cleaned more #6
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name: Model Test on push | |
on: | |
push: | |
branches: ['main'] | |
workflow_dispatch: | |
jobs: | |
test: | |
if: github.repository != 'ersilia-os/eos-template' | |
runs-on: ubuntu-latest | |
steps: | |
- name: Checkout persist credentials | |
uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # pin@v3.5.2 | |
with: | |
persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token | |
fetch-depth: 0 # otherwise, you will failed to push refs to dest repo | |
lfs: 'true' | |
# This might stop working in the future, so we need to keep an eye on it | |
- name: Free Disk Space (Ubuntu) | |
uses: jlumbroso/free-disk-space@main | |
with: | |
# this might remove tools that are actually needed, | |
# if set to "true" but frees about 6 GB | |
tool-cache: true | |
# all of these default to true, but feel free to set to | |
# "false" if necessary for your workflow | |
android: true | |
dotnet: true | |
haskell: true | |
large-packages: true | |
swap-storage: true | |
- name: Add conda to system path | |
run: echo $CONDA/bin >> $GITHUB_PATH | |
- name: Source conda | |
run: source $CONDA/etc/profile.d/conda.sh | |
- name: Set Python to 3.10.10 | |
run: | |
conda install -y python=3.10.10 | |
- name: Install dependencies | |
run: | | |
source activate | |
conda init | |
conda install git-lfs -c conda-forge | |
git-lfs install | |
conda install gh -c conda-forge | |
- name: Install ersilia | |
run: | | |
source activate | |
python --version | |
echo "After conda init" | |
conda init | |
python -m pip install git+https://github.com/ersilia-os/ersilia.git | |
- name: Update metadata to AirTable | |
id: update-metadata-to-airtable | |
env: | |
USER_NAME: ${{ github.repository_owner }} | |
BRANCH: "main" | |
REPO_NAME: ${{ github.event.repository.name }} | |
AIRTABLE_API_KEY: ${{ secrets.AIRTABLE_API_KEY }} | |
uses: nick-fields/retry@v3 | |
with: | |
timeout_minutes: 10 | |
max_attempts: 3 | |
command: | | |
source activate | |
echo "Updating metadata to AirTable looking at owner: $USER_NAME" | |
wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/update_metadata_to_airtable.py | |
python3 update_metadata_to_airtable.py $USER_NAME $REPO_NAME $BRANCH $AIRTABLE_API_KEY | |
rm update_metadata_to_airtable.py | |
- name: Update README file | |
id: update-readme-file | |
env: | |
MODEL_ID: ${{ github.event.repository.name }} | |
run: | | |
source activate | |
echo "Updating README file with AirTable metadata for model: $MODEL_ID" | |
wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/update_readme_from_airtable.py | |
python3 update_readme_from_airtable.py $MODEL_ID . | |
rm update_readme_from_airtable.py | |
less README.md | |
- name: Commit and push changes done to the README file | |
uses: actions-js/push@156f2b10c3aa000c44dbe75ea7018f32ae999772 # pin@v1.4 | |
with: | |
author_name: "ersilia-bot" | |
author_email: "ersilia-bot@users.noreply.github.com" | |
message: "updating readme [skip ci]" | |
repository: "ersilia-os/${{ github.event.repository.name }}" | |
github_token: ${{ secrets.GITHUB_TOKEN }} | |
amend: true | |
force: true | |
- name: Predict output | |
env: | |
MODEL_ID: ${{ github.event.repository.name }} | |
uses: nick-fields/retry@v3 | |
with: | |
timeout_minutes: 10 | |
max_attempts: 3 | |
command: | | |
source activate | |
echo "Sample model id selected: $MODEL_ID" | |
ersilia -v fetch $MODEL_ID --repo_path . | |
ersilia -v serve $MODEL_ID | |
ersilia sample -n 5 -f input.csv | |
ersilia -v run -i input.csv | |
ersilia close | |
- name: Upload log output | |
if: always() | |
uses: actions/upload-artifact@83fd05a356d7e2593de66fc9913b3002723633cb #pin v3.1.1 | |
with: | |
name: debug-logs | |
retention-days: 14 | |
path: /home/runner/eos/*.log |