Update Dockerfile, need to make all tests pass

chempy/util/tests/test_graph.py

@@ -11,7 +11,7 @@
 from ..testing import requires, skipif
 
 try:
-    dot_missing = subprocess.call(["dot", "-?"]) != 0
+    dot_missing = subprocess.run(["dot", "-?"]).returncode != 0
 except OSError:
     dot_missing = True
 

scripts/environment/Dockerfile

@@ -9,11 +9,11 @@ RUN apt-get update && \
     python3-dev python3-pip libboost-dev libgsl-dev liblapack-dev libsuitesparse-dev graphviz && \
     apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-RUN mkdir /tmp/sundials-5.5.0-build && \
-    curl -Ls https://github.com/LLNL/sundials/releases/download/v5.5.0/sundials-5.5.0.tar.gz | tar xz -C /tmp && \
+RUN mkdir /tmp/sundials-5.8.0-build && \
+    curl -Ls https://github.com/LLNL/sundials/releases/download/v5.8.0/sundials-5.8.0.tar.gz | tar xz -C /tmp && \
     FC=gfortran-10 cmake \
-        -S /tmp/sundials-5.5.0 \
-        -B /tmp/sundials-5.5.0-build \
+        -S /tmp/sundials-5.8.0 \
+        -B /tmp/sundials-5.8.0-build \
         -DCMAKE_INSTALL_PREFIX=/usr/local \
         -DCMAKE_BUILD_TYPE=Release \
         -DBUILD_SHARED_LIBS=ON \
@@ -25,15 +25,13 @@ RUN mkdir /tmp/sundials-5.5.0-build && \
         -DENABLE_KLU=ON \
         -DKLU_INCLUDE_DIR=/usr/include/suitesparse \
         -DKLU_LIBRARY_DIR=/usr/lib/x86_64-linux-gnu && \
-    cmake --build /tmp/sundials-5.5.0-build && \
-    cmake --build /tmp/sundials-5.5.0-build --target install && \
-    rm -r /tmp/sundials-5.5.0*/ && \
+    cmake --build /tmp/sundials-5.8.0-build && \
+    cmake --build /tmp/sundials-5.8.0-build --target install && \
+    rm -r /tmp/sundials-5.8.0*/ && \
     python3 -m pip install --upgrade-strategy=eager --upgrade pip && \
-    python3 -m pip install --upgrade-strategy=eager numpy cython setuptools && \
+    python3 -m pip install --upgrade-strategy=eager numpy 'cython>=3.0.10' setuptools && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 
-# http://computation.llnl.gov/projects/sundials/download/sundials-5.5.0.tar.gz
-
 # At this point the system should be able to pip-install the package and all of its dependencies. We'll do so
 # when running the image using the ``host-jupyter-using-docker.sh`` script. Installed packages are cached.

scripts/host-jupyter-using-docker.sh

@@ -51,14 +51,16 @@ else
     LOCALCMD="jupyter notebook --no-browser --port $PORT --ip=* index.ipynb"
     PORTFWD="-p ${4:-127.0.0.1}:$PORT:$PORT"
 fi
-MYCMD="groupadd -f --gid \$HOST_GID \$HOST_WHOAMI; \
-useradd --uid \$HOST_UID --gid \$HOST_GID --home /mount \$HOST_WHOAMI; \
-sudo --login -u \$HOST_WHOAMI PYCVODES_NO_LAPACK=1 PYCVODES_NO_KLU=1 python3 -m pip install --user -e .[all]; \
-sudo --login -u \$HOST_WHOAMI /mount/.local/bin/jupyter-nbextension enable --user --py widgetsnbextension; \
-sudo --login -u \$HOST_WHOAMI LD_LIBRARY_PATH=/usr/local/lib MPLBACKEND=Agg /mount/.local/bin/$LOCALCMD"
+MYCMD="\
+groupadd -f --gid \$HOST_GID \$HOST_WHOAMI; \
+useradd --uid \$HOST_UID --gid \$HOST_GID --home /mount/.env \$HOST_WHOAMI; \
+sudo -u \$HOST_WHOAMI PYCVODES_NO_LAPACK=1 PYCVODES_NO_KLU=1 python3 -m pip install --cache-dir /mount/.env/pypi-cache --user -e .[all]; \
+sudo -u \$HOST_WHOAMI /mount/.env/.local/bin/jupyter-nbextension enable --user --py widgetsnbextension; \
+sudo -u \$HOST_WHOAMI LD_LIBRARY_PATH=/usr/local/lib MPLBACKEND=Agg PYTHONPATH=/mount /mount/.env/.local/bin/$LOCALCMD"
 
 set -x
 
+mkdir -m 777 -p .env
 
 $PODMAN run \
         --rm \

setup.py

@@ -128,7 +128,7 @@ def _path_under_setup(*args):
         "sympy>=1.1.1,!=1.2",
         "quantities>=0.12.1",
         "pyneqsys>=0.5.5",
-        "pyodesys>=0.14.1" if sys.version_info[0] >= 3 else "pyodesys<0.12",
+        "pyodesys>=0.14.3" if sys.version_info[0] >= 3 else "pyodesys<0.12",
         "pyparsing>=2.0.3",
         "sym>=0.3.4",
         "pulp>=1.6.8",