From 29adbb262ff08cda691e06bf1128fd78179d43ec Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Fri, 9 Feb 2024 12:27:14 +0000
Subject: [PATCH 01/11] Merge build and deploy to fix deploy problems

---
 ci-templates/000_3.6.gitlab-ci.yml | 16 +++++-----------
 ci-templates/000_dev.gitlab-ci.yml | 14 ++++----------
 2 files changed, 9 insertions(+), 21 deletions(-)

diff --git a/ci-templates/000_3.6.gitlab-ci.yml b/ci-templates/000_3.6.gitlab-ci.yml
index 8023a68..5422946 100644
--- a/ci-templates/000_3.6.gitlab-ci.yml
+++ b/ci-templates/000_3.6.gitlab-ci.yml
@@ -8,23 +8,16 @@ Build_36:
   rules:
     - when: always
   script:
+    # Build
     - docker pull nest/nest-simulator:3.6 || true
     - docker build
         --cache-from nest/nest-simulator:3.6
         --tag nest/nest-simulator:3.6
         ./src/3.6
-    # Simple test
+    # Test
     - docker run -i --rm nest/nest-simulator:3.6 bash /opt/test-nest.sh
-  tags:
-    - shell-runner
-
-Deploy_36:
-  stage: deploy
-  needs: ["Build_36"]
-  rules:
-    - when: on_success
-  script: 
-    - echo -n $DOCKERHUB_REGISTRY_TOKEN | docker login -u $DOCKERHUB_REGISTRY_USER --password-stdin   
+    # Deploy
+    - echo -n $DOCKERHUB_REGISTRY_TOKEN | docker login -u $DOCKERHUB_REGISTRY_USER --password-stdin
     - docker push nest/nest-simulator:3.6
     - docker tag nest/nest-simulator:3.6 $DOCKER_REGISTRY_IMAGE:3.6
     - docker push $DOCKER_REGISTRY_IMAGE:3.6  
@@ -32,3 +25,4 @@ Deploy_36:
     - docker logout $DOCKER_REGISTRY
   tags:
     - shell-runner
+
diff --git a/ci-templates/000_dev.gitlab-ci.yml b/ci-templates/000_dev.gitlab-ci.yml
index 45c983a..af666ff 100644
--- a/ci-templates/000_dev.gitlab-ci.yml
+++ b/ci-templates/000_dev.gitlab-ci.yml
@@ -8,24 +8,18 @@ Build_Dev:
   rules:
     - when: always
   script:
+    # Build
     - docker pull push nest/nest-simulator:dev || true
     - docker build
         --cache-from nest/nest-simulator:dev
         --tag nest/nest-simulator:dev
         ./src/dev
-    # Simple test
+    # Test
     - docker run -i --rm nest/nest-simulator:dev bash /opt/test-nest.sh
-  tags:
-    - shell-runner
-
-Deploy_Dev:
-  stage: deploy
-  needs: ["Build_Dev"]
-  rules:
-    - when: on_success
-  script:
+    # Deploy
     - echo -n $DOCKERHUB_REGISTRY_TOKEN | docker login -u $DOCKERHUB_REGISTRY_USER --password-stdin
     - docker push nest/nest-simulator:dev
     - docker logout $DOCKERHUB_REGISTRY
   tags:
     - shell-runner
+

From 1adf82e745bbfd587617352a01af2e5b3c6e4266 Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Thu, 4 Apr 2024 09:56:21 +0000
Subject: [PATCH 02/11] Add nest-server requirements

---
 src/3.7rc1/Dockerfile | 1 +
 src/dev/Dockerfile    | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/3.7rc1/Dockerfile b/src/3.7rc1/Dockerfile
index 5ca0e22..fc1cc3e 100644
--- a/src/3.7rc1/Dockerfile
+++ b/src/3.7rc1/Dockerfile
@@ -116,6 +116,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
           make install && \
     python3 -m pip install --upgrade pip && \
     python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements_testing.txt && \
+    python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements_nest_server.txt && \
     python3 -m pip install nest-desktop --pre && \
     python3 -m pip uninstall nestml -y && \
     python3 -m pip install --upgrade https://github.com/nest/nestml/archive/refs/tags/v7.0.1-rc1.zip  && \
diff --git a/src/dev/Dockerfile b/src/dev/Dockerfile
index ade8ee3..01f9f3c 100644
--- a/src/dev/Dockerfile
+++ b/src/dev/Dockerfile
@@ -135,7 +135,7 @@ RUN mkdir ${SRC_PATH}/nest-build && cd $_ && \
 
 # Install NESTML and more
 RUN python3 -m pip install --upgrade pip && \
-    python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements_testing.txt && \
+    python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements.txt && \
     python3 -m pip install nest-desktop --pre && \
     python3 -m pip uninstall nestml -y && \
     python3 -m pip install --upgrade https://github.com/nest/nestml/archive/refs/heads/master.zip 

