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ersilia-os · Nov 6, 2023 · 1464954 · 1464954
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diff --git a/.github/workflows/json-check.yml b/.github/workflows/json-check.yml
@@ -0,0 +1,18 @@
+name: json syntax check
+
+on:
+  push:
+    paths:
+      - "**.json"
+  pull_request:
+
+jobs:
+  json-test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout
+        uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # [email protected]
+
+      - name: json syntax check
+        id: json-yaml-validate
+        uses: GrantBirki/json-yaml-validate@87b2d309a02f4942c5e602183eeea11008a640f9 # [email protected]
diff --git a/.github/workflows/post2slack.yml b/.github/workflows/post2slack.yml
@@ -0,0 +1,17 @@
+name: Send Slack message
+on:
+  issues:
+    types: [opened]
+
+jobs:
+  slack:
+    runs-on: ubuntu-latest
+    steps:
+      - name: post slack
+        uses: slackapi/[email protected]
+        env:
+          SLACK_BOT_TOKEN: ${{ secrets.SLACK_TOKEN }}
+        with:
+          slack-message: |
+              "new issue: https://github.com/${{ github.repository }}/issues/${{ github.event.issue.number }} created."
+          channel-id: ${{ secrets.SLACK_CHANNEL_TESTER }}
diff --git a/.github/workflows/test-model-pr.yml b/.github/workflows/test-model-pr.yml
@@ -0,0 +1,69 @@
+name: Model Test on PR
+
+on: 
+  pull_request:
+
+jobs:
+  test:
+    if: github.repository != 'ersilia-os/eos-template'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # [email protected]
+        with:
+          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: Check metadata before updating to AirTable
+        id: check-metadata
+        env:
+          USER_NAME: ${{ github.event.pull_request.head.repo.owner.login }}
+          BRANCH: "main"
+          REPO_NAME: ${{ github.event.repository.name }}
+        run: |
+          source activate
+          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
+
+      - name: Predict output
+        env:
+          MODEL_ID: ${{ github.event.repository.name }}
+        run: |
+          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 api -i input.csv
+          ersilia close
+          
+      - name: Upload log output
+        uses: actions/upload-artifact@83fd05a356d7e2593de66fc9913b3002723633cb #pin v3.1.1
+        with:
+          name: debug-logs
+          retention-days: 1
+          path: /home/runner/eos/console.log
diff --git a/.github/workflows/test-model.yml b/.github/workflows/test-model.yml
@@ -0,0 +1,129 @@
+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 # [email protected]
+        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 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: Predict output
+        env:
+          MODEL_ID: ${{ github.event.repository.name }}
+        run: |
+          source activate
+          echo "Sample model id selected: $MODEL_ID"
+          ersilia -v fetch $MODEL_ID --repo_path .
+          ersilia -v serve $MODEL_ID
+          ersilia sample -n 5 -f input.csv
+          ersilia -v api -i input.csv
+          ersilia close
+          
+      - name: Upload log output
+        uses: actions/upload-artifact@83fd05a356d7e2593de66fc9913b3002723633cb #pin v3.1.1
+        with:
+          name: debug-logs
+          retention-days: 1
+          path: /home/runner/eos/console.log
+
+      - name: Shuffle assignees
+        id: shuffle
+        run: |
+          export assignees=$(echo "${{ vars.assignees }}" | awk 'BEGIN {FS=","}; {srand();split($0,a,FS); print a[int(rand()*NF+1)]}')
+          echo "$assignees" >> $GITHUB_STEP_SUMMARY
+          echo "shuffled_assignee=$assignees" >> $GITHUB_OUTPUT
+          echo "shuffled_assignee=$assignees" >> $GITHUB_ENV
+
+      - name: Check for existing issue
+        id: check_issue
+        run: |
+          gh auth login --with-token <<< ${{ secrets.GITHUB_TOKEN }}
+          issue_number=$(gh issue list --limit 100 --search "${{ vars.test_issue_title }}" --json number --jq '.[0].number')
+          echo "::set-output name=issue_number::$issue_number"
+   
+      - name: Create a Test issue
+        uses: actions-ecosystem/action-create-issue@b63bc2bbacb6a838dfe4a9f70da6665ae0962a49
+        id: create_issue 
+        with:
+          github_token: ${{ secrets.github_token }}
+          title: ${{ vars.test_issue_title }}
+          assignees: |
+            ${{ steps.shuffle.outputs.shuffled_assignee }}
+          body: |
+            This model is ready for testing. If you are assigned to this issue, please try it out using the CLI, Google Colab and DockerHub and let us know if it works!
+          labels: |
+            test
+        if: steps.check_issue.outputs.issue_number == ''