added assimulo deps to pyproject for worker

biosimulators · Oct 24, 2024 · c9ff61b · c9ff61b
1 parent 1468c39
commit c9ff61b
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diff --git a/Dockerfile-base b/Dockerfile-base
@@ -77,6 +77,7 @@ RUN python3.10 -m pip install --upgrade pip \
     && poetry env use 3.10 \
     && poetry install --without=api,worker
 
+
 # install smoldyn
 # RUN . /app/.venv/bin/activate \
 #     && wget https://www.smoldyn.org/smoldyn-2.73.tgz \

diff --git a/compose_worker/Dockerfile-compose_worker b/compose_worker/Dockerfile-compose_worker
@@ -2,34 +2,6 @@
 
 FROM ghcr.io/biosimulators/bio-check-base:latest
 
-# TODO: start the fenics implementation
-# RUN apt-get update && apt-get install -y petsc-dev \
-#     libopenmpi-dev \
-#     libspdlog-dev \
-#     libpugixml-dev \
-#     cmake \
-#     gcc \
-#     g++ \
-#     gfortran \
-#     && rm -rf /var/lib/apt/lists/* \
-#     && add-apt-repository ppa:fenics-packages/fenics -y \
-#     && apt update \
-#     && apt install -y fenicsx \
-#     && poetry run pip install meson-python meson ninja
-
-# RUN poetry run pip install \
-#     biosimulators-utils[logging] \
-#     biosimulators-amici \
-#     biosimulators-copasi \
-#     biosimulators-pysces \
-#     biosimulators-tellurium
-
-# add deps with extras
-# RUN yes | poetry cache clear PyPI --all \
-#     && poetry add biosimulators-utils --extras=logging \
-#     && poetry add pysces --extras=sbml \
-#     && poetry add biosimulators-copasi --python="^3.10"
-
 # os deps
 RUN apt-get update && apt-get install -y libatlas-base-dev \
     libhdf5-serial-dev \
@@ -49,85 +21,101 @@ RUN apt-get update && apt-get install -y libatlas-base-dev \
 ###################################
 # PySCeS
 
-# SUNDIALS
+# SUNDIALS --> installation path is default cmake (/usr/local) with LD_LIBRARY_PATH as runtime location
 # ignore certificate checking because certificate was expired as of 2021-11-10
-# ARG SUNDIALS_VERSION=2.6.2
-# RUN apt-get install -y --no-install-recommends \
-#         wget \
-#         cmake \
-#         make \
-#         g++ \
-#     \
-#     && cd /tmp \
-#     && wget --no-check-certificate https://computing.llnl.gov/sites/default/files/inline-files/sundials-${SUNDIALS_VERSION}.tar.gz \
-#     && tar xvvf sundials-${SUNDIALS_VERSION}.tar.gz \
-#     && cd sundials-${SUNDIALS_VERSION} \
-#     && mkdir build \
-#     && cd build \
-#     && cmake .. \
-#     && make \
-#     && make install \
-#     \
-#     && cd /tmp \
-#     && rm sundials-${SUNDIALS_VERSION}.tar.gz \
-#     && rm -r sundials-${SUNDIALS_VERSION}
-# ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
-
-# install assimulo because pipenv fails to install it
-# ARG ASSIMULO_VERSION=3.2.9
-# RUN pip install git+https://github.com/modelon-community/Assimulo.git@Assimulo-${ASSIMULO_VERSION}
-
-# RUN pip install "cython<1.0" numpy scipy matplotlib
-
-# install SUNDIALS and Assimulo
-# ARG ASSIMULO_VERSION=3.4.3
-# RUN apt-get update -y \
-#     && apt-get install -y --no-install-recommends \
-#         libsundials-dev \
-#         g++ \
-#         libblas-dev \
-#         liblapack-dev
-#         # libsundials-arkode5 \
-#         # libsundials-cvode6 \
-#         # libsundials-cvodes6 \
-#         # libsundials-ida6 \
-#         # libsundials-idas5 \
-#         # libsundials-kinsol6 \
-#         # libsundials-nvecserial6
-#     # && pip install --install-option="--optimize=1" \
-#     #         --install-option="--extra-fortran-link-flags=-shared" \
-#     #         --install-option="--sundials-home=/usr" \
-#     #         --install-option="--blas-home=/usr/lib/x86_64-linux-gnu" \
-#     #         --install-option="--lapack-home=/usr" \
-#     #         --install-option="--extra-fortran-compile-flags=-fallow-argument-mismatch"  \
-#     #         --install-option="--extra-c-flags=-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION" \
-#     #         git+https://github.com/modelon-community/Assimulo.git@Assimulo-${ASSIMULO_VERSION}  \
-#     # \
-#
-# # fonts for matplotlib
-# RUN apt-get update -y && apt-get install -y --no-install-recommends libfreetype6
-# # && rm -rf /var/lib/apt/lists/*
+ARG SUNDIALS_VERSION=2.6.2
+RUN apt-get install -y --no-install-recommends \
+        wget \
+        cmake \
+        make \
+        g++ \
+    \
+    && cd /tmp \
+    && wget --no-check-certificate https://computing.llnl.gov/sites/default/files/inline-files/sundials-${SUNDIALS_VERSION}.tar.gz \
+    && tar xvvf sundials-${SUNDIALS_VERSION}.tar.gz \
+    && cd sundials-${SUNDIALS_VERSION} \
+    && mkdir build \
+    && cd build \
+    && CFLAGS="-fPIC" cmake .. \
+    && make \
+    && make install \
+    \
+    && cd /tmp \
+    && rm sundials-${SUNDIALS_VERSION}.tar.gz \
+    && rm -r sundials-${SUNDIALS_VERSION}
+ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
 
