.gitignore

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

.gitlab/issue_templates/build-error.md

+<!-- Thanks for taking the time to report this build failure. To proceed with the report please:
+
+1. Title the issue "Installation issue: <name-of-the-package>".
+2. Provide the information required below.
+
+We encourage you to try, as much as possible, to reduce your problem to the minimal example that still reproduces the issue. That would help us a lot in fixing it quickly and effectively! -->
+
+### Summary
+
+|               |                                               |
+|---------------|-----------------------------------------------|
+| Summary       | Spack package build failure                   |
+| Package info  | <!-- Spack package name or entire spec -->    |
+| System        | <!-- HPC cluster name/Collab Lab/other  -->   |
+| Related       | <!-- Other related issues (if applicable) --> |
+
+### Steps to reproduce the issue
+
+<!-- Fill in the console output from the exact spec you are trying to build. -->
+```console
+$ spack spec -I <spec>
+...
+$ spack install <spec>
+...
+```
+
+### Error message
+<!-- Please post the error message from spack inside the <details> tag below: -->
+
+<details><summary>Error message</summary><pre><code>
+(add error logs here)
+</code></pre></details>
+
+### Information on your system
+
+<!-- Please include the output of `spack debug report` -->
+
+<!-- If you have any relevant configuration detail (custom `packages.yaml` or `modules.yaml`, etc.) you can add that here as well. -->
+
+### Additional information
+
+<!-- Please upload the following files. They should be present in the stage directory of the failing build. Also upload any config.log or similar file if one exists. -->
+* [spack-build-out.txt]()
+* [spack-build-env.txt]()
+
+/label ~build-error

.gitlab/issue_templates/test-error.md

+<!-- Thanks for taking the time to report this test failure. To proceed with the report please:
+
+1. Title the issue "Testing issue: <name-of-the-package>".
+2. Provide the information required below.
+
+We encourage you to try, as much as possible, to reduce your problem to the minimal example that still reproduces the issue. That would help us a lot in fixing it quickly and effectively! -->
+
+### Summary
+
+|               |                                               |
+|---------------|-----------------------------------------------|
+| Summary       | Spack package test failure                    |
+| Package info  | <!-- Spack package name or entire spec -->    |
+| System        | <!-- HPC cluster name/Collab Lab/other  -->   |
+| Related       | <!-- Other related issues (if applicable) --> |
+
+### Steps to reproduce the issue
+
+<!-- Fill in the console output from the exact spec you are trying to build and test. -->
+```console
+$ spack spec -I <spec>
+...
+$ spack spack install --test root <spec>
+...
+```
+
+### Error message
+<!-- Please post the error message from install-time-test-log.txt inside the <details> tag below: -->
+
+The test error message (first 1000 lines) from install-time-test-log.txt is the following:
+
+<details><summary>Error message</summary><pre><code>
+(add error logs here)
+</code></pre></details>
+
+### Information on your system
+
+<!-- Please include the output of `spack debug report` -->
+
+### Additional information
+
+<!-- Please upload the following files. They should be present in the stage directory of the failing build. Also upload any config.log or similar file if one exists. -->
+* [spack-build-out.txt]()
+* [spack-build-env.txt]()
+* [install-time-test-log.txt]()
+
+/label ~test-error

.gitlab/merge_request_templates/new-package.md

+### Summary
+
+|               |                                        |
+|---------------|----------------------------------------|
+| Package       | <!-- Spack package name -->            |
+| Contact point | <!-- maintainer GitLab handle -->      |
+| KG entry      | <!-- insert link -->                   |
+
+
+### Checks
+
+<!-- please download the EBRAINS Software Quality checklist, fill it and replace the file below -->
+* [ ] Software Quality Checklist: [SQ-Checklist.pdf](https://drive.ebrains.eu/d/6061531326d048308823/files/?p=%2FSQ-Checklist.pdf) (level: <!-- passing, silver, gold -->)
+* [ ] Current maintainer is listed first in `package.py`
+* [ ] No pinned dependency versions
+* [ ] Post-installation tests are defined
\ No newline at end of file

.gitlab/merge_request_templates/new-version.md

+### Summary
+
+|               |                                        |
+|---------------|----------------------------------------|
+| Package       | <!-- Spack package name -->            |
+| Version added | <!-- version number -->                |
+| Contact point | <!-- maintainer GitLab handle -->      |
+| KG entry      | <!-- insert link -->                   |
+
+
+### Checks
+
+<!-- please download the EBRAINS Software Quality checklist, fill it and replace the file below -->
+* [ ] Software Quality Checklist: [SQ-Checklist.pdf](https://drive.ebrains.eu/d/6061531326d048308823/files/?p=%2FSQ-Checklist.pdf) (level: <!-- passing, silver, gold -->)
+* [ ] Current maintainer is listed first in `package.py`
+* [ ] No pinned dependency versions
+* [ ] Post-installation tests are defined
\ No newline at end of file

.gitmodules

+[submodule "vendor/spack"]
+	path = vendor/spack
+	url = https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/spack.git
+	shallow = true
+[submodule "vendor/yashchiki"]
+	path = vendor/yashchiki
+	url = https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/dedal
+	shallow = true

LICENSE-APACHE

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LICENSE-MIT

+MIT License
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+SOFTWARE.

