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Update mermaid installation and fix sphinx dockumentation build (#248)
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* Merge build and deploy to fix deploy problems

* Add nest-server requirements

* Fix nest-desktop and compose file

* Add v3.7

* Remove test

* Add v3.7 to readme

* Fix nestml version and add pygsl

* Install nestml fix for nest verssion

* Fix merging errors

* Deactivate build of 3.7 and 2.20.2 in CI

* Add rc2

* NEW Version 3.8

* Fix the mermaid installation with a patch and fix some doubles
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steffengraber authored Oct 17, 2024
1 parent cbd06e0 commit 62eb3f3
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Showing 2 changed files with 23 additions and 11 deletions.
21 changes: 10 additions & 11 deletions src/3.8/Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,6 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
libncurses-dev \
libomp-dev \
libopenmpi-dev \
libpcre3 \
libpcre3-dev \
libpython3.10 \
libreadline-dev \
Expand All @@ -57,7 +56,6 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
python3-dev \
python3-flask \
python3-flask-cors \
python3-h5py \
python3-ipython \
python3-junitparser \
python3-jupyter-core \
Expand All @@ -72,7 +70,6 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
python3-restrictedpython \
python3-scipy \
python3-setuptools \
python3-sphinx \
python3-statsmodels \
python3-sympy \
python3-tk \
Expand All @@ -85,22 +82,25 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
wget && \
apt-get autoremove && \
python3 -m pip install --upgrade pip setuptools wheel mock && \
python3 -m pip install --force-reinstall --upgrade --no-binary=h5py h5py && \
python3 -m pip install --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 ${SRC_PATH} && \
tar -xzf v${NEST_VERSION}.tar.gz && \
# 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 sphinx>=6.2.1 sphinx_autobuild>=2021.3.14 sphinx-carousel sphinx-copybutton>=0.5.2 && \
python3 -m pip install sphinx-carousel sphinx-notfound-page>=0.8.3 sphinx-design>=0.4.1 sphinx-gallery>=0.13.0 && \
python3 -m pip install sphinx-material>=0.0.35 sphinxcontrib-mermaid sphinxcontrib-plantuml>=0.26 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' && \
python3 -m pip install "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 && \
mkdir ${SRC_PATH}/nest-build && cd $_ && \
${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_music.sh
WORKDIR ${SRC_PATH}/nest-simulator-${NEST_VERSION}/
COPY patch_1.patch ${SRC_PATH}/nest-simulator-${NEST_VERSION}/
RUN git apply patch_1.patch
RUN mkdir ${SRC_PATH}/nest-build && cd $_ && \
cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/nest \
-Dwith-optimize="-O2" \
-Dwith-warning=ON \
Expand All @@ -119,7 +119,6 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
${SRC_PATH}/nest-simulator-${NEST_VERSION} && \
make && \
make install && \
python3 -m pip install --upgrade pip setuptools wheel && \
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 && \
Expand Down
13 changes: 13 additions & 0 deletions src/3.8/patch_1.patch
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
diff --git a/doc/htmldoc/conf.py b/doc/htmldoc/conf.py
index 2206227a4..66230fda2 100644
--- a/doc/htmldoc/conf.py
+++ b/doc/htmldoc/conf.py
@@ -92,7 +92,7 @@ copybutton_prompt_text = ">>> "
copybutton_only_copy_prompt_lines = True

mermaid_output_format = "raw"
-mermaid_version = "10.2.0"
+mermaid_version = "10.3.0"

# disable require js - mermaid doesn't work if require.js is loaded before it
nbsphinx_requirejs_path = ""

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