Merge branch 'release-0.7.0'

.github/workflows/cffconvert.yml

@@ -9,6 +9,7 @@ jobs:
   validate:
     name: "validate"
     runs-on: ubuntu-latest
+    timeout-minutes: 2
     steps:
       - name: Check out a copy of the repository
         uses: actions/checkout@v2

.github/workflows/ci.yaml

@@ -4,6 +4,7 @@ on: [push, pull_request]
 jobs:
   build:
     runs-on: ubuntu-latest
+    timeout-minutes: 15
 
     steps:
     - uses: actions/checkout@v2
@@ -26,8 +27,3 @@ jobs:
       run: |
         cd $GITHUB_WORKSPACE
         make test
-
-    - name: Upload coverage report to Codacy
-      uses: codacy/codacy-coverage-reporter-action@master
-      with:
-        project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}

.github/workflows/ci_macos11_clang.yaml

@@ -0,0 +1,29 @@
+# Run Continuous Integration on macOS 11 Big Sur, with native Clang and
+# without Fortran.
+
+# This mainly checks for issues/regressions in the native build
+name: compatibility_macos_bigsur_11_clang
+on:
+  schedule:
+    - cron: '30 0 * * 6'
+  push:
+    branches:
+      - 'release-*'
+      - fix_native_compatibility_ci
+jobs:
+  build:
+    runs-on: macos-11
+    timeout-minutes: 30
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Install dependencies
+      run: |
+        python3 -m pip install --upgrade pip
+        pip3 install tox tox-gh-actions
+        brew install openmpi
+
+    - name: Run all tests on macOS Big Sur 11 with Clang
+      run: cd ${GITHUB_WORKSPACE} && make test test_examples
+

.github/workflows/ci_macos11_gcc_gfortran.yaml

@@ -0,0 +1,29 @@
+# Run Continuous Integration on macOS 11 Big Sur with GCC
+# This includes Fortran support
+# This mainly checks for issues/regressions in the native build
+name: compatibility_macos_bigsur_11_gcc_gfortran
+on:
+  schedule:
+    - cron: '00 1 * * 6'
+  push:
+    branches:
+      - 'release-*'
+      - fix_native_compatibility_ci
+jobs:
+  build:
+    runs-on: macos-11
+    timeout-minutes: 30
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Install dependencies
+      run: |
+        brew install gcc
+        brew install openmpi
+        python3 -m pip install --upgrade pip
+        pip3 install tox tox-gh-actions
+
+    - name: Run all tests
+      run: cd ${GITHUB_WORKSPACE} && CXX=g++-12 OMPI_CXX=g++-12 FC=gfortran-12 OMPI_FC=gfortran-12 make test test_examples
+

.github/workflows/ci_macos12_clang.yaml

@@ -0,0 +1,28 @@
+# Run Continuous Integration on macOS 12 Monterey, with native Clang and
+# without Fortran.
+
+# This mainly checks for issues/regressions in the native build
+name: compatibility_macos_monterey_12_clang
+on:
+  schedule:
+    - cron: '30 1 * * 6'
+  push:
+    branches:
+      - 'release-*'
+      - fix_native_compatibility_ci
+jobs:
+  build:
+    runs-on: macos-12
+    timeout-minutes: 30
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Install dependencies
+      run: |
+        python3 -m pip install --upgrade pip
+        pip3 install tox tox-gh-actions
+        brew install openmpi
+
+    - name: Run all tests on macOS Monterey 12 with Clang
+      run: cd ${GITHUB_WORKSPACE} && make test test_examples

.github/workflows/ci_macos12_gcc_gfortran.yaml

@@ -0,0 +1,29 @@
+# Run Continuous Integration on macOS 12 Monterey with GCC
+# This includes Fortran support
+# This mainly checks for issues/regressions in the native build
+name: compatibility_macos_monterey_12_gcc_gfortran
+on:
+  schedule:
+    - cron: '00 2 * * 6'
+  push:
+    branches:
+      - 'release-*'
+      - fix_native_compatibility_ci
+jobs:
+  build:
+    runs-on: macos-12
+    timeout-minutes: 30
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Install dependencies
+      run: |
+        brew install gcc
+        brew install openmpi
+        python3 -m pip install --upgrade pip
+        pip3 install tox tox-gh-actions
+
+    - name: Run all tests
+      run: cd ${GITHUB_WORKSPACE} && CXX=g++-12 OMPI_CXX=g++-12 FC=gfortran-12 OMPI_FC=gfortran-12 make test test_examples
+

