Update Dockerfile, need to make all tests pass

.gitignore

@@ -26,10 +26,7 @@ build/
 *.bak0
 *.bak1
 sundials-*.tar.gz
-.local/
-.ipython/
-.jupyter/*
-!.jupyter/jupyter_notebook_config.py
+.env/
 tmp/
 .coverage
 htmlcov/

README.rst

@@ -107,13 +107,13 @@ Using Docker
 If you have `Docker <https://www.docker.com>`_ installed, you may use it to host a jupyter
 notebook server::
 
-  $ ./scripts/host-jupyter-using-docker.sh . 8888
+  $ ./scripts/host-env.sh host-notebook --port 8888
 
 the first time you run the command, some dependencies will be downloaded. When the installation
 is complete there will be a link visible which you can open in your browser. You can also run
 the test suite using the same docker-image::
 
-  $ ./scripts/host-jupyter-using-docker.sh . 0
+  $ ./scripts/host-env.sh run-tests
 
 there will be a few skipped test (due to some dependencies not being installed by default) and
 quite a few warnings.

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 → scripts/environment/Containerfile

@@ -1,19 +1,20 @@
-FROM docker.io/debian:bullseye
+FROM docker.io/debian:bookworm
 
 MAINTAINER Björn Dahlgren <bjodah@gmail.com>
 
 ENV LANG C.UTF-8
 
 RUN apt-get update && \
-    apt-get --quiet --assume-yes install curl git g++-10 gfortran-10 libgmp-dev binutils-dev bzip2 make cmake sudo \
-    python3-dev python3-pip libboost-dev libgsl-dev liblapack-dev libsuitesparse-dev graphviz && \
+    apt-get --quiet --assume-yes install --no-install-recommends \
+    curl git g++ gfortran libgmp-dev binutils-dev bzip2 make cmake sudo \
+    python3-dev python3-venv 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 && \
-    FC=gfortran-10 cmake \
-        -S /tmp/sundials-5.5.0 \
-        -B /tmp/sundials-5.5.0-build \
+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 cmake \
+        -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 +26,11 @@ 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*/ && \
-    python3 -m pip install --upgrade-strategy=eager --upgrade pip && \
-    python3 -m pip install --upgrade-strategy=eager numpy cython setuptools && \
+    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*/ && \
     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-env.sh

@@ -0,0 +1,110 @@
+#!/bin/bash
+show_help() {
+    echo "Usage:"
+    echo "$(basename $0) host-notebook --port 8888 --listen 127.0.0.1"
+    echo "$(basename $0) run-tests"
+}
+set -euxo pipefail
+
+HOST_NOTEBOOK=0
+RUN_TESTS=0
+PORT=8000
+while [ $# -gt 0 ]; do
+    case "$1" in
+        host-notebook)
+            HOST_NOTEBOOK=1
+            shift
+            ;;
+        --port)
+            shift
+            PORT=$1
+            shift
+            ;;
+        --listen)
+            shift
+            LISTEN=$1
+            shift
+            ;;
+        run-tests)
+            RUN_TESTS=1
+            shift
+            ;;
+        --help|-h)
+            show_help
+            exit 0
+            ;;
+        --)
+            break;
+            ;;
+        *)
+            show_help
+            exit 1
+            ;;
+    esac
+done
+
+if ! which podrun >/dev/null; then
+    SOME_TEMP_DIR=$(mktemp -d)
+    trap 'rm -rf -- "$SOME_TEMP_DIR"' EXIT
+    ( cd "$SOME_TEMP_DIR"; curl -LOs https://raw.githubusercontent.com/bjodah/dotfiles/master/per-leaf-dir/bin/podrun; chmod +x podrun )
+    export PATH="$SOME_TEMP_DIR:$PATH"
+fi
+
+SCRIPTS_DIR=$(dirname $(realpath "$BASH_SOURCE"))
+REPO_DIR=$(realpath "$SCRIPTS_DIR/..")
+ENV_DIR="$REPO_DIR/.env"
+PKG_NAME=${PKG_NAME:-$(basename $REPO_DIR)}
+
+mkdir -p $ENV_DIR
+
+cat <<EOF>$ENV_DIR/setup.sh
+if [ ! -d .env/ ]; then
+   >&2 echo "No .env directory?"
+   exit 1
+fi
+if [ ! -d .env/venv ]; then
+   python3 -m venv .env/venv   
+fi
+source .env/venv/bin/activate
+if ! python -c "import pycvodes" 2>&1 >/dev/null; then
+    python -m pip install --upgrade-strategy=eager --upgrade pip && \
+    python -m pip install --upgrade-strategy=eager numpy 'cython>=3.0.10' setuptools && \
+    env \
+        PYCVODES_NO_LAPACK=1 \
+        PYCVODES_NO_KLU=1 \
+        LDFLAGS='-Wl,--disable-new-dtags -Wl,-rpath,/usr/local/lib -L/usr/local/lib' \
+        python -m pip install --cache-dir .env/pypi-cache -e .[all]
+fi
+if ! python -c "import pyodesys" 2>&1 >/dev/null; then
+   python -m pip install --cache-dir .env/pypi-cache -e .[all]
+   #jupyter-nbextension enable --user --py widgetsnbextension
+fi
+export MPLBACKEND=Agg
+EOF
+
+cat <<EOF>$ENV_DIR/run-tests.sh
+#!/bin/bash
+set -e
+source .env/setup.sh
+pytest -sv -ra --pyargs $PKG_NAME
+EOF
+
+cat <<EOF>$ENV_DIR/host-notebook.sh
+#!/bin/bash
+set -e
+source .env/setup.sh
+jupyter notebook --no-browser --port $PORT --ip=* index.ipynb
+EOF
+
+
+if [ $RUN_TESTS = 1 ]; then
+    podrun --cont-img-dir $SCRIPTS_DIR/environment \
+           --name "${PKG_NAME}_run_tests" \
+           -- bash $ENV_DIR/run-tests.sh
+fi
+if [ $HOST_NOTEBOOK = 1 ]; then
+    podrun --cont-img-dir $SCRIPTS_DIR/environment \
+           --name "${PKG_NAME}_host_notebook_${PORT}" \
+           -p $LISTEN:$PORT:$PORT \
+           -- bash $ENV_DIR/host-notebook.sh
+fi

setup.py

@@ -100,7 +100,7 @@ def _path_under_setup(*args):
 _author, _author_email = open(_path_under_setup("AUTHORS"), "rt").readline().split("<")
 
 extras_req = {
-    "integrators": ["pyodeint>=0.10.4", "pycvodes>=0.14.0", "pygslodeiv2>=0.9.4"],
+    "integrators": ["pyodeint>=0.10.4", "pycvodes>=0.14.5", "pygslodeiv2>=0.9.4"],
     "solvers": ["pykinsol>=0.1.6"],
     "native": ["pycompilation>=0.4.12", "pycodeexport>=0.1.3", "appdirs"],
     "docs": ["Sphinx", "sphinx_rtd_theme", "numpydoc"],
@@ -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>=0.14.4" if sys.version_info[0] >= 3 else "pyodesys<0.12",
         "pyparsing>=2.0.3",
         "sym>=0.3.4",
         "pulp>=1.6.8",