README.md

 # ebrains-spack-builds
 
-Build and distribute software tools with Spack for the EBRAINS Collaboratory Lab containers.  
+Build and distribute EBRAINS software tools with Spack.
 
-**Quickstart for Notebooks**  
-- Open a terminal at a running Collaboratory Lab Container and execute the following:
+## Introduction
+
+Building and deploying EBRAINS tools to make them available for direct use in the Collaboratory Lab environment is a challenging task, mainly due to the number of tools and the increasing complexity of resolving their dependency conflicts. To efficiently solve this problem, we have implemented a delivery strategy based on [Spack](https://spack.io/), a package manager specifically designed to simplify the installation and management of scientific software (more information [here](https://drive.ebrains.eu/f/73bcfe5acf924cef83cc/)).
+
+Spack is highly customizable and flexible, allowing developers to create their own packages and specify their dependencies and custom build configurations. It supports a wide range of programming languages (Python, R, C, C++, Fortran etc), different hardware architectures and operating systems. All an EBRAINS developer needs to do is create a Spack package (simple description of the build logic of their software). Then Spack automatically handles downloading, building, and installing the entire EBRAINS environment, managing all their dependencies and other requirements.
+
+## Repository
+
+This repository is where the EBRAINS Spack packages are maintained. It contains:
+- the EBRAINS [Spack repository](https://spack.readthedocs.io/en/latest/repositories.html), that contains all available EBRAINS Spack packages ([packages/](packages))
+- 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
+
+HBP's developers/component owners that want their EBRAINS tools to be included in the official EBRAINS releases and deployed for direct use from the Lab environment should follow those steps:
+
+- Fork this repository
+- Clone the forked repository to local machine (or use the Gitlab Web IDE)
+- Create a new Spack package for your tool. For instructions on how to do this, see [the Spack documentation](https://spack.readthedocs.io/en/latest/packaging_guide.html) and the developer's section of [our documentation](https://drive.ebrains.eu/f/73bcfe5acf924cef83cc/). **Add the new package** to the repository, by creating a directory inside [packages/](./packages/) and copying the package recipe there. Also don't forget to **add a spec** to [spack.yaml](spack.yaml)
+- Commit the new package and push to a new branch, e.g. `add-packagename`
+- Create a Merge Request to merge your changes into the master branch of the original repository
+- Check the results of the automated test build job and solve any issues
+- Once the tests pass, wait for TC to approve and merge. Once merged, the package will be automatically built and deployed to the integration environment of the Collaboratory Lab (lab-int).
+
+## Installing the EBRAINS official Software release
+
+To install the EBRAINS Spack environment on a new machine, it is recommended to follow exactly the steps from [install_spack_env.sh](install_spack_env.sh), that installs or updates and tests the spack environment defined in this repository. In general, you need to:
+
+Clone this repository. You can use the `ebrains-yy-mm` branches to install the EBRAINS official releases, the `experimental-rel` branch for the experimental release, or the `master` branch for the latest state:
+```
+git clone --branch {branch-name} https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/ebrains-spack-builds.git
 ```
-#update modulepath of JupterLab container to include spack arch modulefiles path
-module use /srv/test-build/spack/share/spack/modules/linux-centos7-broadwell/
-module use /srv/test-build/spack/share/spack/modules/linux-centos7-x86_64/
 
-#start JupyterLab kernel made for spack
-jupyter kernelspec install --user /srv/jupyterlab_kernels/int/release20210930/spack_python_kernel_release_20210930/
+Clone Spack. We currently use version v0.23.1:
 ```
-- Then select File > New Launcher
-- Open a new Notebook with the "EBRAINS_release_20210930" kernel
-- Import the tools available with spack:
+git clone --depth 1 -c advice.detachedHead=false -c feature.manyFiles=true --branch v0.23.1 https://github.com/spack/spack
 ```
-import nest
-import arbor
-import neuron
+
+Activate Spack:
+```
+. spack/share/spack/setup-env.sh
+```
+
+Add the project repository to your Spack environment:
+```
+spack repo add ebrains-spack-builds
 ```
 
