Merge branch 'release-0.7.1'

.github/workflows/cffconvert.yml

@@ -12,7 +12,7 @@ jobs:
     timeout-minutes: 2
     steps:
       - name: Check out a copy of the repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Check whether the citation metadata from CITATION.cff is valid
         uses: citation-file-format/[email protected]

.github/workflows/ci.yaml

@@ -7,10 +7,10 @@ jobs:
     timeout-minutes: 15
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Set up Python 3.8
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: 3.8
 

.github/workflows/ci_macos11_clang.yaml

@@ -16,7 +16,7 @@ jobs:
     timeout-minutes: 30
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Install dependencies
       run: |

.github/workflows/ci_macos11_gcc_gfortran.yaml

@@ -15,7 +15,7 @@ jobs:
     timeout-minutes: 30
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Install dependencies
       run: |

.github/workflows/ci_macos12_clang.yaml

@@ -16,7 +16,7 @@ jobs:
     timeout-minutes: 30
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Install dependencies
       run: |

.github/workflows/ci_macos12_gcc_gfortran.yaml

@@ -15,7 +15,7 @@ jobs:
     timeout-minutes: 30
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Install dependencies
       run: |

.github/workflows/ci_macos13_clang.yaml

@@ -16,7 +16,7 @@ jobs:
     timeout-minutes: 30
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Install dependencies
       run: |

.github/workflows/ci_macos13_gcc_gfortran.yaml

@@ -15,7 +15,7 @@ jobs:
     timeout-minutes: 30
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Install dependencies
       run: |

.github/workflows/ci_python_compatibility.yaml

@@ -7,19 +7,19 @@ jobs:
     timeout-minutes: 5
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
     - name: Check out the source code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache Tox
-      uses: actions/cache@v1
+      uses: actions/cache@v3
       with:
         path: ${{ github.workspace }}/.tox
         key: python-compatibility-${{ matrix.python-version }}-tox

.github/workflows/ci_python_macos.yaml

@@ -7,19 +7,19 @@ jobs:
     timeout-minutes: 10
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
     - name: Check out the source code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache Tox
-      uses: actions/cache@v1
+      uses: actions/cache@v3
       with:
         path: ${{ github.workspace }}/.tox
         key: python-macos-${{ matrix.python-version }}-tox

.github/workflows/ci_ubuntu20.04.yaml

@@ -14,7 +14,7 @@ jobs:
     timeout-minutes: 10
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Run tests on Ubuntu 20.04
       run: docker run -v "${GITHUB_WORKSPACE}:/workspace" --env LC_ALL=C.UTF-8 --env LANG=C.UTF-8 --env DEBIAN_FRONTEND=noninteractive ubuntu:20.04 /bin/bash -c 'apt-get update && apt-get -y dist-upgrade && apt-get -y install build-essential cmake gfortran git valgrind libopenmpi-dev pkg-config python3 python3-pip python3-venv curl && apt-get -y remove libssl-dev zlib1g-dev && useradd -m -d /home/muscle3 muscle3 && su muscle3 -c -- "cp -r --preserve=mode /workspace /home/muscle3/muscle3" && su muscle3 -c -- "pip3 install --user -U \"pip<22\" setuptools wheel" && su muscle3 -c -- "pip3 install --user \"ymmsl>=0.13.0,<0.14\" qcg-pilotjob==0.13.1" && su muscle3 -c -- "cd /home/muscle3/muscle3 && make test_examples"'

