Merge pull request #19 from js2264/PEP621_compliant

.dockerignore

@@ -1,11 +1,9 @@
 *
 Dockerfile*
 .dockerignore
-!metator/*
-!setup.py
-!setup.cfg
+!src/*
+!external/*
 !metator.yaml
-!requirements.txt
+!pyproject.toml
 !MANIFEST.in
 !README.md
-!external

.github/workflows/ci.yml

@@ -0,0 +1,51 @@
+name: Test and Doc
+
+on:
+  push:
+  pull_request:
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+permissions:
+  contents: write
+
+jobs:
+  Test:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [ "3.9", "3.10", "3.11" ]
+        include:
+          - os: ubuntu-latest
+          # - os: windows-latest
+          # - os: macos-latest
+    runs-on: ${{ matrix.os }}
+
+    steps:
+
+      - uses: actions/checkout@v4
+
+      - name: 🛠️ Install Python ${{ matrix.python-version }} and deps with micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+            environment-file: metator.yaml
+            init-shell: bash
+            cache-environment: false
+            post-cleanup: 'none'
+            generate-run-shell: true
+            create-args: >-
+              python=${{ matrix.python-version }}
+
+      - name: 📦 Install package
+        run: |
+          pip install .[test]
+        shell: micromamba-shell {0}
+
+      - name: 🧪 Run tests with Python ${{ matrix.python-version }} 
+        run: |
+          ruff check . --select=E9,F63,F7,F82
+          pytest --cov --cov-report=xml
+        shell: micromamba-shell {0}

.github/workflows/pypi-publish.yml

@@ -5,29 +5,29 @@ name: Upload Python Package on PyPI
 on:
   release:
     types: [created]
-    branches: [master]
 
 jobs:
   deploy:
 
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.10'
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        pip install hatch
         
     - name: Build and publish
       env:
         TWINE_USERNAME: __token__
         TWINE_PASSWORD: ${{secrets.PYPI_TOKEN}}
       run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+        hatch build
+        twine upload dist/*

.gitignore

@@ -35,6 +35,7 @@ wheels/
 .installed.cfg
 *.egg
 MANIFEST
+metator.code-workspace
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -133,6 +134,9 @@ venv.bak/
 dmypy.json
 nf-metator.sif
 
-# Louvain and Leiden installation
-external/gen-louvain/
-networkanalysis
+# Artifacts installation
+artifacts/
+gen-louvain/
+networkanalysis/
+pairix/
+bowtie2/

.pre-commit-config.yaml

@@ -0,0 +1,16 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.3.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+        args: ['--config=./pyproject.toml']
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.6.9
+    hooks:
+      - id: ruff

CHANGELOG.md

@@ -3,6 +3,13 @@
 
 All notable changes to this project will be documented in this file.
 
+## [1.3.4] - 2025-02-19
+- Package now relies on `pyproject.toml` for build configuration with `hatch`. 
+- Binaries for `louvain` and `leiden` clustering algorithms are now embedded in the package.
+- Uses pre-commit hooks for code formatting and linting.
+- Fix deprecated Bio.SeqUtils.GC to Bio.SeqUtils.gc_fraction.
+- `Biopython` is pinned <= 1.80 to work with `micomplete 1.1.1`.
+
 ## [1.3.3] - 2023-11-27
 - Improve ci.
 - Add pairix as requirements.

Dockerfile

@@ -1,39 +1,21 @@
-# syntax=docker/dockerfile:1
-
 FROM mambaorg/micromamba:latest
 
-LABEL Name=metator Version=1.3.3
+LABEL Name=metator Version=1.3.4
 
 COPY --chown=$MAMBA_USER:$MAMBA_USER . ./
 
 # Install 3rd party packages
 USER root
 RUN apt update && \
-    apt install -y --no-install-recommends git make g++ curl default-jre default-jdk zlib1g-dev
-
-# Install Louvain 
-RUN cd ./external && \
-    tar -xzf louvain-generic.tar.gz && \
-    cd gen-louvain && \
-    make && \
-    cd ../
-ENV LOUVAIN_PATH=./external/gen-louvain
-
-# Install Leiden through Network analysis repo
-RUN git clone https://github.com/vtraag/networkanalysis.git && \
-    cd ./networkanalysis && \
-    ./gradlew build && \
-    cd ../
-ENV LEIDEN_PATH=$(pwd)/networkanalysis/build/libs/networkanalysis-1.2.0.jar
+    apt install -y --no-install-recommends git make g++ curl default-jre default-jdk zlib1g-dev unzip
 
-## Install dependencies
+# ## Install dependencies
 USER mambauser
 RUN micromamba install -y -n base --file metator.yaml && \
-    micromamba install -y -n base pip && \
     micromamba clean --all --yes
 
 # Install metator
-RUN micromamba run -n base python3 -m pip install -e .
+RUN micromamba run -n base pip install -e .[dev]
 
 WORKDIR /home/mambauser/
 ENTRYPOINT [ "/bin/bash" ]

MANIFEST.in

@@ -1,4 +1,4 @@
-include requirements.txt
 include README.md
+include external/artifacts/*
 recursive-exclude test_data *
 recursive-exclude tests *