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 01/17] 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 48d2a9d7664e40ab06fbc3c6dc57cc5fce123b9a Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Tue, 12 Mar 2024 10:50:05 +0000
Subject: [PATCH 02/17] Add 1st version of redo

---
 src/base/Dockerfile-deploy-base |   2 +-
 src/dev/Dockerfile              | 110 ++++++++++++++++++--------------
 src/dev/entrypoint.sh           |   2 +-
 3 files changed, 64 insertions(+), 50 deletions(-)

diff --git a/src/base/Dockerfile-deploy-base b/src/base/Dockerfile-deploy-base
index b2ab63d..45b9ac9 100644
--- a/src/base/Dockerfile-deploy-base
+++ b/src/base/Dockerfile-deploy-base
@@ -46,7 +46,7 @@ RUN apt-get update && apt autoremove && apt autoclean && apt-get install -y --no
         wget && \
     update-alternatives --install /usr/bin/python python /usr/bin/python3 10 && \
     update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 10 && \
-    python3 -m pip install jnumpy>=1.17.3,1.25.0 && \
+    python3 -m pip install numpy>=1.17.3,1.25.0 && \
     python3 -m pip install jupyter notebook && \
     python3 -m pip install quantities lazyarray neo && \
     python3 -m pip install --no-binary :all: PyNN && \
diff --git a/src/dev/Dockerfile b/src/dev/Dockerfile
index 90f3b6c..58f342c 100644
--- a/src/dev/Dockerfile
+++ b/src/dev/Dockerfile
@@ -1,32 +1,57 @@
-FROM docker-registry.ebrains.eu/nest/nest-simulator:nest-simulator-build-base as builder
+FROM ubuntu:22.04
 LABEL maintainer="s.graber@fz-juelich.de"
 
 ARG NEST_VERSION=master
 ARG SRC_PATH=/tmp
 ARG CMAKE_C_COMPILER_LAUNCHER=ccache
 ARG CMAKE_CXX_COMPILER_LAUNCHER=ccache
-ARG CXXFLAGS="-O2 -lrt"
-
-
-RUN apt-get update && apt-get install -y --no-install-recommends pandoc \
-    libgsl0-dev libboost-filesystem-dev libboost-regex-dev libboost-wave-dev \
-    libboost-python-dev libboost-program-options-dev libboost-test-dev pkg-config
-RUN python3 -m pip install --force-reinstall --upgrade --no-binary=h5py h5py 
-RUN ldconfig
-
-
-# Install NEST and NESTML
-RUN wget https://github.com/nest/nest-simulator/archive/refs/heads/${NEST_VERSION}.tar.gz -P ${SRC_PATH} && \
-    cd ${SRC_PATH} && tar -xzf ${NEST_VERSION}.tar.gz && ls -l && \
-    python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/doc/requirements.txt && \
-    python3 -m pip install sphinx_gallery==0.10.1
-
-RUN apt-get update && apt-get install -y --no-install-recommends libhdf5-dev 
-RUN python3 -m pip install --force-reinstall --upgrade --no-binary=h5py h5py
-
-RUN mkdir nest-build && cd nest-build
-RUN cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/nest \
-          -Dwith-optimize=ON \
+ARG CXX_FLAGS="-pedantic -Wextra -Wno-unknown-pragmas -D_GLIBCXX_ASSERTIONS"
+
+ENV TERM=xterm \
+    TZ=Europe/Berlin \
+    DEBIAN_FRONTEND=noninteractive \
+    PATH=/root/.local/bin:${PATH}
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    build-essential automake autotools-dev ccache gosu libtool \
+    cmake \
+    gsl-bin \
+    ipython3 \
+    libboost-dev \
+    libgsl-dev \
+    libhdf5-dev \
+    libopenmpi-dev \
+    libreadline-dev \
+    openmpi-bin \
+    pandoc \
+    python3-all-dev \
+    python3-future \
+    python3-nose \ 
+    python3-pip \
+    wget && \
+    apt-get autoremove
+
+# 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
+# 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
+# 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 && \
+    ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_csa-libneurosim.sh $PYLIB_DIR
+# Install sionlib
+RUN chmod +x ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_sionlib.sh && \
+    ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_sionlib.sh
+# Install python requirements
+RUN pip install --user -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements.txt
+# Build nest
+RUN mkdir ${SRC_PATH}/nest-build && cd $_ && \
+    cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/nest \
+          -Dwith-optimize="-O2" \
           -Dwith-warning=ON \
           -Dwith-userdoc=ON \
           -Dwith-boost=ON \
@@ -36,32 +61,21 @@ RUN cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/nest \
           -Dwith-python=ON \
           -Dwith-mpi=ON \
           -Dwith-openmp=ON \
-          -Dwith-libneurosim=OFF \
-          -Dwith-music=ON \ 
+          -Dwith-libneurosim=${HOME}/.cache/libneurosim.install \
+          # -Dwith-sionlib=${HOME}/.cache/sionlib.install\
+          -Dwith-music=${HOME}/.cache/music.install \ 
           -Dwith-hdf5=ON \
-          ${SRC_PATH}/nest-simulator-${NEST_VERSION}
-RUN make -j $(nproc)
-# RUN make docs
-RUN make install
-
-
-
-###############################################################################
-# DEPLOY
-
-FROM docker-registry.ebrains.eu/nest/nest-simulator:nest-simulator-deploy-base
-LABEL maintainer="s.graber@fz-juelich.de"
-
-COPY --from=builder /opt/nest /opt/nest
-COPY --from=builder /opt/music-install /opt/music-install
-# COPY --from=builder /opt/hdf5 /opt/hdf5
-
-RUN python3 -m pip install --upgrade pip && \
-    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 
-
-RUN python3 -m pip install --force-reinstall --upgrade scipy
+          ${SRC_PATH}/nest-simulator-${NEST_VERSION} && \
+          make && \
+          make install
+
+# Install NESTML and more
+RUN python3 -m pip install nest-desktop --pre && \
+    python3 -m pip install --upgrade https://github.com/nest/nestml/archive/refs/heads/master.zip && \
+    python3 -m pip install quantities lazyarray neo && \
+    python3 -m pip install PyNN && \
+    python3 -m pip install elephant[extras] && \
+    python3 -m pip install MarkupSafe==2.0.1
 
 COPY entrypoint.sh /usr/local/bin/entrypoint.sh
 RUN chmod +x /usr/local/bin/entrypoint.sh
diff --git a/src/dev/entrypoint.sh b/src/dev/entrypoint.sh
index f500dee..77e0737 100644
--- a/src/dev/entrypoint.sh
+++ b/src/dev/entrypoint.sh
@@ -8,7 +8,7 @@ source /opt/nest/bin/nest_vars.sh
 # Running NEST to test and to copy the .nestrc into /home/nest
 nest --help
 
