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Merge pull request #211 from blakecaldwell/no_more_compose
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TST: complete base WSL support
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@blakecaldwell
blakecaldwell committed May 15, 2020
2 parents 3edadf6 + 57a305b commit a9c51e4
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292 changes: 165 additions & 127 deletions .travis.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,56 @@ language: c

matrix:
include:
# OSX
- os: osx
name: "MacOS sierra"
osx_image: xcode9.2
env:
- PYTHON_VERSION=3.7
- NEURON_VERSION=7.7
- HOMEBREW_NO_AUTO_UPDATE=1
- HOMEBREW_QEMU=1
- HOMEBREW_SDKROOT=

- os: osx
name: "MacOS el capitan"
osx_image: xcode8
env:
- PYTHON_VERSION=3.7
- NEURON_VERSION=7.7
- HOMEBREW_NO_AUTO_UPDATE=1
- BREW_UNTAP=1
- HOMEBREW_QEMU=1
- HOMEBREW_SDKROOT=

- os: osx
name: "MacOS mojave"
osx_image: xcode11.3
env:
- PYTHON_VERSION=3.7
- NEURON_VERSION=7.7
- HOMEBREW_NO_AUTO_UPDATE=1

- os: osx
name: "MacOS high sierra"
osx_image: xcode10.1
env:
- PYTHON_VERSION=3.7
- NEURON_VERSION=7.7
- HOMEBREW_NO_AUTO_UPDATE=1
- BUILD_QEMU=1

# Windows
- os: windows
name: "Windows"
env:
- PYTHON_VERSION=3.7
- NEURON_VERSION=7.7

# Linux
- os: linux
dist: disco
name: "Ubuntu disco"
dist: xenial
name: "Ubuntu xenial"
env:
- NEURON_VERSION=7.7
services:
Expand All @@ -30,8 +76,8 @@ matrix:
- xvfb

- os: linux
dist: xenial
name: "Ubuntu xenial"
dist: disco
name: "Ubuntu disco"
env:
- NEURON_VERSION=7.7
services:
Expand All @@ -42,96 +88,36 @@ matrix:
packages:
- xvfb

# OSX
- os: osx
name: "MacOS mojave"
osx_image: xcode11.3
env:
- PYTHON_VERSION=3.7
- NEURON_VERSION=7.7
- HOMEBREW_NO_AUTO_UPDATE=1

- os: osx
name: "MacOS high sierra"
osx_image: xcode10.1
env:
- PYTHON_VERSION=3.7
- NEURON_VERSION=7.7
- HOMEBREW_NO_AUTO_UPDATE=1
- BUILD_QEMU=1

- os: osx
name: "MacOS sierra"
osx_image: xcode9.2
env:
- PYTHON_VERSION=3.7
- NEURON_VERSION=7.7
- HOMEBREW_NO_AUTO_UPDATE=1
- HOMEBREW_QEMU=1
- HOMEBREW_SDKROOT=

- os: osx
name: "MacOS el capitan"
osx_image: xcode8
env:
- PYTHON_VERSION=3.7
- NEURON_VERSION=7.7
- HOMEBREW_NO_AUTO_UPDATE=1
- BREW_UNTAP=1
- HOMEBREW_QEMU=1
- HOMEBREW_SDKROOT=