.github/workflows/ci_ubuntu20.04_clang.yaml

@@ -14,7 +14,7 @@ jobs:
     timeout-minutes: 10
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Run tests on Ubuntu 20.04 with Clang
       run: docker run -v "${GITHUB_WORKSPACE}:/workspace" --env LC_ALL=C.UTF-8 --env LANG=C.UTF-8 --env DEBIAN_FRONTEND=noninteractive ubuntu:20.04 /bin/bash -c 'apt-get update && apt-get -y dist-upgrade && apt-get -y install build-essential clang cmake gfortran git valgrind libopenmpi-dev pkg-config python3 python3-pip python3-venv curl && apt-get -y remove libssl-dev zlib1g-dev && useradd -m -d /home/muscle3 muscle3 && su muscle3 -c -- "cp -r --preserve=mode /workspace /home/muscle3/muscle3" && su muscle3 -c -- "pip3 install --user -U \"pip<22\" setuptools wheel" && su muscle3 -c -- "pip3 install --user \"ymmsl>=0.13.0,<0.14\" qcg-pilotjob==0.13.1" && su muscle3 -c -- "cd /home/muscle3/muscle3 && CXXFLAGS=-fPIE OMPI_CXX=clang++ CXX=clang++ make test_examples"'

.github/workflows/ci_ubuntu20.04_intel.yaml

@@ -17,7 +17,7 @@ jobs:
     timeout-minutes: 15
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Run tests on Ubuntu 20.04 with Clang
-      run: docker run -v "${GITHUB_WORKSPACE}:/workspace" --env LC_ALL=C.UTF-8 --env LANG=C.UTF-8 --env DEBIAN_FRONTEND=noninteractive ubuntu:20.04 /bin/bash -c 'apt-get update && apt-get -y install wget && wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB && mv GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB /etc/apt/trusted.gpg.d/intel-sw-products.asc && echo "deb https://apt.repos.intel.com/oneapi all main" >/etc/apt/sources.list.d/oneAPI.list && apt-get update && apt-get -y dist-upgrade && apt-get -y install build-essential cmake git valgrind pkg-config python3 python3-pip python3-venv curl intel-oneapi-compiler-dpcpp-cpp-2021.1.1 intel-oneapi-compiler-fortran-2021.1.1 intel-oneapi-mpi-devel-2021.1.1 && apt-get -y remove libssl-dev zlib1g-dev && useradd -m -d /home/muscle3 muscle3 && su muscle3 -c -- "cp -r --preserve=mode /workspace /home/muscle3/muscle3" && su muscle3 -c -- "pip3 install --user -U \"pip<22\" setuptools wheel" && su muscle3 -c -- "pip3 install --user \"ymmsl>=0.13.0,<0.14\" qcg-pilotjob==0.13.1" && su muscle3 -s /bin/bash -c -- "cd /home/muscle3/muscle3 && . /opt/intel/oneapi/setvars.sh && CXX=icpx MPICXX=\"mpiicpc -cxx=icpx\" FC=ifx MPIFC=\"mpiifort -fc=ifx\" make test_examples"'
+      run: docker run -v "${GITHUB_WORKSPACE}:/workspace" --env LC_ALL=C.UTF-8 --env LANG=C.UTF-8 --env DEBIAN_FRONTEND=noninteractive ubuntu:20.04 /bin/bash -c 'apt-get update && apt-get -y install wget && wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB && mv GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB /etc/apt/trusted.gpg.d/intel-sw-products.asc && echo "deb https://apt.repos.intel.com/oneapi all main" >/etc/apt/sources.list.d/oneAPI.list && apt-get update && apt-get -y dist-upgrade && apt-get -y install build-essential cmake git valgrind pkg-config python3 python3-pip python3-venv curl intel-oneapi-compiler-dpcpp-cpp-2021.2.0 intel-oneapi-compiler-fortran-2021.2.0 intel-oneapi-mpi-devel-2021.2.0 && apt-get -y remove libssl-dev zlib1g-dev && useradd -m -d /home/muscle3 muscle3 && su muscle3 -c -- "cp -r --preserve=mode /workspace /home/muscle3/muscle3" && su muscle3 -c -- "pip3 install --user -U \"pip<22\" setuptools wheel" && su muscle3 -c -- "pip3 install --user \"ymmsl>=0.13.0,<0.14\" qcg-pilotjob==0.13.1" && su muscle3 -s /bin/bash -c -- "cd /home/muscle3/muscle3 && . /opt/intel/oneapi/setvars.sh && CXX=icpx MPICXX=\"mpiicpc -cxx=icpx\" FC=ifx MPIFC=\"mpiifort -fc=ifx\" make test_examples"'

