp/spack.yaml $SPACK_ENV/
     # There is a known spack bug (https://github.com/spack/spack/issues/29447) in installing test dependencies for installation tests. The workaround suggested
     # in the issue is to NOT concretize separately, but simply remove the .lock file and let the enironment be concretized by the spack install command:
     - rm $SPACK_ROOT/var/spack/environments/$SPACK_NFS_ENV/spack.lock || echo "No spack.lock file"

README.md

@@ -15,6 +15,7 @@ This repository is where the EBRAINS Spack packages are maintained. It contains:
 - the latest EBRAINS [Spack environment](https://spack.readthedocs.io/en/latest/environments.html) ([spack.yaml](spack.yaml)), a list of the specific versions of EBRAINS tools that are part of the software release
 - a script ([install_spack_env.sh](install_spack_env.sh)) that can be used to install the latest spack environment on any machine (either install from scratch or update an existing installation)
 - CI/CD pipelines configured for (a) testing the installation of new packages and (b) deploying the environment to the EBRAINS Collaboratory Lab.
+- (WIP) all the site-specific configurations that have been used to install the EBRAINS Spack environment in different systems, such as the EBRAINS Lab and the Fenix HPC systems.
 
 ## Contributing
 
@@ -42,9 +43,8 @@ Clone Spack. We currently use version v0.18.1:
 git clone --depth 1 -c advice.detachedHead=false -c feature.manyFiles=true --branch v0.18.1 https://github.com/spack/spack
 ```
 
-Modify (if needed) and copy the package.yaml file (that contains important package settings for Spack) and activate Spack:
+Activate Spack:
 ```
-cp ebrains-spack-builds/packages.yaml spack/etc/spack/packages.yaml
 . spack/share/spack/setup-env.sh
 ```
 
@@ -53,14 +53,21 @@ Add the project repository to your Spack environment:
 spack repo add ebrains-spack-builds
 ```
 
-Create and activate the environment:
+Create the environment:
 ```
-spack env create ebrains-env ebrains-spack-builds/spack.yaml
-spack env activate ebrains-env
+spack env create -d ebrains-spack-builds/
 ```
 
-Install:
+Define your site-specific configurations:
 ```
+export SYSTEMNAME=<your-system-name>
+mkdir ebrains-spack-builds/site-config/$SYSTEMNAME
+# copy any site-specific .yaml files inside the new dir
+```
+
+Activate the environment and install:
+```
+spack env activate ebrains-spack-builds
 spack install --fresh
 ```
 

create_job.sh

@@ -39,6 +39,8 @@ spec:
             mountPath: /srv
         command: ["/usr/local/bin/deploy-build-env.sh", "$OP", "$INSTALLATION_ROOT", "$SPACK_VERSION", "$SPACK_ENV", "$BRANCH", "$RELEASE_NAME", "$LAB_KERNEL_ROOT"]
         env:
+          - name: SYSTEMNAME
+            value: ebrainslab
           - name: GITLAB_USER
             valueFrom:
               secretKeyRef:

install_spack_env.sh

@@ -17,6 +17,9 @@ EBRAINS_SPACK_ENV=$4  # name of EBRAINS Spack environment to be created/updated
 export SPACK_USER_CACHE_PATH=$INSTALLATION_ROOT/spack/.spack
 export SPACK_USER_CONFIG_PATH=$INSTALLATION_ROOT/spack/.spack
 
+# define SYSTEMNAME variable in sites where it's not already defined
+export SYSTEMNAME=${SYSTEMNAME:-${HPC_SYSTEM:-$BSC_MACHINE}}
+
 # initial setup: clone spack if spack dir doesn't already exist
 if [ ! -d $INSTALLATION_ROOT/spack ]
 then
@@ -26,15 +29,18 @@ then
   sed -i "s/self.file_like, \"w\"/self.file_like, \"a\"/g" $INSTALLATION_ROOT/spack/lib/spack/llnl/util/tty/log.py
 fi
 
-# copy package settings (modify if necessary) and activate Spack
-cp $EBRAINS_REPO/packages.yaml $INSTALLATION_ROOT/spack/etc/spack/packages.yaml
+# activate Spack
 source $INSTALLATION_ROOT/spack/share/spack/setup-env.sh
 