From 53016176d0ec8490b7442238bae9d058aca6865e Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Thu, 4 Apr 2024 10:30:49 +0000
Subject: [PATCH 03/11] Fix nest-desktop and compose file

---
 docker-compose.yml    | 8 ++++----
 src/3.7rc1/Dockerfile | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/docker-compose.yml b/docker-compose.yml
index 96c7ef5..9504522 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -2,7 +2,7 @@ version: "3"
 
 services:
   nest-server:
-    image: nest/nest-simulator:3.6
+    image: nest/nest-simulator:3.7rc1
     environment:
       LOCAL_USER_ID: "`id -u $USER`"
       NEST_CONTAINER_MODE: "nest-server"
@@ -10,7 +10,7 @@ services:
       - "52425:52425"
 
   nest-desktop:
-    image: nest/nest-simulator:3.6
+    image: nest/nest-simulator:3.7rc1
     environment:
       LOCAL_USER_ID: "`id -u $USER`"
       NEST_CONTAINER_MODE: "nest-desktop"
@@ -20,7 +20,7 @@ services:
       - nest-server
 
   nest-notebook:
-    image: nest/nest-simulator:3.6
+    image: nest/nest-simulator:3.7rc1
     volumes:
       - .:/opt/data
     environment:
@@ -30,7 +30,7 @@ services:
       - "8080:8080"
 
   nest-jupyterlab:
-    image: nest/nest-simulator:3.6
+    image: nest/nest-simulator:3.7rc1
     volumes:
       - .:/opt/data
     environment:
diff --git a/src/3.7rc1/Dockerfile b/src/3.7rc1/Dockerfile
index fc1cc3e..421a278 100644
--- a/src/3.7rc1/Dockerfile
+++ b/src/3.7rc1/Dockerfile
@@ -117,7 +117,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     python3 -m pip install --upgrade pip && \
     python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements_testing.txt && \
     python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements_nest_server.txt && \
-    python3 -m pip install nest-desktop --pre && \
+    python3 -m pip install nest-desktop && \
     python3 -m pip uninstall nestml -y && \
     python3 -m pip install --upgrade https://github.com/nest/nestml/archive/refs/tags/v7.0.1-rc1.zip  && \
     python3 -m pip install --force-reinstall --upgrade scipy

From c384fb0a12df94bbbd534048df40099aafea01d5 Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Fri, 12 Apr 2024 12:11:11 +0000
Subject: [PATCH 04/11] Add v3.7

---
 ci-templates/000_3.7.gitlab-ci.yml | 14 +++++++-------
 docker-compose.yml                 |  8 ++++----
 run.sh                             | 16 ++++++++--------
 src/{3.7rc1 => 3.7}/Dockerfile     |  2 +-
 src/{3.7rc1 => 3.7}/entrypoint.sh  |  0
 src/{3.7rc1 => 3.7}/test-nest.sh   |  0
 6 files changed, 20 insertions(+), 20 deletions(-)
 rename src/{3.7rc1 => 3.7}/Dockerfile (99%)
 rename src/{3.7rc1 => 3.7}/entrypoint.sh (100%)
 rename src/{3.7rc1 => 3.7}/test-nest.sh (100%)

diff --git a/ci-templates/000_3.7.gitlab-ci.yml b/ci-templates/000_3.7.gitlab-ci.yml
index ed4fb71..0787e97 100644
--- a/ci-templates/000_3.7.gitlab-ci.yml
+++ b/ci-templates/000_3.7.gitlab-ci.yml
@@ -1,5 +1,5 @@
 ###############################################
-###               3.7rc1                   ###
+###               3.7                  ###
 ###############################################
 
 
@@ -9,16 +9,16 @@ Build_3.7:
     - when: always
   script:
     # Build
-    - docker pull push nest/nest-simulator:3.7rc1 || true
+    - docker pull push nest/nest-simulator:3.7 || true
     - docker build
-        --cache-from nest/nest-simulator:3.7rc1
-        --tag nest/nest-simulator:3.7rc1
-        ./src/3.7rc1
+        --cache-from nest/nest-simulator:3.7
+        --tag nest/nest-simulator:3.7
+        ./src/3.7
     # Test
-    #- docker run -i --rm nest/nest-simulator:3.7rc1 bash /opt/test-nest.sh
+    #- docker run -i --rm nest/nest-simulator:3.7bash /opt/test-nest.sh
     # Deploy
     - echo -n $DOCKERHUB_REGISTRY_TOKEN | docker login -u $DOCKERHUB_REGISTRY_USER --password-stdin
-    - docker push nest/nest-simulator:3.7rc1
+    - docker push nest/nest-simulator:3.7
     - docker logout $DOCKERHUB_REGISTRY
   tags:
     - shell-runner
diff --git a/docker-compose.yml b/docker-compose.yml
index 9504522..1342de2 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -2,7 +2,7 @@ version: "3"
 
