NEURON ModelDB CI #1127
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name: NEURON ModelDB CI | |
on: | |
push: | |
branches: [master] | |
pull_request: | |
branches: [ master ] | |
schedule: | |
# Run at 2am every day | |
- cron: '0 2 * * *' | |
workflow_call: | |
inputs: | |
neuron_v1: | |
description: Last official release (neuron) / NEURON pinned version / Azure drop (artifacts) url | |
default: 'neuron' | |
required: true | |
type: string | |
neuron_v2: | |
description: Last nightly release (neuron-nightly) / NEURON pinned version / Azure drop (artifacts) url | |
default: 'neuron-nightly' | |
required: true | |
type: string | |
models_to_run: | |
description: 'Empty for all models, space separated accession numbers for specific models' | |
default: '' | |
required: false | |
type: string | |
repo: | |
default: 'neuronsimulator/nrn-modeldb-ci' | |
type: string | |
required: false | |
workflow_dispatch: | |
inputs: | |
neuron_v1: | |
description: Last official release (neuron) / NEURON pinned version / Azure drop (artifacts) url | |
default: 'neuron' | |
required: true | |
neuron_v2: | |
description: Last nightly release (neuron-nightly) / NEURON pinned version / Azure drop (artifacts) url | |
default: 'neuron-nightly' | |
required: true | |
models_to_run: | |
description: 'Empty for all models, space separated accession numbers for specific models' | |
default: '' | |
required: false | |
jobs: | |
nrn-modeldb-ci: | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
env: | |
DISPLAY: ${{ ':0' }} | |
NEURON_V1: ${{ github.event.inputs.neuron_v1 || inputs.neuron_v1 || 'neuron' }} | |
NEURON_V2: ${{ github.event.inputs.neuron_v2 || inputs.neuron_v2 || 'neuron-nightly' }} | |
MODELS_TO_RUN: ${{ github.event.inputs.models_to_run || inputs.models_to_run || '' }} | |
steps: | |
- uses: actions/checkout@v3 | |
with: | |
repository: ${{ inputs.repo || github.repository }} | |
- name: check for Azure drop NEURON_V1 -> ${{ env.NEURON_V1 }} | |
if: startsWith(env.NEURON_V1, 'https://dev.azure.com/neuronsimulator/') | |
run: | | |
# check URI | |
curl -sfSI -X GET '${{ env.NEURON_V1 }}' | |
# Download Azure drop and unzip | |
AZURE_DROP_URL="$NEURON_V1" | |
rm -rf drop | |
wget --tries=4 -LO DROP_V1.zip ${AZURE_DROP_URL} | |
unzip DROP_V1.zip | |
mv drop DROP_V1 | |
# Set drop dir in the env | |
echo "DROP_DIR_V1=`pwd`/DROP_V1" >> $GITHUB_ENV | |
- name: check for Azure drop NEURON_V2 -> ${{ env.NEURON_V2 }} | |
if: startsWith(env.NEURON_V2, 'https://dev.azure.com/neuronsimulator/') | |
run: | | |
# check URI | |
curl -sfSI -X GET '${{ env.NEURON_V2 }}' | |
# Download Azure drop and unzip | |
AZURE_DROP_URL="$NEURON_V2" | |
rm -rf drop | |
wget --tries=4 -LO DROP_V2.zip ${AZURE_DROP_URL} | |
unzip DROP_V2.zip | |
mv drop DROP_V2 | |
# Set drop dir in the env | |
echo "DROP_DIR_V2=`pwd`/DROP_V2" >> $GITHUB_ENV | |
- uses: actions/setup-python@v4 | |
with: | |
python-version: 3.9 | |
- name: Set models to run for PR | |
run: | | |
# For PRs we only have a few models for quick sanity checking. | |
# Once the PR is green you need to manually run the ModelDB CI workflow by simply selecting your branch in the UI. | |
# The follwing selection aims to target different features (since we haven't worked on unit testing yet -> #38 ). | |
# Select a few models to run CI for PRs: | |
# 64195 -> run: null | |
# 22203 -> skip: true | |
# 156120 -> several model directories | |
# 97868 -> failed nrnivmodl | |
# 146030 -> curate_patterns | |
# 244679 -> no entry in modeldb-run.yaml | |
# rest: -> currently yielding differences in the pipeline | |
echo 'MODELS_TO_RUN=64195 22203 156120 51781 97868 22203 97756 97917 105507 136803 138379 138382 146030 244679 251881' >> $GITHUB_ENV | |
