Add Dockerfile and CI workflow for Docker image; ignore local assistant state files

Author: Chris2004m

.github/workflows/docker-publish.yml

@@ -0,0 +1,45 @@
+# GitHub Action: Build & Push Docker image to Docker Hub
+# Requires two repository secrets:
+#   DOCKERHUB_USERNAME – your Docker Hub username (e.g. xpert123)
+#   DOCKERHUB_TOKEN    – a Personal Access Token with "write:push" scope
+#
+# On every push to main (or when Docker-related files change) this will
+# build the image and push the tag `latest`.
+# Adjust the `tags:` value if you need versioned tags.
+
+name: Docker Image CI
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - "Dockerfile"
+      - "requirements.txt"
+      - "**/*.py"
+      - ".github/workflows/docker-publish.yml"
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up QEMU (multi-arch builds)
+        uses: docker/setup-qemu-action@v2
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Build and push image
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          push: true
+          tags: xpert123/chris2004m:latest

.gitignore

@@ -7,4 +7,6 @@ data/GCF_000001405.40/protein.faa
 Context.md
 CLAUDE.md
 test.fasta
-process-todos.md
+process-todos.md
+.claude
+.codebuddy

Dockerfile

@@ -0,0 +1,32 @@
+# syntax=docker/dockerfile:1
+
+# Lightweight official Python image
+FROM python:3.10-slim
+
+# Environment settings
+ENV PYTHONDONTWRITEBYTECODE=1 \
+    PYTHONUNBUFFERED=1 \
+    PIP_NO_CACHE_DIR=1 \
+    DEBIAN_FRONTEND=noninteractive
+
+# System deps required by some Python libs (e.g. transformers pulls via git)
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends git curl \
+    && rm -rf /var/lib/apt/lists/*
+
+# Create app directory
+WORKDIR /app
+
+# Copy dependency list first for layer caching
+COPY requirements.txt ./
+
+# Install Python dependencies
+RUN pip install --upgrade pip \
+    && pip install -r requirements.txt
+
+# Copy rest of the project
+COPY . .
+
+# Default entrypoint shows help for the generator script
+ENTRYPOINT ["python", "generate_control_peptides.py"]
+CMD ["--help"]