public release 4.2.0 - see README.md and CHANGES.md for details

extras/docker-docs/Dockerfile

@@ -0,0 +1,30 @@
+FROM python:3.12
+
+# docker container to build PMSCO documentation
+
+WORKDIR /app
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    default-jre \
+    doxygen \
+    gawk \
+    git \
+    graphviz \
+    pandoc \
+    wget \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN pip install --no-cache-dir \
+    doxypypy \
+    meson \
+    meson-python \
+    ninja \
+    pynose
+
+RUN wget -O plantuml.jar https://sourceforge.net/projects/plantuml/files/plantuml.jar/download
+ENV PLANTUML_JAR_PATH=/app/plantuml.jar
+
+COPY . .
+
+CMD ["sh"]
+

extras/singularity/singularity_python3

@@ -1,5 +1,5 @@
 BootStrap: debootstrap
-OSVersion: bionic
+OSVersion: focal
 MirrorURL: http://ch.archive.ubuntu.com/ubuntu/
 
 %help
@@ -32,7 +32,7 @@ path/to/pmsco must point to the directory that contains the __main__.py file.
 %labels
     Maintainer Matthias Muntwiler
     Maintainer_Email matthias.muntwiler@psi.ch
-    Python_Version 3
+    Python_Version 3.8
 
 %environment
     export LC_ALL=C
@@ -43,7 +43,7 @@ path/to/pmsco must point to the directory that contains the __main__.py file.
 
 %post
     export LC_ALL=C
-    export PYTHON_VERSION=3
+    export PYTHON_VERSION=3.8
     export CONDA_ROOT=/opt/miniconda
     export PLANTUML_ROOT=/opt/plantuml
 
@@ -63,33 +63,44 @@ path/to/pmsco must point to the directory that contains the __main__.py file.
         libblas-dev \
         liblapack-dev \
         libopenmpi-dev \
-        make \
+        nano \
         openmpi-bin \
         openmpi-common \
         sqlite3 \
         wget
     apt-get clean
 
-    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
-    bash ~/miniconda.sh -b -p ${CONDA_ROOT}
+    wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh -O ~/miniforge3.sh
+    bash ~/miniforge3.sh -b -p ${CONDA_ROOT}
 
-    . ${CONDA_ROOT}/bin/activate
+    . ${CONDA_ROOT}/etc/profile.d/conda.sh
+    conda activate base
     conda create -q --yes -n pmsco python=${PYTHON_VERSION}
-    conda activate pmsco
-    conda install -q --yes -n pmsco \
-        pip \
-        "numpy>=1.13" \
-        scipy \
-        ipython \
-        matplotlib \
-        nose \
-        mock \
+    conda install -q --yes -n pmsco -c conda-forge \
+        commentjson \
+        fasteners \
         future \
-        statsmodels \
-        swig \
         gitpython
+        ipython \
+        ipykernel \
+        jsonschema \
+        h5py \
+        matplotlib \
+        meson \
+        mock \
+        pynose \
+        "numpy>=1.13" \
+        pandas \
+        periodictable \
+        pip \
+        scikit-learn \
+        scipy \
+        seaborn \
+        sqlalchemy \
+        statsmodels \
+        swig
     conda clean --all -y
-    pip install periodictable attrdict commentjson fasteners mpi4py doxypypy
+    ${CONDA_ROOT}/envs/pmsco/bin/pip install meson-python mpi4py netgraph networkx doxypypy
 
     mkdir ${PLANTUML_ROOT}
     wget -O ${PLANTUML_ROOT}/plantuml.jar https://sourceforge.net/projects/plantuml/files/plantuml.jar/download
@@ -111,11 +122,16 @@ path/to/pmsco must point to the directory that contains the __main__.py file.
     git checkout master
     git checkout -b ${SINGULAR_BRANCH}
 
-    make all
-    nosetests -w tests/
+    meson setup build
+    cd build
+    meson compile
+    meson install
+    meson test
 
 %apprun compile
     . ${CONDA_ROOT}/etc/profile.d/conda.sh
     conda activate pmsco
-    make all
-    nosetests
+    cd build
+    meson compile
+    meson install
+    meson test