Add NEST v3.7 (#228)

* Merge build and deploy to fix deploy problems * Add nest-server requirements * Fix nest-desktop and compose file * Add v3.7
nest · Apr 15, 2024 · 183b390 · 183b390
1 parent 15fd9ce
commit 183b390
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diff --git 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
@@ -2,15 +2,15 @@ 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"
     ports:
       - "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
@@ -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/3.6/entrypoint.sh b/src/3.6/entrypoint.sh
@@ -39,7 +39,7 @@ elif [[ "${MODE}" = 'nest-server' ]]; then
     export NEST_SERVER_STDOUT="${NEST_SERVER_STDOUT:-1}"
 
     export NEST_SERVER_ACCESS_TOKEN="${NEST_SERVER_ACCESS_TOKEN}"
-    export NEST_SERVER_CORS_ORIGINS="${NEST_SERVER_CORS_ORIGINS:-*}"
+    export NEST_SERVER_CORS_ORIGINS="${NEST_SERVER_CORS_ORIGINS:-http://localhost:*}"
     export NEST_SERVER_DISABLE_AUTH="${NEST_SERVER_DISABLE_AUTH:-1}"
     export NEST_SERVER_DISABLE_RESTRICTION="${NEST_SERVER_DISABLE_RESTRICTION:-1}"
     export NEST_SERVER_ENABLE_EXEC_CALL="${NEST_SERVER_ENABLE_EXEC_CALL:-1}"

diff --git a/src/3.7rc1/Dockerfile → src/3.7/Dockerfile b/src/3.7rc1/Dockerfile → src/3.7/Dockerfile
@@ -1,7 +1,7 @@
 FROM ubuntu:22.04
 LABEL maintainer="[email protected]"
 
-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
@@ -15,7 +15,7 @@ ENV TERM=xterm \
 RUN apt-get update && apt-get install -y --no-install-recommends \
     automake \
     autotools-dev \
-    build-essential \
+    build-essential \ 
     ccache \
     cmake \
     curl \
@@ -42,7 +42,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     libpcre3-dev \
     libpython3.10 \
     libreadline-dev \
-    libreadline8 \
+    libreadline8 \ 
     libtool \
     libzmq3-dev \
     llvm-dev \
@@ -64,12 +64,12 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     python3-mpi4py \
     python3-nose \
     python3-numpy \
-    python3-pandas \
+    python3-pandas \    
     python3-path \
     python3-pip \
     python3-pytest \
     python3-pytest-timeout \
-    python3-pytest-xdist \
+    python3-pytest-xdist \    
     python3-restrictedpython \
     python3-scipy \
     python3-setuptools \
@@ -109,7 +109,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
           -Dwith-openmp=ON \
           -Dwith-libneurosim=OFF \
           -Dwith-sionlib=OFF \
-          -Dwith-music='$HOME/.cache/libneurosim.install' \
+          -Dwith-music='$HOME/.cache/libneurosim.install' \ 
           -Dwith-hdf5=ON \
           ${SRC_PATH}/nest-simulator-${NEST_VERSION} && \
           make && \

diff --git a/src/3.7rc1/entrypoint.sh → src/3.7/entrypoint.sh b/src/3.7rc1/entrypoint.sh → src/3.7/entrypoint.sh
@@ -39,7 +39,7 @@ elif [[ "${MODE}" = 'nest-server' ]]; then
     export NEST_SERVER_STDOUT="${NEST_SERVER_STDOUT:-1}"
 
     export NEST_SERVER_ACCESS_TOKEN="${NEST_SERVER_ACCESS_TOKEN}"
-    export NEST_SERVER_CORS_ORIGINS="${NEST_SERVER_CORS_ORIGINS:-*}"
+    export NEST_SERVER_CORS_ORIGINS="${NEST_SERVER_CORS_ORIGINS:-http://localhost:*}"
     export NEST_SERVER_DISABLE_AUTH="${NEST_SERVER_DISABLE_AUTH:-1}"
     export NEST_SERVER_DISABLE_RESTRICTION="${NEST_SERVER_DISABLE_RESTRICTION:-1}"
     export NEST_SERVER_ENABLE_EXEC_CALL="${NEST_SERVER_ENABLE_EXEC_CALL:-1}"

