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Fix issues with the new numpy version in dev (nest#247)
* 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 pygsl installation * Fix numpy/pandas issue
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@@ -12,7 +12,7 @@ ENV TERM=xterm \ | |
| DEBIAN_FRONTEND=noninteractive \ | ||
| PATH=/root/.local/bin:${PATH} | ||
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| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| automake \ | ||
| autotools-dev \ | ||
| build-essential \ | ||
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@@ -24,6 +24,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ | |
| git \ | ||
| gosu \ | ||
| jq \ | ||
| junitparser \ | ||
| less \ | ||
| libboost-filesystem-dev libboost-regex-dev libboost-wave-dev \ | ||
| libboost-python-dev libboost-program-options-dev libboost-test-dev \ | ||
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@@ -60,7 +61,6 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ | |
| python3-ipython \ | ||
| python3-junitparser \ | ||
| python3-jupyter-core \ | ||
| python3-matplotlib \ | ||
| python3-mpi4py \ | ||
| python3-nose \ | ||
| python3-pandas \ | ||
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@@ -70,6 +70,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ | |
| python3-pytest-timeout \ | ||
| python3-pytest-xdist \ | ||
| python3-restrictedpython \ | ||
| python3-scipy \ | ||
| python3-setuptools \ | ||
| python3-sphinx \ | ||
| python3-statsmodels \ | ||
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@@ -82,46 +83,27 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ | |
| uwsgi \ | ||
| vera++ \ | ||
| wget && \ | ||
| apt-get autoremove | ||
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| RUN python3 -m pip install --upgrade scipy numpy numpydoc | ||
| RUN python3 -m pip install --upgrade pip setuptools wheel mock | ||
| RUN python3 -m pip install --force-reinstall --upgrade --no-binary=h5py h5py | ||
| RUN ldconfig | ||
| apt-get autoremove && \ | ||
| python3 -m pip install --upgrade pip setuptools wheel mock && \ | ||
| python3 -m pip install --force-reinstall --upgrade --no-binary=h5py h5py && \ | ||
| ldconfig | ||
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| # 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 | ||
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| # 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 example Image breathe csvkit docutils PyYAML>=4.2b1 tqdm yamllint | ||
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| RUN python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements.txt | ||
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| # RUN python3 -m pip install sphinx_gallery==0.10.1 | ||
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| # 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 | ||
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| # # 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 | ||
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| # Build nest | ||
| RUN mkdir ${SRC_PATH}/nest-build && cd $_ && \ | ||
| # Installing every package fix it. | ||
| RUN python3 -m pip install sphinx>=6.2.1 sphinx_rtd_theme sphinx_autobuild 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==0.13.0 '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 $_ && \ | ||
| cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/nest \ | ||
| -Dwith-optimize="-O2" \ | ||
| -Dwith-warning=ON \ | ||
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@@ -135,21 +117,25 @@ RUN mkdir ${SRC_PATH}/nest-build && cd $_ && \ | |
| -Dwith-openmp=ON \ | ||
| -Dwith-libneurosim=OFF \ | ||
| -Dwith-sionlib=OFF \ | ||
| -Dwith-music=ON \ | ||
| -Dwith-music='$HOME/.cache/libneurosim.install' \ | ||
| -Dwith-hdf5=ON \ | ||
| ${SRC_PATH}/nest-simulator-${NEST_VERSION} && \ | ||
| make && \ | ||
| make install | ||
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| # 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 && \ | ||
| python3 -m pip install nestml-server@git+https://github.com/babsey/[email protected] | ||
| RUN 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 && \ | ||
| python3 -m pip install --upgrade gsl wheel setuptools swig | ||
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| #Latest update to nestml v8.0.0-rc1 | ||
| RUN python3 -m pip install nestml==8.0.0rc2 && \ | ||
| python3 -m pip install nestml-server@git+https://github.com/babsey/[email protected] && \ | ||
| python3 -m pip install --upgrade pygsl@git+https://github.com/pygsl/[email protected] | ||
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| COPY entrypoint.sh /usr/local/bin/entrypoint.sh | ||
| RUN chmod +x /usr/local/bin/entrypoint.sh | ||
| RUN chmod +x /usr/local/bin/entrypoint.sh | ||
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| COPY test-nest.sh /opt/test-nest.sh | ||
| RUN chmod +x /opt/test-nest.sh | ||
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