 # install platform compiler (extract version from packages.yaml)
-EBRAINS_SPACK_COMPILER=$(grep 'compiler' $EBRAINS_REPO/packages.yaml | awk -F'[][]' '{ print $2 }')
-spack compiler find
-spack install $EBRAINS_SPACK_COMPILER
-spack load $EBRAINS_SPACK_COMPILER
+if [ $SYSTEMNAME == ebrainslab ]
+then
+  EBRAINS_SPACK_COMPILER=$(grep 'compiler' $EBRAINS_REPO/site-config/$SYSTEMNAME/packages.yaml | awk -F'[][]' '{ print $2 }')
+  spack compiler find
+  spack install $EBRAINS_SPACK_COMPILER
+  spack load $EBRAINS_SPACK_COMPILER
+fi
+
 spack compiler find
 
 # add repo if it does not exist
@@ -49,12 +55,17 @@ then
   spack env create $EBRAINS_SPACK_ENV
 fi
 
-# update and activate environment
-cp $EBRAINS_REPO/spack.yaml $SPACK_ROOT/var/spack/environments/$EBRAINS_SPACK_ENV/spack.yaml
+# activate environment
 spack env activate $EBRAINS_SPACK_ENV
+# update environment site-configs
+rm -rf $SPACK_ENV/site-config && cp -r $EBRAINS_REPO/site-config $SPACK_ENV
+# update spack.yaml: merge top-level and site-specific spack.yaml files
+spack-python $EBRAINS_REPO/site-config/ymerge.py $EBRAINS_REPO/spack.yaml $EBRAINS_REPO/site-config/$SYSTEMNAME/spack.yaml > /tmp/spack.yaml
+cp /tmp/spack.yaml $SPACK_ENV/
+
 # There is a known spack bug (https://github.com/spack/spack/issues/29447) in installing test dependencies
 # for installation tests. The workaround suggested in the issue is to NOT concretize separately, but simply
-# remove the .lock file and let the enironment be concretized by the spack install command:
+# remove the .lock file and let the environment be concretized by the spack install command:
 rm $SPACK_ROOT/var/spack/environments/$EBRAINS_SPACK_ENV/spack.lock || echo "No spack.lock file"
 # install the environment, use 2 jobs to reduce the amount of required RAM
 spack install -y -j2 --fresh --test root

packages/hxtorch/package.py

@@ -14,10 +14,10 @@ class Hxtorch(WafPackage):
     # This repo provides a waf binary used for the build below
     git      = "https://github.com/electronicvisions/pynn-brainscales.git"
 
-    version('6.0-a1', branch='waf')
+    version('6.0-rc1', branch='waf')
 
     # PPU compiler dependencies
-    depends_on('oppulance@6.0-a1')
+    depends_on('oppulance@6.0-rc1')
 
     # host software dependencies
     depends_on('bitsery', type=('build', 'link', 'run'))

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',    sha256='4504ff7f9cfa051c91a5e85a0761bdd09d23aeeadac22c45f6be18b7fbe2db43')
     version('3.4',    sha256='c56699111f899045ba48e55e87d14eca8763b48ebbb3648beee701a36aa3af20')
     version('3.3',    sha256='179462b966cc61f5785d2fee770bc36f86745598ace9cd97dd620622b62043ed')
     version('3.2',    sha256='583d5725882ad5e8fd4fc7ffab425da97cbbb91fadbc327e940c184e8892b958')

packages/oppulance/package.py

@@ -22,8 +22,8 @@ class Oppulance(Package):
 
     releases = [
         {
-            'version': '6.0-a1',
-            'tag': 'ebrains-6.0-a1'
+            'version': '6.0-rc1',
+            'tag': 'ebrains-6.0-rc1'
         },
     ]
 

packages/py-bluepyefe/package.py

+# (from https://github.com/BlueBrain/spack)
+
+# 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.package import *
+
+
+class PyBluepyefe(PythonPackage):
+    """Blue Brain Python E-feature extraction"""
+
+    homepage = "https://github.com/BlueBrain/BluePyEfe"
+    pypi = "bluepyefe/bluepyefe-0.3.13.tar.gz"
+    git = "https://github.com/BlueBrain/BluePyEfe.git"
+
+    version("2.2.18", sha256="bfb50c6482433ec2ffb4b65b072d2778bd89ae50d92dd6830969222aabb30275")
+
+    depends_on("py-setuptools", type="build")
+
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-neo", type=("build", "run"))
+    depends_on("py-matplotlib", type=("build", "run"))
+    depends_on("py-efel", type=("build", "run"))
+    depends_on("py-scipy", type=("build", "run"))
+    depends_on("py-h5py", type=("build", "run"))
+    depends_on("py-igor", type=("build", "run"))
+
+    def setup_run_environment(self, env):
+        env.set("NEURON_INIT_MPI", "0")
+        env.unset("PMI_RANK")