-**Quickstart for terminal**  
-- Open a terminal at a running Collaboratory Lab Container and execute the following:
+Define your site-specific configurations:
 ```
- git clone https://gitlab.ebrains.eu/akarmas/ebrains-spack-builds.git
- cd ebrains-spack-builds
- source ./load_sim_tools.sh
+export SYSTEMNAME=<your-system-name>
+mkdir ebrains-spack-builds/site-config/$SYSTEMNAME
+# copy any site-specific .yaml files inside the new dir
 ```
-- Then you can start python and import the available tools
-- Currently installed:  
- arbor  
- neuron  
- nest
-
-## Gitlab CI/CD Enviromental variables
-
-The following variable(s) must be set up if not or re-configured if tokens expire.  
-	  
-OPENSHIFT_TOKEN: Token to login to OpenShift cluster (with the "gitlab" service account)  
-OPENSHIFT_DEV_SERVER: The URL of the OpenShift Development cluster needed for deploying software in lab-int environment  
-BUILD_ENV: The name of the environment to deploy the software of the next commit  
-OPERATION: The operation to perform on the spack environment (one of the following: testing, create, update, delete)
-  
-## Copy spack .yaml files and packages to the Openshift job pod that does the build
-
-The gitlab runner copies the various files needed for the build to the OpenShift job pod.
-- It copies the {spack, repo}.yaml files, the create_JupyterLab_kernel.sh script and the packages/ directory
-- The runner waits until the job's pod is running to start copying the files
-- The pod (built from [tc/ebrains-spack-build-env:latest image](https://docker-registry.ebrains.eu/harbor/projects/8/repositories/ebrains-spack-build-env)) waits until the necessary file(s) has finished copying so that it can continue the build process
-
-## Bulding software binaries with Spack
-
-- The build process is powered by Spack a multi-platform package manager that builds and installs multiple versions and configurations of software.
-- A Job (object) in OpenShift is responsible for the build process.
-- The gitlab runner starts a new Job that runs on an OpenShift pod that uses the container image developed in [this](https://gitlab.ebrains.eu/akarmas/ebrains-spack-build-env/) repository that holds all the Spack specifics needed for the build process. All the Spack configuration necessary for a successfull build is to be changed from the Spack configuration files that are found in the present repository.
-- The OpenShift Job's pod mounts an NFS drive that is also mounted by all Collaboratory Lab containers and performs the entire build process with Spack on that NFS drive and as a result all the installed software is readily available to Collaboratory Lab containers
-- A schema of the build process can be found [here](https://drive.ebrains.eu/smart-link/6adcd99f-c088-472e-a596-37ac38869051/)
-
-## Activating software in the Collaboratory Lab containers
-
-- Currently to activate the pre-built simulation tools in the Collaboratory Lab containers refer to **Quickstart** at the beggining of this file
-- There are two options: i) for using the simulation tools directly in the notebooks and ii) for using the simulation tools from a terminal in a Collaboratory Lab container
-
-**ToDo: put the necessary activation commands in the startup script of a JupyterLab conatiner spawned in OpenShift to hide all implementation details from the users**  
+
+Activate the environment and install:
+```
+spack env activate ebrains-spack-builds
+spack install --fresh
+```
+
+## Troubleshooting
+
+If you encounter any issues with installing, testing, or using the EBRAINS Spack environment or a specific package, please [open an issue](https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/ebrains-spack-builds/-/issues/new) using the provided templates, or contact the Technical Coordination team directly.

create_JupyterLab_kernel.sh

 #!/bin/bash
-#title           :create_JupyterLab_kernel.sh
-#description     :Script to create a spackified JupyterLab kernel conf and place it to NFS where it can be loaded by all users.   
-#usage           :./create_JupyterLab_kernel.sh $INSTALLATION_ROOT $ENV $LAB_KERNEL_PATH
-#==============================================================================
 
-INSTALLATION_ROOT=$1
-SPACKIFIED_ENV=$2
-LAB_KERNEL_PATH=$3
+# ===========================================================================================================
+# title         : create_JupyterLab_kernel.sh
+# usage         : ./create_JupyterLab_kernel.sh $INSTALLATION_ROOT $EBRAINS_SPACK_ENV $RELEASE_NAME $LAB_KERNEL_ROOT
+# description   : creates a spackified JupyterLab kernel conf and places it to the NFS where it can be
+#                 loaded by all users.
+# ===========================================================================================================
 
-# capture the empty env
-cd /opt/app-root/src
-env >> before.txt
+set -euo pipefail
 
-# load spack, spack repos and spack env
-cp -r /srv/$INSTALLATION_ROOT/spack/.spack ~
-source /srv/$INSTALLATION_ROOT/spack/share/spack/setup-env.sh
-spack repo add /srv/$INSTALLATION_ROOT/ebrains-spack-builds
-# no need to activate as the env is already activated in the context it is used
-#spack env activate $SPACKIFIED_ENV
+INSTALLATION_ROOT=$1
+EBRAINS_SPACK_ENV=$2
+RELEASE_NAME=$3
+LAB_KERNEL_ROOT=$4
 
-module use /srv/$INSTALLATION_ROOT/spack/share/spack/modules/linux-centos7-broadwell/
-module use /srv/$INSTALLATION_ROOT/spack/share/spack/modules/linux-centos7-x86_64/
-source /srv/$INSTALLATION_ROOT/spack/var/spack/environments/$SPACKIFIED_ENV/loads
-# add also user's .local python3.8 packages to allow package installation at runtime
-# by the user using pip
-export PYTHONPATH=$PYTHONPATH:/opt/app-root/src/.local/lib/python3.8/site-packages
-export PATH=$PATH:/opt/app-root/src/.local/bin
-# export also python modules installed in the base docker Collab image
-export PYTHONPATH=$PYTHONPATH:/usr/local/lib/python3.8/dist-packages
+# kernel name is lowercase release name
+KERNEL_NAME=$(echo "$RELEASE_NAME" | tr '[:upper:]' '[:lower:]')
+# kernel dir is a directory inside LAB_KERNEL_ROOT named after the kernel
+KERNEL_PATH=$LAB_KERNEL_ROOT/$KERNEL_NAME
 
-# capture the env after spack activation
-cd /opt/app-root/src
-env >> after.txt
+# prepare the base env.sh script required for the JupyterLab kernels:
+mkdir -p $KERNEL_PATH/bin
 