-export MUSIC_ROOT_DIR=/opt/music-install
+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

From 26e57f9978cbaf943a048634166cf5d3c3e3ac11 Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Wed, 13 Mar 2024 08:49:39 +0000
Subject: [PATCH 03/17] Error with pip installed requirements.txt -

---
 src/dev/Dockerfile | 110 ++++++++++++++++++++++++++++++++++-----------
 1 file changed, 85 insertions(+), 25 deletions(-)

diff --git a/src/dev/Dockerfile b/src/dev/Dockerfile
index 58f342c..3e0a0f2 100644
--- a/src/dev/Dockerfile
+++ b/src/dev/Dockerfile
@@ -13,41 +13,101 @@ ENV TERM=xterm \
     PATH=/root/.local/bin:${PATH}
 
 RUN apt-get update && apt-get install -y --no-install-recommends \
-    build-essential automake autotools-dev ccache gosu libtool \
+    automake \
+    autotools-dev \
+    build-essential \ 
+    ccache \
     cmake \
-    gsl-bin \
-    ipython3 \
+    curl \
+    cython3 \
+    freeglut3-dev \
+    gosu \
+    jq \
+    less \
+    libboost-filesystem-dev libboost-regex-dev libboost-wave-dev \
+    libboost-python-dev libboost-program-options-dev libboost-test-dev \
     libboost-dev \
-    libgsl-dev \
+    libgomp1 \
+    libgsl-dev  \
+    libgsl0-dev \
     libhdf5-dev \
+    libltdl-dev \
+    libltdl7 \
+    libmusic1v5 \
+    libncurses-dev \
+    libomp-dev \
     libopenmpi-dev \
+    libpcre3 \
+    libpcre3-dev \
+    libpython3.10 \
     libreadline-dev \
+    libreadline8 \ 
+    libtool \
+    libzmq3-dev \
+    llvm-dev \
+    nano \
     openmpi-bin \
+    openssh-client \
+    openssh-server \
     pandoc \
-    python3-all-dev \
-    python3-future \
-    python3-nose \ 
+    pep8 \
+    pkg-config \
+    python3-dev \
+    python3-flask \
+    python3-flask-cors \
+    python3-h5py \
+    python3-ipython \
+    python3-jupyter-core \
+    python3-matplotlib \
+    python3-mpi4py \
+    python3-nose \
+    python3-numpy \
+    python3-pandas \
+    python3-path \
     python3-pip \
+    python3-restrictedpython \
+    python3-scipy \
+    python3-setuptools \
+    python3-sphinx \
+    python3-statsmodels \
+    python3-sympy \
+    python3-tk \
+    python3-tqdm \
+    tcl8.6 \
+    tcl8.6-dev \
+    tk8.6-dev \
+    uwsgi \
+    vera++ \
     wget && \
     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 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
 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
-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 && \
-    ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_csa-libneurosim.sh $PYLIB_DIR
-# Install sionlib
-RUN chmod +x ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_sionlib.sh && \
-    ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_sionlib.sh
+
+# # 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 && \
+#     ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_csa-libneurosim.sh $PYLIB_DIR
+# # Install sionlib
+# RUN chmod +x ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_sionlib.sh && \
+#     ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_sionlib.sh
 # Install python requirements
-RUN pip install --user -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements.txt
+# RUN pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements.txt
+
 # Build nest
 RUN mkdir ${SRC_PATH}/nest-build && cd $_ && \
     cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/nest \
@@ -61,21 +121,21 @@ RUN mkdir ${SRC_PATH}/nest-build && cd $_ && \
           -Dwith-python=ON \
           -Dwith-mpi=ON \
           -Dwith-openmp=ON \
-          -Dwith-libneurosim=${HOME}/.cache/libneurosim.install \
-          # -Dwith-sionlib=${HOME}/.cache/sionlib.install\
-          -Dwith-music=${HOME}/.cache/music.install \ 
+          -Dwith-libneurosim=OFF \
+          -Dwith-sionlib=OFF \
+          -Dwith-music=ON \ 
           -Dwith-hdf5=ON \
           ${SRC_PATH}/nest-simulator-${NEST_VERSION} && \
           make && \
           make install
 
 # Install NESTML and more
-RUN python3 -m pip install nest-desktop --pre && \
-    python3 -m pip install --upgrade https://github.com/nest/nestml/archive/refs/heads/master.zip && \
-    python3 -m pip install quantities lazyarray neo && \
-    python3 -m pip install PyNN && \
-    python3 -m pip install elephant[extras] && \
-    python3 -m pip install MarkupSafe==2.0.1
+RUN python3 -m pip install --upgrade pip && \
+    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 
+
+RUN python3 -m pip install --force-reinstall --upgrade scipy
 
 COPY entrypoint.sh /usr/local/bin/entrypoint.sh
 RUN chmod +x /usr/local/bin/entrypoint.sh

From d0a36b2e95d0870cdc0469fd785f185316aaf479 Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Wed, 13 Mar 2024 08:50:12 +0000
Subject: [PATCH 04/17] Fix for notebook

---
 src/dev/entrypoint.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/dev/entrypoint.sh b/src/dev/entrypoint.sh
index 77e0737..de46708 100644
--- a/src/dev/entrypoint.sh
+++ b/src/dev/entrypoint.sh
@@ -53,7 +53,7 @@ elif [[ "${MODE}" = 'nest-server-mpi' ]]; then
 
 elif [[ "${MODE}" = 'notebook' ]]; then
     mkdir -p /opt/data; cd /opt/data
-    exec jupyter-notebook --ip="${IP_ADDRESS}" --port=8080 --no-browser --allow-root
+    exec /usr/local/bin/jupyter-notebook --ip="${IP_ADDRESS}" --port=8080 --no-browser --allow-root
 
 else
     exec "$@"

From 79880b74118e9be8b704c42182f66614f97f5a4d Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Wed, 13 Mar 2024 08:52:35 +0000
Subject: [PATCH 05/17] Remove need of base,

---
 ci-templates/000_dev.gitlab-ci.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/ci-templates/000_dev.gitlab-ci.yml b/ci-templates/000_dev.gitlab-ci.yml
index af666ff..2b391cc 100644
--- a/ci-templates/000_dev.gitlab-ci.yml
+++ b/ci-templates/000_dev.gitlab-ci.yml
@@ -4,7 +4,6 @@
 
 Build_Dev:
   stage: build
-  needs: ["Build_Base"]
   rules:
     - when: always
   script:

From 117b8be983d29a74664f5c13d5db226c90f0e16f Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Wed, 13 Mar 2024 09:42:35 +0000
Subject: [PATCH 06/17] Use NEST Desktop v3.3.1