diff --git a/src/3.7rc1/test-nest.sh → src/3.7/test-nest.sh b/src/3.7rc1/test-nest.sh → src/3.7/test-nest.sh
diff --git a/src/dev/Dockerfile b/src/dev/Dockerfile
@@ -15,7 +15,7 @@ ENV TERM=xterm \
 RUN apt-get update && apt-get install -y --no-install-recommends \
     automake \
     autotools-dev \
-    build-essential \
+    build-essential \ 
     ccache \
     cmake \
     curl \
@@ -41,7 +41,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     libpcre3-dev \
     libpython3.10 \
     libreadline-dev \
-    libreadline8 \
+    libreadline8 \ 
     libtool \
     libzmq3-dev \
     llvm-dev \
@@ -63,12 +63,12 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     python3-mpi4py \
     python3-nose \
     python3-numpy \
-    python3-pandas \
+    python3-pandas \    
     python3-path \
     python3-pip \
     python3-pytest \
     python3-pytest-timeout \
-    python3-pytest-xdist \
+    python3-pytest-xdist \    
     python3-restrictedpython \
     python3-scipy \
     python3-setuptools \
@@ -86,7 +86,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     apt-get autoremove
 
 RUN python3 -m pip install --upgrade pip setuptools wheel mock
-RUN python3 -m pip install --force-reinstall --upgrade --no-binary=h5py h5py
+RUN python3 -m pip install --force-reinstall --upgrade --no-binary=h5py h5py 
 RUN ldconfig
 
 
@@ -101,7 +101,7 @@ RUN python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/doc/req
 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
 
-# # Install libneurosim
+# # Install libneurosim 
 # RUN cd ${SRC_PATH}/nest-simulator-${NEST_VERSION} && \
 #     PYLIB_DIR="$(python3 -c "import sysconfig; print(sysconfig.get_path('include'))" | sed 's/include/lib/')" && \
 #     chmod +x ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_csa-libneurosim.sh && \
@@ -127,19 +127,18 @@ RUN mkdir ${SRC_PATH}/nest-build && cd $_ && \
           -Dwith-openmp=ON \
           -Dwith-libneurosim=OFF \
           -Dwith-sionlib=OFF \
-          -Dwith-music=ON \
+          -Dwith-music=ON \ 
           -Dwith-hdf5=ON \
           ${SRC_PATH}/nest-simulator-${NEST_VERSION} && \
           make && \
           make install
 
 # 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_nest_server.txt && \
-    python3 -m pip install nest-desktop && \
+    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 --upgrade https://github.com/nest/nestml/archive/refs/heads/master.zip 
 
 RUN python3 -m pip install --force-reinstall --upgrade scipy
 

diff --git a/src/dev/entrypoint.sh b/src/dev/entrypoint.sh
@@ -39,7 +39,7 @@ elif [[ "${MODE}" = 'nest-server' ]]; then
     export NEST_SERVER_STDOUT="${NEST_SERVER_STDOUT:-1}"
 
     export NEST_SERVER_ACCESS_TOKEN="${NEST_SERVER_ACCESS_TOKEN}"
-    export NEST_SERVER_CORS_ORIGINS="${NEST_SERVER_CORS_ORIGINS:-*}"
+    export NEST_SERVER_CORS_ORIGINS="${NEST_SERVER_CORS_ORIGINS:-http://localhost:*}"
     export NEST_SERVER_DISABLE_AUTH="${NEST_SERVER_DISABLE_AUTH:-1}"
     export NEST_SERVER_DISABLE_RESTRICTION="${NEST_SERVER_DISABLE_RESTRICTION:-1}"
     export NEST_SERVER_ENABLE_EXEC_CALL="${NEST_SERVER_ENABLE_EXEC_CALL:-1}"