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Fix pygsl installation #246

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merged 31 commits into from
Sep 26, 2024
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29adbb2
Merge build and deploy to fix deploy problems
steffengraber Feb 9, 2024
3d52979
Merge remote-tracking branch 'upstream/master'
steffengraber Mar 7, 2024
e1cfa85
Merge remote-tracking branch 'upstream/master'
steffengraber Mar 8, 2024
d63f2f4
Merge remote-tracking branch 'upstream/master'
steffengraber Mar 26, 2024
ab7e910
Merge remote-tracking branch 'upstream/master'
steffengraber Apr 4, 2024
1adf82e
Add nest-server requirements
steffengraber Apr 4, 2024
5301617
Fix nest-desktop and compose file
steffengraber Apr 4, 2024
c384fb0
Add v3.7
steffengraber Apr 12, 2024
93b1397
Merge branch 'fix-nest-server'
steffengraber Apr 12, 2024
a52208a
Merge remote-tracking branch 'upstream/master'
steffengraber Apr 15, 2024
d01ede0
Remove test
steffengraber Apr 19, 2024
fa70bbb
Add v3.7 to readme
steffengraber Apr 19, 2024
fe3ca17
Merge remote-tracking branch 'upstream/master'
steffengraber May 15, 2024
52d7575
Fix nestml version and add pygsl
steffengraber May 15, 2024
5fd6274
Merge remote-tracking branch 'upstream/master'
steffengraber Jun 17, 2024
685f670
Merge remote-tracking branch 'upstream/master'
steffengraber Jun 20, 2024
d016e77
Merge remote-tracking branch 'upstream/master'
steffengraber Jul 17, 2024
b2ee7da
Install nestml fix for nest verssion
steffengraber Jul 17, 2024
00d1176
Merge remote-tracking branch 'upstream/master'
steffengraber Jul 18, 2024
28e1391
Fix merging errors
steffengraber Jul 18, 2024
de16dfe
Merge remote-tracking branch 'upstream/master'
steffengraber Jul 22, 2024
4527fa9
Merge remote-tracking branch 'upstream/master'
steffengraber Jul 22, 2024
c567942
Merge remote-tracking branch 'upstream/master'
steffengraber Jul 22, 2024
1174227
Merge remote-tracking branch 'upstream/master'
steffengraber Aug 1, 2024
e99a8a3
Deactivate build of 3.7 and 2.20.2 in CI
steffengraber Aug 1, 2024
fe8fe76
Add rc2
steffengraber Aug 1, 2024
9f9e145
NEW Version 3.8
steffengraber Aug 5, 2024
64354c4
Merge remote-tracking branch 'upstream/master'
steffengraber Aug 6, 2024
2f4ec0f
Merge remote-tracking branch 'upstream/master'
steffengraber Aug 22, 2024
5fcb523
Merge remote-tracking branch 'upstream/master'
steffengraber Sep 26, 2024
4a01baa
Fix pygsl installation
steffengraber Sep 26, 2024
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Merge remote-tracking branch 'upstream/master'
steffengraber committed Jul 18, 2024
commit 00d11761751b68e9b8b170addfd88c8b79caf33c
10 changes: 2 additions & 8 deletions src/3.8/Dockerfile
Original file line number Diff line number Diff line change
@@ -90,13 +90,7 @@ 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 && \
# 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 -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/doc/requirements.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 && \
@@ -138,5 +132,5 @@ 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 52426 54286
EXPOSE 8080 52425 54286
ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]
6 changes: 1 addition & 5 deletions src/3.8/entrypoint.sh
Original file line number Diff line number Diff line change
@@ -11,15 +11,11 @@ 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
23 changes: 8 additions & 15 deletions src/dev/Dockerfile
Original file line number Diff line number Diff line change
@@ -90,23 +90,15 @@ 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

# 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 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

@@ -144,10 +136,11 @@ 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/[email protected]b3
python3 -m pip install nestml-server@git+https://github.com/babsey/[email protected]b1

RUN python3 -m pip install --force-reinstall --upgrade scipy

@@ -157,5 +150,5 @@ 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 52426 54286
EXPOSE 8080 52425 54286
ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]
6 changes: 1 addition & 5 deletions src/dev/entrypoint.sh
Original file line number Diff line number Diff line change
@@ -11,15 +11,11 @@ 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
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