---
 src/3.7/Dockerfile    | 146 ++++++++++++++++++++++++++++++++++++++++++
 src/3.7/entrypoint.sh |  60 +++++++++++++++++
 src/3.7/test-nest.sh  |  13 ++++
 3 files changed, 219 insertions(+)
 create mode 100644 src/3.7/Dockerfile
 create mode 100644 src/3.7/entrypoint.sh
 create mode 100644 src/3.7/test-nest.sh

diff --git a/src/3.7/Dockerfile b/src/3.7/Dockerfile
new file mode 100644
index 0000000..4a7fae6
--- /dev/null
+++ b/src/3.7/Dockerfile
@@ -0,0 +1,146 @@
+FROM ubuntu:22.04
+LABEL maintainer="s.graber@fz-juelich.de"
+
+ARG NEST_VERSION=master
+ARG SRC_PATH=/tmp
+ARG CMAKE_C_COMPILER_LAUNCHER=ccache
+ARG CMAKE_CXX_COMPILER_LAUNCHER=ccache
+ARG CXX_FLAGS="-pedantic -Wextra -Wno-unknown-pragmas -D_GLIBCXX_ASSERTIONS"
+
+ENV TERM=xterm \
+    TZ=Europe/Berlin \
+    DEBIAN_FRONTEND=noninteractive \
+    PATH=/root/.local/bin:${PATH}
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    automake \
+    autotools-dev \
+    build-essential \ 
+    ccache \
+    cmake \
+    curl \
+    cython3 \
+    freeglut3-dev \
+    gosu \
+    jq \
+    less \
+    libboost-filesystem-dev libboost-regex-dev libboost-wave-dev \
+    libboost-python-dev libboost-program-options-dev libboost-test-dev \
+    libboost-dev \
+    libgomp1 \
+    libgsl-dev  \
+    libgsl0-dev \
+    libhdf5-dev \
+    libltdl-dev \
+    libltdl7 \
+    libmusic1v5 \
+    libncurses-dev \
+    libomp-dev \
+    libopenmpi-dev \
+    libpcre3 \
+    libpcre3-dev \
+    libpython3.10 \
+    libreadline-dev \
+    libreadline8 \ 
+    libtool \
+    libzmq3-dev \
+    llvm-dev \
+    nano \
+    openmpi-bin \
+    openssh-client \
+    openssh-server \
+    pandoc \
+    pep8 \
+    pkg-config \
+    python3-dev \
+    python3-flask \
+    python3-flask-cors \
+    python3-h5py \
+    python3-ipython \
+    python3-jupyter-core \
+    python3-matplotlib \
+    python3-mpi4py \
+    python3-nose \
+    python3-numpy \
+    python3-pandas \
+    python3-path \
+    python3-pip \
+    python3-restrictedpython \
+    python3-scipy \
+    python3-setuptools \
+    python3-sphinx \
+    python3-statsmodels \
+    python3-sympy \
+    python3-tk \
+    python3-tqdm \
+    tcl8.6 \
+    tcl8.6-dev \
+    tk8.6-dev \
+    uwsgi \
+    vera++ \
+    wget && \
+    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 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
+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 
+# 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 && \
+#     ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_csa-libneurosim.sh $PYLIB_DIR
+# # Install sionlib
+# RUN chmod +x ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_sionlib.sh && \
+#     ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_sionlib.sh
+# Install python requirements
+# RUN pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements.txt
+
+# Build nest
+RUN mkdir ${SRC_PATH}/nest-build && cd $_ && \
+    cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/nest \
+          -Dwith-optimize="-O2" \
+          -Dwith-warning=ON \
+          -Dwith-userdoc=ON \
+          -Dwith-boost=ON \
+          -Dwith-ltdl=ON \
+          -Dwith-gsl=ON \
+          -Dwith-readline=ON \
+          -Dwith-python=ON \
+          -Dwith-mpi=ON \
+          -Dwith-openmp=ON \
+          -Dwith-libneurosim=OFF \
+          -Dwith-sionlib=OFF \
+          -Dwith-music=ON \ 
+          -Dwith-hdf5=ON \
+          ${SRC_PATH}/nest-simulator-${NEST_VERSION} && \
+          make && \
+          make install
+
+# Install NESTML 
+RUN python3 -m pip install --upgrade pip && \
+    python3 -m pip install nest-desktop && \
+    python3 -m pip install nestml
+
+RUN python3 -m pip install --force-reinstall --upgrade scipy
+
+COPY entrypoint.sh /usr/local/bin/entrypoint.sh
+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
+ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]
diff --git a/src/3.7/entrypoint.sh b/src/3.7/entrypoint.sh
new file mode 100644
index 0000000..de46708
--- /dev/null
+++ b/src/3.7/entrypoint.sh
@@ -0,0 +1,60 @@
+#!/bin/bash
+set -e
+IP_ADDRESS=$(hostname --ip-address)
+
+# NEST environment
+source /opt/nest/bin/nest_vars.sh
+
+# Running NEST to test and to copy the .nestrc into /home/nest
+nest --help
+
+export MUSIC_ROOT_DIR='$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
+
+MODE="${NEST_CONTAINER_MODE:-$1}"
+if [[ "${MODE}" = 'interactive' ]]; then
+    read -p "Your python script: " name
+    echo Starting: $name
+    # Start
+    mkdir -p /opt/data; cd /opt/data
+    exec python3 /opt/data/$name
+
+elif [[ "${MODE}" = 'jupyterlab' ]]; then
+    mkdir -p /opt/data; cd /opt/data
+    exec /usr/local/bin/jupyter-lab --ip="${IP_ADDRESS}" --port=8080 --no-browser --allow-root
+
+elif [[ "${MODE}" = 'nest-desktop' ]]; then
+    export NEST_DESKTOP_HOST="${NEST_DESKTOP_HOST:-0.0.0.0}"
+    export NEST_DESKTOP_PORT="${NEST_DESKTOP_PORT:-54286}"
+    exec nest-desktop start
+
+elif [[ "${MODE}" = 'nest-server' ]]; then
+    export NEST_SERVER_HOST="${NEST_SERVER_HOST:-0.0.0.0}"
+    export NEST_SERVER_PORT="${NEST_SERVER_PORT:-52425}"
+    export NEST_SERVER_STDOUT="${NEST_SERVER_STDOUT:-1}"
+
+    export NEST_SERVER_ACCESS_TOKEN="${NEST_SERVER_ACCESS_TOKEN}"
+    export NEST_SERVER_CORS_ORIGINS="${NEST_SERVER_CORS_ORIGINS:-http://localhost:*}"
+    export NEST_SERVER_DISABLE_AUTH="${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}"
+    export NEST_SERVER_MODULES="${NEST_SERVER_MODULES:-import nest; import numpy; import numpy as np}"
+    exec nest-server start
+
+elif [[ "${MODE}" = 'nest-server-mpi' ]]; then
+    export NEST_SERVER_HOST="${NEST_SERVER_HOST:-0.0.0.0}"
+    export NEST_SERVER_PORT="${NEST_SERVER_PORT:-52425}"
+    exec mpirun -np "${NEST_SERVER_MPI_NUM:-1}" nest-server-mpi
+
+elif [[ "${MODE}" = 'notebook' ]]; then
+    mkdir -p /opt/data; cd /opt/data
+    exec /usr/local/bin/jupyter-notebook --ip="${IP_ADDRESS}" --port=8080 --no-browser --allow-root
+
+else
+    exec "$@"
+fi
diff --git a/src/3.7/test-nest.sh b/src/3.7/test-nest.sh
new file mode 100644
index 0000000..d73492a
--- /dev/null
+++ b/src/3.7/test-nest.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+
+# run mpiexec as root
+export OMPI_ALLOW_RUN_AS_ROOT=1
+export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+
+# install what is needed
+pip3 install pytest-xdist pytest-timeout junitparser
+
+HDF5_DISABLE_VERSION_CHECK=1
+
+cd /opt/nest/share/nest/testsuite/
+bash do_tests.sh --prefix=/opt/nest --with-python=/usr/bin/python

