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cleaned more

cleaned more #6

Workflow file for this run

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