-# prepare the env file required for the JupyterLab kernel
-mkdir $LAB_KERNEL_PATH/bin
-cat <<EOF > $LAB_KERNEL_PATH/bin/env.sh
+# (1) create env.sh bash script
+cat <<EOF > $KERNEL_PATH/bin/env.sh
 #!/usr/bin/env bash
 set -euxo pipefail
 EOF
 
-# load here all tools
-#spack load --sh -r python@3.8.11 py-ipykernel py-pip py-numpy@1.21.0 py-scipy py-pandas py-seaborn py-matplotlib arbor nest@3.0 neuron py-pynn tvb-data tvb-library meta-brainscales %gcc@10.3.0 >> $LAB_KERNEL_PATH/bin/env.sh
+# (2) append the necessary env variables for spack env and tools
+cat $INSTALLATION_ROOT/spack/var/spack/environments/$EBRAINS_SPACK_ENV/load_env.sh >> $KERNEL_PATH/bin/env.sh
+# also copy the script so that it can be used independently:
+cp $INSTALLATION_ROOT/spack/var/spack/environments/$EBRAINS_SPACK_ENV/load_env.sh $KERNEL_PATH/bin/
+
+# (3) also add the user's .local locations to allow package installation at runtime,
+# and the location of python modules installed in the base docker Collab image
+cat <<EOF >> $KERNEL_PATH/bin/env.sh
+export PATH=\$PATH:/opt/app-root/src/.local/bin
+export PYTHONPATH=\$PYTHONPATH:/opt/app-root/src/.local/lib/python3.8/site-packages:/usr/local/lib/python3.8/dist-packages
+export R_LIBS_USER=/opt/app-root/src/.local/lib/R/site-library
+mkdir -p \$R_LIBS_USER
+export R_LIBS=\$R_LIBS_USER:\$R_LIBS
+EOF
+
+# ... and set the SYSTEMNAME env var, to use Spack commands inside the kernel
+cat <<EOF >> $KERNEL_PATH/bin/env.sh
+export SYSTEMNAME=ebrainslab
+EOF
 
-# append the necessary env variables for spack env and tools
-cd /opt/app-root/src
-diff before.txt after.txt|grep ">"|cut -c 3- |awk '$0="export "$0' >> $LAB_KERNEL_PATH/bin/env.sh
+# (4) create startup script for python kernel
+cat $KERNEL_PATH/bin/env.sh > $KERNEL_PATH/bin/env_python.sh
+echo "python -m ipykernel_launcher -f \$@" >> $KERNEL_PATH/bin/env_python.sh
+chmod +x $KERNEL_PATH/bin/env_python.sh
 
-# end of env creation
-cat <<EOF >>$LAB_KERNEL_PATH/bin/env.sh
-python -m ipykernel_launcher -f \$@
+# ... and the new kernel's configuration file
+mkdir -p $KERNEL_PATH/$KERNEL_NAME
+cat <<EOF > $KERNEL_PATH/$KERNEL_NAME/kernel.json
+{
+ "argv": ["$KERNEL_PATH/bin/env_python.sh", "{connection_file}", "--profile=default"],
+ "display_name": "$RELEASE_NAME",
+ "language": "python",
+ "env": { "LAB_KERNEL_NAME": "$RELEASE_NAME", "LAB_KERNEL_RELEASE_DATE": "$(date +"%Y-%m-%d")" }
+}
 EOF
-chmod +x $LAB_KERNEL_PATH/bin/env.sh
-# create the new kernel's configuration file
-mkdir $LAB_KERNEL_PATH/spack_python_kernel_release_202112
-cat <<EOF >$LAB_KERNEL_PATH/spack_python_kernel_release_202112/kernel.json
+
+# ... and add EBRAINS logo to kernel
+cp $(dirname ${BASH_SOURCE[0]})/etc/logo-64x64-python.png $KERNEL_PATH/$KERNEL_NAME/logo-64x64.png
+
+# (5) create startup script for R kernel
+cat $KERNEL_PATH/bin/env.sh > $KERNEL_PATH/bin/env_r.sh
+echo "R --slave -e \"IRkernel::main()\" --args \$@" >> $KERNEL_PATH/bin/env_r.sh
+chmod +x $KERNEL_PATH/bin/env_r.sh
+
+# ... and the new R kernel's configuration file
+mkdir -p $KERNEL_PATH/${KERNEL_NAME}-R
+cat <<EOF > $KERNEL_PATH/${KERNEL_NAME}-R/kernel.json
 {
- "argv": ["$LAB_KERNEL_PATH/bin/env.sh", "{connection_file}", "--profile=default"],
- "display_name": "EBRAINS_release_v0.2_202112",
- "name": "spack_python_kernel_release_202112",
- "language": "python"
+ "argv": ["$KERNEL_PATH/bin/env_r.sh", "{connection_file}"],
+ "display_name": "R-$RELEASE_NAME",
+ "language": "R",
+ "env": { "LAB_KERNEL_NAME": "R-$RELEASE_NAME", "LAB_KERNEL_RELEASE_DATE": "$(date +"%Y-%m-%d")" }
 }
 EOF
+
+# ... and add EBRAINS logo and kernel.js to kernel
+cp $(dirname ${BASH_SOURCE[0]})/etc/logo-64x64-R.png $KERNEL_PATH/${KERNEL_NAME}-R/logo-64x64.png
+cp $(dirname ${BASH_SOURCE[0]})/etc/kernel.js $KERNEL_PATH/${KERNEL_NAME}-R/