From f16462a01721b4269965feb1c777afa8ae72a391 Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Thu, 14 Mar 2024 09:03:27 +0000
Subject: [PATCH 07/17] Use bash and fail to an error

---
 src/3.7/Dockerfile | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/3.7/Dockerfile b/src/3.7/Dockerfile
index 4a7fae6..0959bc1 100644
--- a/src/3.7/Dockerfile
+++ b/src/3.7/Dockerfile
@@ -12,6 +12,8 @@ ENV TERM=xterm \
     DEBIAN_FRONTEND=noninteractive \
     PATH=/root/.local/bin:${PATH}
 
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+
 RUN apt-get update && apt-get install -y --no-install-recommends \
     automake \
     autotools-dev \
@@ -19,14 +21,14 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     ccache \
     cmake \
     curl \
-    cython3 \
+    # cython: https://cython.readthedocs.io/en/latest/src/quickstart/install.html
     freeglut3-dev \
     gosu \
     jq \
     less \
     libboost-filesystem-dev libboost-regex-dev libboost-wave-dev \
     libboost-python-dev libboost-program-options-dev libboost-test-dev \
-    libboost-dev \
+    # libboost-dev \
     libgomp1 \
     libgsl-dev  \
     libgsl0-dev \
@@ -79,14 +81,12 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     uwsgi \
     vera++ \
     wget && \
-    apt-get autoremove
+    apt-get clean && rm -rf /var/lib/apt/lists/*
 
 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} && \

From 08098db7c511cb213d5f0271c939f49593b652ce Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Thu, 14 Mar 2024 10:17:21 +0000
Subject: [PATCH 08/17] Add 3.7 to run skript

---
 run.sh | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/run.sh b/run.sh
index d36f0dd..e181ee3 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','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)
+            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, 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
@@ -88,8 +88,9 @@ case $command in
                 docker build -t nest/nest-simulator:3.2 ./src/3.2
                 docker build -t nest/nest-simulator:3.3 ./src/3.3
                 docker build -t nest/nest-simulator:3.4 ./src/3.4
-                docker build -t nest/nest-simulator:3.4 ./src/3.5
-                docker build -t nest/nest-simulator:3.4 ./src/3.6
+                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/3.7
                 docker build -t nest/nest-simulator:dev ./src/dev
                 docker build -t nest/nest-simulator:latest_daint ./src/latest_daint
                 echo
@@ -113,14 +114,14 @@ case $command in
         echo
         echo "VERSION is the version of NEST"
         echo "(e.g. dev, 2.12.0, 2.14.0, 2.14.2,  2.16.0, 2.18.0, 2.20.0," 
-        echo "2.20.1, 2.20.2, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6)"
+        echo "2.20.1, 2.20.2, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7)"
         echo
     LOCALDIR="$(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 )
+                    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 )
                     echo "Run NEST-$2 with Jupyter Notebook".
                     echo
                     docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` --name my_app  \
@@ -136,7 +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 )
+                    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 )
                     echo
                     docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` --name my_app  \
 							   -v $(pwd):/opt/data -e NEST_CONTAINER_MODE=jupyterlab \
@@ -151,7 +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 )
+                    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 )
                     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 \

From b6e7a5da5836003411fcf424c3c041798ae98224 Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Thu, 14 Mar 2024 10:34:10 +0000
Subject: [PATCH 09/17] Remove all dev packages to shrink the image

---
 src/3.7/Dockerfile | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/3.7/Dockerfile b/src/3.7/Dockerfile
index 0959bc1..8390149 100644
--- a/src/3.7/Dockerfile
+++ b/src/3.7/Dockerfile
@@ -80,8 +80,8 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     tk8.6-dev \
     uwsgi \
     vera++ \
-    wget && \
-    apt-get clean && rm -rf /var/lib/apt/lists/*
+    wget
+    
 
 RUN python3 -m pip install --upgrade pip setuptools wheel mock
 RUN python3 -m pip install --force-reinstall --upgrade --no-binary=h5py h5py 
@@ -136,6 +136,10 @@ RUN python3 -m pip install --upgrade pip && \
 
 RUN python3 -m pip install --force-reinstall --upgrade scipy
 
+# Tidy
+RUN apt-get remove *-dev \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
 COPY entrypoint.sh /usr/local/bin/entrypoint.sh
 RUN chmod +x /usr/local/bin/entrypoint.sh
 

From c556377cab64d6f49e955224244b7125f89bd424 Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Fri, 15 Mar 2024 05:40:06 +0000
Subject: [PATCH 10/17] Goingback to working setup

---
 src/3.7/Dockerfile | 138 ++++++++-------------------------------------
 1 file changed, 23 insertions(+), 115 deletions(-)

diff --git a/src/3.7/Dockerfile b/src/3.7/Dockerfile
index 8390149..f0894fa 100644
--- a/src/3.7/Dockerfile
+++ b/src/3.7/Dockerfile
@@ -1,117 +1,21 @@
-FROM ubuntu:22.04
+FROM docker-registry.ebrains.eu/nest/nest-simulator:nest-simulator-build-base as builder
 LABEL maintainer="s.graber@fz-juelich.de"
 
