Add script to allow running tests locally

.gitignore

@@ -6,11 +6,17 @@ doc/_build/
 dist/
 *.egg-info
 
+# Conda testing environment
+miniconda.sh
+miniconda/
 
 # Test files
+tests.log
 test.png
+test.pdf
 test.svg
 testdb.sqlite*
+ete_test_tmp/
 
 # Coverage files
 .coverage

run_tests.sh

@@ -0,0 +1,287 @@
+#!/bin/bash
+# run_tests.sh -- created 2016-04-28, Renato Alves
+
+export TOP_PID=$$
+
+# If a command in a pipe fails, the whole command fails
+set -o pipefail
+
+usage() {
+    echo >&2 ""
+    echo >&2 "This script runs the test suite provided with ete3."
+    echo >&2 "Without any optional parameters it defaults to running the api tests"
+    echo >&2 "on a Python 3.5 environment."
+    echo >&2 ""
+    echo >&2 "Usage:"
+    echo >&2 "    $0 [option] [-v version] [testset]"
+    echo >&2 ""
+    echo >&2 "Optional parameters:"
+    echo >&2 "       -h --help    = shows the current information"
+    echo >&2 "       --setup-only = configures and updates the testing environment but skips tests"
+    echo >&2 "       --test-only  = skips configuration of environment and runs tests"
+    echo >&2 "       -l           = enable logging to tests.log"
+    echo >&2 "       -s           = show the content of tests.log at the end of execution (implies -l)"
+    echo >&2 "       -x           = install ete3 external apps in the test environment"
+    echo >&2 "       -v           = python version to use for running tests. (default: 3.5)"
+    echo >&2 "       testset      = set of tests to run. (default: api) (for full testsuite use all)"
+    echo >&2 ""
+}
+
+valid_version() {
+    if [ -z "$1" ]; then
+        echo "$2"  # No version was specified
+
+    else
+        if ! [[ $1 =~ ^[2-3](\.[0-9]|\.[1-9][0-9]){0,2}$ ]]; then
+            echo >&2 -e "\nERROR: Python version should be in one of the following formats: 3, 3.5, 3.5.12 not $1"
+            usage
+            kill -s TERM $TOP_PID
+        else
+            echo "$1"
+        fi
+    fi
+}
+
+handle_error() {
+    if [ "$1" != "0" ]; then
+        echo >&2 -e "\n$2"
+        echo >&2 "$3"
+        kill -s TERM $TOP_PID
+    fi
+}
+
+optional() {
+    if [ "x$1" == "x" ]; then
+        echo "$2"
+    else
+        echo "$1"
+    fi
+}
+
+setup_miniconda() {
+    if ! [ -f "${CONDA}/bin/conda" ]; then
+        echo -n ">>> Downloading miniconda... "
+        wget_output=$(wget -nv https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh 2>&1 | tee -a ${LOG})
+        handle_error "$?" "ERROR: Failed to download miniconda installation script" "$wget_output"
+        echo "DONE"
+
+        echo -n ">>> Installing miniconda... "
+        install_output=$(bash miniconda.sh -b -p ${CONDA} 2>&1 | tee -a ${LOG})
+        handle_error "$?" "ERROR: Failed to install miniconda" "$install_output"
+        echo "DONE"
+
+        echo -n ">>> Updating miniconda packages and package information... "
+        conda_update_output=$(${CONDA}/bin/conda update -q -y conda 2>&1 | tee -a ${LOG})
+        handle_error "$?" "ERROR: Failed to update conda packages" "$conda_update_output"
+        echo "DONE"
+
+        echo -n ">>> Cleaning up miniconda installation files... "
+        clean_output=$(rm -f miniconda.sh 2>&1 | tee -a ${LOG})
+        handle_error "$?" "ERROR: Failed to remove miniconda.sh" "$clean_output"
+        echo "DONE"
+
+    fi
+
