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] 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