Merge branch 'release-0.5.0'

.coveragerc

@@ -5,10 +5,6 @@ source =
     libmuscle/python/libmuscle
     integration_test
 
-omit =
-    # Generated code
-    muscle_manager_protocol/muscle_manager_protocol_pb2*
-
 [xml]
 
 output = cobertura.xml

.github/workflows/ci.yaml

@@ -18,7 +18,7 @@ jobs:
         sudo apt-get update
         sudo apt-get install -y build-essential cmake gfortran libopenmpi-dev pkg-config wget valgrind
         sudo apt-get install -y libssl-dev zlib1g-dev
-        pip install ymmsl==0.11.0
+        pip install tox
 
     - name: Build and run the test suite
       env:

.github/workflows/ci_python_compatibility.yaml

@@ -0,0 +1,37 @@
+# Run Continuous Integration on every push
+name: python_compatibility
+on: [push, pull_request]
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.6", "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: ${{ github.workspace }}/.tox
+        key: python-compatibility-${{ 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
+
+    - name: Upload coverage report to Codacy
+      uses: codacy/codacy-coverage-reporter-action@master
+      with:
+        project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}

.github/workflows/ci_ubuntu18.04.yaml

@@ -7,6 +7,7 @@ on:
   push:
     branches:
       - 'release-*'
+      - fix_native_compatibility_ci
 jobs:
   build:
     runs-on: ubuntu-latest
@@ -15,4 +16,4 @@ jobs:
     - uses: actions/checkout@v2
 
     - name: Run tests on Ubuntu 18.04
-      run: docker run -v "${GITHUB_WORKSPACE}:/home/muscle3" --env LC_ALL=C.UTF-8 --env LANG=C.UTF-8 --env DEBIAN_FRONTEND=noninteractive ubuntu:18.04 /bin/bash -c 'apt-get update && apt-get -y dist-upgrade && apt-get -y install build-essential cmake gfortran valgrind libopenmpi-dev pkg-config python3 python3-pip python3-venv curl && apt-get -y remove libssl-dev zlib1g-dev && pip3 install -U pip setuptools wheel && cd /home/muscle3 && pip3 install ymmsl==0.11.0 && make test_examples'
+      run: docker run -v "${GITHUB_WORKSPACE}:/workspace" --env LC_ALL=C.UTF-8 --env LANG=C.UTF-8 --env DEBIAN_FRONTEND=noninteractive ubuntu:18.04 /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 && echo "Added user" && su muscle3 -c -- "cp -r --preserve=mode /workspace /home/muscle3/muscle3" && echo "Copied files" && su muscle3 -c -- "pip3 install --user -U \"pip<22\" setuptools wheel" && su muscle3 -c -- "pip3 install --user \"ymmsl>=0.12.0,<0.13\" qcg-pilotjob==0.13.1" && su muscle3 -c -- "cd /home/muscle3/muscle3 && make test_examples"'

.github/workflows/ci_ubuntu20.04.yaml

@@ -7,6 +7,7 @@ on:
   push:
     branches:
       - 'release-*'
+      - fix_native_compatibility_ci
 jobs:
   build:
     runs-on: ubuntu-latest
@@ -15,4 +16,4 @@ jobs:
     - uses: actions/checkout@v2
 
     - name: Run tests on Ubuntu 20.04
-      run: docker run -v "${GITHUB_WORKSPACE}:/home/muscle3" --env LC_ALL=C.UTF-8 --env LANG=C.UTF-8 --env DEBIAN_FRONTEND=noninteractive ubuntu:20.04 /bin/bash -c 'apt-get update && apt-get -y dist-upgrade && apt-get -y install build-essential cmake gfortran valgrind libopenmpi-dev pkg-config python3 python3-pip python3-venv curl && apt-get -y remove libssl-dev zlib1g-dev && pip3 install -U pip setuptools wheel && cd /home/muscle3 && pip3 install ymmsl==0.11.0 && make test_examples'
+      run: docker run -v "${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 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>=0.12.0,<0.13\" qcg-pilotjob==0.13.1" && su muscle3 -c -- "cd /home/muscle3/muscle3 && make test_examples"'

.github/workflows/ci_ubuntu22.04.yaml

@@ -0,0 +1,19 @@
+# Run Continuous Integration for the latest Ubuntu release
+# This mainly checks for issues/regressions in the native build
+name: native_compatibility_ubuntu22.04
+on:
+  schedule:
+    - cron: '0 4 * * 0'
+  push:
+    branches:
+      - 'release-*'
+      - fix_native_compatibility_ci
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - 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>=0.12.0,<0.13\" qcg-pilotjob==0.13.1" && su muscle3 -c -- "cd /home/muscle3/muscle3 && make test_examples"'

.gitignore

@@ -4,6 +4,7 @@
 
 /dist
 /build
+.tox
 .cache
 .pytest_cache
 .mypy_cache

CHANGELOG.rst

@@ -5,6 +5,43 @@ Change Log
 All notable changes to this project will be documented in this file.
 This project adheres to `Semantic Versioning <http://semver.org/>`_.
 
+0.5.0
+*****
+
+Added
+-----
+
+* MUSCLE3 now starts submodels and other components (using QCG-PilotJob)
+* Automatic resource management for components on HPC
+
+Improved
+--------
+
+* Build and installation process now even easier
+* Improved error messages and reliability
+* Cleaner and more informative logging output
+* TCP performance and scalability improvements
+
+Fixed
+-----
+
+* Various issues when building and running on HPC clusters
+* Many small fixes
+
+Removed
+-------
+
+* Python 3.5 support
+* Removed gRPC for faster and more reliable builds
+* Pipe-based networking, as it had no benefits and some issues
+
+Thanks
+------
+
+* Stefan, Merijn and Maarten for reporting issues
+* Piotr and Bartek for creating and supporting QCG-PilotJob
+
+
 0.4.0
 *****
 

CITATION.cff

@@ -2,11 +2,11 @@
 ---
 cff-version: "1.1.0"
 
-title: "MUSCLE 3: The Multiscale Coupling Library and Environment"
+title: "MUSCLE3: The Multiscale Coupling Library and Environment"
 doi: "10.5281/zenodo.3258864"
 repository-code: "https://github.com/multiscale/muscle3"
 
-message: "If you use MUSCLE 3, please cite it using these metadata."
+message: "If you use MUSCLE3, please cite it using these metadata."
 authors:
   -
     family-names: Veen