+    echo -n ">>> Collecting information about conda... "
+    info_output=$(${CONDA}/bin/conda info -a 2>&1 | tee -a ${LOG})
+    handle_error "$?" "ERROR: Failed to collect information about conda" "$info_output"
+    echo "DONE"
+}
+
+create_env() {
+    env_output=$(${CONDA}/bin/conda env list | grep test_${VERSION})
+    if [ $? == 0 ]; then
+        # Env already created. Nothing to do
+        echo >&2 "### Using existing conda environment test_${VERSION}."
+        return 0
+    fi
+
+    echo -n ">>> Creating test environment for version ${VERSION}... "
+    create_output=$(${CONDA}/bin/conda create -q -y -n test_${VERSION} python=${VERSION} pip pyqt numpy six lxml coverage scikit-bio biopython scipy 2>&1 | tee -a ${LOG})
+    handle_error "$?" "ERROR: Failed to create a new conda environment for python ${VERSION}" "$create_output"
+    echo "DONE"
+}
+
+install_external_apps() {
+    if [ "$EXTERNAL_APPS" == "1" ]; then
+        echo -n ">>> Installing external packages in environment test_${VERSION}... "
+        external_apps_output=$(source ${CONDA}/bin/activate test_${VERSION} 2>&1 && ${CONDA}/bin/conda install -c etetoolkit ete3_external_apps -y 2>&1 | tee -a ${LOG})
+        handle_error "$?" "ERROR: Failed to install ete3 external apps in the conda environment" "$external_apps_output"
+        echo "DONE"
+    fi
+}
+
+update_env() {
+    echo -n ">>> Updating conda packages in environment test_${VERSION}... "
+    update_conda_output=$(source ${CONDA}/bin/activate test_${VERSION} 2>&1 && ${CONDA}/bin/conda update -y --all 2>&1 | tee -a ${LOG})
+    handle_error "$?" "ERROR: Failed to update packages in the conda environment" "$update_conda_output"
+    echo "DONE"
+
+    echo -n ">>> Installing latest ete in test environment... "
+    update_output=$(source ${CONDA}/bin/activate test_${VERSION} 2>&1 && python setup.py install --donottrackinstall 2>&1 | tee -a ${LOG})
+    handle_error "$?" "ERROR: Failed to install/update ete to the latest commit on test_${VERSION}" "$update_output"
+    echo "DONE"
+}
+
+# Find a free X server number by looking at .X*-lock files in /tmp.
+find_free_servernum() {
+    # Start on display 99
+    i=99
+    while [ -f /tmp/.X$i-lock ]; do
+        i=$(($i + 1))
+    done
+    echo $i
+}
+
+start_xvfb() {
+    echo -n ">>> Starting Xvfb on display ${DISPLAY}... "
+    # NOTE -noreset is needed in some versions of Xvfb.
+    # The default is -reset but this causes the server to crash when the last client disconnects
+    Xvfb ${DISPLAY} -noreset -screen 0 1280x800x16 &>> ${LOG} &
+    # Giving xvfb some time to start
+    sleep $SLEEP
+
+    # Checking if Xvfb is still running
+    kill -0 $!
+    handle_error "$?" "ERROR: Xvfb didn't start properly" "Please re-run the test script with option -l and check the log file"
+    echo "DONE"
+}
+
+shutdown_xvfb() {
+    # Don't trap exit codes any longer
+    trap - EXIT HUP INT QUIT TERM KILL
+
+    if [ "$!" != "0" ] && [ "x$!" != "x" ]; then
+        echo -n ">>> Stopping Xvfb... "
+
+        xvfb_stop_output=$(kill $! 2>&1 | tee -a ${LOG})
+        handle_error "$?" "ERROR: Failed to stop Xvfb" "$xvfb_stop_output"
+        echo "DONE"
+    fi
+}
+
+showlog() {
+    if [ "$SHOWLOG" == "1" ]; then
+        echo -e ">>> Showing contents of test log:\n"
+        [ -f "${LOG}" ] && cat ${LOG}
+    fi
+}
+
+run_tests() {
