Merge pull request #1305 from boutproject/v4.2-rc

Version 4.2.0

Author: ZedThree

.codacy.yml

@@ -0,0 +1,33 @@
+---
+languages:
+  cpp:
+    extensions:
+      - '*.hxx'
+      - '*.cxx'
+engines:
+  coverage:
+    enabled: true
+    exclude_paths:
+      - tests/**
+      - examples/**
+  bandit:
+    enabled: true
+    include_paths:
+      - tools/pylib/**
+  cppcheck:
+    enabled: true
+    exclude_paths:
+      - externalpackages/**
+      - tools/**
+  pylint:
+    enable: true
+    include_paths:
+      - tools/pylib/**
+  prospector:
+    enable: true
+    include_paths:
+      - tools/pylib/**
+  shellcheck:
+    enable: true
+    exclude_paths:
+      - build-aux/**

.codacy_coverage.sh

@@ -0,0 +1,11 @@
+#First install the reporter tool
+wget -q -O ~/codacy-coverage-reporter-assembly-latest.jar https://oss.sonatype.org/service/local/repositories/releases/content/com/codacy/codacy-coverage-reporter/4.0.1/codacy-coverage-reporter-4.0.1-assembly.jar > /dev/null
+
+#Analyse the existing gcov files and output in compatible xml format
+#The -g option says to use the existing gcov files, the -k options says to not delete the gcov files
+#The -j option is like make's -j
+#See https://gcovr.com/guide.html for more details
+gcovr --root . -k -j 2 --xml -o gcovr_report.xml --exclude-directories "tests/.*"
+
+#Do the upload
+java -jar ~/codacy-coverage-reporter-assembly-latest.jar report -f --language CPP -r gcovr_report.xml --partial

.codecov.yml

@@ -0,0 +1,7 @@
+comment: false
+
+ignore:
+  - "tests"
+
+codecov:
+  branch: next

.gitignore

@@ -24,14 +24,17 @@
 .tmtags
 autom4te.cache/
 aclocal.m4
-data_*
-test*.py
 /bin/bout-config
 /externalpackages/
 /include/pvode
 /lib/
 /manual/*.pdf
 /tools/vagrant/.vagrant
+\#*#
+.#*
+*.132t.vect
 *.gcda
 *.gcno
 bout-coverage/
+src/.libfast
+.*.mk

.install_miniconda_for_travis.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+export PATH=${HOME}/.local/bin:${PATH}
+pip3 install --user --upgrade pip setuptools
+
+for package in $@
+do
+    if test $package == "cython"
+    then
+        # fast install Cython
+        pip3 install --user Cython --install-option="--no-cython-compile"
+    elif test $package == "something_else"
+    then
+        pip3 install what_we_need
+    else
+        pip3 install --user $package
+    fi
+done

.pip_install_for_travis.sh

@@ -3,57 +3,112 @@ dist: trusty
 language: cpp
 compiler: gcc
 
+git:
+  depth: 3
+
 addons:
   apt:
-    packages:
-    - openmpi-bin
-    - libopenmpi-dev
+    # Note &<name> creates a reference that we can refer to later using
+    # *<name>, see https://en.wikipedia.org/wiki/YAML#Syntax
+    packages: &standard_packages
     - libfftw3-dev
     - libnetcdf-dev
-    - libhdf5-serial-dev
     - netcdf-bin
     - hdf5-tools
+    - python3
+    - python3-pip
+    - python3-numpy
+    - python3-scipy
+    - lcov
+    - libhdf5-mpi-dev
+    - openmpi-bin
+    - libopenmpi-dev
 