-ARG NEST_VERSION=master
+ARG NEST_VERSION=3.6
 ARG SRC_PATH=/tmp
 ARG CMAKE_C_COMPILER_LAUNCHER=ccache
 ARG CMAKE_CXX_COMPILER_LAUNCHER=ccache
-ARG CXX_FLAGS="-pedantic -Wextra -Wno-unknown-pragmas -D_GLIBCXX_ASSERTIONS"
+ARG CXXFLAGS="-O2 -lrt"
 
-ENV TERM=xterm \
-    TZ=Europe/Berlin \
-    DEBIAN_FRONTEND=noninteractive \
-    PATH=/root/.local/bin:${PATH}
 
-SHELL ["/bin/bash", "-o", "pipefail", "-c"]
-
-RUN apt-get update && apt-get install -y --no-install-recommends \
-    automake \
-    autotools-dev \
-    build-essential \ 
-    ccache \
-    cmake \
-    curl \
-    # cython: https://cython.readthedocs.io/en/latest/src/quickstart/install.html
-    freeglut3-dev \
-    gosu \
-    jq \
-    less \
-    libboost-filesystem-dev libboost-regex-dev libboost-wave-dev \
-    libboost-python-dev libboost-program-options-dev libboost-test-dev \
-    # libboost-dev \
-    libgomp1 \
-    libgsl-dev  \
-    libgsl0-dev \
-    libhdf5-dev \
-    libltdl-dev \
-    libltdl7 \
-    libmusic1v5 \
-    libncurses-dev \
-    libomp-dev \
-    libopenmpi-dev \
-    libpcre3 \
-    libpcre3-dev \
-    libpython3.10 \
-    libreadline-dev \
-    libreadline8 \ 
-    libtool \
-    libzmq3-dev \
-    llvm-dev \
-    nano \
-    openmpi-bin \
-    openssh-client \
-    openssh-server \
-    pandoc \
-    pep8 \
-    pkg-config \
-    python3-dev \
-    python3-flask \
-    python3-flask-cors \
-    python3-h5py \
-    python3-ipython \
-    python3-jupyter-core \
-    python3-matplotlib \
-    python3-mpi4py \
-    python3-nose \
-    python3-numpy \
-    python3-pandas \
-    python3-path \
-    python3-pip \
-    python3-restrictedpython \
-    python3-scipy \
-    python3-setuptools \
-    python3-sphinx \
-    python3-statsmodels \
-    python3-sympy \
-    python3-tk \
-    python3-tqdm \
-    tcl8.6 \
-    tcl8.6-dev \
-    tk8.6-dev \
-    uwsgi \
-    vera++ \
-    wget
-    
-
-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 && \
+# Install NEST and NESTML
+RUN wget "https://github.com/nest/nest-simulator/archive/refs/tags/v${NEST_VERSION}.tar.gz" -P ${SRC_PATH} && \
+    cd ${SRC_PATH} && tar -xzf v${NEST_VERSION}.tar.gz && ls -l && \
+    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
-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 
-# 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 && \
-#     ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_csa-libneurosim.sh $PYLIB_DIR
-# # Install sionlib
-# RUN chmod +x ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_sionlib.sh && \
-#     ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_sionlib.sh
-# Install python requirements
-# RUN pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements.txt
-
-# Build nest
-RUN mkdir ${SRC_PATH}/nest-build && cd $_ && \
+RUN mkdir nest-build && cd nest-build && \
     cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/nest \
-          -Dwith-optimize="-O2" \
           -Dwith-warning=ON \
           -Dwith-userdoc=ON \
           -Dwith-boost=ON \
@@ -122,24 +26,28 @@ RUN mkdir ${SRC_PATH}/nest-build && cd $_ && \
           -Dwith-mpi=ON \
           -Dwith-openmp=ON \
           -Dwith-libneurosim=OFF \
-          -Dwith-sionlib=OFF \
-          -Dwith-music=ON \ 
+          -Dwith-music=/opt/music-install \
           -Dwith-hdf5=ON \
           ${SRC_PATH}/nest-simulator-${NEST_VERSION} && \
-          make && \
-          make install
+    make -j $(nproc) && \
+    make docs && \
+    make install
+
+
+
+###############################################################################
+# DEPLOY
+
+FROM docker-registry.ebrains.eu/nest/nest-simulator:nest-simulator-deploy-base
+LABEL maintainer="s.graber@fz-juelich.de"
+
+COPY --from=builder /opt/nest /opt/nest
+COPY --from=builder /opt/music-install /opt/music-install
 
-# Install NESTML 
 RUN python3 -m pip install --upgrade pip && \
     python3 -m pip install nest-desktop && \
     python3 -m pip install nestml
 
-RUN python3 -m pip install --force-reinstall --upgrade scipy
-
-# Tidy
-RUN apt-get remove *-dev \
-    apt-get clean && rm -rf /var/lib/apt/lists/*
-
 COPY entrypoint.sh /usr/local/bin/entrypoint.sh
 RUN chmod +x /usr/local/bin/entrypoint.sh
 

From 6c52a72df2186cd927d5c4f73a6053af4b8c44e9 Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Fri, 15 Mar 2024 05:42:16 +0000
Subject: [PATCH 11/17] Add Dwith-optimize="-O2" to cmake options

---
 src/3.7/Dockerfile | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/src/3.7/Dockerfile b/src/3.7/Dockerfile
index f0894fa..b2eb7e2 100644
--- a/src/3.7/Dockerfile
+++ b/src/3.7/Dockerfile
@@ -1,12 +1,18 @@
 FROM docker-registry.ebrains.eu/nest/nest-simulator:nest-simulator-build-base as builder
 LABEL maintainer="s.graber@fz-juelich.de"
 
-ARG NEST_VERSION=3.6
+ARG NEST_VERSION=master
 ARG SRC_PATH=/tmp
 ARG CMAKE_C_COMPILER_LAUNCHER=ccache
 ARG CMAKE_CXX_COMPILER_LAUNCHER=ccache
-ARG CXXFLAGS="-O2 -lrt"
+ARG CXX_FLAGS="-pedantic -Wextra -Wno-unknown-pragmas -D_GLIBCXX_ASSERTIONS"
 
+ENV TERM=xterm \
+    TZ=Europe/Berlin \
+    DEBIAN_FRONTEND=noninteractive \
+    PATH=/root/.local/bin:${PATH}
+
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
 # Install NEST and NESTML
 RUN wget "https://github.com/nest/nest-simulator/archive/refs/tags/v${NEST_VERSION}.tar.gz" -P ${SRC_PATH} && \
@@ -16,6 +22,7 @@ RUN wget "https://github.com/nest/nest-simulator/archive/refs/tags/v${NEST_VERSI
 
