Merge branch 'master' of github.com:computationalmodelling/fidimag

Author: davidcorteso

.gitignore

@@ -1,2 +1,41 @@
 *.pyc
 /local/
+
+# ignore automatically generated cython files
+fidimag/atomistic/lib/clib.c
+fidimag/common/dipolar/dipolar.c
+fidimag/common/neb/neb_clib.c
+fidimag/common/sundials/cvode.c
+fidimag/micro/lib/baryakhtar/baryakhtar_clib.c
+fidimag/micro/lib/micro_clib.c
+
+# ignore .cache from pytest
+.cache
+
+# ignore simulation data
+*_npys
+*_vtks
+
+# ignore output files from NEB method
+npys
+vtks
+
+/build/
+/doc/build/
+
+
+# ignore *.so created by cython
+fidimag/extensions/baryakhtar_clib.so
+fidimag/extensions/clib.so
+fidimag/extensions/cvode.so
+fidimag/extensions/dipolar.so
+fidimag/extensions/micro_clib.so
+fidimag/extensions/neb_clib.so
+
+
+# ignore output from coverage
+htmlcov
+
+# ignore junit test output
+test-reports
+

.travis.yml

@@ -8,6 +8,7 @@ sudo: false
 before_install:
   # We do this conditionally because it saves us some downloading if the
   # version is the same.
+  - deactivate  # Deactivate virtualenv
   - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
       wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
     else
@@ -17,9 +18,9 @@ before_install:
   - export PATH=/home/travis/miniconda/bin:$PATH
 
 install:
-  - conda create -q -y -n fidimag-test python=$TRAVIS_PYTHON_VERSION cython matplotlib pytest scipy
+  - conda create -q -y -n fidimag-test python=$TRAVIS_PYTHON_VERSION cython matplotlib pytest scipy pytest-cov
   - source activate fidimag-test
-  - pip install pyvtk six
+  - pip install pyvtk six nbval
   # Download and compile FFTW & Sundials locally
   - bash bin/install.sh
 
@@ -36,6 +37,7 @@ before_script:
 # command to run tests
 script:
   - make test-without-run-oommf
+  - make test-ipynb
 
 
 notifications:

Makefile

@@ -6,43 +6,52 @@ EXTENSIONS_DIR = ${PROJECT_DIR}/fidimag/extensions
 #####################
 
 
-build: extensions-directory
-	python setup.py build_ext --build-lib ${EXTENSIONS_DIR}
-	touch ${EXTENSIONS_DIR}/__init__.py
-	rm -rf ${PROJECT_DIR}/build
-
-extensions-directory:
-	mkdir -p ${EXTENSIONS_DIR}
+build:
+	python setup.py build_ext --inplace
 
 clean:
-	rm -rf ${EXTENSIONS_DIR}
+	rm -rf ${EXTENSIONS_DIR}/*
+	touch ${EXTENSIONS_DIR}/__init__.py
 
 #########
 # Tests #
 #########
 
-create-dirs:
-	mkdir -p test-reports/junit
+# Quick tests, also not using OOMMF tests
+test:
+	cd tests && py.test -v -m "not slow and not run_oommf"
+
+test2:
+	# like test, but run also outside the 'tests' directory.
+	# Doesn't work on Hans laptop.
+	py.test -v -m "not slow and not run_oommf"
 
-test: create-dirs
+test-all: create-dirs
 	py.test -v --junitxml=$(PROJECT_DIR)/test-reports/junit/test-pytest.xml
 
 test-without-run-oommf: create-dirs
-	py.test -v --junitxml=$(PROJECT_DIR)/test-reports/junit/test-pytest.xml -m "not run_oommf"
+	py.test -v -m "not run_oommf" --cov=fidimag --cov-report=html --junitxml=$(PROJECT_DIR)/test-reports/junit/test-pytest.xml 
 
 test-basic:
 	cd tests && py.test -v
 
 # Convenience name for commonly used quick running of tests
 tq:
-	make test-quick
-# Quick tests, also not using OOMMF tests
+	$(error This target 'tq' has been removed, please update the code calling this)
+
 test-quick:
-	cd tests && py.test -v -m "not slow and not run_oommf"
+	$(error This target 'test-quick' has been removed, please update the code calling this)
 
 
 test-ipynb: create-dirs
-	cd doc/ipynb && py.test . -v --ipynb --sanitize-with sanitize_file --junitxml=$(PROJECT_DIR)/test-reports/junit/test-ipynb-pytest.xml
+	cd doc/ipynb && py.test . -v --nbval --sanitize-with sanitize_file --junitxml=$(PROJECT_DIR)/test-reports/junit/test-ipynb-pytest.xml
+
+test-oommf:
+	py.test -v -m "oommf"
+
+create-dirs:
+	mkdir -p test-reports/junit
+
 
 #################
 # Documentation #

README.md

@@ -3,6 +3,8 @@ FIDIMAG
 
 [![Build Status](https://travis-ci.org/computationalmodelling/fidimag.svg?branch=master)](https://travis-ci.org/computationalmodelling/fidimag)
 [![Documentation Status](https://readthedocs.org/projects/fidimag/badge/?version=latest)](http://fidimag.readthedocs.org/en/latest/?badge=latest)
+[![codecov](https://codecov.io/gh/computationalmodelling/fidimag/branch/master/graph/badge.svg)](https://codecov.io/gh/computationalmodelling/fidimag)
+
 
 Fidimag solves finite-difference micromagnetic problems and also
 does atomistic simulations.

bin/install-scikit-odes.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+set -e
+
+# This script installs the python bindings to SUNDIALS called scikit ODES.
+# It requires SUNDIALS 2.6.2 to be installed.
+
+echo "Installing dependencies."
+sudo apt-get install python-dev
+sudo pip install scipy numpy cython enum34
+
+HERE_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+FIDIMAG_DIR="$(dirname "$HERE_DIR")"
+LIBS_DIR=${FIDIMAG_DIR}/local
+
+echo "Downloading ODES to "${LIBS_DIR}"."
+mkdir -p ${LIBS_DIR}
+cd ${LIBS_DIR}
+
+git clone git://github.com/bmcage/odes.git odes
+cd odes
+
+# Paths to SUNDIALS are hardcoded in odes/scikits/odes/sundials/setup.py.
+# The README recommends to edit that file if you want to change the paths...
+
+sed -i \
+    "s|LIB_DIRS_SUNDIALS  = \[base_path\,|LIB_DIRS_SUNDIALS = [base_path, '${LIBS_DIR}\/lib',|g" \
+    scikits/odes/sundials/setup.py
+
+python setup.py build
+sudo python setup.py install
+
+cd ${HERE_DIR}

bin/install-sundials.sh

@@ -0,0 +1,64 @@
+#!/bin/bash
+set -e
+
+# This script installs any SUNDIALS version starting with version 2.6.0
+# when SUNDIALS moved to a CMake-based installation. Will install locally.
+# It may need environment variables to work, like `export CC=gcc` in ARCHER.
+
+SUNDIALS=sundials-2.6.2
+
+# Make sure CMake is installed, since SUNDIALS requires it.
+which cmake > /dev/null
+if [ $? -eq 0 ]
+then
+    echo "Found CMake."
+else
+    echo "CMake required to build SUNDIALS. Installing."
+    sudo apt-get install cmake
+fi
+
+HERE_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+FIDIMAG_DIR="$(dirname "$HERE_DIR")"
+LIBS_DIR=${FIDIMAG_DIR}/local
+
+echo "Will install SUNDIALS to "${LIBS_DIR}" using CC="${CC}"."
+mkdir -p ${LIBS_DIR}
+cd ${LIBS_DIR}
+
+download_and_cmake_install() {
+    # $1 name of the package
+    # $2 URL where ${1}.tar.gz can be obtained
+    # $3 configure options
+    if [ ! -e ${1}.tar.gz ]; then
+        echo "Downloading "${1}"."
+        wget -q ${2}/${1}.tar.gz
+    fi;
+
+    if [ ! -e ${1} ]; then
+        tar -xzf ${1}.tar.gz
+
+        echo "Configuring "${1}"."
+        mkdir ${1}_build
+        cd ${1}_build
+        cmake ${3} ../${1}
+
+        echo "Compiling and installing "${1}"."
+        {
+            make
+            make install
+        } > /dev/null
+
+        echo "Cleaning up."
+        cd ..
+        rm -rf ${1}
+        rm -rf ${1}_build
+
+        cd ${HERE_DIR}
+        echo "Done."
+    fi;
+}
+
+download_and_cmake_install \
+    ${SUNDIALS} \
+    http://computation.llnl.gov/projects/sundials-suite-nonlinear-differential-algebraic-equation-solvers/download \
+    "-DBUILD_STATIC_LIBS=OFF -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX="${LIBS_DIR}" -DEXAMPLES_ENABLE=OFF -DLAPACK_ENABLE=ON -DOPENMP_ENABLE=ON"