updating readme [skip ci]

ersilia-os · Apr 11, 2024 · 5849d98 · 5849d98
1 parent e75358b
commit 5849d98
Show file tree

Hide file tree

Showing 6 changed files with 115 additions and 31 deletions.
diff --git a/.github/workflows/test-model-pr.yml b/.github/workflows/test-model-pr.yml
@@ -18,6 +18,10 @@ jobs:
       - 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

diff --git a/.github/workflows/test-model.yml b/.github/workflows/test-model.yml
@@ -23,6 +23,10 @@ jobs:
       - 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
@@ -102,7 +106,14 @@ jobs:
           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 
@@ -115,3 +126,4 @@ jobs:
             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 == ''
diff --git a/.github/workflows/upload-model-to-dockerhub.yml b/.github/workflows/upload-model-to-dockerhub.yml
@@ -9,17 +9,17 @@ on:
 
 jobs:
   upload_model_to_dockerhub:
-    if: github.repository != 'ersilia-os/eos-template'
+    if: ${{ github.repository != 'ersilia-os/eos-template' && github.event.workflow_run.conclusion == 'success' }}
     runs-on: ubuntu-latest
     steps:
       # https://github.com/docker/setup-qemu-action
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v3
 
       # https://github.com/docker/setup-buildx-action
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
 
       # log in to dockerhub
       - name: Login to Docker Hub
@@ -35,7 +35,22 @@ jobs:
           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: 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: Generate the Dockerfile
         id: generate-dockerfile
         env:
@@ -44,11 +59,67 @@ jobs:
           wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/place_a_dockerfile_in_current_eos_repo.py
           python -m pip install requests
           python place_a_dockerfile_in_current_eos_repo.py $REPO_NAME
-                                          
+
+      # We cannot tag it as anything other than latest because 
+      # ersilia cli only looks for the 'latest' tag
+      - name: Build only AMD64 Image for Testing
+        id: buildForTest
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          load: true
+          tags: ersiliaos/${{ github.event.repository.name }}:latest
+
+      - 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
+          
+      # TODO This is very hacky, maybe we want to use the ersilia test command in the future for this
+      - name: Test Built Image
+        id: testBuiltImage
+        run: |
+          ersilia -v fetch ${{ github.event.repository.name }} --from_dockerhub
+          ersilia -v serve ${{ github.event.repository.name }}
+          ersilia -v run -i "CCCC" -o "output.json"
+          expected=$(jq '.[0].output.outcome[]' output.json | wc -l)
+          result=$(jq '.[0].output.outcome[] | select(. != null)' output.json | wc -l)
+          echo "Expected correct outcomes $expected"
+          echo "Returned correct outcomes $result"
+          if ! ([ $result -gt 0 ] && [ $result -le $expected ])
+            then
+              echo "Error in model output, aborting build and push"
+              exit 1
+          fi
+        env:
+          PULL_IMAGE: n
+
       - name: Build and push
         id: buildMultiple
         continue-on-error: true
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
+        timeout-minutes: 45
         with:
           context: .
           platforms: linux/amd64,linux/arm64
@@ -69,15 +140,15 @@ jobs:
       - name: Build only for Linux/amd64
         id: buildSingle
         if: steps.buildCheck.outputs.failed == 'true'
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           context: .
           platforms: linux/amd64
           push: ${{ github.event_name != 'pull_request' }}
           tags: ersiliaos/${{ github.event.repository.name }}:latest
 
       - name: Update Metadata JSON file with DockerHub info
-        id: UpdateMetadata
+        id: updateMetadata
         run: |
           mv Dockerfile_legacy Dockerfile
           python3 -c "
@@ -94,6 +165,7 @@ jobs:
              json.dump(data, f, indent=4)
           "
           rm arch.txt
+          rm place_a_dockerfile_in_current_eos_repo.py
           
       - name: Commit and push changes done to the Metadata JSON file
         uses: actions-js/push@156f2b10c3aa000c44dbe75ea7018f32ae999772 # pin@v1.4
@@ -105,28 +177,6 @@ jobs:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           amend: true
           force: 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: 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

diff --git a/.github/workflows/upload-model-to-s3.yml b/.github/workflows/upload-model-to-s3.yml
@@ -9,7 +9,7 @@ on:
 
 jobs:
   upload_model_to_s3:
-    if: github.repository != 'ersilia-os/eos-template'
+    if: ${{ github.repository != 'ersilia-os/eos-template' && github.event.workflow_run.conclusion == 'success' }}
     runs-on: ubuntu-latest
     steps:
       - name: Checkout persist credentials
@@ -25,6 +25,10 @@ jobs:
       - 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

diff --git a/output.json b/output.json
@@ -0,0 +1,14 @@
+[
+    {
+        "input": {
+            "key": "IJDNQMDRQITEOD-UHFFFAOYSA-N",
+            "input": "CCCC",
+            "text": "CCCC"
+        },
+        "output": {
+            "outcome": [
+                1.605723
+            ]
+        }
+    }
+]
diff --git a/place_a_dockerfile_in_current_eos_repo.py → place_a_dockerfile_in_current_eos_repo.py.1 b/place_a_dockerfile_in_current_eos_repo.py → place_a_dockerfile_in_current_eos_repo.py.1