Merge branch 'tag_update_3.0.0'

.github/workflows/checks.yml

@@ -0,0 +1,195 @@
+name: checks
+
+on:
+  pull_request:
+    types: [opened, synchronize]
+    branches:
+      - master
+      - dev
+
+
+
+jobs:
+  linux-clang-build:
+
+    runs-on: ubuntu-latest
+
+    env:
+      CFLAGS: -Werror
+      QT_SELECT: qt5
+
+    steps:
+    - uses: actions/checkout@v1
+
+    - name: install dependencies
+      run: |
+         sudo apt-get update
+         sudo apt-get install clang-8 libqt5opengl5-dev libqt5svg5-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev 
+
+    - name: configure
+      run: ./configure -assert || { cat configure.log; false; }
+
+    - name: build
+      run: ./build -nowarnings -persistent -nopaginate || { cat build.log; false; }
+
+    - name: unit tests
+      run: ./run_tests units || { cat testing_units.log; false; }
+
+    - name: binary tests
+      run: ./run_tests binaries || { cat testing_binaries.log; false; }
+
+
+
+
+
+
+  linux-gcc-build:
+
+    runs-on: ubuntu-latest
+
+    env:
+      CXX: g++-9
+      CFLAGS: -Werror
+      QT_SELECT: qt5
+
+    steps:
+    - uses: actions/checkout@v1
+
+    - name: install dependencies
+      run: |
+         sudo apt-get update
+         sudo apt-get install g++-9 libqt5opengl5-dev libqt5svg5-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev 
+
+    - name: configure
+      run: ./configure -nooptim || { cat configure.log; false; }
+
+    - name: build
+      run: ./build -nowarnings -persistent -nopaginate || { cat build.log; false; }
+
+
+
+
+
+
+  macos-build:
+
+    runs-on: macos-latest
+
+    env:
+      CFLAGS: -Werror
+
+    steps:
+    - uses: actions/checkout@v1
+
+    - name: install dependencies
+      run: |
+         brew update
+         brew install qt5 eigen pkg-config libtiff fftw libpng
+         brew link --force qt5
+
+    - name: configure
+      run: ./configure -assert || { cat configure.log; false; }
+
+    - name: build
+      run: ./build -nowarnings -persistent -nopaginate || { cat build.log; false; }
+
+    - name: unit tests
+      run: ./run_tests units || { cat testing_units.log; false; }
+
+    - name: binary tests
+      run: ./run_tests binaries || { cat testing_binaries.log; false; }
+
+    - name: check command documentation
+      run: ./docs/generate_user_docs.sh && git diff --exit-code docs/
+
+
+
+
+
+  windows-build:
+
+    runs-on: windows-latest
+
+    env:
+      CFLAGS: -Werror
+      MSYSTEM: MINGW64
+      MSYSCON: defterm
+      CHERE_INVOKING: enabled_from_arguments
+      MSYS2_NOSTART: yes
+
+    steps:
+
+    - uses: actions/checkout@v1
+
+    - name: fetch and install MSYS2
+      run: bash -c 'curl -sL https://github.com/MRtrix3/MinGW/releases/download/1.0/msys2.tar.{0,1} | tar xf -'
+
+    - name: run qtbinpatcher
+      shell: cmd
+      run: msys64\msys2_shell.cmd -c "qtbinpatcher --qt-dir=$(dirname $(which qmake))"
+
+    - name: configure
+      shell: cmd
+      run: msys64\msys2_shell.cmd -c "./configure -assert || { cat configure.log; false; }"
+
+    - name: build
+      shell: cmd
+      run: msys64\msys2_shell.cmd -c "./build -nowarnings -persistent -nopaginate || { cat build.log; false; }"
+
+    - name: unit tests
+      shell: cmd
+      run: msys64\msys2_shell.cmd -c "./run_tests units || { cat testing_units.log; false; }"
+
+    - name: binary tests
+      shell: cmd
+      run: msys64\msys2_shell.cmd -c "./run_tests binaries || { cat testing_binaries.log; false; }"
+
+
+
+
+  secondary-checks:
+
+    runs-on: ubuntu-latest
+
+    env:
+      QT_SELECT: qt5
+
+    steps:
+    - uses: actions/checkout@v1
+
+    - name: install dependencies
+      run: |
+         sudo apt-get update
+         sudo apt-get install pylint pylint3 python3-sphinx sphinx-rtd-theme-common python3-recommonmark python3-sphinx-rtd-theme
+
+
+    - name: check syntax
+      run: ./check_syntax || { cat syntax.log; false; }
+
+    - name: pylint (Python 2)
+      run: |
+         echo "__version__ = 'pylint testing' #pylint: disable=unused-variable" > ./lib/mrtrix3/_version.py
+         PYTHON=python2 ./run_pylint || { cat pylint.log; false; }
+
+    - name: pylint (Python 3)
+      run: |
+         echo "__version__ = 'pylint testing' #pylint: disable=unused-variable" > ./lib/mrtrix3/_version.py
+         PYTHON=python3 ./run_pylint || { cat pylint.log; false; }
+
+    - name: check building of documentation
+      run: python3 -m sphinx -n -N -W -w sphinx.log docs/ tmp/
+
+    - name: install build dependencies
+      run: sudo apt-get install clang-8 libqt5opengl5-dev libqt5svg5-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev
+
+    - name: check configure with Python 2
+      run: python2 ./configure || { cat configure.log; false; }
+
+    - name: check build with Python 2
+      run: python2 ./build -dryrun || { cat build.log; false; }
+
+    - name: check configure with Python 3
+      run: python3 ./configure || { cat configure.log; false; }
+
+    - name: check build with Python 3
+      run: python3 ./build -dryrun || { cat build.log; false; }

