minor changes in CI/CD

Author: ypriverol

.github/workflows/quantms-rescoring-containers.yml

@@ -36,6 +36,13 @@ jobs:
       RETRY_DELAY: 30
 
     steps:
+    - name: Free up disk space before build
+      run: |
+        sudo rm -rf /usr/share/dotnet /usr/local/lib/android /opt/ghc
+        docker system prune -af || true
+        sudo apt-get clean
+        sudo rm -rf /var/lib/apt/lists/*
+
     - name: Checkout repository
       uses: actions/checkout@v4
 
@@ -55,7 +62,6 @@ jobs:
         VERSION=$(grep '^version = ' pyproject.toml | cut -d'"' -f2)
         echo "VERSION=$VERSION" >> $GITHUB_OUTPUT
         echo "Extracted version: $VERSION"
-        
         # Extract major and minor version
         MAJOR=$(echo $VERSION | cut -d'.' -f1)
         MINOR=$(echo $VERSION | cut -d'.' -f2)
@@ -77,6 +83,12 @@ jobs:
         # Note: Only building for linux/amd64 as pyopenms doesn't have ARM64 wheels
         platforms: linux/amd64
 
+    - name: Free up disk space after build
+      run: |
+        docker system prune -af || true
+        sudo apt-get clean
+        sudo rm -rf /var/lib/apt/lists/*
+
     - name: Set up Singularity
       if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }}
       uses: eWaterCycle/setup-singularity@v7
@@ -86,17 +98,13 @@ jobs:
     - name: Pull Docker image for Singularity conversion
       if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }}
       run: |
-        # Pull the Docker image from GitHub Container Registry
         docker pull ghcr.io/bigbio/quantms-rescoring:latest
-        # Save the Docker image to a tar file
         docker save ghcr.io/bigbio/quantms-rescoring:latest -o quantms-rescoring.tar
 
     - name: Convert Docker image to Singularity
       if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }}
       run: |
-        # Convert Docker tar to Singularity SIF
         singularity build quantms-rescoring.sif docker-archive://quantms-rescoring.tar
-        # Verify the SIF file exists
         ls -la quantms-rescoring.sif
 
     - name: Login and Deploy Container
@@ -105,11 +113,7 @@ jobs:
         IS_RELEASE: ${{ github.event_name == 'release' }}
       run: |
         echo ${{ secrets.GHCR_TOKEN }} | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io
-        
-        # Push with exact version tag
         singularity push quantms-rescoring.sif oras://ghcr.io/bigbio/quantms-rescoring-sif:${{ steps.version.outputs.VERSION }}
-        
-        # If this is a release event, also tag as latest
         if [[ "${{ env.IS_RELEASE }}" == "true" || "${{ github.event_name }}" == "release" ]]; then
           singularity push quantms-rescoring.sif oras://ghcr.io/bigbio/quantms-rescoring-sif:latest
         fi

Dockerfile

@@ -1,74 +1,61 @@
-FROM ubuntu:22.04
-
-# Some metadata
-LABEL base_image="ubuntu:22.04"
-LABEL version="1"
-LABEL software="quantms-rescoring"
-LABEL software.version="0.0.11"
-LABEL about.summary="quantms-rescoring: Python scripts and helpers for the quantMS workflow"
-LABEL about.home="https://github.com/bigbio/quantms-rescoring"
-LABEL about.documentation="https://github.com/bigbio/quantms-rescoring"
-LABEL about.license_file="https://github.com/bigbio/quantms-rescoring/blob/main/LICENSE"
-LABEL about.tags="Proteomics,MS2PIP,DeepLC,OpenMS"
-LABEL maintainer="Yasset Perez-Riverol <ypriverol@gmail.com>"
+# ===================
+# Stage 1: Build
+# ===================
+FROM python:3.11-slim as builder
 
 ENV DEBIAN_FRONTEND=noninteractive
 
-# Update package lists and install necessary packages in a single RUN command
 RUN apt-get update && apt-get install -y --no-install-recommends \
-    python3.11 \
+    build-essential \
     python3.11-dev \
     python3.11-venv \
-    python3-pip \
-    build-essential \
-    curl \
-    git \
-    wget \
-    locales \
-    # pyOpenMS dependencies
     libglib2.0-0 \
     libgomp1 \
-    # Additional dependencies for proteomics tools
     libboost-all-dev \
     libhdf5-dev \
     libnetcdf-dev \
     libxml2-dev \
     libxslt1-dev \
     libssl-dev \
     libffi-dev && \
-    # Configure locale
-    locale-gen en_US.UTF-8 && \
-    update-locale LANG=en_US.UTF-8 && \
-    # Clean up package cache
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/*
+    apt-get clean && rm -rf /var/lib/apt/lists/*
 
-# Set environment variables for locale
-ENV LANG=en_US.UTF-8
-ENV LANGUAGE=en_US:en
-ENV LC_ALL=en_US.UTF-8
-
-# Set work directory
 WORKDIR /app
-
-# Copy application code first
 COPY . .
 
-# Install Poetry and dependencies using the same strategy as CI/CD
-RUN python3.11 -m pip install --upgrade pip && \
-    python3.11 -m pip install flake8==7.3.0 pytest==8.4.1 && \
-    python3.11 -m pip install -r requirements.txt && \
-    python3.11 -m pip install poetry==2.1.3 && \
+RUN pip install --no-cache-dir --upgrade pip && \
+    pip install --no-cache-dir poetry==2.1.3 && \
     poetry build && \
-    python3.11 -m pip install dist/*.whl && \
-    python3.11 -m pip cache purge
+    pip install --no-cache-dir dist/*.whl && \
+    pip cache purge
 
-# Test pyOpenMS import
-RUN python3.11 -c "import pyopenms; print('pyOpenMS imported successfully')"
+# ===================
+# Stage 2: Runtime
+# ===================
+FROM python:3.11-slim as final
+
+ENV DEBIAN_FRONTEND=noninteractive
+ENV LANG=en_US.UTF-8
+ENV LANGUAGE=en_US:en
+ENV LC_ALL=en_US.UTF-8
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    libglib2.0-0 \
+    libgomp1 \
+    libhdf5-103-1 \
+    libnetcdf19 \
+    libxml2 \
+    libxslt1.1 \
+    libssl3 \
+    libffi8 && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+COPY --from=builder /usr/local /usr/local
 
-# Create a non-root user
 RUN useradd --create-home --shell /bin/bash app && \
-    chown -R app:app /app
+    mkdir /data && chown -R app:app /data
 USER app
 
-WORKDIR /data/
+WORKDIR /data
+
+RUN python3.11 -c "import pyopenms; print('pyOpenMS imported successfully')"