packages/py-bluepymm/package.py

+# (from https://github.com/BlueBrain/spack)
+
+# 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.package import *
+
+
+class PyBluepymm(PythonPackage):
+    """Blue Brain Model Management Python Library"""
+
+    homepage = "https://github.com/BlueBrain/BluePyMM"
+    pypi = "bluepymm/bluepymm-0.7.49.tar.gz"
+
+    version("0.7.65", sha256="024b009decd8d967b3b885421196d53670e3c0a6b75aaaa55559f148b0b0d7d4")
+
+    depends_on("py-setuptools", type="build")
+    depends_on("py-bluepyopt", type="run")
+    depends_on("py-matplotlib", type="run")
+    # The below dependency should disappear once
+    # the matplotlib package is fixed
+    depends_on("py-backports-functools-lru-cache", type="run", when="^python@:3.3.99")
+    depends_on("py-pandas", type="run")
+    depends_on("py-numpy", type="run")
+    depends_on("py-ipyparallel", type="run")
+    depends_on("py-lxml", type="run")
+    depends_on("py-sh", type="run")
+    depends_on("neuron", type="run")
+    depends_on("py-h5py", type="run")
+    depends_on("py-pyyaml", type="run")
+
+    def setup_run_environment(self, env):
+        env.unset("PMI_RANK")
+        env.set("NEURON_INIT_MPI", "0")

packages/py-bluepyopt/package.py

-# (this package was adapted from https://github.com/BlueBrain/spack/blob/develop/bluebrain/repo-bluebrain/packages/py-bluepyopt/package.py)
+# (from https://github.com/BlueBrain/spack)
 
+# 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 *
+from spack.package import *
 
 
 class PyBluepyopt(PythonPackage):
@@ -10,11 +14,8 @@ class PyBluepyopt(PythonPackage):
     homepage = "https://github.com/BlueBrain/BluePyOpt"
     pypi = "bluepyopt/bluepyopt-1.9.27.tar.gz"
 
-    maintainers = ["hjorth", "elmath"]
-
     # NOTE : while adding new release check pmi_rank.patch compatibility
-    version("1.12.63", sha256="ec33abe2113767420cae0317da4d61554eb934e5447cadb54d66620576b97714")
-    version("1.11.47", sha256="cffe1698930e3e89544c441674a5f66e310c72db27f8265b17200713d9d16614")
+    version("1.13.86", sha256="37b4abcc4a53ed5af50fa0b3bc4d0003332b7f2f2b6e4d9f0b9de8638254e753")
     version("1.10.38", sha256="fb1411c6a8fbfac52d36b837225bae882fd6524acfb4d0580189312ef3c1cfcc")
     version("1.9.37", sha256="4399af71de48b288832e92f0de73c431bf88d6e76e2c4ea250c3b38fb38a45a8")
     version("1.9.27", sha256="4cce15b92b32311c808cae5e005b664deb6e8dc5df4ca13ea7b59252ae346522")
@@ -28,19 +29,19 @@ class PyBluepyopt(PythonPackage):
 
     variant("neuron", default=True, description="Use BluePyOpt together with NEURON")
 
-    depends_on("py-setuptools",         type=("build"))
-    depends_on("py-pandas@0.18:",       type=("build","run"))
-    depends_on("py-numpy@1.6:",         type=("build","run"))
-    depends_on("py-efel@2.13:",         type=("build","run"))
-    depends_on("py-deap",               type=("build","run"))
-    depends_on("py-deap@1.3.3:",        type=("build","run"), when="@1.12.63:")
-    depends_on("py-scoop@0.7:",         type=("build","run"), when="@:1.9.37")
-    depends_on("py-ipyparallel",        type=("build","run"))
-    depends_on("py-pickleshare@0.7.3:", type=("build","run"))
-    depends_on("py-future",             type=("build","run"))
-    depends_on("py-jinja2@2.8:",        type=("build","run"))
-    depends_on("py-pebble@4.3.10:",     type=("build","run"))
-    depends_on("neuron",                type=("build","run"), when="+neuron")
+    depends_on("py-setuptools", type="build")
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-pandas", type=("build", "run"))
+    depends_on("py-deap", type=("build", "run"))
+    depends_on("py-deap@1.3.3:", type=("build","run"), when="@1.13.86:")
+    depends_on("py-efel", type=("build", "run"))
+    depends_on("py-ipyparallel", type=("build", "run"))
+    depends_on("py-pickleshare", type=("build", "run"))
+    depends_on("py-jinja2", type=("build", "run"))
+    depends_on("py-future", type=("build", "run"))
+    depends_on("py-pebble@4.3.10:", type=("build", "run"))
+    depends_on("py-scoop@0.7:", type=("build", "run"), when="@:1.9.37")
+    depends_on("neuron", type=("build", "run"), when="+neuron")
 
     def setup_run_environment(self, env):
         env.unset("PMI_RANK")

packages/py-efel/package.py

-# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
+# (from https://github.com/BlueBrain/spack)
+
+# 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 *
+from spack.package import *
 
 
 class PyEfel(PythonPackage):
-    """Electrophys Feature Extract Library (eFEL)
-    """
+    """The Electrophys Feature Extract Library (eFEL) allows
+    neuroscientists to automatically extract features from time series data
+    recorded from neurons (both in vitro and in silico).
+    Examples are the action potential width and amplitude in
+    voltage traces recorded during whole-cell patch clamp experiments.
+    The user of the library provides a set of traces and selects the
+    features to be calculated. The library will then extract the requested
+    features and return the values to the user."""
 
     homepage = "https://github.com/BlueBrain/eFEL"
-    pypi     = "efel/efel-4.0.4.tar.gz"
-    git      = "https://github.com/BlueBrain/eFEL.git"
+    pypi = "efel/efel-3.0.80.tar.gz"
 
     version("4.0.4", sha256="258c506776df609edc799338fd773e78f0f0315fd6f3e2f969478bda401a8894")
 
-    depends_on("python@3.6.9:")
-    depends_on("py-setuptools", type=("build"))
-    depends_on("py-numpy@1.6:", type=("build", "run"))
-    depends_on("py-six",        type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+    depends_on("py-numpy", type="run")
+    depends_on("py-six", type="run")

packages/py-igor/package.py

+# (backported from Spack v0.20.0)
+
+# Copyright 2013-2023 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.package import *
+
+
+class PyIgor(PythonPackage):
+    """igor: interface for reading binary IGOR files."""
+
+    homepage = "http://blog.tremily.us/posts/igor/"
+    pypi = "igor/igor-0.3.tar.gz"
+
+    version("0.3", sha256="b04ac38c68fb81cf3167a9981dc5a20379112d40268bb72c5a8514dc8051abba")
+
+    depends_on("py-setuptools", type="build")
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-matplotlib", type=("build", "run"))
\ No newline at end of file

packages/py-libsonata/package.py

-# (this package was adapted from https://github.com/BlueBrain/spack/blob/develop/bluebrain/repo-bluebrain/packages/py-libsonata/package.py)
+# (from https://github.com/BlueBrain/spack)
 
+# 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 *
+from spack.package import *
 
 
 class PyLibsonata(PythonPackage):
@@ -10,12 +14,15 @@ class PyLibsonata(PythonPackage):
     homepage = "https://github.com/BlueBrain/libsonata"
     git = "https://github.com/BlueBrain/libsonata.git"
     pypi = "libsonata/libsonata-0.1.14.tar.gz"
-    
-    maintainers = ["hjorth", "elmath"]
 
     submodules = True
 
-    version("develop", branch="master")
+    version("develop", branch="master", get_full_repo=True)
+    version("0.1.22", sha256="4adbb32ed2fac5d3c74bde03a5e2adb319724d324318a2a7dc2ef3c30f817b2c")
+    version("0.1.21", sha256="5b280d82cb21a745d9cdb736c00446e0209494c21d2d17a2c878fabf23a08b68")
+    version("0.1.20", sha256="f2e63a26dcf045bb7424e236e12f9b9ef8c46c356e953d26555f313f5763651e")
+    version("0.1.18", sha256="1b13728cbffbcb74cc864c7bc186e568945e25c260f732ffa872437c081fd9b4")
+    version("0.1.17", sha256="d122dd9fce82c8ce1621746ed9029e7db0d319fb94f6a737fb14f572f632f7b4")
     version("0.1.16", sha256="49ced56992ba8be8aa6638525e8078b7e3ce0d5c05c34ee90746cab02bb5185a")
     version("0.1.15", sha256="8c7c509db692b482cba5b0453579747db5a981ce5b3c13da96b14ae0332a6e81")
     version("0.1.14", sha256="a5c75df1c3ef6fac10d92fb6781643e0834e5c35debe77693686dab8bfcf221f")
@@ -24,9 +31,10 @@ class PyLibsonata(PythonPackage):
     version("0.1.11", sha256="95f302818971fec3f19ef18febd5c31c580490692138c8e4fe3534104d88b5e0")
     version("0.1.10", sha256="7ef9f911f7ea31da5ff5306d8372ec194d223850aede0878ac2a921ce049bbb2")
 
+    depends_on("cmake@3.3:", type="build")
     depends_on("hdf5")
     depends_on("py-pybind11")
-    depends_on("cmake@3.3:",        type=("build"))
-    depends_on("py-setuptools",     type=("build"), when="@0.1:")
-    depends_on("py-setuptools-scm", type=("build"), when="@0.1:")
-    depends_on("py-numpy@1.17:",    type=("build", "run"))
+
+    depends_on("py-numpy@1.17:", type=("build", "run"))
+    depends_on("py-setuptools", type="build", when="@0.1:")
+    depends_on("py-setuptools-scm", type="build", when="@0.1:")

packages/py-morph-tool/package.py

+# (from https://github.com/BlueBrain/spack)
+
+# 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.package import *
 
 
@@ -25,5 +32,5 @@ class PyMorphTool(PythonPackage):
     depends_on("neuron+python@7.8:", type=("build", "run"))
     depends_on("py-bluepyopt@1.9.37:", type=("build", "run"))
 
-    depends_on("py-neurom@3.0:3.999", type=("build", "run"))
-    depends_on("py-morphio@3.0:3.999", type=("build", "run"))
+    depends_on("py-neurom@3.0:3.999,develop", type=("build", "run"))
+    depends_on("py-morphio@3.0:3.999,develop", type=("build", "run"))

packages/py-morphio/package.py

-# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# (from https://github.com/BlueBrain/spack)
+
+# 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 https://github.com/BlueBrain/spack/blob/develop/bluebrain/repo-bluebrain/packages/py-morphio/package.py
 
 from spack.package import *
 
@@ -18,6 +18,7 @@ class PyMorphio(PythonPackage):
     version("develop", branch="master", submodules=True)
     version("unifurcation", branch="unifurcation", submodules=True)
 
+    version("3.3.5", sha256="9e6cfebaea32080131b2b08a4a32dfbe92b18427a3e557861e27c4131f7542ac")
     version("3.3.4", sha256="b70c6884e9b835560501f798c75c9cc7eaf3162cba1d930b5a9b854bb9ea60dc")
     version("3.3.3", sha256="f6d91970cfd734b2e5fb8f9239a0bfa00519fe082dd8e403e4cc204dbdf0a9fa")
     version("3.3.2", sha256="fc961defbfbfb3f11360954fb3ec51373eaff25b154fa31d6b31decca6937780")

packages/py-neurom/package.py

-# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# (from https://github.com/BlueBrain/spack)
+
+# 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 https://github.com/BlueBrain/spack/blob/develop/bluebrain/repo-bluebrain/packages/py-neurom/package.py
 
 from spack.package import *
 

packages/py-neuror/package.py

+# (from https://github.com/BlueBrain/spack)
+
+# Copyright 2013-2021 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.package import *
 
 

packages/pynn-brainscales/package.py

@@ -13,10 +13,10 @@ class PynnBrainscales(WafPackage):
     homepage = "https://github.com/electronicvisions/pynn-brainscales"
     git      = "https://github.com/electronicvisions/pynn-brainscales.git"
 
-    version('6.0-a1', branch='waf')
+    version('6.0-rc1', branch='waf')
 
     # PPU compiler dependencies
-    depends_on('oppulance@6.0-a1')
+    depends_on('oppulance@6.0-rc1')
 
     # host software dependencies
     depends_on('bitsery', type=('build', 'link', 'run'))

site-config/.gitignore

+# exclude all files to allow sites to add own configs
+*/
+
+# un-exclude the configs tracked in this repository
+!ebrainslab
+!g100
+!jurecadc
+!jusuf
+!hsmcompute
+