bump versions

scripts/environment/Containerfile

@@ -1,17 +1,18 @@
-FROM docker.io/debian:bullseye
+FROM docker.io/debian:bookworm
 
 MAINTAINER Björn Dahlgren <[email protected]>
 
 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-5.8.0-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 \
+    FC=gfortran cmake \
         -S /tmp/sundials-5.8.0 \
         -B /tmp/sundials-5.8.0-build \
         -DCMAKE_INSTALL_PREFIX=/usr/local \
@@ -28,8 +29,6 @@ RUN mkdir /tmp/sundials-5.8.0-build && \
     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>=3.0.10' setuptools && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 

scripts/host-env.sh

@@ -4,10 +4,12 @@ show_help() {
     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
+while [ $# -gt 0 ]; do
     case "$1" in
         host-notebook)
             HOST_NOTEBOOK=1
@@ -33,15 +35,15 @@ while [ $# -gt 0]; do
             ;;
         --)
             break;
+            ;;
         *)
             show_help
             exit 1
             ;;
     esac
 done
 
-set -euxo pipefail
-if ! which pod-run >/dev/null; then
+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 )
@@ -63,27 +65,33 @@ fi
 if [ ! -d .env/venv ]; then
    python3 -m venv .env/venv   
 fi
-source .env/venv/activate
+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
-   pip install --cache-dir .env/pypi-cache -e .[all]
-   jupyter-nbextension enable --user --py widgetsnbextension
+   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
@@ -92,15 +100,11 @@ EOF
 if [ $RUN_TESTS = 1 ]; then
     podrun --cont-img-dir $SCRIPTS_DIR/environment \
            --name "${PKG_NAME}_run_tests" \
-           --image $DOCKERIMAGE \
-           -- $ENV_DIR/run-tests.sh
+           -- 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}" \
-           --image $DOCKERIMAGE \
            -p $LISTEN:$PORT:$PORT \
-           -- $ENV_DIR/host-notebook.sh
+           -- bash $ENV_DIR/host-notebook.sh
 fi
-
-

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>=0.14.3" 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",