create_job.sh

 #!/bin/bash
 
-INSTALLATION_ROOT=$1
-SPACKIFIED_ENV=$2
-OP=$3
-SPACK_ENV_TAR_FILE=$4
-OC_JOB_ID=$5
-BUILD_ENV_DOCKER_IMAGE=$6
-LAB_KERNEL_PATH=$7
-OKD_CLUSTER_UID=$8
+# ===========================================================================================================
+# title         : create_job.sh
+# usage         : ./create_job.sh $OC_JOB_ID $BUILD_ENV_DOCKER_IMAGE $INSTALLATION_ROOT
+#                 $SPACK_ENV $COMMIT_SHA $RELEASE_NAME $LAB_KERNEL_ROOT
+# description   : creates OKD job yaml file that builds/updates spack environment and creates Lab kernel
+# ===========================================================================================================
+
+OC_JOB_ID=$1
+BUILD_ENV_DOCKER_IMAGE=$2
+INSTALLATION_ROOT=$3
+EBRAINS_SPACK_ENV=$4
+COMMIT_SHA=$5
+RELEASE_NAME=$6
+LAB_KERNEL_ROOT=$7
+UPDATE_SPACK_OCI_CACHES=$8
+OCI_CACHE_PREFIX=$9
 
 cat <<EOT >> simplejob.yml
 apiVersion: batch/v1
@@ -15,32 +23,88 @@ kind: Job
 metadata:
   name: simplejob${OC_JOB_ID}
 spec:
-  parallelism: 1    
+  parallelism: 1
   completions: 1
-  backoffLimit: 0    
-  template:         
+  backoffLimit: 0
+  template:
     metadata:
       name: testjob
     spec:
-      #securityContext:
-      #  supplementalGroups: [1000410000]
-      #  seLinuxOptions:
-      #    level: s0:c25,c10
       containers:
       - name: simplejob
         image: ${BUILD_ENV_DOCKER_IMAGE}
         imagePullPolicy: Always
-        securityContext:
-          runAsUser: ${OKD_CLUSTER_UID}
+        resources:
+          limits:
+            cpu: '8'
+            memory: '32Gi'
+          requests:
+            cpu: '4'
+            memory: '20Gi'
         volumeMounts:
           - name: sharedbin
             mountPath: /srv
-        command: ["/usr/local/bin/deploy-build-env.sh", "$INSTALLATION_ROOT", "$SPACKIFIED_ENV", "$OP", "$SPACK_ENV_TAR_FILE", "$LAB_KERNEL_PATH"]
+          - name: tmp
+            mountPath: /tmp
+        command:
+        - /bin/bash
+        - -c
+        - |
+          # create root dir if it doesn't exist
+          mkdir -p \$INSTALLATION_ROOT
+          
+          # reset spack repository dir by cloning the selected version
+          if [ ! -d \$EBRAINS_REPO_PATH ]; then git clone ${CI_PROJECT_URL} --recurse-submodules \$EBRAINS_REPO_PATH; fi
+          cd \$EBRAINS_REPO_PATH
+          git fetch origin
+          git reset --hard \$COMMIT_SHA
+          git submodule update --force
+
+          # reset build error log dir (delete previous logs to save space)
+          rm -rf \$BUILD_LOGS_DIR
+          mkdir -p \$BUILD_LOGS_DIR
+          cd \$BUILD_LOGS_DIR
+          
+          # run installation script
+          bash \$EBRAINS_REPO_PATH/install_spack_env.sh \$SPACK_JOBS \$INSTALLATION_ROOT \$EBRAINS_REPO_PATH \$EBRAINS_SPACK_ENV "" \$UPDATE_SPACK_OCI_CACHES \$OCI_CACHE_PREFIX
+          
+          if [ \$? -eq 0 ]
+          then
+            # build process succeeded - create or update kernel on the NFS based on the current spack environment
+            bash \$EBRAINS_REPO_PATH/create_JupyterLab_kernel.sh \$INSTALLATION_ROOT \$EBRAINS_SPACK_ENV \$RELEASE_NAME \$LAB_KERNEL_ROOT && exit 0
+          else
+            # build process failed - keep spack build logs and fail the pipeline
+            cp -r /tmp/spack/spack-stage/* \$BUILD_LOGS_DIR
+            exit 1
+          fi
+        env:
+          - name: SYSTEMNAME
+            value: ebrainslab
+          - name: INSTALLATION_ROOT
+            value: $INSTALLATION_ROOT
+          - name: EBRAINS_SPACK_ENV
+            value: $EBRAINS_SPACK_ENV
+          - name: UPDATE_SPACK_OCI_CACHES
+            value: '$UPDATE_SPACK_OCI_CACHES'
+          - name: OCI_CACHE_PREFIX
+            value: $OCI_CACHE_PREFIX
+          - name: COMMIT_SHA
+            value: $COMMIT_SHA
+          - name: RELEASE_NAME
+            value: $RELEASE_NAME
+          - name: LAB_KERNEL_ROOT
+            value: $LAB_KERNEL_ROOT
+          - name: BUILD_LOGS_DIR
+            value: /srv/build_logs/$EBRAINS_SPACK_ENV
+          - name: EBRAINS_REPO_PATH
+            value: $INSTALLATION_ROOT/ebrains-spack-builds
+          - name: SPACK_JOBS
+            value: '6'
       volumes:
         - name: sharedbin
           persistentVolumeClaim:
             claimName: shared-binaries
+        - name: tmp
+          emptyDir: {}
       restartPolicy: Never
-      #nodeSelector:
-      #  kubernetes.io/hostname: okd-worker-3.dev.hbp.eu     
 EOT