# Windows
- os: windows
name: "Windows"
env:
- PYTHON_VERSION=3.7
- NEURON_VERSION=7.7

before_install:
- set -e
- |
- set -e # error on any command failure
- | # function exports
export TRAVIS_TESTING=1
source scripts/utils.sh
source scripts/docker_functions.sh
# source utility functions
export LOGFILE="hnn_travis.log"
set_globals
# override cleanup function in docker_functions.sh
function cleanup {
check_var LOGFILE
local __failed
__failed=$1
echo -e "\n=====================" >> $LOGFILE
echo "cleanup() called from: ${FUNCNAME[1]} (L:${BASH_LINENO[0]})" >> $LOGFILE
if [[ $__failed -ne "0" ]]; then
echo -e "\n======================================"
echo "Error: Please see log output for more details"
cat $LOGFILE
return $__failed
fi
}
source scripts/docker_functions.sh
source scripts/utils.sh
export -f cleanup
export DOCKER_IMAGE_NAME="jonescompneurolab/hnn:master"
export BASE_QEMU_OPTS="--disable-cocoa --disable-curses --disable-vnc --disable-vde \
--disable-pie --disable-libusb --disable-hax --disable-kvm \
--disable-debug-info --disable-docs --disable-nettle \
--disable-sparse --disable-guest-agent --disable-qom-cast-debug \
--disable-lzo --disable-bzip2 --disable-fdt \
--disable-tpm --disable-replication --disable-modules --disable-blobs \
--disable-gnutls --disable-vhost-crypto --disable-live-block-migration \
--disable-user --disable-vhost-net"
# some functions require $docker_cmd and $CONTAINER_TYPE
set_globals
- |
if [ "${TRAVIS_OS_NAME}" == "osx" ]; then # install osx prerequisites
echo "Installing macOS prerequisites"
scripts/setup-travis-mac.sh
export PATH=${HOME}/miniconda/bin:$PATH
export PATH=$PATH:/Applications/NEURON-${NEURON_VERSION}/nrn/x86_64/bin
export PYTHONPATH=/Applications/NEURON-${NEURON_VERSION}/nrn/lib/python:$PYTHONPATH
export PATH=$PATH:/Applications/Docker.app/Contents/Resources/bin
export PYTHON=python3
eval "$(docker-machine env default)"
# check container type
find_program_print docker && export docker_cmd || script_fail
get_docker_container_type && export CONTAINER_TYPE || script_fail
# set up DISPLAY and make sure that xquartz is ready
check_xquartz_listening || {
Expand All @@ -141,17 +127,16 @@ before_install:
# accept TCP connections in hnn_docker.sh later
xset -display $DISPLAY -q > /dev/null
export PATH=${HOME}/miniconda/bin:$PATH
export PATH=$PATH:/Applications/NEURON-${NEURON_VERSION}/nrn/x86_64/bin
export PYTHONPATH=/Applications/NEURON-${NEURON_VERSION}/nrn/lib/python:$PYTHONPATH
export PATH=$PATH:/Applications/Docker.app/Contents/Resources/bin
export PYTHON=python3
eval "$(docker-machine env default)"
source activate hnn && echo "activated conda HNN environment"
fi
- |
if [ "${TRAVIS_OS_NAME}" == "windows" ]; then # install windows prerequisites
- | # windows
if [ "${TRAVIS_OS_NAME}" == "windows" ]; then
echo "Installing windows prerequisites"
# check container type
find_program_print docker && export docker_cmd || script_fail
get_docker_container_type && export CONTAINER_TYPE || script_fail
scripts/setup-travis-windows.sh
# add miniconda python to the path
Expand All @@ -160,34 +145,55 @@ before_install:
export PATH=$HOME/Miniconda3/envs/hnn/Scripts:$PATH
export PATH=$HOME/Miniconda3/envs/hnn/Library/bin:$PATH
# for using X server
export PATH="$PATH:/c/Program\ Files/VcXsrv"
# for MESA dll's
export PATH=$PATH:/c/tools/msys64/mingw64/bin
# for sharing with WSL environment
export WSLENV=TRAVIS_TESTING/u
# set other variables for neuron and HNN
export PATH=$PATH:/c/nrn/bin
export DISPLAY="localhost:0"
export NEURONHOME=/c/nrn
export PYTHON=python
fi
- |
- | # Linux
if [ "${TRAVIS_OS_NAME}" == "linux" ]; then
echo "Installing Linux prerequisites"
# check container type
find_program_print docker && export docker_cmd || script_fail
get_docker_container_type && export CONTAINER_TYPE || script_fail
echo "Starting fake Xserver"
Xvfb :0 -listen tcp -screen 0 1024x768x24 > /dev/null &
export DISPLAY=:0
export PATH=/usr/bin:/usr/local/bin:$PATH
echo "Starting Ubuntu install script"
bash -xe ./installer/ubuntu/installer.sh
echo "Install finished"
installer/ubuntu/hnn-ubuntu.sh
NLOPT_LIB=$(ls -d $HOME/.local/lib/python*/site-packages)
echo $NLOPT_LIB
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NLOPT_LIB
export PYTHON=python3
# test X server
xset -display $DISPLAY -q > /dev/null;
fi
install:
- if [[ ! "${TRAVIS_OS_NAME}" == "windows" ]]; then
make;
fi;
- |
- | # for mac build HNN .mod files
if [[ "${TRAVIS_OS_NAME}" == "osx" ]]; then
make -j2
fi
- | # start the docker image build on linux
if [[ "${TRAVIS_OS_NAME}" == "linux" ]]; then
make -j2
if [[ "$TRAVIS_PULL_REQUEST" =~ "false" ]]; then