.github/workflows/ci_ubuntu22.04.yaml

@@ -14,7 +14,7 @@ jobs:
     timeout-minutes: 10
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Run tests on Ubuntu 22.04
       run: docker run -v "${GITHUB_WORKSPACE}:/workspace" --env LC_ALL=C.UTF-8 --env LANG=C.UTF-8 --env DEBIAN_FRONTEND=noninteractive ubuntu:22.04 /bin/bash -c 'apt-get update && apt-get -y dist-upgrade && apt-get -y install build-essential cmake gfortran git valgrind libopenmpi-dev pkg-config python3 python3-pip python3-venv curl && apt-get -y remove libssl-dev && useradd -m -d /home/muscle3 muscle3 && su muscle3 -c -- "cp -r --preserve=mode /workspace /home/muscle3/muscle3" && su muscle3 -c -- "pip3 install -U pip setuptools wheel" && su muscle3 -c -- "pip3 install \"ymmsl>=0.13.0,<0.14\" qcg-pilotjob==0.13.1" && su muscle3 -c -- "cd /home/muscle3/muscle3 && make test_examples"'

.github/workflows/ci_ubuntu22.04_clang.yaml

@@ -14,7 +14,7 @@ jobs:
     timeout-minutes: 10
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Run tests on Ubuntu 22.04 with Clang
       run: docker run -v "${GITHUB_WORKSPACE}:/workspace" --env LC_ALL=C.UTF-8 --env LANG=C.UTF-8 --env DEBIAN_FRONTEND=noninteractive ubuntu:22.04 /bin/bash -c 'apt-get update && apt-get -y dist-upgrade && apt-get -y install build-essential clang cmake gfortran git valgrind libopenmpi-dev pkg-config python3 python3-pip python3-venv curl && apt-get -y remove libssl-dev && useradd -m -d /home/muscle3 muscle3 && su muscle3 -c -- "cp -r --preserve=mode /workspace /home/muscle3/muscle3" && su muscle3 -c -- "pip3 install -U pip setuptools wheel" && su muscle3 -c -- "pip3 install \"ymmsl>=0.13.0,<0.14\" qcg-pilotjob==0.13.1" && su muscle3 -c -- "cd /home/muscle3/muscle3 && CXXFLAGS=-fPIE OMPI_CXX=clang++ CXX=clang++ make test_examples"'

.github/workflows/ci_ubuntu22.04_intel.yaml

@@ -15,7 +15,7 @@ jobs:
     timeout-minutes: 10
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Run tests on Ubuntu 22.04 with the Intel compiler
       run: docker run -v "${GITHUB_WORKSPACE}:/workspace" --env LC_ALL=C.UTF-8 --env LANG=C.UTF-8 --env DEBIAN_FRONTEND=noninteractive ubuntu:22.04 /bin/bash -c 'apt-get update && apt-get -y install wget && wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB && mv GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB /etc/apt/trusted.gpg.d/intel-sw-products.asc && echo "deb https://apt.repos.intel.com/oneapi all main" >/etc/apt/sources.list.d/oneAPI.list && apt-get update && apt-get -y dist-upgrade && apt-get -y install build-essential cmake git valgrind pkg-config python3 python3-pip python3-venv curl intel-oneapi-compiler-dpcpp-cpp intel-oneapi-compiler-fortran intel-oneapi-mpi-devel && apt-get -y remove libssl-dev && useradd -m -d /home/muscle3 muscle3 && su muscle3 -c -- "cp -r --preserve=mode /workspace /home/muscle3/muscle3" && su muscle3 -c -- "pip3 install -U pip setuptools wheel" && su muscle3 -c -- "pip3 install \"ymmsl>=0.13.0,<0.14\" qcg-pilotjob==0.13.1" && su muscle3 -c -- "cd /home/muscle3/muscle3 && . /opt/intel/oneapi/setvars.sh && MPICXX=\"mpiicpc -cxx=icpx\" CXX=icpx MPIFC=\"mpiifort -fc=ifx\" FC=ifx make test_examples"'

