Merge pull request #1763 from boutproject/v4.3.0-rc

Release new minor version v4.3.0

.build_sundials_for_travis.sh

@@ -0,0 +1,39 @@
+#!/bin/bash
+
+set -e
+
+if [[ ! -d $HOME/local/include/sundials ]]; then
+    echo "****************************************"
+    echo "Building SUNDIALS"
+    echo "****************************************"
+    sundials_ver=4.1.0
+    tarball_name=sundials-${sundials_ver}.tar.gz
+    llnl_url=https://computation.llnl.gov/projects/sundials/download/${tarball_name}
+    github_url=https://github.com/LLNL/sundials/releases/download/v${sundials_ver}/${tarball_name}
+    wget ${llnl_url} \
+        || wget ${github_url} \
+        || (echo "Could not download SUNDIALS! Aborting"; exit 1)
+    tar xvf ${tarball_name}
+    mkdir -p sundials-${sundials_ver}/build && cd sundials-${sundials_ver}/build
+    cmake -DCMAKE_INSTALL_PREFIX="$HOME/local" \
+          -DEXAMPLES_INSTALL=off \
+          -DMPI_ENABLE=on \
+          -DOPENMP_ENABLE=off \
+          -DBUILD_CVODES=off \
+          -DBUILD_IDAS=off \
+          -DBUILD_KINSOL=off \
+          -DBUILD_TESTING=off \
+          -DMPI_C_COMPILER="$(command -v mpicc)" \
+          -DMPI_CXX_COMPILER="$(command -v mpic++)" \
+          -DMPIEXEC_EXECUTABLE="$(command -v mpiexec)" \
+          ..
+    make && make install
+    cd "${TRAVIS_BUILD_DIR}"
+    echo "****************************************"
+    echo "Finished building SUNDIALS"
+    echo "****************************************"
+else
+    echo "****************************************"
+    echo "SUNDIALS already installed"
+    echo "****************************************"
+fi

