Docker image publishing and change CI infrastructure

.github/workflows/ci-test.yml

@@ -0,0 +1,75 @@
+name: Run Tests with Docker image 
+
+on:
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+jobs:
+  start-aws-runner:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      contents: read
+    outputs:
+      mapping: ${{ steps.aws-start.outputs.mapping }}
+      instances: ${{ steps.aws-start.outputs.instances }}
+    steps:
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          role-to-assume: arn:aws:iam::203627415330:role/of-gha-runner 
+          aws-region: us-east-1
+      - name: Create cloud runner
+        id: aws-start
+        uses: omsf/start-aws-gha-runner@v1.0.0
+        with:
+          aws_image_id: ami-0754c6e75b3b97dcd  # Deep Learning AMI Neuron (Ubuntu 22.04)
+          aws_instance_type: t3.2xlarge 
+          aws_home_dir: /home/ubuntu
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
+
+  test-openfold-docker:
+    runs-on: ${{ fromJSON(needs.start-aws-runner.outputs.instances) }}
+    needs:
+      - start-aws-runner
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Pull pre-built Docker image
+        run: docker pull openfoldconsortium/openfold3:stable
+
+      - name: Build test layers on Docker image 
+        run: docker build -t openfold3-test-runner -f openfold3/tests/Dockerfile . 
+
+      - name: Run unit tests
+        run: docker run -v ${{ github.workspace }}:/opt/openfold3 openfold3-test-runner:latest pytest openfold3/tests
+
+  stop-aws-runner:
+    runs-on: ubuntu-latest
+    permissions:
+        id-token: write
+        contents: read
+    needs:
+      - start-aws-runner
+      - test-openfold-docker 
+    if: ${{ always() }}
+    steps:
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          role-to-assume: arn:aws:iam::203627415330:role/of-gha-runner 
+          aws-region: us-east-1
+      - name: Stop instances
+        uses: omsf/stop-aws-gha-runner@v1.0.0
+        with:
+          instance_mapping: ${{ needs.start-aws-runner.outputs.mapping }}
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}

.github/workflows/docker.yml

@@ -0,0 +1,110 @@
+name: Publish Docker image
+
+on:
+  workflow_dispatch:  # Allow manual creation of docker images
+    inputs:
+      version:
+        description: 'Version tag (e.g., 1.0.0)'
+        required: true
+        type: string
+      additional_tags:
+        description: 'Additional tags (comma-separated, e.g., latest,stable)'
+        required: false
+        type: string
+        default: ''
+  release:
+    types: [published]
+
+jobs:
+  start-aws-runner:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      contents: read
+    outputs:
+      mapping: ${{ steps.aws-start.outputs.mapping }}
+      instances: ${{ steps.aws-start.outputs.instances }}
+    steps:
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          role-to-assume: arn:aws:iam::203627415330:role/of-gha-runner 
+          aws-region: us-east-1
+      - name: Create cloud runner
+        id: aws-start
+        uses: omsf/start-aws-gha-runner@v1.1.0
+        with:
+          aws_image_id: ami-0754c6e75b3b97dcd  # Deep Learning AMI Neuron (Ubuntu 22.04)
+          aws_instance_type: trn1.2xlarge 
+          aws_home_dir: /home/ubuntu
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
+
+  push-to-registry:
+    name: Push Docker image to Docker Hub
+    runs-on: ${{ fromJSON(needs.start-aws-runner.outputs.instances) }}
+    needs:
+      - start-aws-runner
+    permissions:
+      packages: write
+      contents: read
+      attestations: write
+      id-token: write
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v5
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+        with:
+          images: openfoldconsortium/openfold3
+          tags: |
+            type=raw,value=${{ inputs.version }},enable=${{ github.event_name == 'workflow_dispatch' }}
+            type=raw,value=${{ inputs.additional_tags }},enable=${{ inputs.additional_tags != '' && github.event_name == 'workflow_dispatch' }}
+            type=semver,pattern={{major}}.{{minor}}
+
+      - name: Build and push Docker image
+        id: push
+        uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671
+        with:
+          context: .
+          file: ./Dockerfile
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+
+      - name: Generate artifact attestation
+        uses: actions/attest-build-provenance@v3
+        with:
+          subject-name: index.docker.io/openfoldconsortium/openfold3
+          subject-digest: ${{ steps.push.outputs.digest }}
+          push-to-registry: true
+
+  stop-aws-runner:
+    runs-on: ubuntu-latest
+    permissions:
+        id-token: write
+        contents: read
+    needs:
+      - start-aws-runner
+      - push-to-registry 
+    if: ${{ always() }}
+    steps:
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          role-to-assume: arn:aws:iam::203627415330:role/of-gha-runner 
+          aws-region: us-east-1
+      - name: Stop instances
+        uses: omsf/stop-aws-gha-runner@v1.0.0
+        with:
+          instance_mapping: ${{ needs.start-aws-runner.outputs.mapping }}
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}

docs/source/Installation.md

@@ -38,22 +38,14 @@ mamba install kalign2 -c bioconda
 
 ### OpenFold3 Docker Image
 
-A compressed version of the OpenFold3 image is available on HuggingFace at this [link](https://huggingface.co/OpenFold/OpenFold3/tree/main/docker_image) The size of the compressed image is ~14GB.
+The OpenFold3 Docker Image is now available on Docker Hub: [openfoldconsortium/openfold3](https://hub.docker.com/repository/docker/openfoldconsortium/openfold3/general)
 
-To verify the compressed file is not unintentionally corrupted, you can check against the md5 checksum file provided with the following command and expected output.
+To get the latest stable version, you can use the following command
 
 ```bash
-$ md5sum -c openfold3_image.tar.bz2.md5
-openfold3_image.tar.bz2: OK
+docker pull openfoldconsortium/openfold3:stable
 ```
 
-The image may then be unpacked with the following command:
-
-```bash
-docker load --input openfold3_image.tar.bz2
-```
-
-
 ### Building the OpenFold3 Docker Image 
 
 If you would like to build an OpenFold docker image locally, we provide a dockerfile. You may build this image with the following command:

openfold3/tests/Dockerfile

@@ -1,7 +1,9 @@
-FROM openfold-base
+# Copy Openfold3 folder and build dependencies needed for testing
+FROM openfoldconsortium/openfold3:stable
 
-COPY openfold3/tests /opt/openfold3/tests
+COPY openfold3 /opt/openfold3
 COPY environments/development.txt /opt/openfold3/development.txt
 
 WORKDIR /opt/openfold3
 RUN pip install -r development.txt
+RUN pip install --force-reinstall --no-deps .