+    echo -n ">>> Obtaining deployed python version... "
+    py_version_output=$(source ${CONDA}/bin/activate test_${VERSION} &>/dev/null && python --version 2>&1 | tee -a ${LOG})
+    handle_error "$?" "ERROR: couldn't obtain python version" "$py_version_output"
+    echo "DONE"
+
+    echo -n ">>> Obtaining ete3 version... "
+    ete_version_output=$(source ${CONDA}/bin/activate test_${VERSION} &>/dev/null && ete3 version 2>&1 | tee -a ${LOG})
+    handle_error "$?" "ERROR: couldn't obtain ete3 version" "$ete_version_output"
+    echo "DONE"
+
+    echo -n ">>> Running tests on ete ${ete_version_output} using ${py_version_output}... "
+    tests_output=$(source ${CONDA}/bin/activate test_${VERSION} 2>&1 && coverage run -m ete3.test.test_${TESTSET} 2>&1 | tee -a ${LOG})
+    handle_error "$?" "ERROR: One or more tests failed on test_${VERSION}" "$tests_output"
+    echo "DONE"
+
+    echo "### All tests passed successfully"
+}
+
+# Location of current script
+FILEDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+CONDA="${FILEDIR}/test_tmp/miniconda"
+EXTERNAL_APPS=0
+SETUP=1
+TEST=1
+
+# Logfile
+NULL_LOG="/dev/null"
+LOG="${NULL_LOG}"
+DEFAULT_LOG="${FILEDIR}/tests.log"
+SHOWLOG=0
+
+# Parse args using getopt (instead of getopts) to allow arguments before options
+ARGS="$(getopt -o v:lshx -l help,test-only,setup-only -n "$0" -- "$@" 2>/dev/null)"
+if [ "$?" != "0" ]; then
+    usage
+    handle_error "1" "ERROR: Check the arguments passed. At least one was not valid."
+fi
+
+# reorganize arguments as returned by getopt
+eval set -- "$ARGS"
+
+while true; do
+    case "$1" in
+        # Shift before to throw away option
+        # Shift after if option has a required positional argument
+        -l)
+            shift
+            LOG="${DEFAULT_LOG}"
+            ;;
+        -s)
+            shift
+            SHOWLOG=1
+            LOG="${DEFAULT_LOG}"
+            ;;
+        -v)
+            shift
+            # Validate provided python version to use for tests
+            VERSION="$1"
+            shift
+            ;;
+        -x)
+            shift
+            EXTERNAL_APPS=1
+            ;;
+        --setup-only)
+            shift
+            TEST=0
+            ;;
+        --test-only)
+            shift
+            SETUP=0
+            ;;
+        -h|--help)
+            usage
+            exit
+            ;;
+        --)
+            shift
+            break
+            ;;
+    esac
+done
+
+VERSION="$(valid_version ${VERSION} 3.5)"
+TESTSET="$(optional $1 api)"
+export DISPLAY=":$(find_free_servernum)"
+SLEEP=2  # Time to wait for xvfb to start and be functional
+
+[ ! -f "ete3/test/test_${TESTSET}.py" ] && usage && handle_error "1" "ERROR: Invalid testset selected ${TESTSET}"
+
+if [ "${LOG}" == "${NULL_LOG}" ]; then
+    echo "### Running ${TESTSET} tests with Python ${VERSION}"
+else
+    echo "### Running ${TESTSET} tests with Python ${VERSION} and logging to ${LOG}"
+fi
+
+# Empty logfile
+echo -n > ${LOG}
+
+# At any of these signals shutdown xvfb first and conditionally show the
+# contents of the logfile
+trap 'exitcode=$? ; shutdown_xvfb ; showlog ; exit $exitcode' EXIT HUP INT QUIT TERM KILL
+
+if [ "${SETUP}" == "1" ]; then
+    setup_miniconda
+    create_env
+    install_external_apps
+    update_env
+fi
+if [ "${TEST}" == "1" ]; then
+    start_xvfb
+    run_tests
+    shutdown_xvfb
+fi
+showlog
+
+# vi: