Merge pull request #236 from databio/dev

Release 0.15.0

Author: nsheff

.github/workflows/black.yml

@@ -8,4 +8,8 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
-      - uses: psf/black@stable
+        with:
+          python-version: "3.12"
+      - run: pip install ruff
+      - run: ruff check .
+      - run: ruff format --check .

.github/workflows/python-publish.yml

@@ -22,10 +22,9 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        pip install build
     - name: Build and publish
       run: |
-        python setup.py sdist bdist_wheel
+        python -m build
     - name: Publish package distributions to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
-

.github/workflows/run-pytest.yml

@@ -5,13 +5,13 @@ on:
     branches: [master, dev]
   workflow_dispatch:
     inputs: null
-    
+
 jobs:
   pytest:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.13"]
+        python-version: ["3.10", "3.14"]
         os: [ubuntu-latest]
 
     steps:
@@ -22,14 +22,8 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install dev dependencies
-        run: if [ -f requirements/requirements-dev.txt ]; then pip install -r requirements/requirements-dev.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 -x -vv --remote-data

.gitignore

@@ -89,3 +89,7 @@ piper.egg-info/
 
 
 example_pipelines/pipeline_output
+
+# Test output folders
+tests/Data/pipeline_output/
+tests/Data/pipeline_output3/

.travis.yml

@@ -2,10 +2,7 @@
 
 # Pypiper
 
-[![Documentation Status](https://readthedocs.org/projects/pypiper/badge/?version=latest)](http://pypiper.readthedocs.org/en/latest/?badge=latest)
 [![Build Status](https://github.com/databio/pypiper/actions/workflows/run-pytest.yml/badge.svg)](https://github.com/databio/pypiper/actions/workflows/run-pytest.yml)
-[![PEP compatible](https://pepkit.github.io/img/PEP-compatible-green.svg)](http://pepkit.github.io)
 [![pypi-badge](https://img.shields.io/pypi/v/piper)](https://pypi.org/project/piper)
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
-A lightweight python toolkit for gluing together restartable, robust shell pipelines. Learn more in the [documentation](http://pypiper.databio.org).
+A lightweight Python toolkit for gluing together restartable, robust shell pipelines. Pypiper manages shell command execution with automatic restartability, file integrity protection, resource monitoring, and detailed logging -- useful for any multi-step workflow that calls command-line tools. Learn more in the [documentation](https://pep.databio.org/pypiper/).