.clang-format

@@ -1,57 +1,111 @@
 ---
+# Note: commented out lines require clang-format >= 6
 Language:        Cpp
 BasedOnStyle:  LLVM
 AccessModifierOffset: -2
-ConstructorInitializerIndentWidth: 4
-AlignEscapedNewlinesLeft: false
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+# AlignEscapedNewlines: Right
+AlignEscapedNewlinesLeft: true
+AlignOperands:   true
 AlignTrailingComments: true
 AllowAllParametersOfDeclarationOnNextLine: true
 AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: All
 AllowShortIfStatementsOnASingleLine: false
 AllowShortLoopsOnASingleLine: false
-AllowShortFunctionsOnASingleLine: All
-AlwaysBreakTemplateDeclarations: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
 AlwaysBreakBeforeMultilineStrings: false
-BreakBeforeBinaryOperators: false
+AlwaysBreakTemplateDeclarations: true
+BinPackArguments: true
+BinPackParameters: true
+BraceWrapping:
+  AfterClass:      false
+  AfterControlStatement: false
+  AfterEnum:       false
+  AfterFunction:   false
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+#  AfterExternBlock: false
+  BeforeCatch:     false
+  BeforeElse:      false
+  IndentBraces:    false
+#  SplitEmptyFunction: true
+#  SplitEmptyRecord: true
+#  SplitEmptyNamespace: true
+BreakBeforeBinaryOperators: NonAssignment
+BreakBeforeBraces: Attach
+# BreakBeforeInheritanceComma: false
 BreakBeforeTernaryOperators: true
 BreakConstructorInitializersBeforeComma: false
-BinPackParameters: true
+# BreakConstructorInitializers: BeforeColon
+#BreakAfterJavaFieldAnnotations: false
+#BreakStringLiterals: true
 ColumnLimit:     90
+CommentPragmas:  '^ IWYU pragma:'
+# CompactNamespaces: false
 ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
 DerivePointerAlignment: false
+DisableFormat:   false
 ExperimentalAutoDetectBinPacking: false
+# FixNamespaceComments: true
+ForEachMacros:
+  - foreach
+  - Q_FOREACH
+  - BOOST_FOREACH
+# IncludeBlocks:   Regroup
+IncludeCategories:
+  - Regex:           '^(<|")bout/'
+    Priority:        2
+  - Regex:           '^(<|"(gtest|gmock|isl|json)/)'
+    Priority:        3
+  - Regex:           '^<.*>'
+    Priority:        4
+  - Regex:           '.*'
+    Priority:        1
+#IncludeIsMainRegex: '(Test)?$'
 IndentCaseLabels: false
+# IndentPPDirectives: None
+IndentWidth:     2
 IndentWrappedFunctionNames: false
-IndentFunctionDeclarationAfterType: false
-MaxEmptyLinesToKeep: 1
 KeepEmptyLinesAtTheStartOfBlocks: true
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
 NamespaceIndentation: None
 ObjCSpaceAfterProperty: false
 ObjCSpaceBeforeProtocolList: true
+# PenaltyBreakAssignment: 2
 PenaltyBreakBeforeFirstCallParameter: 19
 PenaltyBreakComment: 300
-PenaltyBreakString: 1000
 PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
 PenaltyExcessCharacter: 1000000
 PenaltyReturnTypeOnItsOwnLine: 60
-PointerAlignment: Right
+PointerAlignment: Left
+ReflowComments:  true
+SortIncludes:    true
+# SortUsingDeclarations: true
+SpaceAfterCStyleCast: false
+#SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: ControlStatements
+SpaceInEmptyParentheses: false
 SpacesBeforeTrailingComments: 1
-Cpp11BracedListStyle: true
+SpacesInAngles:  false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
 Standard:        Cpp11
-IndentWidth:     2
 TabWidth:        8
 UseTab:          Never
-BreakBeforeBraces: Attach
-SpacesInParentheses: false
-SpacesInAngles:  false
-SpaceInEmptyParentheses: false
-SpacesInCStyleCastParentheses: false
-SpacesInContainerLiterals: true
-SpaceBeforeAssignmentOperators: true
-ContinuationIndentWidth: 4
-CommentPragmas:  '^ IWYU pragma:'
-ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
-SpaceBeforeParens: ControlStatements
-DisableFormat:   false
 ...
-

.gitignore

@@ -25,7 +25,6 @@
 autom4te.cache/
 aclocal.m4
 /bin/bout-config
-/externalpackages/
 /include/pvode
 /lib/
 /manual/*.pdf
@@ -38,3 +37,7 @@ aclocal.m4
 bout-coverage/
 src/.libfast
 .*.mk
+*.mo
+.BOUT.pid.*
+build/
+build*/

.gitmodules

@@ -1,6 +1,9 @@
 [submodule "googletest"]
-	path = googletest
+	path = externalpackages/googletest
 	url = https://github.com/google/googletest.git
 [submodule "externalpackages/git-archive-all.sh"]
 	path = externalpackages/git-archive-all.sh
 	url = https://github.com/meitar/git-archive-all.sh/
+[submodule "mpark.variant"]
+	path = externalpackages/mpark.variant
+	url = https://github.com/mpark/variant.git

.pip_install_for_travis.sh

@@ -1,7 +1,10 @@
 #!/bin/bash
-export PATH=${HOME}/.local/bin:${PATH}
-pip3 install --user --upgrade pip setuptools
 
+set -e
+
+export PATH=${HOME}/.local/bin:${PATH}
+pip3 install --user --upgrade pip==18.1 setuptools==40.6.3
+pip3 install --user --upgrade scipy==1.2 numpy==1.16
 for package in $@
 do
     if test $package == "cython"

.travis.yml

@@ -30,7 +30,9 @@ addons:
     - netcdf-bin
     - hdf5-tools
     - python3
+    - python3-h5py
     - python3-pip
+    - python3-pytest
     - python3-numpy
     - python3-scipy
     - lcov
@@ -42,13 +44,18 @@ addons:
     - liblapack-dev
     - libparpack2-dev
 