 services:
   nest-server:
-    image: nest/nest-simulator:3.7rc1
+    image: nest/nest-simulator:3.7
     environment:
       LOCAL_USER_ID: "`id -u $USER`"
       NEST_CONTAINER_MODE: "nest-server"
@@ -10,7 +10,7 @@ services:
       - "52425:52425"
 
   nest-desktop:
-    image: nest/nest-simulator:3.7rc1
+    image: nest/nest-simulator:3.7
     environment:
       LOCAL_USER_ID: "`id -u $USER`"
       NEST_CONTAINER_MODE: "nest-desktop"
@@ -20,7 +20,7 @@ services:
       - nest-server
 
   nest-notebook:
-    image: nest/nest-simulator:3.7rc1
+    image: nest/nest-simulator:3.7
     volumes:
       - .:/opt/data
     environment:
@@ -30,7 +30,7 @@ services:
       - "8080:8080"
 
   nest-jupyterlab:
-    image: nest/nest-simulator:3.7rc1
+    image: nest/nest-simulator:3.7
     volumes:
       - .:/opt/data
     environment:
diff --git a/run.sh b/run.sh
index 03955bf..f208944 100755
--- a/run.sh
+++ b/run.sh
@@ -50,11 +50,11 @@ case $command in
         echo
 
         echo "Provisioning needs an argument: 'dev' 'latest_daint' '2.12.0', '2.14.0', '2.14.2',"
-        echo "'2.16.0', '2.18.0', '2.20.0', '2.20.1', '2.20.2', '3.0','3.1', '3.2', '3.3', '3.4', '3.5', '3.6', '3.7rc1','all' or 'base'."
+        echo "'2.16.0', '2.18.0', '2.20.0', '2.20.1', '2.20.2', '3.0','3.1', '3.2', '3.3', '3.4', '3.5', '3.6', '3.7','all' or 'base'."
         echo
         while test $# -gt 0; do
             case "$1" in
-            dev | latest_daint | 2.12.0 | 2.14.0 | 2.14.2 | 2.16.0 | 2.18.0 | 2.20.0 | 2.20.1 | 2.20.2 | 3.0 | 3.1 | 3.2 | 3.3 | 3.4 | 3.5 | 3.6 | 3.7rc1 )
+            dev | latest_daint | 2.12.0 | 2.14.0 | 2.14.2 | 2.16.0 | 2.18.0 | 2.20.0 | 2.20.1 | 2.20.2 | 3.0 | 3.1 | 3.2 | 3.3 | 3.4 | 3.5 | 3.6 | 3.7 )
                 echo "Build the NEST image for NEST $1"
                 echo
                 docker build -t nest/nest-simulator:"$1" ./src/"$1"
@@ -73,7 +73,7 @@ case $command in
             all)
                 echo "Build the NEST image for NEST 2.12.0, 2.14.0, 2.14.2"
                 echo "2.16.0, 2.18.0, 2.20.0, 2.20.1, 2.20.2, 3.0, 3.1, 3.2," 
-                echo "3.3, 3.4, 3.5, 3.6, 3.7rc1, dev and latest_daint"
+                echo "3.3, 3.4, 3.5, 3.6, 3.7, dev and latest_daint"
                 echo
                 docker build -t nest/nest-simulator:2.12.0 ./src/2.12.0
                 docker build -t nest/nest-simulator:2.14.0 ./src/2.14.0
@@ -90,7 +90,7 @@ case $command in
                 docker build -t nest/nest-simulator:3.4 ./src/3.4
                 docker build -t nest/nest-simulator:3.5 ./src/3.5
                 docker build -t nest/nest-simulator:3.6 ./src/3.6
-                docker build -t nest/nest-simulator:3.7rc1 ./src/3.7rc1
+                docker build -t nest/nest-simulator:3.7 ./src/3.7
                 docker build -t nest/nest-simulator:dev ./src/dev
                 docker build -t nest/nest-simulator:latest_daint ./src/latest_daint
                 echo
@@ -114,14 +114,14 @@ case $command in
         echo
         echo "VERSION is the version of NEST"
         echo "(e.g. dev, 2.12.0, 2.14.0, 2.14.2,  2.16.0, 2.18.0, 2.20.0," 
-        echo "2.20.1, 2.20.2, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7rc1)"
+        echo "2.20.1, 2.20.2, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7)"
         echo
     LOCALDIR="$(pwd)"
     while test $# -gt 1; do
         case "$1" in
             notebook)
                 case "$2" in
-                    dev | 2.12.0 | 2.14.0 | 2.14.2 | 2.16.0 | 2.18.0 | 2.20.0 | 2.20.1 | 2.20.2 | 3.0 | 3.1 | 3.2 | 3.3 | 3.4 | 3.5 | 3.6 | 3.7rc1 )
+                    dev | 2.12.0 | 2.14.0 | 2.14.2 | 2.16.0 | 2.18.0 | 2.20.0 | 2.20.1 | 2.20.2 | 3.0 | 3.1 | 3.2 | 3.3 | 3.4 | 3.5 | 3.6 | 3.7 )
                     echo "Run NEST-$2 with Jupyter Notebook".
                     echo
                     docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` --name my_app  \
@@ -137,7 +137,7 @@ case $command in
             ;;
             jupyterlab)
                 case "$2" in
-                    dev | 2.12.0 | 2.14.0 | 2.14.2 | 2.16.0 | 2.18.0 | 2.20.0 | 2.20.1 | 2.20.2 | 3.0 | 3.1 | 3.2 | 3.3 | 3.4 | 3.5 | 3.6 | 3.7rc1 )
+                    dev | 2.12.0 | 2.14.0 | 2.14.2 | 2.16.0 | 2.18.0 | 2.20.0 | 2.20.1 | 2.20.2 | 3.0 | 3.1 | 3.2 | 3.3 | 3.4 | 3.5 | 3.6 | 3.7 )
                     echo
                     docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` --name my_app  \
 							   -v $(pwd):/opt/data -e NEST_CONTAINER_MODE=jupyterlab \
@@ -152,7 +152,7 @@ case $command in
             ;;
             interactive)
                 case "$2" in
-                    dev | 2.12.0 | 2.14.0 | 2.14.2 | 2.16.0 | 2.18.0 | 2.20.0 | 2.20.1 | 2.20.2 | 3.0 | 3.1 | 3.2 | 3.3 | 3.4 | 3.5 | 3.6 | 3.7rc1 )
+                    dev | 2.12.0 | 2.14.0 | 2.14.2 | 2.16.0 | 2.18.0 | 2.20.0 | 2.20.1 | 2.20.2 | 3.0 | 3.1 | 3.2 | 3.3 | 3.4 | 3.5 | 3.6 | 3.7 )
                     echo "Run NEST-$2 in interactive mode."
                     echo
                     docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` --name my_app  -e NEST_CONTAINER_MODE=interactive \
diff --git a/src/3.7rc1/Dockerfile b/src/3.7/Dockerfile
similarity index 99%
rename from src/3.7rc1/Dockerfile
rename to src/3.7/Dockerfile
index 421a278..551368b 100644
--- a/src/3.7rc1/Dockerfile
+++ b/src/3.7/Dockerfile
@@ -1,7 +1,7 @@
 FROM ubuntu:22.04
 LABEL maintainer="s.graber@fz-juelich.de"
 
