first commit

Author: wikiselev

.github/workflows/docker-deploy.yml

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+name: Docker Deploy to AWS ECR Public
+
+on:
+  push:
+    # branches: [ dev ]
+    branches: [ '**' ]  # This will match all branches
+    paths:
+      - 'Dockerfile'
+      - 'requirements.txt'
+  workflow_dispatch:  # This enables manual triggering
+    inputs:
+      version:
+        description: 'Override version tag (optional)'
+        required: false
+        default: ''
+        
+env:
+  REPO: 'artemis-paper'
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      contents: read
+    
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v3
+      with:
+        fetch-depth: 0  # Fetch all history for tags and branches
+      
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v2
+      
+    - name: Set dynamic version
+      id: version
+      run: |
+        # If this is a tag push, use the tag name without the 'v' prefix
+        if [[ $GITHUB_REF == refs/tags/* ]]; then
+          TAG=${GITHUB_REF#refs/tags/v}
+          echo "VERSION=${TAG}" >> $GITHUB_OUTPUT
+          echo "Using tag: ${TAG}"
+        else
+          # Otherwise use short SHA
+          SHORT_SHA=$(git rev-parse --short HEAD)
+          echo "VERSION=${SHORT_SHA}" >> $GITHUB_OUTPUT
+          echo "Using commit SHA: ${SHORT_SHA}"
+        fi
+
+    - name: Debug OIDC Token
+      run: |
+        echo "GitHub Repository: $GITHUB_REPOSITORY"
+        echo "GitHub Ref: $GITHUB_REF"
+        echo "GitHub Actor: $GITHUB_ACTOR"
+        
+    - name: Configure AWS credentials
+      uses: aws-actions/configure-aws-credentials@v4
+      with:
+        role-to-assume: ${{ secrets.AWS_ROLE_ARN }}
+        aws-region: us-east-1     # ECR Public requires us-east-1
+        role-session-name: GitHubActions-${{ github.run_id }}
+        role-duration-seconds: 3600
+
+    - name: Login to Amazon ECR
+      id: login-ecr
+      uses: aws-actions/amazon-ecr-login@v2
+      with:
+        registry-type: public
+        
+    - name: Build and push Docker image
+      env:
+        PUBLIC_URI: ${{ steps.login-ecr.outputs.registry }}/alethiotx
+        VERSION: ${{ steps.version.outputs.VERSION }}
+      run: |        
+        echo "Building version: ${VERSION}"
+        
+        # Build and push the Docker image
+        docker build \
+          --platform linux/amd64 \
+          -t ${PUBLIC_URI}/${REPO}:${VERSION} \
+          -t ${PUBLIC_URI}/${REPO}:latest \
+          --push \
+          -f Dockerfile .

.gitignore

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+# Jupyter
+*ipynb_checkpoints
+*.ipynb_checkpoints/
+
+# Terraform
+**.terraform**
+*.tfstate
+*.tfstate.*
+*.tfvars
+.terraform.lock.hcl
+backend.hcl
+
+# Nextflow
+**.nextflow**
+**.nextflow.log**
+work/
+.nextflow/
+
+# Python
+.venv/
+venv/
+__pycache__/
+*.py[cod]
+*$py.class
+*.egg-info/
+dist/
+build/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+
+# Output directories
+results/
+output/
+plots/
+data/local/
+
+# Local testing
+test/
+for_ed/
+check/
+targets/
+
+# Documentation build
+docs/_build/
+docs/.doctrees/
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Credentials (extra safety)
+*.pem
+*.key
+credentials
+secrets.yml

Dockerfile

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+FROM ubuntu:25.10
+
+# Install dependencies
+RUN apt-get update && apt-get install -y \
+    python3-dev \
+    gcc \
+    python3-venv
+
+RUN apt-get clean
+RUN rm -rf /var/lib/apt/lists/*
+
+COPY requirements.txt .
+
+# Install packages with CodeArtifact as additional index
+RUN python3 -m venv artemis
+RUN artemis/bin/pip3 install --no-cache-dir \
+    -r requirements.txt
+
+RUN find . -name "__pycache__" -type d -exec rm -rf {} +
+RUN rm -rf *.egg-info
+
+# Activate the virtual environment by default
+ENV PATH="/artemis/bin:$PATH"

LICENSE

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+MIT License
+
+Copyright (c) 2025 Alethio Therapeutics
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.