SOURCE_REPO="https://github.com/${TRAVIS_REPO_SLUG}.git"
SOURCE_BRANCH=$TRAVIS_BRANCH
Expand All @@ -202,16 +208,28 @@ install:
--build-arg SOURCE_REPO=${SOURCE_REPO} \
installer/docker > docker_build.txt 2>&1 || echo "Failed build" >> docker_build.txt) &
fi
- pip install flake8 pytest pytest-cov coverage coveralls mne
- |
pip install flake8 pytest pytest-cov coverage coveralls mne &
PIP_PID=$!
if [[ "${TRAVIS_OS_NAME}" == "windows" ]]; then
wsl -- pip install flake8 pytest pytest-cov coverage coveralls mne
fi
echo "Waiting for pip installation to finish..."
NAME="installing python test prerequisites"
wait_for_pid "${PIP_PID}" "$NAME"
script:
- echo "Running Python tests" && py.test tests/
- echo "Testing GUI on host OS" && $PYTHON hnn.py
- |
- | # Check that the GUI starts on host OS
echo "Testing GUI on host OS..."
$PYTHON hnn.py
- | # Run py.test that includes running a simulation and verifying results
echo "Running Python tests on host OS..."
py.test tests/
- | # wait for docker image to be fully loaded into docker daemon
if [[ "${TRAVIS_OS_NAME}" = "linux" ]]; then
find "$HOME/hnn_out" -type d -exec chmod 777 {} \; && \
find "$HOME/hnn_out" -type f -exec chmod 666 {} \;
echo "Waiting on docker build:"
echo "Waiting on docker build..."
cat docker_build.txt
while ! cat docker_build.txt|grep "Successfully built"; do
if cat docker_build.txt|grep "Failed build"; then
Expand All @@ -223,36 +241,56 @@ script:
done
tail -1 docker_build.txt
else
echo "Waiting for docker image to be loaded..."
while ! test -e $HOME/docker_image_loaded; do
echo "Sleeping for 10s while waiting for docker image download to complete"
sleep 10
sleep 1
done
fi
- |
if [[ "${TRAVIS_OS_NAME}" = "windows" ]]; then
echo "Testing GUI in docker without ssh as user 'test user'"
- | # test HNN using Docker without SSH
echo "Testing GUI in docker without ssh..."
if [[ "${CONTAINER_TYPE}" = "windows" ]]; then
echo "Running as user 'test user'"
powershell -executionpolicy bypass -File "scripts\start-test-as-user.ps1"
else
echo "Testing GUI in docker without ssh"
USE_SSH=0 ./hnn_docker.sh start || script_fail
fi
- |
- | # Testing hnn_docker.sh upgrade command
echo "Testing hnn_docker.sh upgrade"
if [[ "${TRAVIS_OS_NAME}" = "linux" ]]; then
echo "Testing MPI in docker"
make clean
# only run on linux because it's not virtualized through qemu
timeout 120 docker exec hnn_container bash -c "sudo apt-get install --no-install-recommends -y \
make gcc libc6-dev libtinfo-dev libncurses-dev libx11-dev libreadline-dev"
timeout 300 docker exec -u $UID:hnn_group hnn_container bash -c "make && source /home/hnn_user/hnn_envs && \
mpiexec -np 2 --oversubscribe nrniv -mpi -python run.py param/default.param && echo finished simulation" || { \
echo -e "\nMPI test failed\n"
docker ps -a | grep hnn_container
false
}
echo "Testing hnn_docker.sh upgrade" && ./hnn_docker.sh upgrade || script_fail
./hnn_docker.sh upgrade || script_fail
else
echo "Skipping"
fi
- |
if [[ ! "${TRAVIS_OS_NAME}" = "windows" ]]; then
echo "Testing GUI in docker with ssh" && USE_SSH=1 ./hnn_docker.sh start || script_fail
echo "Testing hnn_docker.sh uninstall command" && ./hnn_docker.sh uninstall || script_fail
- | # For linux containers (mac/windows/linux OS), start HNN with docker using ssh
if [[ ! "${CONTAINER_TYPE}" = "windows" ]]; then
echo "Testing GUI in docker with ssh"
USE_SSH=1 ./hnn_docker.sh start || script_fail
fi
- | # test running a MPI simulation within container
if [[ $TRAVIS_OSX_IMAGE == "xcode8" ]] || [[ $TRAVIS_OSX_IMAGE == "xcode9.2" ]]; then
# tests on mac take a long time. sierra and el capitan are close to maximum build times
echo "Skipping"
else
if [[ "${TRAVIS_OS_NAME}" == "windows" ]]; then
find_command_suggested_path "vcxsrv" "/c/Program Files/VcXsrv" && \
start_vcxsrv_print || script_fail
wsl -- //home/hnn_user/hnn/scripts/run-travis-wsl.sh
stop_vcxsrv || script_fail
else
echo "Testing MPI in docker..."
if [[ "$CONTAINER_TYPE" == "linux" ]]; then
timeout 120 docker exec hnn_container bash -c "sudo apt-get install --no-install-recommends -y \
make gcc libc6-dev libtinfo-dev libncurses-dev libx11-dev libreadline-dev"
timeout 120 docker exec -u hnn_user hnn_container bash -c "make clean && make"
fi
timeout 300 docker exec -u hnn_user hnn_container bash -c "source /home/hnn_user/hnn_envs && \
mpiexec -np 2 nrniv -mpi -python run.py && echo finished simulation" || { \
echo -e "\nMPI test failed\n"
docker ps -a | grep hnn_container
false
} || script_fail
fi
fi
- | # Test hnn_docker.sh uninstall command
echo "Testing hnn_docker.sh uninstall command"
./hnn_docker.sh uninstall || script_fail

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