-ARG NEST_VERSION=3.7_rc1
+ARG NEST_VERSION=3.7
 ARG SRC_PATH=/tmp
 ARG CMAKE_C_COMPILER_LAUNCHER=ccache
 ARG CMAKE_CXX_COMPILER_LAUNCHER=ccache
diff --git a/src/3.7rc1/entrypoint.sh b/src/3.7/entrypoint.sh
similarity index 100%
rename from src/3.7rc1/entrypoint.sh
rename to src/3.7/entrypoint.sh
diff --git a/src/3.7rc1/test-nest.sh b/src/3.7/test-nest.sh
similarity index 100%
rename from src/3.7rc1/test-nest.sh
rename to src/3.7/test-nest.sh

From d01ede09a8187ded22642a8baa8efaf485727796 Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Fri, 19 Apr 2024 04:49:25 +0000
Subject: [PATCH 05/11] Remove test

---
 ci-templates/000_3.6.gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ci-templates/000_3.6.gitlab-ci.yml b/ci-templates/000_3.6.gitlab-ci.yml
index 5422946..f27929e 100644
--- a/ci-templates/000_3.6.gitlab-ci.yml
+++ b/ci-templates/000_3.6.gitlab-ci.yml
@@ -15,7 +15,7 @@ Build_36:
         --tag nest/nest-simulator:3.6
         ./src/3.6
     # Test
-    - docker run -i --rm nest/nest-simulator:3.6 bash /opt/test-nest.sh
+    # - docker run -i --rm nest/nest-simulator:3.6 bash /opt/test-nest.sh
     # Deploy
     - echo -n $DOCKERHUB_REGISTRY_TOKEN | docker login -u $DOCKERHUB_REGISTRY_USER --password-stdin
     - docker push nest/nest-simulator:3.6

From fa70bbb2b3226c7623397c166074e6af4b0b6c3f Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Fri, 19 Apr 2024 04:53:26 +0000
Subject: [PATCH 06/11] Add v3.7 to readme

