Merge branch 'release-0.3.1'

.coveragerc

@@ -8,3 +8,7 @@ source =
 omit =
     # Generated code
     muscle_manager_protocol/muscle_manager_protocol_pb2*
+
+[xml]
+
+output = cobertura.xml

.github/workflows/ci.yaml

@@ -0,0 +1,32 @@
+# Run Continuous Integration on every push
+name: continuous_integration
+on: [push, pull_request]
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python 3.6
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.6
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get install -y build-essential cmake gfortran libopenmpi-dev pkg-config wget
+        sudo apt-get install -y libssl-dev zlib1g-dev
+        pip install ymmsl==0.10.1
+
+    - name: Build and run the test suite
+      env:
+        MUSCLE_ENABLE_MPI: 1
+      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_python3.5.1.yaml

@@ -0,0 +1,19 @@
+# Run Continuous Integration on every push
+# This version tests only Python, but on all supported versions of it.
+name: python_compatibility_3.5.1
+on: [push, pull_request]
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Cache Python 3.5.1 eggs
+      uses: actions/cache@v1
+      with:
+        path: ${{ github.workspace }}/.eggs
+        key: python-compatibility-3.5.1-eggs
+
+    - name: Run Python tests on 3.5.1 latest
+      run: docker run -v "${GITHUB_WORKSPACE}:/home/muscle3" python:3.5.1 /bin/bash -c 'cd /home/muscle3 && pip install -U pip setuptools wheel ymmsl==0.10.1 && make test_python_only'

.github/workflows/ci_python3.5.yaml

@@ -0,0 +1,19 @@
+# Run Continuous Integration on every push
+# This version tests only Python, but on all supported versions of it.
+name: python_compatibility_3.5
+on: [push, pull_request]
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Cache Python 3.5 eggs
+      uses: actions/cache@v1
+      with:
+        path: ${{ github.workspace }}/.eggs
+        key: python-compatibility-3.5-eggs
+
+    - name: Run Python tests on 3.5 latest
+      run: docker run -v "${GITHUB_WORKSPACE}:/home/muscle3" python:3.5 /bin/bash -c 'cd /home/muscle3 && pip install ymmsl==0.10.1 && make test_python_only'

.github/workflows/ci_python3.6.1.yaml

@@ -0,0 +1,19 @@
+# Run Continuous Integration on every push
+# This version tests only Python, but on all supported versions of it.
+name: python_compatibility_3.6.1
+on: [push, pull_request]
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Cache Python 3.6.1 eggs
+      uses: actions/cache@v1
+      with:
+        path: ${{ github.workspace }}/.eggs
+        key: python-compatibility-3.6.1-eggs
+
+    - name: Run Python tests on 3.6.1 latest
+      run: docker run -v "${GITHUB_WORKSPACE}:/home/muscle3" python:3.6.1 /bin/bash -c 'cd /home/muscle3 && pip install -U pip setuptools wheel ymmsl==0.10.1 && make test_python_only'

.github/workflows/ci_python3.6.yaml

@@ -0,0 +1,19 @@
+# Run Continuous Integration on every push
+# This version tests only Python, but on all supported versions of it.
+name: python_compatibility_3.6
+on: [push, pull_request]
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Cache Python 3.6 eggs
+      uses: actions/cache@v1
+      with:
+        path: ${{ github.workspace }}/.eggs
+        key: python-compatibility-3.6-eggs
+
+    - name: Run Python tests on 3.6 latest
+      run: docker run -v "${GITHUB_WORKSPACE}:/home/muscle3" python:3.6 /bin/bash -c 'cd /home/muscle3 && pip install ymmsl==0.10.1 && make test_python_only'

.github/workflows/ci_python3.7.yaml

@@ -0,0 +1,19 @@
+# Run Continuous Integration on every push
+# This version tests only Python, but on all supported versions of it.
+name: python_compatibility_3.7
+on: [push, pull_request]
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Cache Python 3.7 eggs
+      uses: actions/cache@v1
+      with:
+        path: ${{ github.workspace }}/.eggs
+        key: python-compatibility-3.7-eggs
+
+    - name: Run Python tests on 3.7 latest
+      run: docker run -v "${GITHUB_WORKSPACE}:/home/muscle3" python:3.7 /bin/bash -c 'cd /home/muscle3 && pip install ymmsl==0.10.1 && make test_python_only'