.github/workflows/ci_macos13_clang.yaml

@@ -0,0 +1,30 @@
+# Run Continuous Integration on macOS 13 Ventura, with native Clang and
+# without Fortran.
+
+# This mainly checks for issues/regressions in the native build
+name: compatibility_macos_ventura_13_clang
+on:
+  schedule:
+    - cron: '30 2 * * 6'
+  push:
+    branches:
+      - 'release-*'
+      - fix_native_compatibility_ci
+jobs:
+  build:
+    runs-on: macos-13
+    timeout-minutes: 30
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Install dependencies
+      run: |
+        brew install openmpi
+        brew install pkg-config
+        python3 -m pip install --upgrade pip
+        pip3 install tox tox-gh-actions
+
+    - name: Run all tests on macOS Ventura 13 with Clang
+      run: cd ${GITHUB_WORKSPACE} && make test test_examples
+

.github/workflows/ci_macos13_gcc_gfortran.yaml

@@ -0,0 +1,30 @@
+# Run Continuous Integration on macOS 13 Ventura with GCC
+# This includes Fortran support
+# This mainly checks for issues/regressions in the native build
+name: compatibility_macos_ventura_13_gcc_gfortran
+on:
+  schedule:
+    - cron: '00 3 * * 6'
+  push:
+    branches:
+      - 'release-*'
+      - fix_native_compatibility_ci
+jobs:
+  build:
+    runs-on: macos-13
+    timeout-minutes: 30
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Install dependencies
+      run: |
+        brew install gcc
+        brew install openmpi
+        brew install pkg-config
+        python3 -m pip install --upgrade pip
+        pip3 install tox tox-gh-actions
+
+    - name: Run all tests
+      run: cd ${GITHUB_WORKSPACE} && CXX=g++-12 OMPI_CXX=g++-12 FC=gfortran-12 OMPI_FC=gfortran-12 make test test_examples
+

.github/workflows/ci_python_compatibility.yaml

@@ -4,6 +4,7 @@ on: [push, pull_request]
 jobs:
   build:
     runs-on: ubuntu-latest
+    timeout-minutes: 5
     strategy:
       matrix:
         python-version: ["3.7", "3.8", "3.9", "3.10"]

.github/workflows/ci_python_macos.yaml

@@ -0,0 +1,33 @@
+# Run Continuous Integration on every push
+name: python_compatibility_macos
+on: [push, pull_request]
+jobs:
+  build:
+    runs-on: macos-latest
+    timeout-minutes: 10
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+
+    steps:
+    - name: Check out the source code
+      uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Cache Tox
+      uses: actions/cache@v1
+      with:
+        path: ${{ github.workspace }}/.tox
+        key: python-macos-${{ matrix.python-version }}-tox
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install tox tox-gh-actions
+
+    - name: Run the test suite
+      run: make test_python_only

.github/workflows/ci_ubuntu20.04.yaml

@@ -3,14 +3,15 @@
 name: native_compatibility_ubuntu20.04
 on:
   schedule:
-    - cron: '0 3 * * 0'
+    - cron: '0 4 * * 6'
   push:
     branches:
       - 'release-*'
       - fix_native_compatibility_ci
 jobs:
   build:
     runs-on: ubuntu-latest
+    timeout-minutes: 10
 
     steps:
     - uses: actions/checkout@v2

.github/workflows/ci_ubuntu20.04_clang.yaml

@@ -3,14 +3,15 @@
 name: native_compatibility_ubuntu20.04_clang
 on:
   schedule:
-    - cron: '30 3 * * 0'
+    - cron: '30 3 * * 6'
   push:
     branches:
       - 'release-*'
       - fix_native_compatibility_ci
 jobs:
   build:
     runs-on: ubuntu-latest
+    timeout-minutes: 10
 