.github/workflows/package-linux-anaconda.yml

@@ -0,0 +1,33 @@
+name: package-linux-anaconda
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  package:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - name: install conda-build # and anaconda-client
+      run: $CONDA/bin/conda install -y conda-build #anaconda-client
+
+    - name: fetch recipe
+      run: |
+        git clone https://github.com/MRtrix3/conda-build.git
+        mv conda-build/* .
+
+    - name: build package
+      run: ./run.sh ${GITHUB_REF#refs/*/} ${GITHUB_REPOSITORY%/*} conda-linux
+
+#    - name: upload package to Anaconda.org
+#      run: $CONDA/bin/anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u MRtrix3 $(sudo $CONDA/bin/conda build conda-build/ --output)
+
+    - name: Upload package to GitHub Release
+      uses: AButler/upload-release-assets@v2.0
+      with:
+        files: '*.tar.bz2'
+        repo-token: ${{ secrets.GITHUB_TOKEN }}
+

.github/workflows/package-macos-anaconda.yml

@@ -0,0 +1,38 @@
+name: package-macos-anaconda
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  package:
+
+    runs-on: macos-latest
+
+    steps:
+
+    - name: fetch MacOSX 10.11 SDK
+      run: curl -L https://github.com/phracker/MacOSX-SDKs/releases/download/MacOSX10.11.sdk/MacOSX10.11.sdk.tar.xz | sudo tar xf - -C /opt/
+
+    - name: install conda-build # and anaconda-client
+      run: sudo $CONDA/bin/conda install -y conda-build # anaconda-client
+
+    - name: fetch recipe
+      run: |
+        git clone https://github.com/MRtrix3/conda-build.git
+        mv conda-build/* .
+        { echo "CONDA_BUILD_SYSROOT:"; echo "  - /opt/MacOSX10.11.sdk        # [osx]"; } > conda_build_config.yaml
+
+    - name: build package
+      run: sudo CONDA="$CONDA" ./run.sh ${GITHUB_REF#refs/*/} ${GITHUB_REPOSITORY%/*} conda-macos
+
+#    - name: upload package
+#      run: $CONDA/bin/anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u MRtrix3 $(sudo $CONDA/bin/conda build conda-build/ --output)
+
+    - name: Upload package to GitHub Release
+      uses: AButler/upload-release-assets@v2.0
+      with:
+        files: '*.tar.bz2'
+        repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+

.github/workflows/package-macos-native.yml

@@ -0,0 +1,27 @@
+name: package-macos-native
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  package:
+
+    runs-on: macos-latest
+
+    steps:
+
+    - name: fetch recipe
+      run: git clone https://github.com/MRtrix3/macos-installer.git
+
+    - name: build packages
+      run: ./build ${GITHUB_REF#refs/*/}
+      working-directory: ./macos-installer
+
+    - name: Upload package to GitHub Release
+      uses: AButler/upload-release-assets@v2.0
+      with:
+        files: 'macos-installer/mrtrix3-macos-*.tar.gz'
+        repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+

.github/workflows/package-windows-msys2.yml

@@ -0,0 +1,40 @@
+name: package-windows-msys2
+
+on:
+  release:
+    types: [created]
+
+
+jobs:
+  package:
+
+    runs-on: windows-latest
+
+    env:
+      MSYSTEM: MINGW64
+      MSYSCON: defterm
+      CHERE_INVOKING: enabled_from_arguments
+      MSYS2_NOSTART: yes
+
+    steps:
+
+    - name: fetch and install MSYS2
+      run: bash -c 'curl -sL https://github.com/MRtrix3/MinGW/releases/download/1.0/msys2.tar.{0,1} | tar xf -'
+
+    - name: run qtbinpatcher
+      shell: cmd
+      run: msys64\msys2_shell.cmd -c "qtbinpatcher --qt-dir=$(dirname $(which qmake))"
+
+    - name: fetch PKGBUILD
+      shell: cmd
+      run: msys64\msys2_shell.cmd -c "git clone https://github.com/MRtrix3/MinGW.git && mv MinGW/* ."
+
+    - name: run makepkg
+      shell: cmd
+      run: msys64\msys2_shell.cmd -c "./run.sh ${GITHUB_REF#refs/*/} ${GITHUB_REPOSITORY%%/*}"
+
+    - name: Upload package to GitHub Release
+      uses: AButler/upload-release-assets@v2.0
+      with:
+        files: '*.tar.xz'
+        repo-token: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -31,6 +31,7 @@ build.*
 /dev/
 /bin/
 /tmp/
+/.vscode/
 .cproject
 .idea
 .project
@@ -43,6 +44,7 @@ build.*
 *.creator.user
 *.files
 *.includes
+*.code-workspace
 /debug/
 /assert/
 testing.log
@@ -51,3 +53,5 @@ testing/bin/
 testing/src/project_version.cpp
 testing/src/project_version.h
 .__tmp.log
+.check_syntax.tmp
+.check_syntax2.tmp

.gitmodules

@@ -1,3 +1,6 @@
 [submodule "testing/data"]
-	path = testing/data
+	path = testing/binaries/data
 	url = https://github.com/MRtrix3/test_data
+[submodule "testing/script_data"]
+	path = testing/scripts/data
+	url = https://github.com/MRtrix3/script_test_data.git