feature: pixi-beta

.dockerignore

@@ -4,6 +4,8 @@
 # Allow specific files
 !CITATION.cff
 !LICENSE
+!pixi.toml
+!pixi.lock
 !pyproject.toml
 !README.md
 

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.github/workflows/ci-integration-test-reusable.yml → .github/workflows/ci-integration-test-conda-reusable.yml

@@ -67,16 +67,16 @@ jobs:
         uses: docker/build-push-action@v7.1.0
         with:
           context: .
-          file: docker/Dockerfile
+          file: docker/Dockerfile.conda
           target: test
           push: true
           build-args: |
             CUDA_BASE_IMAGE_TAG=${{ inputs.cuda_base_image_tag }}
             BUILD_MODE=${{ inputs.build_mode }}
           tags: |
             ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:test-${{ inputs.cuda_base_image_tag }}-${{ github.sha }}
-          cache-from: type=registry,ref=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:cache-${{ inputs.cuda_base_image_tag }}
-          cache-to: type=registry,ref=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:cache-${{ inputs.cuda_base_image_tag }},mode=max
+          cache-from: type=registry,ref=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:cache-conda-${{ inputs.cuda_base_image_tag }}
+          cache-to: type=registry,ref=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:cache-conda-${{ inputs.cuda_base_image_tag }},mode=max
 
       - name: Create parameter cache directory
         run: mkdir -p ~/.openfold3

.github/workflows/ci-integration-test-pixi-reusable.yml

@@ -0,0 +1,128 @@
+name: Reusable Docker Test for running heavy test loads (Pixi)
+
+on:
+  # Can only be called by another workflow, not directly by the user
+  workflow_call:
+    inputs:
+      pixi_env:
+        description: 'Pixi environment name (e.g., openfold3-cuda12, openfold3-cuda13)'
+        required: true
+        type: string
+      base_image:
+        description: 'Base Docker image'
+        required: false
+        type: string
+        default: 'ubuntu:22.04'
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}/openfold3-docker
+
+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@v6
+        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@v1.1.1
+        with:
+          aws_image_id: ami-00839c71d8f6096b4  # Deep Learning Base AMI with Single CUDA (Ubuntu 22.04)
+          aws_instance_type: "g5.4xlarge" # A10G 64 GB
+          aws_home_dir: /home/ubuntu
+          aws_root_device_size: 200
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
+
+  test-openfold-docker-pixi:
+    runs-on: ${{ fromJSON(needs.start-aws-runner.outputs.instances) }}
+    needs:
+      - start-aws-runner
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Log in to GHCR
+        uses: docker/login-action@v4
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v4
+
+      - name: Build and push test image
+        uses: docker/build-push-action@v7
+        with:
+          context: .
+          file: docker/Dockerfile.pixi
+          target: test
+          push: true
+          build-args: |
+            PIXI_ENV=${{ inputs.pixi_env }}
+            BASE_IMAGE=${{ inputs.base_image }}
+          tags: |
+            ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:test-pixi-${{ inputs.pixi_env }}-${{ github.sha }}
+          cache-from: type=registry,ref=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:cache-pixi-${{ inputs.pixi_env }}
+          cache-to: type=registry,ref=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:cache-pixi-${{ inputs.pixi_env }},mode=max
+
+      - name: Create parameter cache directory
+        run: mkdir -p ~/.openfold3
+
+      - name: Cache download of parameters
+        id: cache-openfold_parameters
+        uses: actions/cache@v4
+        with:
+          path: ~/.openfold3/
+          key: shared-params_of3
+          restore-keys: |
+            shared-params_of3
+
+      - name: Install AWS CLI and Download OpenFold parameters
+        if: steps.cache-openfold_parameters.outputs.cache-hit != 'true'
+        run: |
+          echo "Cache miss: Downloading OpenFold parameters..."
+          aws s3 cp s3://openfold3-data/openfold3-parameters/of3-p2-155k.pt ~/.openfold3/ --no-sign-request
+
+      - name: Run integration test
+        run: |
+          docker run --gpus all\
+            -v ${{ github.workspace }}:/opt/openfold3 \
+            -v ~/.openfold3:/root/.openfold3 \
+            ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:test-pixi-${{ inputs.pixi_env }}-${{ github.sha }} \
+            pytest -x openfold3/tests/ -m slow -vvv
+
+  stop-aws-runner:
+    runs-on: ubuntu-latest
+    permissions:
+        id-token: write
+        contents: read
+    needs:
+      - start-aws-runner
+      - test-openfold-docker-pixi
+    if: ${{ always() }}
+    steps:
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v6
+        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/ci-test-reusable.yml → .github/workflows/ci-test-conda-reusable.yml

@@ -69,16 +69,16 @@ jobs:
         uses: docker/build-push-action@v7.1.0
         with:
           context: .
-          file: docker/Dockerfile
+          file: docker/Dockerfile.conda
           target: test
           push: true
           build-args: |
             CUDA_BASE_IMAGE_TAG=${{ inputs.cuda_base_image_tag }}
             BUILD_MODE=${{ inputs.build_mode }}
           tags: |
             ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:test-${{ inputs.cuda_base_image_tag }}-${{ github.sha }}
-          cache-from: type=registry,ref=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:cache-${{ inputs.cuda_base_image_tag }}
-          cache-to: type=registry,ref=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:cache-${{ inputs.cuda_base_image_tag }},mode=max
+          cache-from: type=registry,ref=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:cache-conda-${{ inputs.cuda_base_image_tag }}
+          cache-to: type=registry,ref=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:cache-conda-${{ inputs.cuda_base_image_tag }},mode=max
 
