Merge branch 'master' into jw/type-hint-commands-modules

.github/workflows/tests.yml → .github/workflows/ci.yml

@@ -1,53 +1,46 @@
-name: Run tests and upload coverage
-
-on: ["push", "pull_request"]
+# This workflow installs Gens and runs test suite
+name: CI
 
+on:
+  push:
+    branches: ["master"]
+  pull_request:
+    branches: ["master"]
 
 jobs:
-  test-python:
+  python-unit-tests:
     name: Coverage
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: ["3.11", "3.12"]
         mongodb-version: ["7"]
 
     steps:
-
-    # Check out Scout code
     - uses: actions/checkout@v4
-
     # Set up python
     - name: Set up Python ${{ matrix.python-version}}
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version}}
-
-    - name: Production Dependencies
+    - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
         pip install -e .
-        pip install pytest-cov
-        pip install coveralls
-    - name: Test with pytest & Coveralls
-      run: |
         pip install -r requirements-dev.txt
+    - name: Run unit-tests and coveralls
+      run: |
         pytest --cov=./
         coveralls
       env: 
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
 
-  test-js:
-
+  js-unit-tests:
     runs-on: ubuntu-latest
-
     strategy:
       matrix:
         node-version: [17.x]
-        # See supported Node.js release schedule at https://nodejs.org/en/about/releases/
-
     steps:
     - uses: actions/checkout@v4
     - name: Use Node.js ${{ matrix.node-version }}

CHANGELOG.md

@@ -4,6 +4,11 @@ This project adheres to [Semantic Versioning](http://semver.org/)
 
 About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
+## Unreleased
+
+### Changed
+ - Migrated from setup.py to pyproject.toml using hatchling
+ - Updated python to version 3.12 and thawed some dependencies.
 
 ## 3.0.1
 

Dockerfile

@@ -2,23 +2,26 @@
 # BUILDER PYTHON #
 ##################
 
-FROM python:3.8.1-slim AS python-builder
+FROM python:3.12 AS python-builder
 
 # Set build variables
 ENV PYTHONDONTWRITEBYTECODE=1
 ENV PYTHONUNBUFFERED=1
 
 WORKDIR /usr/src/app
-COPY MANIFEST.in setup.py setup.cfg requirements.txt ./
+
 COPY gens gens/
+COPY README.md LICENSE pyproject.toml ./
+
 RUN apt-get update &&                                                     \
     apt-get upgrade -y &&                                                 \
     apt-get install -y --no-install-recommends python3-pip                \
     python3-wheel &&                                                      \
     pip install --no-cache-dir --upgrade pip &&                           \
-    pip install --no-cache-dir gunicorn &&                                \
-    pip wheel --no-cache-dir --no-deps --wheel-dir /usr/src/app/wheels    \
-    --requirement requirements.txt
+    pip install --no-cache-dir hatch &&                                   \
+    hatch build -t wheel /usr/src/app/wheels
+    #pip wheel --no-cache-dir --no-deps --wheel-dir /usr/src/app/wheels  --requirement requirements.txt  \
+
 
 ################
 # BUILDER NODE #
@@ -34,37 +37,46 @@ RUN npm install && npm run build
 # FINAL #
 #########
 
-FROM python:3.8.1-slim
+FROM python:3.12-slim
 
-LABEL base_image="python:3.8.1-slim"
+LABEL base_image="python:3.12-slim"
 LABEL about.home="https://github.com/Clinical-Genomics-Lund/Gens"
 
 # Run commands as non-root user
-RUN useradd -m app && mkdir -p /home/app/app
-WORKDIR /home/app/app
+# Create non-root user to run Gens
+RUN groupadd --gid 1000 worker \
+    && useradd -g worker --uid 1000 --shell /user/sbin/nologin --create-home worker
 
-# Copy pyhon wheels and install software
+# Copy project to worker dir
+WORKDIR /home/worker
+
+# Copy pyhon wheels
 COPY --from=python-builder /usr/src/app/wheels /wheels
+
+# Install production dependencies
 RUN apt-get update &&                              \
     apt-get install -y ssh sshfs &&                \
     pip install --no-cache-dir --upgrade pip &&    \
     pip install --no-cache-dir /wheels/* &&        \
+    pip install --no-cache-dir gunicorn &&         \
     rm -rf /var/lib/apt/lists/* &&                 \
     rm -rf /wheels
 
 # Chown all the files to the app user
-COPY gens gens
-COPY utils utils
+COPY --chown=worker:worker gens ./gens
+COPY --chown=worker:worker utils ./utils
 
 # copy compiled web assetes
 COPY --from=node-builder /usr/src/app/build/css/error.min.css gens/static/css/
 COPY --from=node-builder /usr/src/app/build/css/home.min.css /usr/src/app/build/css/landing.min.css /usr/src/app/build/css/about.min.css gens/blueprints/home/static/
 COPY --from=node-builder /usr/src/app/build/*/gens.min.* gens/blueprints/gens/static/
 
