Diff (formatted)

.dockerignore

@@ -0,0 +1,50 @@
+# Ignore Git repository files
+.git
+.gitignore
+
+# Ignore Python virtual environments
+.venv/
+env/
+venv/
+
+# Ignore log files
+*.log
+
+# Ignore Python cache and compiled files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Ignore pytest cache
+.pytest_cache/
+
+# Ignore mypy cache
+.mypy_cache/
+
+# Ignore coverage reports
+.coverage
+htmlcov/
+
+# Ignore temporary files
+*.swp
+*~
+*.tmp
+*.temp
+
+# Ignore build artifacts
+build/
+dist/
+.eggs/
+*.egg-info/
+
+# Ignore IDE/editor configurations
+.vscode/
+.idea/
+
+# Ignore macOS Finder files
+.DS_Store
+
+# Ignore other system files
+Thumbs.db
+desktop.ini
+

.github/workflows/docker-image.yml

@@ -0,0 +1,32 @@
+name: Build and Push Docker Image
+
+on:
+  push:
+    branches:
+      - main  # Push to dockerhub when a new version is merged to `main`
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Check Out Code
+      uses: actions/checkout@v3
+
+    - name: Extract Package Version
+      # run: echo "PACKAGE_VERSION=$(python -c 'from jointly_hic import __version__; print(__version__)')" >> $GITHUB_ENV
+      run: echo 2.0.0
+
+    - name: Log in to Docker Hub
+      uses: docker/login-action@v1
+      with:
+        username: ${{ secrets.DOCKERHUB_USERNAME }}
+        password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+    - name: Build and Push Docker Image
+      uses: docker/build-push-action@v2
+      with:
+        context: .
+        file: Dockerfile
+        push: true
+        tags: treimonn/ldsc-python3:latest, treimonn/ldsc-python3:${{ env.PACKAGE_VERSION }}

.github/workflows/python-package.yml

@@ -0,0 +1,52 @@
+# This workflow will install Python dependencies using Poetry, run tests, and lint with multiple Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python Package CI
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11"]
+
+    steps:
+    - name: Check out code
+      uses: actions/checkout@v3
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install Poetry
+      run: |
+        python -m pip install --upgrade pip
+        pip install poetry
+
+    - name: Install dependencies with Poetry
+      run: |
+        poetry install --no-interaction --no-root
+
+    - name: Lint with flake8 and black
+      run: |
+        # poetry run flake8 --max-line-length 120 ldscore test
+        poetry run black --check ldscore test
+
+    - name: Run tests with nose2
+      run: |
+        poetry run nose2
+
+    - name: Run type checks with mypy
+      run: |
+        # poetry run mypy ldscore
+
+

.gitignore

@@ -46,7 +46,6 @@ coverage.xml
 .ropeproject
 
 # Django stuff:
-*.log
 *.pot
 
 # Sphinx documentation
@@ -84,3 +83,6 @@ docs/_build/
 # sublime text
 *.idea*
 *sublime*
+
+# Env
+.venv/

.pre-commit-config.yaml

@@ -0,0 +1,16 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 24.10.0
+    hooks:
+      - id: black
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+
+#  - repo: https://github.com/pre-commit/mirrors-mypy
+#    rev: v1.13.0
+#    hooks:
+#      - id: mypy
+

Dockerfile

@@ -0,0 +1,46 @@
+# --------------------- Stage 1: Build the wheel ---------------------
+# Use the official Ubuntu 23.04 as the base image for the builder
+FROM ubuntu:23.04 AS builder
+
+# Set environment variables
+ENV PYTHONUNBUFFERED=1 \
+    POETRY_VIRTUALENVS_CREATE=false \
+    POETRY_NO_INTERACTION=1
+
+# Update and install system dependencies for building
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    build-essential \
+    curl \
+    python3.11 \
+    python3.11-venv \
+    python3.11-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# Ensure python3 and pip3 are the default
+RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.11 1
+RUN update-alternatives --install /usr/bin/python python /usr/bin/python3.11 10
+
+# Install Poetry
+RUN curl -sSL https://install.python-poetry.org | python3 -
+
+# Add Poetry to PATH
+ENV PATH="/root/.local/bin:$PATH"
+
+# Set the working directory inside the container
+WORKDIR /app
+
+# Copy pyproject.toml and poetry.lock if available
+COPY pyproject.toml poetry.lock* /app/
+
+# Install project dependencies without installing the package itself
+RUN poetry install --only main
+
+# Copy the rest of the project files
+COPY . /app
+
+# Install the package
+RUN poetry install
+
+# Set the entrypoint to ldsc
+ENTRYPOINT ["poetry", "run"]