Fix ipygsl install #266

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Merged

steffengraber merged 59 commits into nest:master from steffengraber:fix-gsl

Oct 17, 2025

.github/workflows/docker-image-build.yml

            
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    @@ -34,26 +34,26 @@ jobs:
  
              DOCKER_HUB_USERNAME: ${{ secrets.DOCKER_HUB_USERNAME }}

              DOCKER_HUB_ACCESS_TOKEN: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}

      build-3-9-rc1:

      build-3-9:

        runs-on: ubuntu-latest

        steps:

          - name: Checkout code

            uses: actions/checkout@v4

          - name: Build 3.9-rc1 Docker image

          - name: Build 3.9 Docker image

            run: |

              docker build ./src/3.9 --tag nest/nest-simulator:3.9-rc1

              docker build ./src/3.9 --tag nest/nest-simulator:3.9

          - name: Check NEST 3.9-rc1

          - name: Check NEST 3.9

            run: |

              docker run --rm nest/nest-simulator:3.9-rc1 python3 -c "import nest" | grep "Version:"

              docker run --rm nest/nest-simulator:3.9 python3 -c "import nest" | grep "Version:"

          - name: Push 3.9-rc1 to Docker Hub

          - name: Push 3.9 to Docker Hub

            uses: docker/build-push-action@v5

            with:

              context: ./src/3.9

              push: true

              tags: nest/nest-simulator:3.9-rc1

              tags: nest/nest-simulator:3.9

            env:

              DOCKER_HUB_USERNAME: ${{ secrets.DOCKER_HUB_USERNAME }}

              DOCKER_HUB_ACCESS_TOKEN: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}

README.md

            
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    @@ -1,8 +1,39 @@
  
    # Docker image for the NEST simulator

    [![Docker Hub](https://img.shields.io/badge/Docker%20Hub-nest--simulator-blue?logo=docker)](https://hub.docker.com/r/nest/nest-simulator)

    [![NEST Simulator](https://img.shields.io/badge/NEST-Simulator-green?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAADUlEQVR42mNkYPhfDwAChwGA60e6kgAAAABJRU5ErkJggg==)](https://www.nest-simulator.org/)

    [![License: GPL v2](https://img.shields.io/badge/License-GPL%20v2-blue.svg)](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)

    [![Latest Version](https://img.shields.io/badge/Latest-v3.9-brightgreen)](https://github.com/nest/nest-docker)

    ## Table of Contents

    - [What is it for?](#what-is-it-for)

    - [Quick Start](#quick-start)

    - [Usage](#usage)

      - [NEST 2.20.2](#nest-2202)

      - [NEST 3.9](#nest-39)

      - [NEST dev](#nest-dev)

      - [On Windows](#on-windows)

    - [Local Build System (run.sh)](#usage-of-the-local-build-system-runsh)

      - [Quick Reference](#quick-reference)

      - [Step-by-Step Guide](#1---2---3)

    - [Using NEST with MUSIC](#using-nest-with-music)

    - [Useful Docker commands](#useful-docker-commands)

    - [Publishing to Registry](#add-image-to-ebrans-registry)

    ## What is it for?

    If you know how to use docker, you know how to use NEST.

    **If you know how to use Docker, you know how to use NEST.**

    This repository provides Docker images for the [NEST simulator](https://www.nest-simulator.org/), making it easy to run NEST simulations without complex installation procedures. Whether you're a researcher, student, or developer, these Docker images provide:

    - ✅ **Zero-installation experience** - No dependency management headaches

    - ✅ **Consistent environment** - Same setup across different systems  

    - ✅ **Multiple interfaces** - Jupyter notebooks, JupyterLab, or interactive shell

    - ✅ **Latest versions** - From legacy 2.x to cutting-edge development builds

    - ✅ **NEST Desktop integration** - Full graphical interface support

    ### Available Docker Images

    Currently the following docker images are provided

    @@ -17,14 +48,41 @@ Currently the following docker images are provided
  
        - nest/nest-simulator:3.6

        - nest/nest-simulator:3.7

        - nest/nest-simulator:3.8

        - nest/nest-simulator:3.9

    ## Quick Start

    **🚀 Get started in 30 seconds:**

    1. **Pull the latest NEST image:**

       ```bash

       docker pull nest/nest-simulator:3.9

       ```

    2. **Start Jupyter Notebook:**

       ```bash

       docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -v $(pwd):/opt/data \

                  -e NEST_CONTAINER_MODE=notebook -p 8080:8080 nest/nest-simulator:3.9

       ```

    3. **Open your browser** to the displayed URL and start exploring NEST!

    **🛠️ For local development with build tools:**

    ```bash

    git clone https://github.com/nest/nest-docker.git

    cd nest-docker

    ./run.sh list                    # See all available options

    ./run.sh run notebook 3.9        # Start notebook with NEST 3.9

    ```

    ## Usage

    You can use the docker images direct out of docker-registry.ebrains.eu like this:

    You can use the docker images directly from docker-registry.ebrains.eu like this:

        docker pull nest/nest-simulator:TAG

    TAG is '2.20.2', '3.2', '3.3', '3.4', '3.5', '3.6', '3.7', '3.8'or 'dev'.

    TAG is '2.20.2', '3.2', '3.3', '3.4', '3.5', '3.6', '3.7', '3.8', '3.9' or 'dev'.

    #### NEST 2.20.2

    @@ -33,12 +91,12 @@ Jupyter notebook with NEST 2.20.2:
  
        docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -v $(pwd):/opt/data -e NEST_CONTAINER_MODE=notebook \

                   -p 8080:8080 nest/nest-simulator:2.20.2

    Jupyter lab with NEST 2.20.2

    JupyterLab with NEST 2.20.2:

        docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -v $(pwd):/opt/data -e NEST_CONTAINER_MODE=jupyterlab \

                   -p 8080:8080 nest/nest-simulator:2.20.2

    #### NEST 3.8

    #### NEST 3.9

    To use 'docker-compose' you need the definition file from the git repository. Download it:

    @@ -51,7 +109,7 @@ To use 'docker-compose' you need the definition file from the git repository. Do
  
      or

          docker run -it --rm -e NEST_CONTAINER_MODE=nest-server -p 52425:52425 \

               nest/nest-simulator:3.8

               nest/nest-simulator:3.9

      Starts the NEST API server container and opens the corresponding port 52425. Test it with `curl localhost:52425/api`.

    @@ -62,9 +120,9 @@ To use 'docker-compose' you need the definition file from the git repository. Do
  
      or

          docker run -it --rm -e NEST_CONTAINER_MODE=nest-server -p 52425:52425 \

              nest/nest-simulator:3.8

              nest/nest-simulator:3.9

          docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -p 54286:54286  \

              -e NEST_CONTAINER_MODE=nest-desktop nest/nest-simulator:3.8

              -e NEST_CONTAINER_MODE=nest-desktop nest/nest-simulator:3.9

      Starts the NEST server and the NEST desktop web interface. Port 54286 is also made available.

      Open in the web browser: `http://localhost:54286`

    @@ -76,26 +134,26 @@ To use 'docker-compose' you need the definition file from the git repository. Do
  
      or

          docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -v $(pwd):/opt/data -e NEST_CONTAINER_MODE=notebook \

              -p 8080:8080 nest/nest-simulator:3.8

              -p 8080:8080 nest/nest-simulator:3.9

      Starts a notebook server with pre-installed NEST 3.8. The corresponding URL is displayed in the console.

      Starts a notebook server with pre-installed NEST 3.9. The corresponding URL is displayed in the console.

    - Jupyter lab with NEST

    - JupyterLab with NEST

          docker-compose up nest-jupyterlab

      or

          docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -v $(pwd):/opt/data -e NEST_CONTAINER_MODE=jupyterlab \

              -p 8080:8080 nest/nest-simulator:3.8

              -p 8080:8080 nest/nest-simulator:3.9

      Starts a jupyter lab server with pre-installed NEST 3.8. The corresponding URL is displayed in the console.

      Starts a JupyterLab server with pre-installed NEST 3.9. The corresponding URL is displayed in the console.

    To stop and delete running containers use `docker-compose down`.

    #### NEST dev

    If you want to use the compose configurtion for the dev NEST version, use the file option, e.g.:

    If you want to use the compose configuration for the dev NEST version, use the file option, e.g.:

        wget https://raw.githubusercontent.com/steffengraber/nest-docker/master/docker-compose.yml

        docker-compose -f docker-compose-dev.yml up nest-notebook

    @@ -111,8 +169,8 @@ In Powershell, '%cd%' might not work for the current directory. Then
  
    you should explicitly specify a folder with existing write permissions.

    In any case, this will download the docker image with the pre-installed

    NEST master from docker-registry.ebrains.eu and start it. After booting an URL is presented.

    Click on it or copy it to your browser. Voilá jupyter notebook starts from

    NEST master from docker-registry.ebrains.eu and start it. After booting, a URL is presented.

    Click on it or copy it to your browser. Voilà! Jupyter notebook starts from

    the docker image.

    You can update the image with:

    @@ -126,22 +184,36 @@ You can clone this repository and use the shell script:
  
        sh run.sh [--help] <command> [<args>] [<version>]

        --help      print this usage information.

        <command>   can be either 'provision', 'run' or 'clean'.

        [<args>]    can be either 'notebook', 'jupyterlab', or 'interactice'.

        <command>   can be either 'provision', 'run', 'clean', or 'list'.

        [<args>]    can be either 'notebook', 'jupyterlab', or 'interactive'.

        [<version>] kind of docker image (e.g. 'dev', '2.12.0', '2.14.0',

                    '2.16.0', '2.18.0', '3.0', '3.1', '3.2', '3.3', '3.4', '3.5', 

                    '3.6', '3.7', '3.8' or 'all').

                    '3.6', '3.7', '3.8', '3.9' or 'all').

        Example:    sh run.sh provision dev

        Examples:   sh run.sh list

                    sh run.sh provision dev

                    sh run.sh provision all-parallel

                    sh run.sh provision 3.9 --no-cache

                    sh run.sh run notebook dev

                    sh run.sh run jupyterlab dev

                    sh run.sh run jupyterlab 3.9

    ### Quick Reference

    To see all available versions and commands:

        sh run.sh list

    This will display:

    - All available NEST versions (categorized by legacy 2.x, NEST 3.x, and special versions)

    - Available run modes (notebook, jupyterlab, interactive)

    - Available provision commands

    ## 1 - 2 (- 3)

    ## Step-by-Step Guide

    In the next steps, VERSION is the kind of docker image you want to use (3.8, dev, ...)

    In the next steps, `VERSION` is the kind of docker image you want to use (3.9, dev, ...)

    Two little steps to get started

    **Two simple steps to get started:**

    ### 1 - Provisioning

    @@ -150,7 +222,30 @@ from the docker files.
  
        sh run.sh provision VERSION

    Be careful with the version 'all'. This really takes a long time.

    **Build Options:**

    - Build a single version:

      ```

      sh run.sh provision 3.9

      ```

    - Build all versions sequentially:

      ```

      sh run.sh provision all

      ```

    - Build all versions in parallel (faster, but uses more system resources):

      ```

      sh run.sh provision all-parallel

      ```

    - Force rebuild without using Docker cache:

      ```

      sh run.sh provision 3.9 --no-cache

      sh run.sh provision all --no-cache

      ```

    Be careful with the version 'all'. This really takes a long time. Use 'all-parallel' for faster builds if your system has sufficient resources.

    After every build of a NEST docker image, there are two more images - the one

    with the name of the NEST version (e.g. 'nest/nest-simulator:latest') and

    @@ -180,21 +275,21 @@ More information about this so called 'multi-stage build' here:
  
        be in the path where you start the script.

    ### (3) - Delete the NEST Images

    ### 3 - Clean Up (Optional)

        sh run.sh clean

    Be careful. This stops EVERY container and delete then EVERY NEST Images.

    ⚠️ **Warning:** This stops EVERY container and deletes EVERY NEST image.

    ## Using NEST with music

    ## Using NEST with MUSIC

    In the folder with your music scripts run:

    In the folder with your MUSIC scripts run:

        docker run -it --rm -e LOCAL_USER_ID=`id -u $USER`  \

                   -v $(pwd):/opt/data  \

                   nest/nest-simulator:3.8 /bin/bash

                   nest/nest-simulator:3.9 /bin/bash

    You are now on container's shell.

    You are now in the container's shell.

        cd /opt/nest/share/doc/nest/examples/music/

        mpirun --allow-run-as-root -np 2 music ./minimalmusicsetup.music

    @@ -207,7 +302,7 @@ You are now on container's shell.
  
    -   Export a docker image

            docker save nest/nest-simulator:3.8 | gzip -c > nest-docker.tar.gz  

            docker save nest/nest-simulator:3.9 | gzip -c > nest-docker.tar.gz  

    -   Import a docker image

    @@ -221,7 +316,7 @@ You are now on container's shell.
  
            docker exec -it --workdir /root --user root <nest_container_name> bash

    ## Add image to ebrans registry

    ## Add image to EBRAINS registry

        docker login docker-registry.ebrains.eu

        docker build -t nest-simulator:<VERSION> /path/to/recipe --squash

docker-compose.yml

            
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    @@ -1,14 +1,14 @@
  
    services:

      nest-server:

        image: nest/nest-simulator:3.9-rc2

        image: nest/nest-simulator:3.9

        environment:

          LOCAL_USER_ID: "`id -u $USER`"

          NEST_CONTAINER_MODE: "nest-server"

        ports:

          - "52425:52425"

      nest-server-mpi:

        image: nest/nest-simulator:3.9-rc2

        image: nest/nest-simulator:3.9

        environment:

          LOCAL_USER_ID: "`id -u $USER`"

          NEST_CONTAINER_MODE: "nest-server-mpi"

    @@ -17,7 +17,7 @@ services:
  
          - "52425:52425"

      nest-desktop:

        image: nest/nest-simulator:3.9-rc2

        image: nest/nest-simulator:3.9

        environment:

          LOCAL_USER_ID: "`id -u $USER`"

          NEST_CONTAINER_MODE: "nest-desktop"

    @@ -27,7 +27,7 @@ services:
  
          - nest-server

      nest-notebook:

        image: nest/nest-simulator:3.9-rc2

        image: nest/nest-simulator:3.9

        volumes:

          - .:/opt/data

        environment:

    @@ -37,7 +37,7 @@ services:
  
          - "8080:8080"

      nest-jupyterlab:

        image: nest/nest-simulator:3.9-rc2

        image: nest/nest-simulator:3.9

        volumes:

          - .:/opt/data

        environment:

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