.github/workflows/ci_ubuntu23.04.yaml

@@ -0,0 +1,20 @@
+# Run Continuous Integration for the latest Ubuntu release
+# This mainly checks for issues/regressions in the native build
+name: native_compatibility_ubuntu23.04
+on:
+  schedule:
+    - cron: '30 7 * * 6'
+  push:
+    branches:
+      - 'release-*'
+      - fix_native_compatibility_ci
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Run tests on Ubuntu 23.04
+      run: docker run -v "${GITHUB_WORKSPACE}:/workspace" --env LC_ALL=C.UTF-8 --env LANG=C.UTF-8 --env DEBIAN_FRONTEND=noninteractive ubuntu:23.04 /bin/bash -c 'apt-get update && apt-get -y dist-upgrade && apt-get -y install build-essential cmake gfortran git valgrind libopenmpi-dev pkg-config python3 python3-pip python3-venv curl && apt-get -y remove libssl-dev && useradd -m -d /home/muscle3 muscle3 && su muscle3 -c -- "cp -r --preserve=mode /workspace /home/muscle3/muscle3" && su muscle3 -c -- "cd /home/muscle3/muscle3 && make test_examples"'

.github/workflows/ci_ubuntu23.04_clang.yaml

@@ -0,0 +1,20 @@
+# Run Continuous Integration for the latest Ubuntu release
+# This mainly checks for issues/regressions in the native build
+name: native_compatibility_ubuntu23.04_clang
+on:
+  schedule:
+    - cron: '30 6 * * 6'
+  push:
+    branches:
+      - 'release-*'
+      - fix_native_compatibility_ci
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Run tests on Ubuntu 23.04 with Clang
+      run: docker run -v "${GITHUB_WORKSPACE}:/workspace" --env LC_ALL=C.UTF-8 --env LANG=C.UTF-8 --env DEBIAN_FRONTEND=noninteractive ubuntu:23.04 /bin/bash -c 'apt-get update && apt-get -y dist-upgrade && apt-get -y install build-essential clang cmake gfortran git valgrind libopenmpi-dev pkg-config python3 python3-pip python3-venv curl && apt-get -y remove libssl-dev && useradd -m -d /home/muscle3 muscle3 && su muscle3 -c -- "cp -r --preserve=mode /workspace /home/muscle3/muscle3" && su muscle3 -c -- "cd /home/muscle3/muscle3 && CXXFLAGS=-fPIE OMPI_CXX=clang++ CXX=clang++ make test_examples"'

.github/workflows/ci_ubuntu23.04_intel.yaml

@@ -0,0 +1,21 @@
+# Run Continuous Integration for the latest Ubuntu release
+# This mainly checks for issues/regressions in the native build
+name: native_compatibility_ubuntu23.04_intel
+on:
+  schedule:
+    - cron: '0 7 * * 6'
+  push:
+    branches:
+      - 'release-*'
+      - fix_native_compatibility_ci
+      - issue-25-intel-compiler-support
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Run tests on Ubuntu 23.04 with the Intel compiler
+      run: docker run -v "${GITHUB_WORKSPACE}:/workspace" --env LC_ALL=C.UTF-8 --env LANG=C.UTF-8 --env DEBIAN_FRONTEND=noninteractive ubuntu:23.04 /bin/bash -c 'apt-get update && apt-get -y install wget && wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB && mv GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB /etc/apt/trusted.gpg.d/intel-sw-products.asc && echo "deb https://apt.repos.intel.com/oneapi all main" >/etc/apt/sources.list.d/oneAPI.list && apt-get update && apt-get -y dist-upgrade && apt-get -y install build-essential cmake git valgrind pkg-config python3 python3-pip python3-venv curl intel-oneapi-compiler-dpcpp-cpp intel-oneapi-compiler-fortran intel-oneapi-mpi-devel && apt-get -y remove libssl-dev && useradd -m -d /home/muscle3 muscle3 && su muscle3 -c -- "cp -r --preserve=mode /workspace /home/muscle3/muscle3" && su muscle3 -c -- "cd /home/muscle3/muscle3 && . /opt/intel/oneapi/setvars.sh && MPICXX=\"mpiicpc -cxx=icpx\" CXX=icpx MPIFC=\"mpiifort -fc=ifx\" FC=ifx make test_examples"'

CHANGELOG.rst

@@ -5,6 +5,34 @@ Change Log
 All notable changes to this project will be documented in this file.
 This project adheres to `Semantic Versioning <http://semver.org/>`_.
 
