Modernize stages 1-3

.github/workflows/black.yml

@@ -1,13 +1,15 @@
 name: Lint
 
-on:
-  pull_request:
-    branches: [ main ]
+on: [push, pull_request]
 
 jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-      - uses: psf/black@stable
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+      - run: pip install ruff
+      - run: ruff check .
+      - run: ruff format --check .

.github/workflows/cli-coverage.yml

@@ -6,23 +6,16 @@ on:
 
 jobs:
   cli-coverage-report:
-    strategy:
-      matrix:
-        python-version: [ "3.12" ]
-        os: [ ubuntu-latest ]
-        r: [ release ]
-    runs-on: ${{ matrix.os }}
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
-          python-version: '3.12'
+          python-version: "3.13"
 
-      - name: Install test dependencies
-        run: if [ -f requirements/requirements-test.txt ]; then pip install -r requirements/requirements-test.txt; fi
-
-      - run: pip install .
+      - name: Install package with test dependencies
+        run: pip install ".[test]"
 
       - name: Run tests
         run: coverage run -m pytest
@@ -37,4 +30,4 @@ jobs:
           SMOKESHOW_GITHUB_CONTEXT: coverage
           SMOKESHOW_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           SMOKESHOW_GITHUB_PR_HEAD_SHA: ${{ github.event.pull_request.head.sha }}
-          SMOKESHOW_AUTH_KEY: ${{ secrets.SMOKESHOW_AUTH_KEY }}
+          SMOKESHOW_AUTH_KEY: ${{ secrets.SMOKESHOW_AUTH_KEY }}

.github/workflows/pytest-windows.yml

@@ -11,25 +11,19 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.11"]
+        python-version: ["3.13"]
         os: [windows-latest]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v6
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install all dependencies
-      run: pip install -r requirements/requirements-all.txt
-
-    - name: Install test dependencies
-      run: pip install -r requirements/requirements-test.txt
-
-    - name: Install package
-      run: python -m pip install .
+    - name: Install package with test dependencies
+      run: python -m pip install ".[test]"
 
     - name: Run pytest tests
-      run: pytest tests -v
+      run: pytest tests -v

.github/workflows/pytest.yml

@@ -11,25 +11,19 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.9", "3.13"]
+        python-version: ["3.10", "3.13"]
         os: [ubuntu-latest]
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install all dependencies
-      run: if [ -f requirements/requirements-all.txt ]; then pip install -r requirements/requirements-all.txt; fi
-
-    - name: Install test dependencies
-      run: if [ -f requirements/requirements-test.txt ]; then pip install -r requirements/requirements-test.txt; fi
-
-    - name: Install package
-      run: python -m pip install .
+    - name: Install package with test dependencies
+      run: python -m pip install ".[test]"
 
     - name: Run pytest tests
       run: pytest tests -v

.github/workflows/python-publish.yml

@@ -6,22 +6,21 @@ on:
 
 jobs:
   deploy:
-    name: upload release to PyPI
     runs-on: ubuntu-latest
+    name: upload release to PyPI
     permissions:
+      contents: read
       id-token: write
+
     steps:
     - uses: actions/checkout@v6
     - name: Set up Python
       uses: actions/setup-python@v6
       with:
         python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-    - name: Build and publish
-      run: |
-        python setup.py sdist bdist_wheel
+    - name: Install build dependencies
+      run: python -m pip install --upgrade pip build
+    - name: Build package
+      run: python -m build
     - name: Publish package distributions to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
+      uses: pypa/gh-action-pypi-publish@release/v1

peppy/__init__.py

@@ -7,12 +7,15 @@
 
 """
 
-from ._version import __version__
+from importlib.metadata import version
+
 from .const import *
 from .exceptions import *
 from .project import Project
 from .sample import Sample
 
+__version__ = version("peppy")
+
 __classes__ = ["Project", "Sample"]
 __all__ = __classes__ + ["PeppyError", "__version__"]
 

peppy/cli.py

@@ -1,14 +1,15 @@
+from importlib.metadata import version
+
 import typer
 
-from ._version import __version__
 from .const import PKG_NAME
 from .eido.cli import app as eido_app
 from .pephubclient.cli import app as phc_app
 
 
 def version_callback(value: bool):
     if value:
-        typer.echo(f"{PKG_NAME} version: {__version__}")
+        typer.echo(f"{PKG_NAME} version: {version(PKG_NAME)}")
         raise typer.Exit()
 
 

peppy/eido/conversion.py

@@ -1,12 +1,8 @@
-import sys
-
-if sys.version_info < (3, 10):
-    from importlib_metadata import entry_points
-else:
-    from importlib.metadata import entry_points
+from importlib.metadata import entry_points
 
 import inspect
 import os
+import sys
 from logging import getLogger
 from typing import Callable, Dict, List, NoReturn, Optional
 

pyproject.toml

@@ -0,0 +1,78 @@
+[project]
+name = "peppy"
+version = "0.50.0a2"
+description = "A python-based project metadata manager for portable encapsulated projects"
+readme = "README.md"
+license = "BSD-2-Clause"
+requires-python = ">=3.10"
+authors = [
+    { name = "Michal Stolarczyk" },
+    { name = "Nathan Sheffield" },
+    { name = "Vince Reuter" },
+    { name = "Andre Rendeiro" },
+    { name = "Oleksandr Khoroshevskyi" },
+]
+keywords = ["project", "metadata", "bioinformatics", "sequencing", "ngs", "workflow"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "License :: OSI Approved :: BSD License",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dependencies = [
+    "pandas>=2.2.0",
+    "pyyaml>=6.0.0",
+    "rich>=10.3.0",
+    "ubiquerg>=0.6.2",
+    "numpy",
+    "logmuse>=0.2.8",
+    "jsonschema>=3.0.1",
+    "typer>=0.20.0",
+    "requests>=2.28.2",
+    "pydantic>2.5.0",
+    "coloredlogs>=15.0.1",
+]
+
+[project.urls]
+Homepage = "https://github.com/pepkit/peppy/"
+
+[project.scripts]
+peppy = "peppy.cli:main"
+
+[project.entry-points."pep.filters"]
+basic = "peppy.eido.conversion_plugins:basic_pep_filter"
+yaml = "peppy.eido.conversion_plugins:yaml_pep_filter"
+csv = "peppy.eido.conversion_plugins:csv_pep_filter"
+yaml-samples = "peppy.eido.conversion_plugins:yaml_samples_pep_filter"
+
+[project.optional-dependencies]
+test = [
+    "pytest",
+    "pytest-cov",
+    "pytest-remotedata",
+    "pytest-mock",
+    "python-dotenv",
+    "coverage",
+    "smokeshow",
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.pytest.ini_options]
+addopts = "-rfE"
+testpaths = ["tests"]
+
+[tool.ruff]
+line-length = 88
+
+[tool.ruff.lint]
+select = ["E", "F", "I"]
+ignore = ["F403", "F405", "E501"]
+
+[tool.ruff.lint.isort]
+known-first-party = ["peppy"]