 RUN mkdir nest-build && cd nest-build && \
     cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/nest \
+          -Dwith-optimize="-O2" \
           -Dwith-warning=ON \
           -Dwith-userdoc=ON \
           -Dwith-boost=ON \

From d335b33c363bcbbf187e8d8f735c1c242ffcf97f Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Fri, 15 Mar 2024 08:21:00 +0000
Subject: [PATCH 12/17] Fix numpy version and rename to 3.7rc1

---
 run.sh                            | 10 +++++-----
 src/{3.7 => 3.7rc1}/Dockerfile    | 29 +++++++++++++----------------
 src/{3.7 => 3.7rc1}/entrypoint.sh |  0
 src/{3.7 => 3.7rc1}/test-nest.sh  |  0
 4 files changed, 18 insertions(+), 21 deletions(-)
 rename src/{3.7 => 3.7rc1}/Dockerfile (77%)
 rename src/{3.7 => 3.7rc1}/entrypoint.sh (100%)
 rename src/{3.7 => 3.7rc1}/test-nest.sh (100%)

diff --git a/run.sh b/run.sh
index e181ee3..03955bf 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', '3.7','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', '3.7rc1','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 | 3.7)
+            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 )
                 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, 3.7, dev and latest_daint"
+                echo "3.3, 3.4, 3.5, 3.6, 3.7rc1, 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/3.7
+                docker build -t nest/nest-simulator:3.7rc1 ./src/3.7rc1
                 docker build -t nest/nest-simulator:dev ./src/dev
                 docker build -t nest/nest-simulator:latest_daint ./src/latest_daint
                 echo
@@ -114,7 +114,7 @@ case $command in
         echo
         echo "VERSION is the version of NEST"
         echo "(e.g. dev, 2.12.0, 2.14.0, 2.14.2,  2.16.0, 2.18.0, 2.20.0," 
-        echo "2.20.1, 2.20.2, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7)"
+        echo "2.20.1, 2.20.2, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7rc1)"
         echo
     LOCALDIR="$(pwd)"
     while test $# -gt 1; do
diff --git a/src/3.7/Dockerfile b/src/3.7rc1/Dockerfile
similarity index 77%
rename from src/3.7/Dockerfile
rename to src/3.7rc1/Dockerfile
index b2eb7e2..65c6849 100644
--- a/src/3.7/Dockerfile
+++ b/src/3.7rc1/Dockerfile
@@ -1,7 +1,7 @@
 FROM docker-registry.ebrains.eu/nest/nest-simulator:nest-simulator-build-base as builder
 LABEL maintainer="s.graber@fz-juelich.de"
 
-ARG NEST_VERSION=master
+ARG NEST_VERSION=3.6
 ARG SRC_PATH=/tmp
 ARG CMAKE_C_COMPILER_LAUNCHER=ccache
 ARG CMAKE_CXX_COMPILER_LAUNCHER=ccache
@@ -17,10 +17,10 @@ SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 # Install NEST and NESTML
 RUN wget "https://github.com/nest/nest-simulator/archive/refs/tags/v${NEST_VERSION}.tar.gz" -P ${SRC_PATH} && \
     cd ${SRC_PATH} && tar -xzf v${NEST_VERSION}.tar.gz && ls -l && \
+    apt-get remove -y python3-numpy && \
     python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/doc/requirements.txt && \
-    python3 -m pip install sphinx_gallery==0.10.1
-
-RUN mkdir nest-build && cd nest-build && \
+    python3 -m pip install sphinx_gallery==0.10.1 numpy>=1.17.3,1.25.0 && \
+    mkdir nest-build && cd nest-build && \
     cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/nest \
           -Dwith-optimize="-O2" \
           -Dwith-warning=ON \
@@ -40,8 +40,6 @@ RUN mkdir nest-build && cd nest-build && \
     make docs && \
     make install
 
-
-
 ###############################################################################
 # DEPLOY
 
@@ -50,16 +48,15 @@ LABEL maintainer="s.graber@fz-juelich.de"
 
 COPY --from=builder /opt/nest /opt/nest
 COPY --from=builder /opt/music-install /opt/music-install
-
-RUN python3 -m pip install --upgrade pip && \
-    python3 -m pip install nest-desktop && \
-    python3 -m pip install nestml
-
-COPY entrypoint.sh /usr/local/bin/entrypoint.sh
-RUN chmod +x /usr/local/bin/entrypoint.sh
-
-COPY test-nest.sh /opt/test-nest.sh
-RUN chmod +x /opt/test-nest.sh
+COPY entrypoint.sh /usr/local/bin/
+COPY test-nest.sh /opt/
+
+RUN python3 -m pip install nest-desktop && \
+    python3 -m pip install nestml && \
+    apt-get remove -y python3-scipy && \
+    python3 -m pip install scipy numpy && \
+    chmod +x /usr/local/bin/entrypoint.sh && \
+    chmod +x /opt/test-nest.sh
 
 EXPOSE 8080 52425 54286
 ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]
diff --git a/src/3.7/entrypoint.sh b/src/3.7rc1/entrypoint.sh
similarity index 100%
rename from src/3.7/entrypoint.sh
rename to src/3.7rc1/entrypoint.sh
diff --git a/src/3.7/test-nest.sh b/src/3.7rc1/test-nest.sh
similarity index 100%
rename from src/3.7/test-nest.sh
rename to src/3.7rc1/test-nest.sh

From 501a9b5004aeaf52c6bc93d0e3c5e34c339ab943 Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Mon, 25 Mar 2024 12:45:46 +0000
Subject: [PATCH 13/17] Add 3.7rc1 to CI

---
 ci-templates/000_3.7.gitlab-ci.yml | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 ci-templates/000_3.7.gitlab-ci.yml

diff --git a/ci-templates/000_3.7.gitlab-ci.yml b/ci-templates/000_3.7.gitlab-ci.yml
new file mode 100644
index 0000000..27f244b
--- /dev/null
+++ b/ci-templates/000_3.7.gitlab-ci.yml
@@ -0,0 +1,28 @@
+###############################################
+###               v3.6                     ###
+###############################################
+
+Build_36:
+  stage: build
+  needs: ["Build_Base"]
+  rules:
+    - when: always
+  script:
+    # Build
+    - docker pull nest/nest-simulator:3.7rc1 || true
+    - docker build
+        --cache-from nest/nest-simulator:3.7rc1
+        --tag nest/nest-simulator:3.7rc1
+        ./src/3.7rc1
+    # Test
+    - docker run -i --rm nest/nest-simulator:3.7rc1 bash /opt/test-nest.sh
+    # Deploy
+    - echo -n $DOCKERHUB_REGISTRY_TOKEN | docker login -u $DOCKERHUB_REGISTRY_USER --password-stdin
+    - docker push nest/nest-simulator:3.7rc1
+    - docker tag nest/nest-simulator:3.7rc1 $DOCKER_REGISTRY_IMAGE:3.7rc1
+    - docker push $DOCKER_REGISTRY_IMAGE:3.7rc1  
+    - docker logout $DOCKERHUB_REGISTRY
+    - docker logout $DOCKER_REGISTRY
+  tags:
+    - shell-runner
+