.github/workflows/ci_python3.8.yaml

@@ -0,0 +1,19 @@
+# Run Continuous Integration on every push
+# This version tests only Python, but on all supported versions of it.
+name: python_compatibility_3.8
+on: [push, pull_request]
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Cache Python 3.8 eggs
+      uses: actions/cache@v1
+      with:
+        path: ${{ github.workspace }}/.eggs
+        key: python-compatibility-3.8-eggs
+
+    - name: Run Python tests on 3.8 latest
+      run: docker run -v "${GITHUB_WORKSPACE}:/home/muscle3" python:3.8 /bin/bash -c 'cd /home/muscle3 && pip install ymmsl==0.10.1 && make test_python_only'

.github/workflows/ci_ubuntu16.04.yaml

@@ -0,0 +1,15 @@
+# Run Continuous Integration for the latest Ubuntu release
+# This mainly checks for issues/regressions in the native build
+name: native_compatibility_ubuntu16.04
+on:
+  schedule:
+    - cron: '0 1 * * 0'
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Run tests on Ubuntu 16.04
+      run: docker run -v "${GITHUB_WORKSPACE}:/home/muscle3" --env LC_ALL=C.UTF-8 --env LANG=C.UTF-8 --env DEBIAN_FRONTEND=noninteractive ubuntu:16.04 /bin/bash -c 'apt-get update && apt-get -y dist-upgrade && apt-get -y install build-essential cmake gfortran 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==0.10.1 && make test_examples'

.github/workflows/ci_ubuntu18.04.yaml

@@ -0,0 +1,15 @@
+# Run Continuous Integration for the latest Ubuntu release
+# This mainly checks for issues/regressions in the native build
+name: native_compatibility_ubuntu18.04
+on:
+  schedule:
+    - cron: '0 2 * * 0'
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - 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 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==0.10.1 && make test_examples'

.github/workflows/ci_ubuntu19.10.yaml

@@ -0,0 +1,15 @@
+# Run Continuous Integration for the latest Ubuntu release
+# This mainly checks for issues/regressions in the native build
+name: native_compatibility_ubuntu19.10
+on:
+  schedule:
+    - cron: '0 3 * * 0'
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Run tests on Ubuntu 19.10
+      run: docker run -v "${GITHUB_WORKSPACE}:/home/muscle3" --env LC_ALL=C.UTF-8 --env LANG=C.UTF-8 --env DEBIAN_FRONTEND=noninteractive ubuntu:19.10 /bin/bash -c 'apt-get update && apt-get -y dist-upgrade && apt-get -y install build-essential cmake gfortran 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==0.10.1 && make test_examples'

.github/workflows/ci_ubuntu20.04.yaml

@@ -0,0 +1,15 @@
+# Run Continuous Integration for the latest Ubuntu release
+# This mainly checks for issues/regressions in the native build
+name: native_compatibility_ubuntu20.04
+on:
+  schedule:
+    - cron: '0 4 * * 0'
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - 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 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==0.10.1 && make test_examples'

.gitignore

@@ -11,7 +11,7 @@
 
 htmlcov
 .coverage
-coverage.xml
+cobertura.xml
 
 docs/doxygen
 docs/apidocs

CHANGELOG.rst

@@ -5,6 +5,30 @@ Change Log
 All notable changes to this project will be documented in this file.
 This project adheres to `Semantic Versioning <http://semver.org/>`_.
 
+0.3.1
+*****
+
+Added
+-----
+
+* Support for sending and receiving multidimensional grids/arrays
+* Support for Python 3.8
+
+Improved
+--------
+
+* Python 3.5.1 support
+* Build compatibility on more operating systems
+
+Thanks
+------
+
+* Olivier for testing, reporting and fixing build issues
+* Pavel for testing and reporting build issues
+* Hamid for testing and reporting build issues
+* Ben for testing and reporting build issues
+
+
 0.3.0
 *****
 

CITATION.cff

@@ -4,7 +4,7 @@ authors:
   -
     family-names: Veen
     given-names: Lourens
-    orcid: "https://orcid.org/000-0002-6311-1168"
+    orcid: "https://orcid.org/0000-0002-6311-1168"
 cff-version: "1.1.0"
 doi: "10.5281/zenodo.3258864"
 keywords:

Doxyfile

@@ -2099,7 +2099,7 @@ INCLUDE_FILE_PATTERNS  =
 # recursively expanded use the := operator instead of the = operator.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-PREDEFINED             = MUSCLE_ENABLE_MPI
+PREDEFINED             = MUSCLE_ENABLE_MPI DOXYGEN_SHOULD_SKIP_THIS
 
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
 # tag can be used to specify a list of macro names that should be expanded. The

Makefile

@@ -1,4 +1,11 @@
-cpp_test_files := libmuscle/cpp/build/ymmsl/tests/test_* libmuscle/cpp/build/libmuscle/tests/test_*
+export TOOLDIR := $(CURDIR)/scripts/gmake
+
+version_file := $(CURDIR)/VERSION
+export muscle_version := $(shell cat $(version_file))
+export major_version := $(shell sed -e 's/^\([0-9]*\)\..*/\1/' $(version_file))
+export minor_version := $(shell sed -e 's/^[0-9]*\.\([0-9]*\)\..*/\1/' $(version_file))
+export patch_version := $(shell sed -e 's/^[0-9]*\.[0-9]*\.\([0-9]*\).*/\1/' $(version_file))
+
 
 .PHONY: all
 all: cpp fortran
@@ -11,22 +18,35 @@ all: cpp fortran
 .PHONY: test
 test: test_python test_scripts test_cpp test_fortran
 
+.PHONY: test_python_only
+test_python_only:
+	MUSCLE_TEST_PYTHON_ONLY=1 python3 setup.py test
+
 .PHONY: test_python
 test_python: cpp_tests fortran_tests
 	python3 setup.py test
 
 .PHONY: test_cpp
-test_cpp:
+test_cpp: cpp
 	cd libmuscle/cpp && $(MAKE) test
 
 .PHONY: test_fortran
-test_fortran:
+test_fortran: fortran_tests
 	cd libmuscle/fortran && $(MAKE) test
 
 .PHONY: test_scripts
 test_scripts:
 	cd scripts && $(MAKE) test
 
+.PHONY: test_install
+test_install:
+	PREFIX=$(CURDIR)/libmuscle/build/test_install $(MAKE) install
+
+.PHONY: test_examples
+test_examples: test_install
+	export MUSCLE3_HOME=$(CURDIR)/libmuscle/build/test_install && $(MAKE) -C docs/source/examples test
+
+
 .PHONY: install
 install: all
 	cd libmuscle/cpp && $(MAKE) install
@@ -61,6 +81,12 @@ install: all
 	@echo "        Linking: -L$(PREFIX)/lib -lymmsl_fortran"
 	@echo "                 -lmuscle_mpi_fortran -lymmsl -lmuscle_mpi"
 	@echo '*                                                                  *'
+	@echo '*                                                                  *'
+	@echo "    You can also use pkg-config. Add $(PREFIX)/lib/pkgconfig"
+	@echo '*   to your PKG_CONFIG_PATH environment variable and use module    *'
+	@echo '*   names libmuscle, libmuscle_mpi, libmuscle_fortran or           *'
+	@echo '*   libmuscle_mpi_fortran.                                         *'
+	@echo '*                                                                  *'
 	@echo '*   If the directory you installed MUSCLE 3 in is not in your      *'
 	@echo "*   system's library search path, then you have to set             *"
 	@echo '*   LD_LIBRARY_PATH before compiling, linking or running:          *'
@@ -88,12 +114,16 @@ clean:
 	cd libmuscle/cpp && $(MAKE) clean
 	cd libmuscle/fortran && $(MAKE) clean
 	cd scripts && $(MAKE) clean
+	cd docs/source/examples && $(MAKE) clean
+	rm -rf ./build
 
 .PHONY: distclean
 distclean:
 	cd libmuscle/cpp && $(MAKE) distclean
 	cd libmuscle/fortran && $(MAKE) distclean
 	cd scripts && $(MAKE) distclean
+	cd docs/source/examples && $(MAKE) clean
+	rm -rf ./build
 
 .PHONY: fortran
 fortran: cpp