+cache:
+  directories:
+  - $HOME/local
+
 matrix:
   fast_finish: true
   include:
   - env: &default_env
-      - CONFIGURE_OPTIONS='--enable-checks=no --enable-optimize=3 --disable-signal --disable-track --disable-backtrace --with-petsc --with-slepc'
+      - CONFIGURE_OPTIONS="--enable-checks=no --enable-optimize=3 --disable-signal --disable-track --disable-backtrace --with-petsc --with-slepc --with-sundials=$HOME/local"
       - SCRIPT_FLAGS='-uim'
       - PIP_PACKAGES='cython==0.29.6 netcdf4==1.4.2 sympy==1.3'
+      - LD_LIBRARY_PATH=$HOME/local/lib:$LD_LIBRARY_PATH
       - *petsc_vars
   - addons:
       apt:
@@ -59,21 +66,36 @@ matrix:
           - *standard_packages
     env:
       - *default_env
-      - CONFIGURE_OPTIONS='--enable-debug --with-petsc --with-slepc'
+      - CONFIGURE_OPTIONS="--enable-sigfpe --enable-debug --with-petsc --with-slepc --with-sundials=$HOME/local"
       - CC=gcc-7 CXX=g++-7
       - MATRIX_EVAL="CC=gcc-7 && CXX=g++-7"
   - env:
       - *default_env
-      - CONFIGURE_OPTIONS='--enable-shared --with-petsc --with-slepc'
+      - CONFIGURE_OPTIONS="--enable-shared --with-petsc --with-slepc --with-sundials=$HOME/local"
       - SCRIPT_FLAGS="-uim -t python -t shared"
   - env:
       - *default_env
-      - CONFIGURE_OPTIONS='--enable-openmp --with-petsc --with-slepc'
+      - CONFIGURE_OPTIONS="--enable-shared --with-petsc --with-slepc --with-sundials=$HOME/local"
+      - SCRIPT_FLAGS="-uim5t python"
+  - env:
+      - *default_env
+      - CONFIGURE_OPTIONS="--enable-openmp --with-petsc --with-slepc --with-sundials=$HOME/local"
+      - OMP_NUM_THREADS=2
+#CMAKE
+  - env:
+      - *default_env
       - OMP_NUM_THREADS=2
+      - PYTHONPATH="${TRAVIS_BUILD_DIR}/tools/pylib:$PYTHONPATH"
+    script:
+      - ./.build_sundials_for_travis.sh
+      - mkdir build && cd build
+      - cmake .. -DUSE_PETSC=ON -DUSE_SLEPC=ON -DUSE_SUNDIALS=ON -DSUNDIALS_ROOT="$HOME/local" -DENABLE_OPENMP=ON
+      - cmake --build .
+      - ctest --output-on-failure
 #CLANG
   - env:
       - *default_env
-      - CONFIGURE_OPTIONS='--enable-debug --with-petsc --with-slepc'
+      - CONFIGURE_OPTIONS="--enable-debug --with-petsc --with-slepc --with-sundials=$HOME/local"
       - MPICH_CC=clang MPICH_CXX=clang++
       - OMPI_CC=clang OMPI_CXX=clang++
     compiler: clang
@@ -85,8 +107,9 @@ matrix:
           - *standard_packages
           - jq
     env:
-      - CONFIGURE_OPTIONS='--enable-code-coverage --enable-debug --enable-track --enable-checks=3 --with-petsc --with-lapack --with-slepc --enable-openmp'
+      - CONFIGURE_OPTIONS="--enable-code-coverage --enable-debug --enable-track --enable-checks=3 --with-petsc --with-lapack --with-slepc --enable-openmp --with-sundials=$HOME/local"
       - OMP_NUM_THREADS=2
+      - LD_LIBRARY_PATH=$HOME/local/lib:$LD_LIBRARY_PATH
       - *coverage_vars
       - *petsc_vars
       - *codecov_secure
@@ -97,7 +120,7 @@ matrix:
           - *standard_packages
           - jq
     env:
-      - CONFIGURE_OPTIONS='--enable-code-coverage --disable-debug --disable-checks'
+      - CONFIGURE_OPTIONS="--enable-code-coverage --disable-debug --disable-checks"
       - *coverage_vars
       - *codecov_secure