 # make mountpoints and change ownership of app
-RUN mkdir -p /access /fs1/results /fs1/results_dev && chown -R app:app /home/app/app /access /fs1 /fs1/results_dev
-# Change the user to app
-USER app
+RUN mkdir -p /access /fs1/results /fs1/results_dev && \
+    chown -R worker:worker /access /fs1 /fs1/results_dev
+
+# Setup non-root user and variables
+USER worker
 
 ENV GUNICORN_WORKERS=1
 ENV GUNICORN_THREADS=1
@@ -76,11 +88,11 @@ CMD gunicorn \
     --bind=$GUNICORN_BIND  \
     --threads=$GUNICORN_THREADS \
     --timeout=$GUNICORN_TIMEOUT \
-    --chdir /home/app/app/ \
+    --chdir /home/worker/ \
     --proxy-protocol \
     --forwarded-allow-ips="10.0.2.100,127.0.0.1" \
     --log-syslog \
     --access-logfile - \
     --error-logfile - \
-    --log-level="debug" \
+    --log-level="warning" \
     gens.wsgi:app

Dockerfile.dev

@@ -16,7 +16,7 @@ RUN npm install && npm run build
 # FINAL #
 #########
 
-FROM python:3.8.1
+FROM python:3.12
 
 # Create non-root user to run Gens
 RUN groupadd --gid 1000 worker \
@@ -28,7 +28,7 @@ WORKDIR /home/worker
 # Chown all the files to the app user
 COPY --chown=worker:worker gens ./gens
 COPY --chown=worker:worker utils ./utils
-COPY --chown=worker:worker setup.cfg setup.py ./
+COPY --chown=worker:worker README.md LICENSE pyproject.toml ./
 
 # copy compiled web assetes
 COPY --chown=worker:worker --from=node-builder /usr/src/app/build/css/error.min.css gens/static/css/

pyproject.toml

@@ -0,0 +1,96 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "Gens"
+dynamic = ["version"]
+description = 'Visualise copy number profiles from WGS data'
+readme = "README.md"
+requires-python = ">=3.8"
+license = "MIT"
+keywords = ["WGS", "scout", "CNV", "cancer", "rare disease", "variant", "NGS", "browser"]
+authors = [
+  { name = "Markus Johansson", email = "[email protected]" },
+  { name = "Jakob Willforss", email = "[email protected]" },
+]
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3.8",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: Implementation :: CPython",
+  "Programming Language :: Python :: Implementation :: PyPy",
+]
+dependencies = [
+  "Click",
+  "Flask",
+  "flask-caching",
+  "flask_login",
+  "authlib",
+  "pymongo",
+  "gtfparse",
+  "pysam",
+  "pyyaml",
+  "attrs",
+  "cattrs",
+  "connexion==2.14.2",
+  "flask-compress",
+  "tabulate",
+]
+
+[project.urls]
+Documentation = "https://github.com/SMD-Bioinformatics-Lund/gens#readme"
+Issues = "https://github.com/SMD-Bioinformatics-Lund/gens/issues"
+Changelog = "https://github.com/SMD-Bioinformatics-Lund/gens/blob/master/CHANGELOG.md"
+
+[project.scripts]
+gens = "gens.commands:cli"
+
+[tool.hatch.version]
+path = "gens/__version__.py"
+
+[tool.hatch.build]
+include = [
+  "gens/templates/*.html",
+  "gens/static/**/*",
+  "gens/static/**/*",
+  "gens/blueprints/**/static/*",
+  "gens/openapi/openapi.yaml",
+]
+
+[tool.hatch.build.targets.wheel]
+packages = ["gens"]
+
+[tool.hatch.envs.types]
+extra-dependencies = [
+  "mypy>=1.0.0",
+]
+[tool.hatch.envs.types.scripts]
+check = "mypy --install-types --non-interactive {args:src/temporary tests}"
+
+[tool.coverage.run]
+source_pkgs = ["gens", "tests"]
+branch = true
+parallel = true
+omit = [
+  "gens/__version__.py",
+]
+
+[tool.coverage.paths]
+gens = ["gens",]
+tests = ["tests", "*/temporary/tests"]
+
+[tool.coverage.report]
+exclude_lines = [
+  "no cov",
+  "if __name__ == .__main__.:",
+  "if TYPE_CHECKING:",
+]
+
+[tool.isort]
+profile = "black"
+src_paths = ["gens"]

requirements-dev.txt

@@ -3,6 +3,7 @@ pytest
 pytest-cov
 pytest-flask
 pytest-mongodb
+coveralls
 
 # utils
 black