From aedb4904134d88298f98f404be21cc8ff14e443f Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Mon, 25 Mar 2024 12:46:22 +0000
Subject: [PATCH 14/17] Add 3.7rc1

---
 src/3.7rc1/Dockerfile | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/3.7rc1/Dockerfile b/src/3.7rc1/Dockerfile
index 65c6849..72fec69 100644
--- a/src/3.7rc1/Dockerfile
+++ b/src/3.7rc1/Dockerfile
@@ -1,7 +1,7 @@
 FROM docker-registry.ebrains.eu/nest/nest-simulator:nest-simulator-build-base as builder
 LABEL maintainer="s.graber@fz-juelich.de"
 
-ARG NEST_VERSION=3.6
+ARG NEST_VERSION=3.7_rc1
 ARG SRC_PATH=/tmp
 ARG CMAKE_C_COMPILER_LAUNCHER=ccache
 ARG CMAKE_CXX_COMPILER_LAUNCHER=ccache
@@ -37,7 +37,6 @@ RUN wget "https://github.com/nest/nest-simulator/archive/refs/tags/v${NEST_VERSI
           -Dwith-hdf5=ON \
           ${SRC_PATH}/nest-simulator-${NEST_VERSION} && \
     make -j $(nproc) && \
-    make docs && \
     make install
 
 ###############################################################################

From e90ba73badab1f67577ecacfded1dbff99d8f084 Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Tue, 26 Mar 2024 04:21:21 +0000
Subject: [PATCH 15/17] Complet rework of dockerfile

---
 ci-templates/000_3.7.gitlab-ci.yml |  10 +-
 src/3.7rc1/Dockerfile              | 142 +++++++++++++++++++++++------
 2 files changed, 117 insertions(+), 35 deletions(-)

diff --git a/ci-templates/000_3.7.gitlab-ci.yml b/ci-templates/000_3.7.gitlab-ci.yml
index 27f244b..8f8efb2 100644
--- a/ci-templates/000_3.7.gitlab-ci.yml
+++ b/ci-templates/000_3.7.gitlab-ci.yml
@@ -1,15 +1,14 @@
 ###############################################
-###               v3.6                     ###
+###               3.7rc1                   ###
 ###############################################
 
-Build_36:
+Build_Dev:
   stage: build
-  needs: ["Build_Base"]
   rules:
     - when: always
   script:
     # Build
-    - docker pull nest/nest-simulator:3.7rc1 || true
+    - docker pull push nest/nest-simulator:3.7rc1 || true
     - docker build
         --cache-from nest/nest-simulator:3.7rc1
         --tag nest/nest-simulator:3.7rc1
@@ -19,10 +18,7 @@ Build_36:
     # Deploy
     - echo -n $DOCKERHUB_REGISTRY_TOKEN | docker login -u $DOCKERHUB_REGISTRY_USER --password-stdin
     - docker push nest/nest-simulator:3.7rc1
-    - docker tag nest/nest-simulator:3.7rc1 $DOCKER_REGISTRY_IMAGE:3.7rc1
-    - docker push $DOCKER_REGISTRY_IMAGE:3.7rc1  
     - docker logout $DOCKERHUB_REGISTRY
-    - docker logout $DOCKER_REGISTRY
   tags:
     - shell-runner
 
diff --git a/src/3.7rc1/Dockerfile b/src/3.7rc1/Dockerfile
index 72fec69..9ef7641 100644
--- a/src/3.7rc1/Dockerfile
+++ b/src/3.7rc1/Dockerfile
@@ -1,7 +1,7 @@
-FROM docker-registry.ebrains.eu/nest/nest-simulator:nest-simulator-build-base as builder
+FROM ubuntu:22.04
 LABEL maintainer="s.graber@fz-juelich.de"
 
-ARG NEST_VERSION=3.7_rc1
+ARG NEST_VERSION=v3.7_rc1
 ARG SRC_PATH=/tmp
 ARG CMAKE_C_COMPILER_LAUNCHER=ccache
 ARG CMAKE_CXX_COMPILER_LAUNCHER=ccache
@@ -12,15 +12,104 @@ ENV TERM=xterm \
     DEBIAN_FRONTEND=noninteractive \
     PATH=/root/.local/bin:${PATH}
 
-SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    automake \
+    autotools-dev \
+    build-essential \ 
+    ccache \
+    cmake \
+    curl \
+    cython3 \
+    freeglut3-dev \
+    gosu \
+    jq \
+    less \
+    libboost-filesystem-dev libboost-regex-dev libboost-wave-dev \
+    libboost-python-dev libboost-program-options-dev libboost-test-dev \
+    libboost-dev \
+    libgomp1 \
+    libgsl-dev  \
+    libgsl0-dev \
+    libhdf5-dev \
+    libltdl-dev \
+    libltdl7 \
+    libmusic1v5 \
+    libncurses-dev \
+    libomp-dev \
+    libopenmpi-dev \
+    libpcre3 \
+    libpcre3-dev \
+    libpython3.10 \
+    libreadline-dev \
+    libreadline8 \ 
+    libtool \
+    libzmq3-dev \
+    llvm-dev \
+    nano \
+    openmpi-bin \
+    openssh-client \
+    openssh-server \
+    pandoc \
+    pep8 \
+    pkg-config \
+    python3-dev \
+    python3-flask \
+    python3-flask-cors \
+    python3-h5py \
+    python3-ipython \
+    python3-jupyter-core \
+    python3-matplotlib \
+    python3-mpi4py \
+    python3-nose \
+    python3-numpy \
+    python3-pandas \
+    python3-path \
+    python3-pip \
+    python3-restrictedpython \
+    python3-scipy \
+    python3-setuptools \
+    python3-sphinx \
+    python3-statsmodels \
+    python3-sympy \
+    python3-tk \
+    python3-tqdm \
+    tcl8.6 \
+    tcl8.6-dev \
+    tk8.6-dev \
+    uwsgi \
+    vera++ \
+    wget && \
+    apt-get autoremove
 