 ############################################
 # App content
 
 COPY . /app/worker
 
-# install requirements in poetry via pip prox
-# RUN poetry run pip install -r /app/worker/requirements.worker.txt
+ENV PATH="/root/.local/bin:$PATH"
 
-# install masspy TODO: do this
-# RUN poetry run pip install biosimulators-masspy
+# Install only worker deps
+RUN poetry install --only=worker --no-cache
 
-# install with poetry TODO: remove this eventually
-# RUN /app/assets/install_deps.sh /app/worker/requirements.worker.txt
-
-ENV PATH="/root/.local/bin:$PATH"
+# Install Assimulo from source for Pysces
+RUN apt-get update \
+    && apt-get install -y libblas-dev \
+    liblapack-dev \
+    libatlas-base-dev \
+    python3-distutils \
+    python3-dev \
+    && git clone https://github.com/modelon-community/Assimulo.git \
+    && cd Assimulo \
+    && poetry run pip install --upgrade setuptools pip wheel Cython numpy \
+    && poetry run python3 setup.py install --sundials-home=/usr/local --blas-home=/usr/lib/x86_64-linux-gnu
+
+# && cd Assimulo \
+# && rm -rf build \
+# && poetry run python3 setup.py install --sundials-home=/usr/local --blas-home=/usr/lib/x86_64-linux-gnu
 
-RUN poetry install --only=worker
+# install masspy TODO: do this
+# RUN poetry run pip install biosimulators-masspy
 
 WORKDIR /app/worker
 
 RUN python3 -c "import os;files=os.listdir();import shutil;[shutil.rmtree(f) if '__pycache__' in f else None for f in files]"
 
 ENTRYPOINT ["poetry", "run", "python3", "main.py"]
+
+#############################
+# Fenics
+
+# TODO: start the fenics implementation
+# RUN apt-get update && apt-get install -y petsc-dev \
+#     libopenmpi-dev \
+#     libspdlog-dev \
+#     libpugixml-dev \
+#     cmake \
+#     gcc \
+#     g++ \
+#     gfortran \
+#     && rm -rf /var/lib/apt/lists/* \
+#     && add-apt-repository ppa:fenics-packages/fenics -y \
+#     && apt update \
+#     && apt install -y fenicsx \
+#     && poetry run pip install meson-python meson ninja
+
+# RUN poetry run pip install \
+#     biosimulators-utils[logging] \
+#     biosimulators-amici \
+#     biosimulators-copasi \
+#     biosimulators-pysces \
+#     biosimulators-tellurium
+
+# add deps with extras
+# RUN yes | poetry cache clear PyPI --all \
+#     && poetry add biosimulators-utils --extras=logging \
+#     && poetry add pysces --extras=sbml \
+#     && poetry add biosimulators-copasi --python="^3.10"
+
+# install requirements in poetry via pip prox
+# RUN poetry run pip install -r /app/worker/requirements.worker.txt
+
+# install masspy TODO: do this
+# RUN poetry run pip install biosimulators-masspy
+
+# install with poetry TODO: remove this eventually
+# RUN /app/assets/install_deps.sh /app/worker/requirements.worker.txt