install HOLE for full tests (see #898)

.travis.yml

@@ -15,6 +15,7 @@ env:
     - GIT_CI_USER: TravisCI
     - GIT_CI_EMAIL: TravisCI@mdanalysis.org
     - MDA_DOCDIR: package/doc/html
+    - MDA_OPTPACKAGES: opt/packages
   matrix:
     - SETUP=minimal PYTHON_VERSION=2.7
     - SETUP=full PYTHON_VERSION=2.7
@@ -45,6 +46,16 @@ install:
   - pip install testsuite/
   - pip install coveralls
   - chmod +x testsuite/MDAnalysisTests/mda_nosetests
+# additional external tools (Isssue #898) -- HOLE
+  - |
+     if [[ $SETUP == 'full' ]]; then \
+         bash ./maintainer/install_hole.sh $TRAVIS_OS_NAME "${HOME}/${MDA_OPTPACKAGES}"; \
+         HOLE_BINDIR="${HOME}/${MDA_OPTPACKAGES}/hole2/exe"; \
+         export PATH=${PATH}:${HOLE_BINDIR}; \
+     fi
+  # we should still be here but make doubly sure:
+  - cd ${TRAVIS_BUILD_DIR}
+
 # command to run tests
 script:
   - ./testsuite/MDAnalysisTests/mda_nosetests --with-coverage --cover-package MDAnalysis --processes=2 --process-timeout=300 --with-memleak

maintainer/install_hole.sh

@@ -0,0 +1,86 @@
+#!/bin/bash
+# Install HOLE from http://www.smartsci.uk/hole/
+#
+# arguments
+#    OSNAME : linux | darwin
+#    PREFIX : "path/to/installdir"
+#
+# PREFIX can be relative to HOME or an absolute path; it will be created
+# and HOLE unpacked under PREFIX (the tar file contains "hole2/...")
+
+set -o errexit -o nounset
+
+SCRIPT=$(basename $0)
+
+DOWNLOAD_URL_LINUX='https://www.dropbox.com/s/jukpwlohhi20r17/hole2-NotForProfit-2.2.004-Linux-x86_64.tar.gz?dl=1'
+TARFILE_LINUX='hole2-NotForProfit-2.2.004-Linux-x86_64.tar.gz'
+
+DOWNLOAD_URL_DARWIN='https://www.dropbox.com/s/5mzrsyp48i32je4/hole2-NotForProfit-2.2.004-Darwin-i386.tar.gz?dl=1'
+TARFILE_DARWIN=hole2-NotForProfit-2.2.004-Darwin-i386.tar.gz
+
+# path to dir with executables in the current HOLE distribution
+HOLE_EXE_DIR=hole2/exe
+
+function die () {
+    local msg="$1" err=$2
+    echo "[${SCRIPT}] ERROR: $msg [$err]"
+    exit $err
+}
+
+function is_native_executable () {
+    local filename="$1" OSNAME="$2"
+    file "${filename}" | grep -qi ${OFORMAT}
+    return $?
+}
+
+OSNAME="$1"
+case "$OSNAME" in
+    Linux|linux)
+	OSNAME=Linux
+	OFORMAT=Linux
+	DOWNLOAD_URL="${DOWNLOAD_URL_LINUX}"
+	TARFILE=${TARFILE_LINUX}
+	;;
+    OSX|osx|Darwin|darwin)
+	OSNAME=Darwin
+	OFORMAT="Mach-O"
+	DOWNLOAD_URL="${DOWNLOAD_URL_DARWIN}"
+	TARFILE=${TARFILE_DARWIN}
+	;;
+    *)
+	die "OS '${OSNAME}' not supported." 10;;
+esac
+
+PREFIX="$2"
+test -n "$PREFIX" || die "missing second argument PREFIX (installation directory)" 10
+
+#------------------------------------------------------------
+# start installation
+#------------------------------------------------------------
+
+cd ~
+mkdir -p "$PREFIX" && cd "$PREFIX" || die "Failed to create and cd to $PREFIX" 1
+test -f ${TARFILE} || \
+    curl -L ${DOWNLOAD_URL} -o ${TARFILE} || \
+    die "Failed to download ${TARFILE} from ${DOWNLOAD_URL}" 1
+
+# only install the executables in HOLE_EXE_DIR 
+tar xvf ${TARFILE} ${HOLE_EXE_DIR} || die "Failed 'tar xvf ${TARFILE} ${HOLE_EXE_DIR}'" 1
+
+MDA_HOLE_BINDIR="${PWD}/${HOLE_EXE_DIR}"
+HOLE_EXE="${MDA_HOLE_BINDIR}/hole"
+
+test -d "${MDA_HOLE_BINDIR}" || { \
+    echo "Content of ${PWD}:";
+    ls -la;
+    die "no HOLE exe dir ${MDA_HOLE_BINDIR} in $PWD" 2; }
+test -f "${HOLE_EXE}" || die "hole executable ${HOLE_EXE} not installed" 2
+is_native_executable ${HOLE_EXE} ${OFORMAT} || \
+    { file ${HOLE_EXE}; \
+      die "${HOLE_EXE} will not run on ${OSNAME} (object format ${OFORMAT})" 3; }
+
+echo "HOLE executables were installed into ${MDA_HOLE_BINDIR}"
+echo ">>> export PATH=\${PATH}:${MDA_HOLE_BINDIR}"
+
+# repeat this line in .travis.yml
+export PATH=${PATH}:${MDA_HOLE_BINDIR}