etc/kernel.js

+const cmd_key = /Mac/.test(navigator.platform) ? 'Cmd' : 'Ctrl'const edit_actions = [
+        {
+                name: 'R Assign',
+                shortcut: 'Alt--',
+                icon: 'fa-long-arrow-left',
+                help: 'R: Inserts the left-assign operator (<-)',
+                handler(cm) {
+                        cm.replaceSelection(' <- ')
+                },
+        },
+        {
+                name: 'R Pipe',
+                shortcut: `Shift-${cmd_key}-M`,
+                icon: 'fa-angle-right',
+                help: 'R: Inserts the magrittr pipe operator (%>%)',
+                handler(cm) {
+                        cm.replaceSelection(' %>% ')
+                },
+        },
+        {
+                name: 'R Help',
+                shortcut: 'F1',
+                icon: 'fa-book',
+                help: 'R: Shows the manpage for the item under the cursor',
+                handler(cm, cell) {
+                        const {anchor, head} = cm.findWordAt(cm.getCursor())
+                        const word = cm.getRange(anchor, head)
+
+                        const callbacks = cell.get_callbacks()
+                        const options = {silent: false, store_history: false, stop_on_error: true}
+                        cell.last_msg_id = cell.notebook.kernel.execute(`help(\`${word}\`)`, callbacks, options)
+                },
+        },
+]
+
+const prefix = 'irkernel'
+
+function add_edit_shortcut(notebook, actions, keyboard_manager, edit_action) {
+        const {name, shortcut, icon, help, handler} = edit_action
+
+        const action = {
+                icon, help,
+                help_index : 'zz',
+                handler: () => {
+                        const cell = notebook.get_selected_cell()
+                        handler(cell.code_mirror, cell)
+                },
+        }
+
+        const full_name = actions.register(action, name, prefix)
+
+        Jupyter.keyboard_manager.edit_shortcuts.add_shortcut(shortcut, full_name)
+}
+
+function render_math(pager, html) {
+        if (!html) return
+        const $container = pager.pager_element.find('#pager-container')
+        $container.find('p[style="text-align: center;"]').map((i, e) =>
+                e.outerHTML = `\\[${e.querySelector('i').innerHTML}\\]`)
+        $container.find('i').map((i, e) =>
+                e.outerHTML = `\\(${e.innerHTML}\\)`)
+        MathJax.Hub.Queue(['Typeset', MathJax.Hub, $container[0]])
+}
+
+define(['base/js/namespace'], ({
+        notebook,
+        actions,
+        keyboard_manager,
+        pager,
+}) => ({
+        onload() {
+                edit_actions.forEach(a => add_edit_shortcut(notebook, actions, keyboard_manager, a))
+
+                pager.events.on('open_with_text.Pager', (event, {data: {'text/html': html}}) =>
+                        render_math(pager, html))
+        },
+}))

