Merge pull request #5 from Genentech/docker

docker ci

Author: joshua-gould

.github/workflows/docker.yml

@@ -0,0 +1,55 @@
+name: CI/CD - Build and Push Docker Image to GHCR
+
+on:
+  push:
+    branches: [ "main" ]
+    tags:
+      - '*' # Matches any tag name
+  # Optional: Allows manual triggering of the workflow from the GitHub Actions tab
+  workflow_dispatch:
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write # Grant write permission to the GITHUB_TOKEN for packages
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      - name: Log in to the GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ghcr.io/${{ github.repository }}
+          tags: |
+            type=schedule,pattern=nightly
+            type=ref,event=branch
+            type=ref,event=tag
+            type=ref,event=pr
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+            type=semver,pattern={{major}}
+            type=sha,format=long
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max

.github/workflows/test.yml

@@ -1,4 +1,4 @@
-name: Python package
+name: Python tests
 
 on:
   push:

Dockerfile

@@ -1,58 +1,18 @@
-FROM ghcr.io/astral-sh/uv:python3.12-bookworm-slim
-SHELL ["/bin/bash", "-c"]
+FROM python:3.12-slim
 
-# Configure environment
-ENV UV_COMPILE_BYTECODE=1 \
-    UV_LINK_MODE=copy \
-    PYTHONUNBUFFERED=1 \
-    VIRTUAL_ENV=/opt/venv \
-    PATH="/opt/venv/bin:$PATH" \
-    AWS_RETRY_MODE=adaptive \
-    AWS_MAX_ATTEMPTS=10 \
-    DEBIAN_FRONTEND=noninteractive
-
-WORKDIR /software/scallops
-
-# --- DEPENDENCY LAYER ---
-COPY pyproject.toml setup.py requirements.txt requirements.cellpose.txt requirements.ufish.txt ./
-
-ARG TF_PKG="tensorflow==2.19.0"
-
-RUN --mount=type=cache,target=/root/.cache/uv \
-    --mount=type=cache,target=/var/cache/apt \
-    --mount=type=cache,target=/var/lib/apt \
-    set -eux; \
-    # Install system dependencies
-    apt-get update && \
-    apt-get install --no-install-recommends -y \
+ENV AWS_RETRY_MODE=adaptive \
+    AWS_MAX_ATTEMPTS=10
+RUN apt-get update -qq && \
+    apt-get install -qq --no-install-recommends -y \
       build-essential \
       git \
-      ca-certificates && \
-    # Create virtual environment
-    uv venv /opt/venv && \
-    # Filter out tensorflow from requirements
-    grep -vE '^tensorflow(==|>=|<=|~=|!=)' requirements.txt > /tmp/requirements.no-tf.txt && \
-    # Install Python dependencies
-    uv pip install --no-cache-dir \
-      -r /tmp/requirements.no-tf.txt \
-      -r requirements.cellpose.txt \
-      -r requirements.ufish.txt \
-      "${TF_PKG}" && \
-    # Cleanup
-    apt-get remove -y build-essential git && \
-    apt-get autoremove -y && \
-    apt-get clean && \
-    rm -rf /tmp/* /var/tmp/*
-
-# --- APPLICATION LAYER ---
-COPY scallops scallops/
-
-# Install the application itself
-RUN --mount=type=bind,source=.git,target=.git \
-    apt-get update && \
-    apt-get install --no-install-recommends -y build-essential git && \
-    # Install app in editable mode into the venv
-    uv pip install -e . && \
-    apt-get remove -y build-essential git && \
-    apt-get autoremove -y && \
-    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+      ca-certificates
+WORKDIR /app
+COPY requirements.txt requirements.ufish.txt ./
+RUN pip install -q --no-cache-dir --upgrade pip && pip install -q --no-cache-dir -r requirements.txt
+RUN pip install -q --no-cache-dir -r requirements.ufish.txt
+COPY . ./
+RUN pip install .
+RUN apt-get remove -qq -y build-essential git && \
+    apt-get autoremove -qq -y && apt-get clean -qq && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /app/