+0.7.1
+*****
+
+Added
+-----
+
+* Support for Python 3.11 (working already, now official)
+* Enabled type checking support for the libmuscle Python API
+
+Improved
+--------
+
+* Easier crash debugging due to improved root cause detection
+* Fixed crash in profiling timeline plot
+* Better performance of timeline plot
+* Better visual quality of timeline plot
+* Improved profiling of shutdown process
+* Fixed crash in profiler for large simulations
+* Fixed several (harmless) compiler warnings
+* Small documentation rendering improvements
+
+
+Thanks
+------
+
+* David for reporting many of these and submitting a fix too!
+
+
 0.7.0
 *****
 

CITATION.cff

@@ -12,6 +12,9 @@ authors:
     family-names: Veen
     given-names: Lourens
     orcid: "https://orcid.org/0000-0002-6311-1168"
+  -
+    family-names: Sebregts
+    given-names: Maarten
 
 keywords:
   - multiscale

MANIFEST.in

@@ -2,3 +2,5 @@ include LICENSE
 include README.rst
 include NOTICE
 include VERSION
+include muscle3/py.typed
+include libmuscle/python/libmuscle/py.typed

README.rst

@@ -1,8 +1,8 @@
 .. image:: https://github.com/multiscale/muscle3/raw/develop/docs/source/muscle3_logo_readme.png
     :alt: MUSCLE3
 
-.. image:: https://readthedocs.org/projects/muscle3/badge/?version=latest
-    :target: https://muscle3.readthedocs.io/en/develop/?badge=latest
+.. image:: https://readthedocs.org/projects/muscle3/badge/?version=master
+    :target: https://muscle3.readthedocs.io/en/develop/?badge=master
     :alt: Documentation Build Status
 
 .. image:: https://github.com/multiscale/muscle3/workflows/continuous_integration/badge.svg?branch=master
@@ -18,12 +18,22 @@
 |
 
 MUSCLE3 is the third incarnation of the MUSCLE Multiscale Coupling Library and
-Environment. It is developed by the e-MUSC project of the University of
-Amsterdam and the Netherlands eScience Center.
+Environment. With MUSCLE3, you can connect multiple simulation models together into
+a multiscale simulation.
 
 Browse to `the MUSCLE3 documentation`_ to get started.
 
 
+Collaboration
+=============
+
+For academic collaboration, please contact `prof. Alfons Hoekstra (UvA CSL) <https://www.uva.nl/profiel/h/o/a.g.hoekstra/a.g.hoekstra.html>`_
+and/or `Lourens Veen (NLeSC) <https://www.esciencecenter.nl/team/lourens-veen-msc/>`_.
+
+Commercial support for MUSCLE3 is provided by
+`Ignition Computing <https://www.ignitioncomputing.com>`_.
+
+
 Legal
 =====
 

VERSION

@@ -1 +1 @@
-0.7.0
+0.7.1

docs/source/conf.py

@@ -136,6 +136,13 @@ def patch_installation_version():
 import subprocess
 subprocess.call('cd ../.. ; doxygen', shell=True)
 
+# -- Remove impl namespaces for exported symbols --
+for p in pathlib.Path('..', 'doxygen', 'xml').iterdir():
+    contents = p.read_text()
+    contents = contents.replace('::_MUSCLE_IMPL_NS', '')
+    contents = contents.replace('::impl', '')
+    p.write_text(contents)
+
 # -- Run apidoc plug-in manually, as readthedocs doesn't support it -------
 # See https://github.com/rtfd/readthedocs.org/issues/1139
 def run_apidoc(_):