install_spack_env.sh

+#!/bin/bash
+
+# =========================================================================================================================================
+# title         : install_spack_env.sh
+# usage         : ./install_spack_env.sh $SPACK_JOBS $INSTALLATION_ROOT $EBRAINS_REPO $EBRAINS_SPACK_ENV $UPSTREAM_INSTANCE \
+#                                        $UPDATE_SPACK_OCI_CACHES $OCI_CACHE_PREFIX
+# description   : installs or updates the spack environment defined in the EBRAINS spack repo
+#                 (if the specified spack instance doesn't exist, it also creates it)
+# =========================================================================================================================================
+
+set -eo pipefail
+
+SPACK_JOBS=$1         # number of jobs
+INSTALLATION_ROOT=$2  # where to set up the installation
+EBRAINS_REPO=$3       # location of ebrains-spack-builds repository
+EBRAINS_SPACK_ENV=$4  # name of EBRAINS Spack environment to be created/updated
+UPSTREAM_INSTANCE=$5  # path to Spack instance to use as upstream (optional)
+UPDATE_SPACK_OCI_CACHES=$6 # "true" enables updating the OCI cache for spack sources and build results
+export OCI_CACHE_PREFIX=$7
+
+# make sure spack uses the symlinked folder as path
+export CI_SPACK_ROOT=${INSTALLATION_ROOT}/spack
+
+# disable local configuration and cache directories
+export SPACK_DISABLE_LOCAL_CONFIG=true
+export SPACK_USER_CACHE_PATH=/tmp/spack
+
+# define SYSTEMNAME variable in sites where it's not already defined
+export SYSTEMNAME=${SYSTEMNAME:-${HPC_SYSTEM:-$BSC_MACHINE}}
+
+# cache related variables
+export CACHE_SPECFILE=${CACHE_SPECFILE:-"env_specfile.yaml"}
+export YASHCHIKI_HOME=${EBRAINS_REPO}/vendor/yashchiki
+export SPACK_CACHE_SOURCE=${SPACK_CACHE_SOURCE:-${CI_SPACK_ROOT}/var/spack/cache}
+export SPACK_CACHE_BUILD=${SPACK_CACHE_BUILD:-${CI_SPACK_ROOT}/var/spack/cache}
+
+if [ ! -d ${INSTALLATION_ROOT} ]; then
+    mkdir -p ${INSTALLATION_ROOT}
+fi
+
+# initial setup: use spack submodule if spack dir doesn't already exist
+SPACK_ROOT_EXISTED=1
+if [ ! -d ${CI_SPACK_ROOT} ]; then
+  ln -s ${EBRAINS_REPO}/vendor/spack ${CI_SPACK_ROOT}
+  SPACK_ROOT_EXISTED=0
+fi
+
+# activate Spack
+source ${CI_SPACK_ROOT}/share/spack/setup-env.sh
+
+if [[ $UPSTREAM_INSTANCE ]]; then
+    UPSTREAM_PREFIX=$(find $UPSTREAM_INSTANCE/spack/opt/spack/ -type d -name ".spack-db" 2>/dev/null | xargs -I {} dirname {})
+    spack config add upstreams:upstream-spack-instance:install_tree:$UPSTREAM_PREFIX
+fi
+
+if [ "${SPACK_ROOT_EXISTED}" -eq 0 ]; then
+    # for caching purposes it's nice if we can relocate into long paths, but we
+    # can't do that for existing installations -> else path
+    # ECM (2025-01-23) true seems to yield too large paths for some packages (e.g., gcc)
+    spack config add config:install_tree:padded_length:128
+fi
+
+# add repo if it does not exist
+if [[ ! $(spack repo list | grep ebrains-spack-builds$) ]]
+then
+  spack repo add $EBRAINS_REPO
+fi
+
+# make sure all fetching/clingo stuff happens before anything else
+spack spec aida
+
+# rebuild spack's database (could be an debugging session)
+spack reindex
+
+# add local mirror if it does not exist
+if [[ ! $(spack mirror list | grep local_cache) ]]; then
+    # TODO for newer spack versions, add: --autopush --unsigned, drop create cache command below
+    # (Note: spack expects `build_cache/` below the folder we specify here
+    spack mirror add local_cache ${SPACK_CACHE_BUILD}
+fi
+
+spack compiler find
+
+# create environment if it does not exist
+if [ ! -d "${CI_SPACK_ROOT}/var/spack/environments/$EBRAINS_SPACK_ENV" ]
+then
+  spack env create $EBRAINS_SPACK_ENV
+fi
+
+# update environment site-configs
+rm -rf ${CI_SPACK_ROOT}/var/spack/environments/$EBRAINS_SPACK_ENV/site-config && cp -r $EBRAINS_REPO/site-config ${CI_SPACK_ROOT}/var/spack/environments/$EBRAINS_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 ${CI_SPACK_ROOT}/var/spack/environments/$EBRAINS_SPACK_ENV/
+
+# activate environment
+spack env activate --without-view $EBRAINS_SPACK_ENV
+
+# deactivate view during concretization and installation
+spack env view disable
+
+spack concretize --force --fresh --test root
+
+# dump dag to file
+spack spec -y > "${CACHE_SPECFILE}"
+if [ -n "${OCI_CACHE_PREFIX}" ]; then
+    # fetch missing sources (if packages not yet installed)
+    python3 ${YASHCHIKI_HOME}/fetch_cached_sources.py \
+        --local-cache=${SPACK_CACHE_SOURCE} \
+        --remote-cache-type=oci \
+        --remote-cache=${OCI_CACHE_PREFIX}/source_cache \
+        --yashchiki-home=${YASHCHIKI_HOME} \
+        /tmp/missing_paths_sources.dat ${CACHE_SPECFILE}
+    # fetch missing build results (if packages not yet installed)
+    python3 ${YASHCHIKI_HOME}/fetch_cached_buildresults.py \
+        --local-cache=${SPACK_CACHE_BUILD}/build_cache \
+        --remote-cache-type=oci \
+        --remote-cache=${OCI_CACHE_PREFIX}/build_cache \
+        --yashchiki-home=${YASHCHIKI_HOME} \
+        /tmp/missing_paths_buildresults.dat ${CACHE_SPECFILE}
+fi
+spack-python -c "exit(not len(spack.environment.active_environment().uninstalled_specs()))" && (
+    # fetch all sources but delay exit code handling
+    spack fetch --dependencies --missing && ret=$? || ret=$?;
+    if [ -n "${OCI_CACHE_PREFIX}" ] && [ "${UPDATE_SPACK_OCI_CACHES:-false}" = "true" ]; then
+        # push freshly fetched sources to remote cache
+        echo "Performing update of the source cache"
+        python3 ${YASHCHIKI_HOME}/update_cached_sources.py \
+            --local-cache=${SPACK_CACHE_SOURCE} \
+            --remote-cache-type=oci \
+            --remote-cache=${OCI_CACHE_PREFIX}/source_cache \
+            /tmp/missing_paths_sources.dat;
+    else
+        echo "Updating of the source cache disabled."
+    fi
+    if [ "$ret" -ne 0 ]; then
+        (exit $ret)
+    fi
+)
+
+if [ -n "${OCI_CACHE_PREFIX}" ]; then
+    # record the state of installed/uninstalled packages before actually installing them
+    dag_hashes_pre_install=$(spack-python ${YASHCHIKI_HOME}/specfile_dag_hash.py ${CACHE_SPECFILE})
+fi
+
+# install the environment, use 2 jobs to reduce the amount of required RAM
+# delay exit code until we have updated the cache below
+spack install --no-check-signature -y -j$SPACK_JOBS --fresh --test root && spack_install_ret=$? || spack_install_ret=$?
+
+# re-enable view
+spack env view enable
+spack env view regenerate
+
+# no need to update the local cache nor the remote cache if we don't want to update
+if [ -n "${OCI_CACHE_PREFIX}" ] && [ "${UPDATE_SPACK_OCI_CACHES:-false}" = "true" ]; then
+    # push previously missing (but now installed) packages to the local cache
+    for dag_hash in $dag_hashes_pre_install; do
+        spack buildcache create --unsigned --only package ${SPACK_CACHE_BUILD} /${dag_hash} && ret=$? || ret=$?
+        if [ $ret -ne 0 ]; then
+            echo "Failed to push ${dag_hash}, trying to call spack find on it:"
+            spack find -Lvp /${dag_hash} || true
+        fi
+    done
+
+    # upload packages from local to remote cache
+    echo "Performing update of the build cache"
+    python3 ${YASHCHIKI_HOME}/update_cached_buildresults.py \
+        --local-cache=${SPACK_CACHE_BUILD}/build_cache \
+        --remote-cache-type=oci \
+        --remote-cache=${OCI_CACHE_PREFIX}/build_cache \
+        /tmp/missing_paths_buildresults.dat
+else
+    echo "Updating of the build cache disabled."
+fi
+
+# propagate spack install exit code
+if [ $spack_install_ret -ne 0 ]; then
+    (exit "$spack_install_ret")
+fi
+
+# remove local cache content
+if [ -d ${SPACK_CACHE_BUILD} ]; then
+    spack mirror destroy --mirror-name local_cache
+fi
+
+# TODO: when using spack remote OCI build caches require an index file
+#spack mirror add ebrains oci://docker-registry.ebrains.eu/esd/build_cache
+#spack buildcache list -a ebrains && ret=$? || ret=$?
+
+# rebuild spack's database
+spack reindex
+
+# create load script that when sourced activates and loads the installed spack environment, using views
+# this needs deactivating the environment first:
+spack env deactivate
+unset SPACK_LD_LIBRARY_PATH
+spack env activate --sh $EBRAINS_SPACK_ENV > ${CI_SPACK_ROOT}/var/spack/environments/$EBRAINS_SPACK_ENV/load_env.sh
+
+# create modules files with spack
+# spack module tcl refresh -y
+# create loads script that when sourced activates and loads the installed spack environment, using modules
+# spack env loads -r

load_sim_tools.sh

-#!/bin/bash
-#title           :load_sim_tools.sh
-#description     :Script to load simulation software on the Collaboratory Lab containers from the Object Storage at CSCS.
-#author          :Athanasios Karmas
-#date            :20210601   
-#usage           :source ./load_sim_tools.sh
-#==============================================================================
-
-echo "Setting up environment..."
-
-INSTALLATION_ROOT="test-build"
-SPACKIFIED_ENV="ebrains-spack-builds"
-
-cp -r /srv/$INSTALLATION_ROOT/spack/.spack ~
-source /srv/$INSTALLATION_ROOT/spack/share/spack/setup-env.sh
-
-cd /srv/$INSTALLATION_ROOT
-spack repo add ebrains-spack-builds
-spack env activate $SPACKIFIED_ENV
-
-module use /srv/$INSTALLATION_ROOT/spack/share/spack/modules/linux-centos7-x86_64/
-source /srv/$INSTALLATION_ROOT/spack/var/spack/environments/$SPACKIFIED_ENV/loads
-
-echo "Everything ready!"

operations/cleanup_script.py

+# ensure compatability with Spack v0.18.0
+try:
+    from spack.package_base import PackageStillNeededError
+except:
+    from spack.package import PackageStillNeededError
+
+needed = set()
+# keep packages that are part of an environment
+for e in spack.environment.all_environments():
+    needed.update(e.all_hashes())
+# also keep packages that provide compilers (and their dependencies)
+for c in spack.compilers.all_compiler_specs():
+    pkg_spec = spack.compilers.pkg_spec_for_compiler(c)
+    needed.update([dep.dag_hash() for pkg in spack.store.db.query(pkg_spec) for dep in pkg.traverse()])
+
+installed = {spec.dag_hash(): spec for spec in spack.store.db.query()}
+to_remove = set(installed) - needed
+
+# this will try to uninstall ANY package that is not part of an environment
+# including test dependencies
+# for a list of all the packages that will be uninstalled:
+print('The following packages will be uninstalled:')
+print('\n'.join(sorted([installed[h].short_spec+' ('+h+')' for h in to_remove])))
+
+# iteratively uninstall packages with no dependents
+while to_remove:
+    # print('New iteration')
+    for hash in to_remove.copy():
+        spec = installed[hash]
+        try:
+            spec.package.do_uninstall()
+            to_remove.discard(hash)
+        except PackageStillNeededError:
+            pass
+            # print('Not ready to remove', spec.short_spec, 'in this iteration')