---
 README.md | 25 +++++++++++++------------
 1 file changed, 13 insertions(+), 12 deletions(-)

diff --git a/README.md b/README.md
index 3779168..0d0df63 100644
--- a/README.md
+++ b/README.md
@@ -15,6 +15,7 @@ Currently the following docker images are provided
     - nest/nest-simulator:3.4
     - nest/nest-simulator:3.5
     - nest/nest-simulator:3.6
+    - nest/nest-simulator:3.7
 
 ## Usage
 
@@ -22,7 +23,7 @@ You can use the docker images direct out of 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' or 'dev'.
+TAG is '2.20.2', '3.2', '3.3', '3.4', '3.5', '3.6', '3.7' or 'dev'.
 
 #### NEST 2.20.2
 
@@ -36,7 +37,7 @@ Jupyter lab 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 3.6
+#### NEST 3.7
 
 To use 'docker-compose' you need the definition file from the git repository. Download it:
 
@@ -49,7 +50,7 @@ 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:3.6 
+           nest/nest-simulator:3.7 
 
   Starts the NEST API server container and opens the corresponding port 52425. Test it with `curl localhost:52425/api`.
 
@@ -60,9 +61,9 @@ 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:3.6
+          nest/nest-simulator:3.7
       docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -p 54286:54286  \
-          -e NEST_CONTAINER_MODE=nest-desktop nest/nest-simulator:3.6
+          -e NEST_CONTAINER_MODE=nest-desktop nest/nest-simulator:3.7
 
   Starts the NEST server and the NEST desktop web interface. Port 54286 is also made available.
   Open in the web browser: `http://localhost:54286`
@@ -74,9 +75,9 @@ 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:3.6
+          -p 8080:8080 nest/nest-simulator:3.7
 
-  Starts a notebook server with pre-installed NEST 3.4. The corresponding URL is displayed in the console.
+  Starts a notebook server with pre-installed NEST 3.7. The corresponding URL is displayed in the console.
 
 - Jupyter lab with NEST
 
@@ -85,9 +86,9 @@ 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=jupyterlab \
-          -p 8080:8080 nest/nest-simulator:3.6
+          -p 8080:8080 nest/nest-simulator:3.7
 
-  Starts a jupyter lab server with pre-installed NEST 3.4. The corresponding URL is displayed in the console.
+  Starts a jupyter lab server with pre-installed NEST 3.7. The corresponding URL is displayed in the console.
 
 To stop and delete running containers use `docker-compose down`.
 
@@ -128,7 +129,7 @@ You can clone this repository and use the shell script:
     [<args>]    can be either 'notebook', 'jupyterlab', or 'interactice'.
     [<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' or 'all').
+                '3.6', '3.7' or 'all').
 
     Example:    sh run.sh provision dev
                 sh run.sh run notebook dev
@@ -137,7 +138,7 @@ You can clone this repository and use the shell script:
 
 ## 1 - 2 (- 3)
 
-In the next steps, VERSION is the kind of docker image you want to use (3.2, dev, ...)
+In the next steps, VERSION is the kind of docker image you want to use (3.7, dev, ...)
 
 Two little steps to get started
 
@@ -190,7 +191,7 @@ 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:3.6 /bin/bash
+               nest/nest-simulator:3.7 /bin/bash
 
 You are now on container's shell.
 

From 52d757518a4592aacdda23e1ed2da9fdc05fe79f Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Wed, 15 May 2024 12:32:58 +0000
Subject: [PATCH 07/11] Fix nestml version and add pygsl

---
 src/3.7/Dockerfile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/3.7/Dockerfile b/src/3.7/Dockerfile
index 551368b..6c02a42 100644
--- a/src/3.7/Dockerfile
+++ b/src/3.7/Dockerfile
@@ -117,9 +117,9 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     python3 -m pip install --upgrade pip && \
     python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements_testing.txt && \
     python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements_nest_server.txt && \
-    python3 -m pip install nest-desktop && \
-    python3 -m pip uninstall nestml -y && \
-    python3 -m pip install --upgrade https://github.com/nest/nestml/archive/refs/tags/v7.0.1-rc1.zip  && \
+    python3 -m pip install --upgrade pygsl && \
+    python3 -m pip install --upgrade nest-desktop && \
+    python3 -m pip install --upgrade nestml && \
     python3 -m pip install --force-reinstall --upgrade scipy
 
 COPY entrypoint.sh /usr/local/bin/entrypoint.sh

From b2ee7dac15611b3ed917c3f8d4a42e83fb1c64ea Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Wed, 17 Jul 2024 06:46:19 +0000
Subject: [PATCH 08/11] Install nestml fix for nest verssion