-# Install NEST and NESTML
-RUN wget "https://github.com/nest/nest-simulator/archive/refs/tags/v${NEST_VERSION}.tar.gz" -P ${SRC_PATH} && \
-    cd ${SRC_PATH} && tar -xzf v${NEST_VERSION}.tar.gz && ls -l && \
-    apt-get remove -y python3-numpy && \
-    python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/doc/requirements.txt && \
-    python3 -m pip install sphinx_gallery==0.10.1 numpy>=1.17.3,1.25.0 && \
-    mkdir nest-build && cd nest-build && \
+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 ${SRC_PATH} && \
+    wget "https://github.com/nest/nest-simulator/archive/refs/tags/v${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
+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 
+# 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 && \
+#     ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_csa-libneurosim.sh $PYLIB_DIR
+# # Install sionlib
+# RUN chmod +x ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_sionlib.sh && \
+#     ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_sionlib.sh
+# Install python requirements
+# RUN pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements.txt
+
+# Build nest
+RUN mkdir ${SRC_PATH}/nest-build && cd $_ && \
     cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/nest \
           -Dwith-optimize="-O2" \
           -Dwith-warning=ON \
@@ -33,29 +122,26 @@ RUN wget "https://github.com/nest/nest-simulator/archive/refs/tags/v${NEST_VERSI
           -Dwith-mpi=ON \
           -Dwith-openmp=ON \
           -Dwith-libneurosim=OFF \
-          -Dwith-music=/opt/music-install \
+          -Dwith-sionlib=OFF \
+          -Dwith-music=ON \ 
           -Dwith-hdf5=ON \
           ${SRC_PATH}/nest-simulator-${NEST_VERSION} && \
-    make -j $(nproc) && \
-    make install
+          make && \
+          make install
 
-###############################################################################
-# DEPLOY
+# Install NESTML and more
+RUN python3 -m pip install --upgrade pip && \
+    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 docker-registry.ebrains.eu/nest/nest-simulator:nest-simulator-deploy-base
-LABEL maintainer="s.graber@fz-juelich.de"
+RUN python3 -m pip install --force-reinstall --upgrade scipy
+
+COPY entrypoint.sh /usr/local/bin/entrypoint.sh
+RUN chmod +x /usr/local/bin/entrypoint.sh
 
-COPY --from=builder /opt/nest /opt/nest
-COPY --from=builder /opt/music-install /opt/music-install
-COPY entrypoint.sh /usr/local/bin/
-COPY test-nest.sh /opt/
-
-RUN python3 -m pip install nest-desktop && \
-    python3 -m pip install nestml && \
-    apt-get remove -y python3-scipy && \
-    python3 -m pip install scipy numpy && \
-    chmod +x /usr/local/bin/entrypoint.sh && \
-    chmod +x /opt/test-nest.sh
+COPY test-nest.sh /opt/test-nest.sh
+RUN chmod +x /opt/test-nest.sh
 
 EXPOSE 8080 52425 54286
 ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]

From d01dbc9d61574af305267f46803722cde33a59ee Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Tue, 26 Mar 2024 06:14:14 +0000
Subject: [PATCH 16/17] Combine image layers

---
 src/3.7rc1/Dockerfile | 54 +++++++++++++------------------------------
 1 file changed, 16 insertions(+), 38 deletions(-)

diff --git a/src/3.7rc1/Dockerfile b/src/3.7rc1/Dockerfile
index 9ef7641..8192aa2 100644
--- a/src/3.7rc1/Dockerfile
+++ b/src/3.7rc1/Dockerfile
@@ -1,7 +1,7 @@
 FROM ubuntu:22.04
 LABEL maintainer="s.graber@fz-juelich.de"
 
-ARG NEST_VERSION=v3.7_rc1
+ARG NEST_VERSION=3.7_rc1
 ARG SRC_PATH=/tmp
 ARG CMAKE_C_COMPILER_LAUNCHER=ccache
 ARG CMAKE_CXX_COMPILER_LAUNCHER=ccache
@@ -79,37 +79,18 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     uwsgi \
     vera++ \
     wget && \
-    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 ldconfig
-
-
-
-# Download NEST
-RUN cd ${SRC_PATH} && \
+    apt-get autoremove && \
+    python3 -m pip install --upgrade pip setuptools wheel mock && \
+    python3 -m pip install --force-reinstall --upgrade --no-binary=h5py h5py && \
+    ldconfig && \
+    cd ${SRC_PATH} && \
     wget "https://github.com/nest/nest-simulator/archive/refs/tags/v${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
-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 
-# 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 && \
-#     ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_csa-libneurosim.sh $PYLIB_DIR
-# # Install sionlib
-# RUN chmod +x ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_sionlib.sh && \
-#     ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_sionlib.sh
-# Install python requirements
-# RUN pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements.txt
-
-# Build nest
-RUN mkdir ${SRC_PATH}/nest-build && cd $_ && \
+    tar -xzf v${NEST_VERSION}.tar.gz && \
+    python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/doc/requirements.txt && \
+    python3 -m pip install sphinx_gallery==0.10.1 && \
+    chmod +x ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_music.sh && \
+    ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_music.sh && \
+    mkdir ${SRC_PATH}/nest-build && cd $_ && \
     cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/nest \
           -Dwith-optimize="-O2" \
           -Dwith-warning=ON \
@@ -127,15 +108,12 @@ RUN mkdir ${SRC_PATH}/nest-build && cd $_ && \
           -Dwith-hdf5=ON \
           ${SRC_PATH}/nest-simulator-${NEST_VERSION} && \
           make && \
-          make install
-
-# Install NESTML and more
-RUN python3 -m pip install --upgrade pip && \
+          make install && \
+    python3 -m pip install --upgrade pip && \
     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 
-
-RUN python3 -m pip install --force-reinstall --upgrade scipy
+    python3 -m pip install --upgrade https://github.com/nest/nestml/archive/refs/heads/master.zip  && \
+    python3 -m pip install --force-reinstall --upgrade scipy
 
 COPY entrypoint.sh /usr/local/bin/entrypoint.sh
 RUN chmod +x /usr/local/bin/entrypoint.sh

From 996613ed8a898a0c9a6d0fe51a277480e71734ac Mon Sep 17 00:00:00 2001
From: Steffen Graber <s.graber@fz-juelich.de>
Date: Tue, 26 Mar 2024 06:23:01 +0000
Subject: [PATCH 17/17] Fix naming

---
 ci-templates/000_3.7.gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ci-templates/000_3.7.gitlab-ci.yml b/ci-templates/000_3.7.gitlab-ci.yml
index 8f8efb2..8615677 100644
--- a/ci-templates/000_3.7.gitlab-ci.yml
+++ b/ci-templates/000_3.7.gitlab-ci.yml
@@ -2,7 +2,7 @@
 ###               3.7rc1                   ###
 ###############################################
 
-Build_Dev:
+Build_3.7:
   stage: build
   rules:
     - when: always