setting up workflow

.dockerignore

@@ -0,0 +1,42 @@
+# Secret files and resources
+.secret*
+resources/*
+
+# Python cache files
+__pycache__/
+*.py[cod]
+.pytest_cache/
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# IDE or editor files
+.vscode/
+.idea/
+*.swp
+
+# Jupyter Notebook checkpoints
+.ipynb_checkpoints/
+
+# Log and temporary files
+*.log
+*.tmp
+*.temp
+
+# Environment files (pip and conda)
+.env
+.venv/
+env/
+venv/
+*.conda
+*.condarc
+
+# Distribution / packaging files
+bin/
+.Python
+build/
+dist/
+lib/
+lib64/
+*.egg-info/

.github/workflows/bifrost_sp_cdiff_workflow.yml

@@ -0,0 +1,62 @@
+name: bifrost sp cdiff workflow
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["main"]
+  repository_dispatch:  # webhook event to trigger this action workflow upon push to the submodule cdiff_fbi 
+    types: 
+      - cdiff-fbi-webhook 
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: ["3.11"]
+
+    steps:
+      # Step 1: Checkout repository
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          submodules: 'true'  #Initialize and update submodules -> git submodule init && git submodule update
+
+      # Step 2: Update submodule to the latest commit
+      - name: Update submodule
+        run: |
+          cd bifrost_sp_cdiff/cdiff_fbi
+          git fetch origin
+          git checkout main  # or the specific branch you want to track
+          git pull origin main  # pull the latest changes
+          
+          # print the latest commit of cdiff_fbi
+          LATEST_COMMIT=$(git rev-parse HEAD)
+          echo "Updated cdiff_fbi to latest commit: $LATEST_COMMIT"
+
+      # Step 3: Set environment variables
+      - name: Set environment variables
+        run: |
+          echo "BIFROST_INSTALL_DIR='${{ github.workspace }}'" >> $GITHUB_ENV
+
+      # Step 4: Extract version from __init__.py and set ENV_NAME
+      - name: Set ENV_NAME
+        run: |
+          VERSION=$(grep "__version__" bifrost_sp_cdiff/__init__.py | cut -d "'" -f 2)
+          REPO_NAME=$(basename "${{ github.workspace }}")
+          ENV_NAME="${REPO_NAME}_v${VERSION}"
+          # Echo the ENV_NAME to the log for debugging
+          echo "Setting ENV_NAME to: $ENV_NAME"
+          echo "ENV_NAME=$ENV_NAME" >> $GITHUB_ENV
+
+      # Step 5: Build Docker image
+      - name: Build Docker image
+        run: |
+          docker build --build-arg BIFROST_DB_KEY="${{ secrets.MONGODB_ATLAS_TEST }}" --build-arg CONDA_ENV_NAME="${{ env.ENV_NAME }}" -t bifrost_sp_cdiff_image .
+
+      # Step 6: Run Docker container and execute the command
+      - name: Run Docker container
+        run: |
+          docker run --env BIFROST_DB_KEY="${{ secrets.MONGODB_ATLAS_TEST  }}" --env CONDA_ENV_NAME="${{ env.ENV_NAME }}" bifrost_sp_cdiff_image

.gitignore

@@ -0,0 +1,42 @@
+# Secret files and resources
+.secret*
+resources/*
+
+# Python cache files
+__pycache__/
+*.py[cod]
+.pytest_cache/
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# IDE or editor files
+.vscode/
+.idea/
+*.swp
+
+# Jupyter Notebook checkpoints
+.ipynb_checkpoints/
+
+# Log and temporary files
+*.log
+*.tmp
+*.temp
+
+# Environment files (pip and conda)
+.env
+.venv/
+env/
+venv/
+*.conda
+*.condarc
+
+# Distribution / packaging files
+bin/
+.Python
+build/
+dist/
+lib/
+lib64/
+*.egg-info/

Dockerfile

@@ -0,0 +1,35 @@
+# syntax=docker/dockerfile:1
+
+# Use a base image with Miniconda
+FROM continuumio/miniconda3:latest
+
+# Set the working directory as base
+WORKDIR /app
+
+# Install app dependencies and git necessary for submodules when using info from ecoli_fbi github repository
+RUN apt-get update && apt-get install -y git
+
+# Copy the entire repository into the container
+COPY . .
+
+# Copy the install.sh and environment.yml into the container
+COPY install.sh .
+#COPY environment.yml .
+
+# Ensure install.sh is executable
+RUN chmod +x install.sh
+
+# Initialize conda for bash shell
+RUN /opt/conda/bin/conda init bash
+
+# Install the tool using the install script
+RUN bash install.sh -i LOCAL
+
+# Set environment variables
+ENV BIFROST_INSTALL_DIR='/app'
+# Use ARG for database key and set at runtime
+ARG BIFROST_DB_KEY=''
+
+# Set the default command to run the Python module
+CMD ["bash", "-c", "BIFROST_DB_KEY=\"$BIFROST_DB_KEY\" conda run -n $CONDA_ENV_NAME python cmd_test.py"]
+

install.sh

@@ -9,6 +9,12 @@ helpFunction()
    exit 1 # Exit script after printing help
 }
 
+# Check if the conda command exist in order to setup the conda environment
+if ! command -v conda &> /dev/null; then
+    echo "conda could not be found, please install Anaconda/Miniconda"
+    exit 1
+fi
+
 while getopts "i:" opt
 do
    case "$opt" in
@@ -56,6 +62,24 @@ then
   fi
 fi
 
+# Update ecoli_fbi submodule
+echo "Updating ecoli_fbi submodule to the most current commit"
+git submodule update --init --recursive
+cd bifrost_sp_ecoli/ecoli_fbi || exit
+
+# Fetch the latest changes from the remote repository
+git fetch origin
+git checkout main  # or the specific branch you want to track
+git pull origin main
+
+# Optionally, echo the latest commit SHA
+LATEST_COMMIT=$(git rev-parse HEAD)
+echo "Updated ecoli_fbi to latest commit: $LATEST_COMMIT"
+
+# Navigate back to the main project directory
+cd ../../
+pwd
+
 # Begin script
 if $(conda config --show channels | grep -q "bioconda")
 then