       - name: Run unit tests
         run: |

.github/workflows/ci-test-pixi-reusable.yml

@@ -0,0 +1,132 @@
+name: Reusable Docker Test (Pixi)
+
+on:
+  # Can only be called by another workflow, not directly by the user
+  workflow_call:
+    inputs:
+      pixi_env:
+        description: 'Pixi environment name (e.g., openfold3-cuda12, openfold3-cuda13)'
+        required: true
+        type: string
+      base_image:
+        description: 'Base Docker image'
+        required: false
+        type: string
+        default: 'ubuntu:22.04'
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}/openfold3-docker
+
+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@v6
+        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@v1.1.1
+        with:
+          aws_image_id: ami-0754c6e75b3b97dcd  # Deep Learning AMI Neuron (Ubuntu 22.04)
+          aws_instance_type: t3.2xlarge
+          aws_home_dir: /home/ubuntu
+          aws_root_device_size: 200
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
+
+  test-openfold-docker-pixi:
+    runs-on: ${{ fromJSON(needs.start-aws-runner.outputs.instances) }}
+    needs:
+      - start-aws-runner
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          ref: ${{ github.event.pull_request.head.sha || github.sha }}
+
+      - name: Log in to GHCR
+        uses: docker/login-action@v4
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v4
+
+      - name: Build and push test image
+        uses: docker/build-push-action@v7
+        with:
+          context: .
+          file: docker/Dockerfile.pixi
+          target: test
+          push: true
+          build-args: |
+            PIXI_ENV=${{ inputs.pixi_env }}
+            BASE_IMAGE=${{ inputs.base_image }}
+          tags: |
+            ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:test-pixi-${{ inputs.pixi_env }}-${{ github.sha }}
+          cache-from: type=registry,ref=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:cache-pixi-${{ inputs.pixi_env }}
+          cache-to: type=registry,ref=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:cache-pixi-${{ inputs.pixi_env }},mode=max
+
+      - name: Run unit tests
+        run: |
+          docker run \
+            -v ${{ github.workspace }}:/opt/openfold3 \
+            ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:test-pixi-${{ inputs.pixi_env }}-${{ github.sha }} \
+            pytest openfold3/tests -vvv -n auto --cov=openfold3 --cov-report=xml --cov-report=term
+
+      - name: Debug - List files and find coverage
+        if: always()
+        run: |
+          echo "=== Current directory ==="
+          pwd
+          echo "=== Files in workspace root ==="
+          ls -la ${{ github.workspace }}
+          echo "=== Looking for coverage files ==="
+          find ${{ github.workspace }} -name "coverage.xml" -o -name ".coverage" 2>/dev/null || echo "No coverage files found"
+
+      - name: Upload coverage report
+        uses: actions/upload-artifact@v7
+        if: always()
+        with:
+          name: coverage-report-pixi-${{ inputs.pixi_env }}
+          path: |
+            coverage.xml
+            .coverage
+          include-hidden-files: true
+          retention-days: 30
+
+  stop-aws-runner:
+    runs-on: ubuntu-latest
+    permissions:
+        id-token: write
+        contents: read
+    needs:
+      - start-aws-runner
+      - test-openfold-docker-pixi
+    if: ${{ always() }}
+    steps:
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v6
+        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/ci-test.yml

@@ -10,7 +10,7 @@ on:
   workflow_dispatch:
 
 jobs:
-  test:
+  test-conda:
     if: |
       (github.event_name == 'push') ||
       (github.event_name == 'workflow_dispatch') ||
@@ -29,10 +29,36 @@ jobs:
           - cuda_base_image_tag: "12.1.1-cudnn8-devel-ubuntu22.04"
             build_mode: "yaml"
     concurrency:
-      group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}-${{ matrix.cuda_base_image_tag }}
+      group: ${{ github.workflow }}-conda-${{ github.head_ref || github.ref }}-${{ matrix.cuda_base_image_tag }}
       cancel-in-progress: true
-    uses: ./.github/workflows/ci-test-reusable.yml
+    uses: ./.github/workflows/ci-test-conda-reusable.yml
     with:
       cuda_base_image_tag: ${{ matrix.cuda_base_image_tag }}
       build_mode: ${{ matrix.build_mode }}
     secrets: inherit
+
+  test-pixi:
+    if: |
+      (github.event_name == 'push') ||
+      (github.event_name == 'workflow_dispatch') ||
+      (github.event_name == 'pull_request_target' &&
+       (github.repository == 'aqlaboratory/openfold-3' &&
+        github.event.action == 'labeled' &&
+        github.event.label.name == 'safe-to-test') ||
+       (github.repository != 'aqlaboratory/openfold-3'))
+    permissions:
+      id-token: write
+      contents: read
+      packages: write
+    strategy:
+      matrix:
+        include:
+          - pixi_env: "openfold3-cuda12"
+          - pixi_env: "openfold3-cuda13"
+    concurrency:
+      group: ${{ github.workflow }}-pixi-${{ github.head_ref || github.ref }}-${{ matrix.pixi_env }}
+      cancel-in-progress: true
+    uses: ./.github/workflows/ci-test-pixi-reusable.yml
+    with:
+      pixi_env: ${{ matrix.pixi_env }}
+    secrets: inherit