     steps:
     - uses: actions/checkout@v2

.github/workflows/ci_ubuntu20.04_intel.yaml

@@ -5,7 +5,7 @@
 name: native_compatibility_ubuntu20.04_intel
 on:
   schedule:
-    - cron: '30 5 * * 0'
+    - cron: '30 4 * * 6'
   push:
     branches:
       - 'release-*'
@@ -14,9 +14,10 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
+    timeout-minutes: 15
 
     steps:
     - uses: actions/checkout@v2
 
     - name: Run tests on Ubuntu 20.04 with Clang
-      run: docker run -v "${GITHUB_WORKSPACE}:/workspace" --env LC_ALL=C.UTF-8 --env LANG=C.UTF-8 --env DEBIAN_FRONTEND=noninteractive ubuntu:20.04 /bin/bash -c 'apt-get update && apt-get -y install wget && wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB && mv GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB /etc/apt/trusted.gpg.d/intel-sw-products.asc && echo "deb https://apt.repos.intel.com/oneapi all main" >/etc/apt/sources.list.d/oneAPI.list && apt-get update && apt-get -y dist-upgrade && apt-get -y install build-essential cmake git valgrind pkg-config python3 python3-pip python3-venv curl intel-oneapi-compiler-dpcpp-cpp-2021.1.1 intel-oneapi-compiler-fortran-2021.1.1 intel-oneapi-mpi-devel-2021.1.1 && apt-get -y remove libssl-dev zlib1g-dev && useradd -m -d /home/muscle3 muscle3 && su muscle3 -c -- "cp -r --preserve=mode /workspace /home/muscle3/muscle3" && su muscle3 -c -- "pip3 install --user -U \"pip<22\" setuptools wheel" && su muscle3 -c -- "pip3 install --user \"ymmsl>=0.13.0,<0.14\" qcg-pilotjob==0.13.1" && su muscle3 -c -s /bin/bash -- "cd /home/muscle3/muscle3 && . /opt/intel/oneapi/setvars.sh && CXX=icpx MPICXX=\"mpiicpc -cxx=icpx\" FC=ifx MPIFC=\"mpiifort -fc=ifx\" make test_examples"'
+      run: docker run -v "${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-2021.1.1 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"'

.github/workflows/ci_ubuntu22.04.yaml

@@ -3,14 +3,15 @@
 name: native_compatibility_ubuntu22.04
 on:
   schedule:
-    - cron: '0 4 * * 0'
+    - cron: '30 5 * * 6'
   push:
     branches:
       - 'release-*'
       - fix_native_compatibility_ci
 jobs:
   build:
     runs-on: ubuntu-latest
+    timeout-minutes: 10
 
     steps:
     - uses: actions/checkout@v2

.github/workflows/ci_ubuntu22.04_clang.yaml

@@ -3,14 +3,15 @@
 name: native_compatibility_ubuntu22.04_clang
 on:
   schedule:
-    - cron: '30 4 * * 0'
+    - cron: '00 5 * * 6'
   push:
     branches:
       - 'release-*'
       - fix_native_compatibility_ci
 jobs:
   build:
     runs-on: ubuntu-latest
+    timeout-minutes: 10
 
     steps:
     - uses: actions/checkout@v2

.github/workflows/ci_ubuntu22.04_intel.yaml

@@ -3,7 +3,7 @@
 name: native_compatibility_ubuntu22.04_intel
 on:
   schedule:
-    - cron: '0 5 * * 0'
+    - cron: '0 6 * * 6'
   push:
     branches:
       - 'release-*'
@@ -12,6 +12,7 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
+    timeout-minutes: 10
 
     steps:
     - uses: actions/checkout@v2

.gitignore

@@ -17,5 +17,6 @@ cobertura.xml
 docs/doxygen
 docs/apidocs
 docs/source/examples/*.log
+docs/source/examples/python/performance.sqlite
 
 libmuscle/python/libmuscle/version.py

.readthedocs.yml

@@ -12,6 +12,7 @@ build:
       # let tox set up a build environment
       - tox -e docs --notest
       # export tox installed packages as requirements for the install step
-      - .tox/docs/bin/pip freeze > docs/requirements.txt
+      - .tox/docs/bin/pip freeze | grep -v '^muscle3' > docs/requirements.txt
+      - cat docs/requirements.txt
     post_install:
       - pip install -r docs/requirements.txt