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upload-model-to-s3.yml
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name: Upload model to S3
on:
workflow_dispatch:
workflow_run:
workflows: ["Model test on push"]
types:
- completed
jobs:
upload_model_to_s3:
if: ${{ github.repository != 'ersilia-os/eos-template' && github.event.workflow_run.conclusion == 'success' }}
runs-on: ubuntu-latest
steps:
- name: Checkout persist credentials
uses: actions/checkout@master
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'
- name: Add conda to system path
run: echo $CONDA/bin >> $GITHUB_PATH
- name: Source conda
run: source $CONDA/etc/profile.d/conda.sh
- name: Set Python to 3.10.10
run:
conda install -y python=3.10.10
- name: Install dependencies
run: |
source activate
conda init
conda install git-lfs -c conda-forge
git-lfs install
conda install gh -c conda-forge
- name: Install ersilia
run: |
source activate
python --version
echo "After conda init"
conda init
python -m pip install git+https://github.com/ersilia-os/ersilia.git
- name: Update Metadata JSON file with DockerHub info
id: UpdateMetadata
run: |
python3 -c "
import json
with open('metadata.json', 'r') as f:
data = json.load(f)
data['S3'] = 'https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/{0}.zip'.format(data['Identifier'])
with open('metadata.json', 'w') as f:
json.dump(data, f, indent=4)
"
- name: Commit and push changes done to the Metadata JSON file
uses: actions-js/push@156f2b10c3aa000c44dbe75ea7018f32ae999772 # [email protected]
with:
author_name: "ersilia-bot"
author_email: "[email protected]"
message: "updating metadata [skip ci]"
repository: "ersilia-os/${{ github.event.repository.name }}"
github_token: ${{ secrets.GITHUB_TOKEN }}
amend: true
force: true
- 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 }}
run: |
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 $MODEL_ID .
rm update_readme_from_airtable.py
less README.md
- name: Commit and push changes done to the README file
uses: actions-js/push@156f2b10c3aa000c44dbe75ea7018f32ae999772 # [email protected]
with:
author_name: "ersilia-bot"
author_email: "[email protected]"
message: "updating readme [skip ci]"
repository: "ersilia-os/${{ github.event.repository.name }}"
github_token: ${{ secrets.GITHUB_TOKEN }}
amend: true
force: true
- name: Upload model to S3
id: upload-model-to-s3
env:
REPO_NAME: ${{ github.event.repository.name }}
AWS_ACCESS_KEY: ${{ secrets.AWS_ACCESS_KEY }}
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
run: |
source activate
echo "Uploading model to S3 bucket"
wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/upload_model_to_s3.py
python3 upload_model_to_s3.py $REPO_NAME $AWS_ACCESS_KEY $AWS_SECRET_ACCESS_KEY .
rm upload_model_to_s3.py