# parse PR description for models to run | |
parse_models=$(gh pr view $PR_URL --json body -q '.body | capture("(MODELS_TO_RUN=)(?<models>\\d+( \\d+)*)")') | |
if [ ! -z "$parse_models" ]; then | |
echo "MODELS_TO_RUN=$(echo $parse_models | jq -r .models)" >> $GITHUB_ENV | |
fi | |
if: github.event_name == 'pull_request' && inputs.repo == '' | |
env: | |
PR_URL: ${{ github.event.pull_request.html_url }} | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
- name: Install dependencies and project | |
id: install-deps | |
run: | | |
set | |
# Set up Xvfb | |
sudo apt-get install xvfb | |
sudo /usr/bin/Xvfb $DISPLAY -screen 0 1600x1200x24 -noreset -nolock -shmem & # run in bg | |
# Install python dependencies | |
python -m pip install --upgrade pip | |
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
#Install project in editable mode | |
python -m pip install -e . | |
- name: Cache ModelDB models | |
uses: actions/cache@v3 | |
with: | |
path: | | |
cache | |
modeldb/modeldb-meta.yaml | |
key: dynamic-models | |
- name: Get ModelDB models | |
run: getmodels $MODELS_TO_RUN | |
- name: Run Models with NEURON V1 -> ${{ env.NEURON_V1 }} | |
run: | | |
# Install NEURON V1 | |
if [[ -d "${DROP_DIR_V1}" ]]; then | |
python -m pip install --user --find-links ${DROP_DIR_V1} neuron-nightly | |
else | |
python -m pip install $NEURON_V1 | |
fi | |
nrn_ver=`python -c "from neuron import __version__ as nrn_ver; print(nrn_ver)"` | |
runmodels --gout --workdir=$nrn_ver $MODELS_TO_RUN | |
# Filter out the gout data before generating HTML reports. The HTML | |
# diff uses the original gout files on disk anyway. Compress the large | |
# JSON file including gout data for inclusion in the artifacts | |
mv ${nrn_ver}.json ${nrn_ver}-full.json | |
jq -r 'del(.[].gout)' ${nrn_ver}-full.json > ${nrn_ver}.json | |
xz ${nrn_ver}-full.json | |
report2html ${nrn_ver}.json | |
if [[ -d "${DROP_DIR_V1}" ]]; then | |
python -m pip uninstall --yes neuron-nightly==${nrn_ver} | |
else | |
python -m pip uninstall --yes $NEURON_V1 | |
fi | |
echo "nrn1_ver=$nrn_ver" >> $GITHUB_ENV | |
- name: Run Models with NEURON V2 -> ${{ env.NEURON_V2 }} | |
if: env.NEURON_V1 != env.NEURON_V2 | |
run: | | |
# Install NEURON V2 | |
if [[ -d "${DROP_DIR_V2}" ]]; then | |
python -m pip install --user --find-links ${DROP_DIR_V2} neuron-nightly | |
else | |
python -m pip install $NEURON_V2 | |
fi | |
nrn_ver=`python -c "from neuron import __version__ as nrn_ver; print(nrn_ver)"` | |
runmodels --gout --workdir=$nrn_ver $MODELS_TO_RUN | |
# Filter out the gout data before generating HTML reports. The HTML | |
# diff uses the original gout files on disk anyway. Compress the large | |
# JSON file including gout data for inclusion in the artifacts | |
mv ${nrn_ver}.json ${nrn_ver}-full.json | |
jq -r 'del(.[].gout)' ${nrn_ver}-full.json > ${nrn_ver}.json | |
xz ${nrn_ver}-full.json | |
report2html ${nrn_ver}.json | |
if [[ -d "${DROP_DIR_V2}" ]]; then | |
python -m pip uninstall --yes neuron-nightly==${nrn_ver} | |
else | |
python -m pip uninstall --yes $NEURON_V2 | |
fi | |
echo "nrn2_ver=$nrn_ver" >> $GITHUB_ENV | |
- name: diffreports2html ${{ env.nrn1_ver }}.json <-> ${{ env.nrn2_ver }}.json | |
if: env.NEURON_V1 != env.NEURON_V2 | |
run: | | |
diffreports2html ${nrn1_ver}.json ${nrn2_ver}.json | |
- uses: actions/upload-artifact@v3 | |
if: ${{ always() }} | |
with: | |
name: ${{ env.nrn1_ver }}-vs-${{ env.nrn2_ver }} | |
path: | | |
./*.json.xz | |
./*.html |