---
 src/3.8/Dockerfile | 10 +++++++---
 src/dev/Dockerfile |  1 +
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/src/3.8/Dockerfile b/src/3.8/Dockerfile
index a6f038e..d33cd81 100644
--- a/src/3.8/Dockerfile
+++ b/src/3.8/Dockerfile
@@ -117,9 +117,13 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements.txt && \
     python3 -m pip install --upgrade nest-desktop && \
     python3 -m pip install --upgrade scipy && \
-    python3 -m pip install --upgrade gsl wheel setuptools swig && \
-    python3 -m pip install nestml==8.0.0rc1 && \
-    python3 -m pip install nestml-server@git+https://github.com/babsey/nestml-server@v1.0-b1 && \
+    python3 -m pip install --upgrade gsl wheel setuptools swig
+
+RUN python3 -m pip install https://api.github.com/repos/nest/nestml/zipball/pull/1087/head
+
+    # python3 -m pip install nestml==8.0.0rc1 && \
+
+RUN python3 -m pip install nestml-server@git+https://github.com/babsey/nestml-server@v1.0-b1 && \
     python3 -m pip install --upgrade pygsl@git+https://github.com/pygsl/pygsl@v2.3.3
 
 COPY entrypoint.sh /usr/local/bin/entrypoint.sh
diff --git a/src/dev/Dockerfile b/src/dev/Dockerfile
index 10472cd..c302eea 100644
--- a/src/dev/Dockerfile
+++ b/src/dev/Dockerfile
@@ -21,6 +21,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     curl \
     cython3 \
     freeglut3-dev \
+    git \
     gosu \
     jq \
     less \

From 28e1391f2339adeb4ecf89322c49c13780c8a69c Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Thu, 18 Jul 2024 08:49:47 +0000
Subject: [PATCH 09/11] Fix merging errors

---
 src/3.8/Dockerfile    | 13 ++++++++++---
 src/3.8/entrypoint.sh |  6 +++++-
 src/dev/Dockerfile    | 23 +++++++++++++++--------
 src/dev/entrypoint.sh |  6 +++++-
 4 files changed, 35 insertions(+), 13 deletions(-)

diff --git a/src/3.8/Dockerfile b/src/3.8/Dockerfile
index d33cd81..5ea9258 100644
--- a/src/3.8/Dockerfile
+++ b/src/3.8/Dockerfile
@@ -90,7 +90,13 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     cd ${SRC_PATH} && \
     wget "https://github.com/nest/nest-simulator/archive/refs/tags/v${NEST_VERSION}.tar.gz" -P ${SRC_PATH} && \
     tar -xzf v${NEST_VERSION}.tar.gz && \
-    python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/doc/requirements.txt && \
+    # Installing the requirements_docs.txt stops at some time with an error
+    # Installing every package fix it.
+    python3 -m pip install sphinx>=6.2.1 sphinx_rtd_theme sphinx_autobuild sphinx_gallery sphinx-tabs && \
+    python3 -m pip install sphinx_design sphinx-material sphinx-copybutton sphinx-carousel && \
+    python3 -m pip install sphinx-notfound-page sphinxcontrib-mermaid sphinxcontrib-plantuml nbsphinx && \
+    python3 -m pip install  numpydoc example Image breathe csvkit docutils PyYAML>=4.2b1 tqdm yamllint && \
+    # RUN python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements_docs.txt
     python3 -m pip install sphinx_gallery==0.10.1 'numpy<=1.26' && \
     chmod +x ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_music.sh && \
     ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_music.sh && \
@@ -119,11 +125,12 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     python3 -m pip install --upgrade scipy && \
     python3 -m pip install --upgrade gsl wheel setuptools swig
 
+#Latest update to nestml v8.0.0-rc1
 RUN python3 -m pip install https://api.github.com/repos/nest/nestml/zipball/pull/1087/head
 
     # python3 -m pip install nestml==8.0.0rc1 && \
 
-RUN python3 -m pip install nestml-server@git+https://github.com/babsey/nestml-server@v1.0-b1 && \
+RUN python3 -m pip install nestml-server@git+https://github.com/babsey/nestml-server@v1.0-b3 && \
     python3 -m pip install --upgrade pygsl@git+https://github.com/pygsl/pygsl@v2.3.3
 
 COPY entrypoint.sh /usr/local/bin/entrypoint.sh
@@ -132,5 +139,5 @@ RUN chmod +x /usr/local/bin/entrypoint.sh
 COPY test-nest.sh /opt/test-nest.sh
 RUN chmod +x /opt/test-nest.sh
 
-EXPOSE 8080 52425 54286
+EXPOSE 8080 52425 52426 54286
 ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]
diff --git a/src/3.8/entrypoint.sh b/src/3.8/entrypoint.sh
index 5b3df93..b27435e 100644
--- a/src/3.8/entrypoint.sh
+++ b/src/3.8/entrypoint.sh
@@ -11,11 +11,15 @@ nest --help
 export MUSIC_ROOT_DIR='$HOME/.cache/music.install'
 export MUSIC_ROOT=${MUSIC_ROOT_DIR}
 MUSIC_PATH=${MUSIC_ROOT_DIR}
-export LD_LIBRARY_PATH=${MUSIC_PATH}/lib:$LD_LIBRARY_PATH
 export PATH=${MUSIC_PATH}/bin:$PATH
 export CPATH=${MUSIC_PATH}/include:$CPATH
 export PYTHONPATH=${MUSIC_PATH}/lib/python3.8/site-packages:$PYTHONPATH
 
+export NESTML_MODULES_PATH=${NESTML_MODULES_PATH:-/tmp/nestmlmodules}
+
+# Set LD_LIBRARY_PATH for music and nestml modules
+export LD_LIBRARY_PATH=${MUSIC_PATH}/lib:${NESTML_MODULES_PATH}:$LD_LIBRARY_PATH
+
 MODE="${NEST_CONTAINER_MODE:-$1}"
 if [[ "${MODE}" = 'interactive' ]]; then
     read -p "Your python script: " name
diff --git a/src/dev/Dockerfile b/src/dev/Dockerfile
index c302eea..1282183 100644
--- a/src/dev/Dockerfile
+++ b/src/dev/Dockerfile
@@ -90,15 +90,23 @@ RUN python3 -m pip install --upgrade pip setuptools wheel mock
 RUN python3 -m pip install --force-reinstall --upgrade --no-binary=h5py h5py
 RUN ldconfig
 
-
-
 # Download NEST
 RUN cd ${SRC_PATH} && \
     wget https://github.com/nest/nest-simulator/archive/refs/heads/${NEST_VERSION}.tar.gz -P ${SRC_PATH} && \
     tar -xzf ${NEST_VERSION}.tar.gz
-RUN python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/doc/requirements.txt && \
-    python3 -m pip install sphinx_gallery==0.10.1
-# Install music
+
+# Installing the requirements_docs.txt stops at some time with an error
+# Installing every package fix it.
+RUN python3 -m pip install sphinx>=6.2.1 sphinx_rtd_theme sphinx_autobuild sphinx_gallery sphinx-tabs 
+RUN python3 -m pip install sphinx_design sphinx-material sphinx-copybutton sphinx-carousel 
+RUN python3 -m pip install sphinx-notfound-page sphinxcontrib-mermaid sphinxcontrib-plantuml nbsphinx
+RUN python3 -m pip install  numpydoc example Image breathe csvkit docutils PyYAML>=4.2b1 tqdm yamllint
+
+# RUN python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements_docs.txt
+
+RUN python3 -m pip install sphinx_gallery==0.10.1
+
+    # Install music
 RUN chmod +x ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_music.sh && \
     ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_music.sh
 
@@ -136,11 +144,10 @@ RUN mkdir ${SRC_PATH}/nest-build && cd $_ && \
 
 # Install NESTML and more
 RUN python3 -m pip install --upgrade pip && \
-    python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements.txt && \
     python3 -m pip install nest-desktop --pre && \
     python3 -m pip uninstall nestml -y && \
     python3 -m pip install --upgrade https://github.com/nest/nestml/archive/refs/heads/master.zip && \
-    python3 -m pip install nestml-server@git+https://github.com/babsey/nestml-server@v1.0-b1
+    python3 -m pip install nestml-server@git+https://github.com/babsey/nestml-server@v1.0-b3
 
 RUN python3 -m pip install --force-reinstall --upgrade scipy
 
@@ -150,5 +157,5 @@ RUN chmod +x /usr/local/bin/entrypoint.sh
 COPY test-nest.sh /opt/test-nest.sh
 RUN chmod +x /opt/test-nest.sh
 
-EXPOSE 8080 52425 54286
+EXPOSE 8080 52425 52426 54286
 ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]
diff --git a/src/dev/entrypoint.sh b/src/dev/entrypoint.sh
index 5b3df93..b27435e 100644
--- a/src/dev/entrypoint.sh
+++ b/src/dev/entrypoint.sh
@@ -11,11 +11,15 @@ nest --help
 export MUSIC_ROOT_DIR='$HOME/.cache/music.install'
 export MUSIC_ROOT=${MUSIC_ROOT_DIR}
 MUSIC_PATH=${MUSIC_ROOT_DIR}
-export LD_LIBRARY_PATH=${MUSIC_PATH}/lib:$LD_LIBRARY_PATH
 export PATH=${MUSIC_PATH}/bin:$PATH
 export CPATH=${MUSIC_PATH}/include:$CPATH
 export PYTHONPATH=${MUSIC_PATH}/lib/python3.8/site-packages:$PYTHONPATH
 
+export NESTML_MODULES_PATH=${NESTML_MODULES_PATH:-/tmp/nestmlmodules}
+
+# Set LD_LIBRARY_PATH for music and nestml modules
+export LD_LIBRARY_PATH=${MUSIC_PATH}/lib:${NESTML_MODULES_PATH}:$LD_LIBRARY_PATH
+
 MODE="${NEST_CONTAINER_MODE:-$1}"
 if [[ "${MODE}" = 'interactive' ]]; then
     read -p "Your python script: " name

From e99a8a360a85b65315a5a60c6a945e48cf1d6a2e Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Thu, 1 Aug 2024 06:38:26 +0000
Subject: [PATCH 10/11] Deactivate build of 3.7 and 2.20.2 in CI

---
 ci-templates/000_3.7.gitlab-ci.yml    | 2 +-
 ci-templates/003_2.20.2.gitlab-ci.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/ci-templates/000_3.7.gitlab-ci.yml b/ci-templates/000_3.7.gitlab-ci.yml
index d8a05a0..0166eb9 100644
--- a/ci-templates/000_3.7.gitlab-ci.yml
+++ b/ci-templates/000_3.7.gitlab-ci.yml
@@ -6,7 +6,7 @@
 Build_3.7:
   stage: build
   rules:
-    - when: always
+    - when: never
   script:
     # Build
     - docker pull nest/nest-simulator:3.7 || true
diff --git a/ci-templates/003_2.20.2.gitlab-ci.yml b/ci-templates/003_2.20.2.gitlab-ci.yml
index bb5c1ef..7ddb05d 100644
--- a/ci-templates/003_2.20.2.gitlab-ci.yml
+++ b/ci-templates/003_2.20.2.gitlab-ci.yml
@@ -7,7 +7,7 @@ Build_2202:
   stage: build
   # needs: ["Build_Base"]
   rules:
-    - when: always
+    - when: never
   script:
     # Build
     - docker pull nest/nest-simulator:2.20.2 || true

From fe8fe76c17d2282fd805ffbfa60c4d70385f5db7 Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Thu, 1 Aug 2024 06:38:44 +0000
Subject: [PATCH 11/11] Add rc2

---
 ci-templates/000_3.8.gitlab-ci.yml | 4 ++--
 src/3.8/Dockerfile                 | 6 ++----
 2 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/ci-templates/000_3.8.gitlab-ci.yml b/ci-templates/000_3.8.gitlab-ci.yml
index d65cb83..29757d7 100644
--- a/ci-templates/000_3.8.gitlab-ci.yml
+++ b/ci-templates/000_3.8.gitlab-ci.yml
@@ -12,13 +12,13 @@ Build_3.8:
     - docker pull nest/nest-simulator:3.8 || true
     - docker build
         --cache-from nest/nest-simulator:3.8
-        --tag nest/nest-simulator:3.8_rc1
+        --tag nest/nest-simulator:3.8_rc2
         ./src/3.8
     # Test
     #- docker run -i --rm nest/nest-simulator:3.8bash /opt/test-nest.sh
     # Deploy
     - echo -n $DOCKERHUB_REGISTRY_TOKEN | docker login -u $DOCKERHUB_REGISTRY_USER --password-stdin
-    - docker push nest/nest-simulator:3.8_rc1
+    - docker push nest/nest-simulator:3.8_rc2
     - docker logout $DOCKERHUB_REGISTRY
   tags:
     - shell-runner
diff --git a/src/3.8/Dockerfile b/src/3.8/Dockerfile
index fbfc53e..0045661 100644
--- a/src/3.8/Dockerfile
+++ b/src/3.8/Dockerfile
@@ -1,7 +1,7 @@
 FROM ubuntu:22.04
 LABEL maintainer="s.graber@fz-juelich.de"
 
-ARG NEST_VERSION=3.8_rc1
+ARG NEST_VERSION=3.8_rc2
 ARG SRC_PATH=/tmp
 ARG CMAKE_C_COMPILER_LAUNCHER=ccache
 ARG CMAKE_CXX_COMPILER_LAUNCHER=ccache
@@ -126,9 +126,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     python3 -m pip install --upgrade gsl wheel setuptools swig
 
 #Latest update to nestml v8.0.0-rc1
-RUN python3 -m pip install https://api.github.com/repos/nest/nestml/zipball/pull/1087/head
-
-    # python3 -m pip install nestml==8.0.0rc1 && \
+RUN python3 -m pip install nestml==8.0.0rc1
 
 RUN python3 -m pip install nestml-server@git+https://github.com/babsey/nestml-server@v1.0-b4 && \
     python3 -m pip install --upgrade pygsl@git+https://github.com/pygsl/pygsl@v2.3.3