 matrix:
+  fast_finish: true
   include:
-  - env: CONFIGURE_OPTIONS=''
-  - env: CONFIGURE_OPTIONS='--enable-openmp' OMP_NUM_THREADS=2
-  - env: CONFIGURE_OPTIONS='--enable-debug'
-  - env: CONFIGURE_OPTIONS='--enable-checks=no --enable-optimize=3 --disable-signal --disable-track --disable-backtrace'
-  - env: CONFIGURE_OPTIONS='' MPICH_CC=clang MPICH_CXX=clang++ OMPI_CC=clang OMPI_CXX=clang++
-    compiler: clang
-  - env: CONFIGURE_OPTIONS='--enable-debug' MPICH_CC=clang MPICH_CXX=clang++ OMPI_CC=clang OMPI_CXX=clang++
-    compiler: clang
+  - env: &default_env
+      - CONFIGURE_OPTIONS='--enable-checks=no --enable-optimize=3 --disable-signal --disable-track --disable-backtrace'
+      - SCRIPT_FLAGS='-uim'
+      - PIP_PACKAGES='netcdf4'
   - addons:
       apt:
+        sources:
+          - ubuntu-toolchain-r-test
         packages:
-          - openmpi-bin
-          - libopenmpi-dev
-          - libfftw3-dev
-          - libnetcdf-dev
-          - libhdf5-serial-dev
-          - netcdf-bin
-          - hdf5-tools
+          - g++-7
+          - *standard_packages
+    env:
+      - *default_env
+      - CONFIGURE_OPTIONS='--enable-debug'
+      - CC=gcc-7 CXX=g++-7
+      - MATRIX_EVAL="CC=gcc-7 && CXX=g++-7"
+      #The -Wno-literal-suffix flag in CXXFLAGS above is a temporary workaround to
+      #disable a noisy message arising from the relatively old version of openmpi
+      #in use in combination with the relatively new version of gcc. We should be able
+      #to remove this if a newer openmpi version is introduced.
+      - CXXFLAGS="-Wno-literal-suffix -Wall -Wextra"
+  - env:
+      - *default_env
+      - CONFIGURE_OPTIONS='--enable-shared'
+      - SCRIPT_FLAGS="-uim -t python -t shared"
+      - PIP_PACKAGES='netcdf4 cython'
+  - env:
+      - *default_env
+      - CONFIGURE_OPTIONS='--enable-openmp'
+      - OMP_NUM_THREADS=2
+#CLANG
+  - env:
+      - *default_env
+      - CONFIGURE_OPTIONS='--enable-debug'
+      - MPICH_CC=clang MPICH_CXX=clang++
+      - OMPI_CC=clang OMPI_CXX=clang++
+    compiler: clang
+#COVERAGE
+  - if: branch IN (master, next) OR commit_message =~ /build coverage/
+    addons:
+      apt:
+        packages:
+          - *standard_packages
           - libpetsc3.4.2-dev
-    env: CONFIGURE_OPTIONS='--with-petsc' PETSC_DIR=/usr/lib/petscdir/3.4.2 PETSC_ARCH=linux-gnu-c-opt
-  - addons:
+          - libslepc3.4.2-dev
+          - liblapack-dev
+          - libparpack2-dev
+          - jq
+    env:
+      - CONFIGURE_OPTIONS='--enable-code-coverage --enable-debug --enable-track --enable-checks=3 --with-petsc --with-lapack --with-slepc --enable-openmp'
+      - OMP_NUM_THREADS=2
+      - PETSC_DIR=/usr/lib/petscdir/3.4.2
+      - PETSC_ARCH=linux-gnu-c-opt
+      - SLEPC_DIR=/usr/lib/slepcdir/3.4.2
+      - SLEPC_ARCH=linux-gnu-c-opt
+      - SCRIPT_FLAGS='-cu'
+      - PIP_PACKAGES='gcovr'
+      - secure: "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"
+  - if: branch IN (master, next) OR commit_message =~ /build coverage/
+    addons:
+      apt:
+        packages:
+          - *standard_packages
+          - jq
+    env:
+      - CONFIGURE_OPTIONS='--enable-code-coverage --disable-debug --disable-checks'
+      - SCRIPT_FLAGS='-cu'
+      - PIP_PACKAGES='gcovr'
+      - secure: "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"
+
+  - stage: Finalise Coverage
+    if: branch IN (master, next) OR commit_message =~ /build coverage/
+    addons:
       apt:
-        sources:
-          - ubuntu-toolchain-r-test
         packages:
-          - g++-6
-          - openmpi-bin
-          - libopenmpi-dev
-          - libfftw3-dev
-          - libnetcdf-dev
-          - libhdf5-serial-dev
-          - netcdf-bin
-          - hdf5-tools
-    env: CONFIGURE_OPTIONS='' CC=gcc-6 CXX=g++-6 MPICH_CC=gcc-6 MPICH_CXX=g++-6 OMPI_CC=gcc-6 OMPI_CXX=g++-6 MATRIX_EVAL="CC=gcc-6 && CXX=g++-6" CXXFLAGS=-Wno-literal-suffix
-    #The -Wno-literal-suffix flag in CXXFLAGS above is a temporary workaround to
-    #disable a noisy message arising from the relatively old version of openmpi
-    #in use in combination with the relatively new version of gcc. We should be able
-    #to remove this if a newer openmpi version is introduced.
+          - *standard_packages
+          - jq
+    env:
+      - SCRIPT_FLAGS='-cu'
+      - PIP_PACKAGES='gcovr'
+      - secure: "M5U3I81hzK41Kw7KB+DpEMxP/sgkWkFI4uiRZQDMDFRlhcitsJQQ/YGeBt3a0vo153m2P2PmmeKUl/lTo5WS5SfAVFI8BkcyBjpxZQXV3OD8ru7JsMgVc5pGwl2dvR8Qz02gUIbrIpAlf3YDnNVb6F1C9ofDaCnZU3GUTLH5Fy5z5Z8OpuTaLmTVMMnT2ZEcRawHbmlVhIB/9PUQUa+fM7iC+dtszFxZ2ma5LOHxPS2sGpRCKE5Sae1/xAFWjo4oO0ZqYu5JFvKdb+/2yWKTg/1aTyxCdqAzLg4ldzDlX759zXgtWn+k3TLiVyQ+gsvF8QZkh4BKvl/w2KZ20vRP3blzmxvdsSH+ZP92MZIIK9EkNPGd+UJJd5Hu+zwecEFyfO8bXB9l00kzUsVx+lo7VHbANuNO3b5a6FRiihTCgk+dfOxxrow/fci+lQ9BkmJg0680SIj2e6UM/P9lFgfQLH3IoacN1PtkyqnpJqdHUdbWmpqMtmitmQhXHjnJ+wDb5+i9b1fy5yEsB64rjgF9PBr1/Nos1XD4oGWAknXmQTgWhNyy6f+e0wBNcSUd5nrReLTOAscyXYpcTqONp1W999JSFQEH+YTwBfXytdkWaAGAFEhaaAXQ2jCwHO7jl/TODPfSeZgXkQiT5jgg63i5tlPB4Xn0MTSCX74bYIi16Tk="
+    script: wget -q -O ~/codacy-coverage-reporter-assembly-latest.jar https://oss.sonatype.org/service/local/repositories/releases/content/com/codacy/codacy-coverage-reporter/4.0.1/codacy-coverage-reporter-4.0.1-assembly.jar ; java -jar ~/codacy-coverage-reporter-assembly-latest.jar final
 
 before_install:
   ##################################################
@@ -64,19 +119,13 @@ before_install:
   - eval "${MATRIX_EVAL}"
   - echo "${CC} $(${CC} --version)"
   ##################################################
-  # Install Conda for python 3
+  # Install remaining python3 packages using pip
   ##################################################
-  - source .install_miniconda_for_travis.sh
-
-  ##################################################
-
-  # Make sure to use the system NetCDF/HDF5 libraries, or we end up
-  # using the Conda libraries, which causes no end of headaches
-  - export CONFIGURE_OPTIONS="--with-netcdf=/usr/bin/nc-config --with-hdf5=/usr/bin/h5cc $CONFIGURE_OPTIONS"
+  - source .pip_install_for_travis.sh ${PIP_PACKAGES}
 
 script:
   # Configure, compile and run test_suite
-  - "./.travis_script.sh"
+  - "./.travis_script.sh ${SCRIPT_FLAGS}"
 
 notifications:
   # Send a notification to the BOUT++ Slack team