Adds support for pypoetry (https://python-poetry.org) (#222)

* introduces python poetry to maintain and build the package

* allows building wheels for PyPI  (fixes #212) 

* uses `pyproject.toml` instead of `setup.py` and thus fixes  #143 and fixes #137 

* sets up Github Actions for general testing (replaces Travis)

* bumps version to 1.0.0-beta

Co-authored-by: Konstantin (Tino) Sering <[email protected]>

Author: Trybnetic

.github/workflows/python-test.yml

@@ -0,0 +1,72 @@
+name: Linux & OSX tests
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  build:
+    name: ${{ matrix.os }} ${{ matrix.python-version }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macOS-latest]
+        python-version: ['3.8', '3.10']
+        poetry-version: [1.1.13]
+      fail-fast: false
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Get full Python version
+        id: full-python-version
+        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+
+      - name: Setup poetry
+        uses: abatilo/[email protected]
+        with:
+          poetry-version: ${{ matrix.poetry-version }}
+
+      - name: Update PATH
+        if: ${{ runner.os != 'Windows' }}
+        run: echo "$HOME/.local/bin" >> $GITHUB_PATH
+
+      - name: Update Path for Windows
+        if: ${{ runner.os == 'Windows' }}
+        run: echo "$APPDATA\Python\Scripts" >> $GITHUB_PATH
+
+      - name: Configure poetry
+        run: poetry config virtualenvs.in-project true
+
+      - name: Set up cache
+        uses: actions/cache@v2
+        id: cache
+        with:
+          path: .venv
+          key: venv-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }}
+
+      - name: Install dependencies
+        run: poetry install
+
+      - name: Run linux tests
+        if: ${{ runner.os == 'Linux' }}
+        run: poetry run pytest --cov=pyndl --cov-report=xml --disable-pytest-warnings
+
+      - name: Run tests on other distributions (skip linux-only tests)
+        if: ${{ runner.os != 'Linux' }}
+        run: poetry run pytest --no-linux
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v2
+        with:
+          file: ./coverage.xml
+          flags: unittests
+          env_vars: OS,PYTHON

.gitignore

@@ -3,6 +3,7 @@ pyndl/ndl_parallel.c
 pyndl/ndl_openmp.c
 pyndl/corr_parallel.c
 pyndl/wh_parallel.c
+pyndl/correlation_openmp.c
 latex/
 *.pyc
 __pycache__/
@@ -28,4 +29,7 @@ doc/data/levent.tab.filtered
 doc/data/weights.nc
 
 # copybutton js script
-doc/source/_static/copybutton.js
+copybutton.js
+
+# pypoetry
+poetry.lock

.readthedocs.yml

@@ -1,5 +1,25 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: doc/source/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+formats: all
+
+# Optionally declare the Python requirements required to build your docs
 python:
-   setup_py_install: true
-   pip_install: true
-   extra_requirements:
-        - docs
+   install:
+     - path: .
+     - requirements: doc/requirements.txt

.travis.yml

@@ -2,11 +2,11 @@
 Pyndl - Naive Discriminative Learning in Python
 ===============================================
 
-.. image:: https://travis-ci.com/quantling/pyndl.svg?branch=master
-    :target: https://travis-ci.com/quantling/pyndl
+.. image:: https://github.com/quantling/pyndl/actions/workflows/python-test.yml/badge.svg?branch=master
+    :target: https://github.com/quantling/pyndl/actions/workflows/python-test.yml
 
-.. image:: https://coveralls.io/repos/github/quantling/pyndl/badge.svg?branch=master
-    :target: https://coveralls.io/github/quantling/pyndl?branch=master
+.. image:: https://codecov.io/gh/quantling/pyndl/branch/master/graph/badge.svg?token=2GWUXRA9PD
+    :target: https://codecov.io/gh/quantling/pyndl
 
 .. image:: https://img.shields.io/lgtm/grade/python/g/quantling/pyndl.svg?logo=lgtm&logoWidth=18
     :target: https://lgtm.com/projects/g/quantling/pyndl/context:python
@@ -87,4 +87,3 @@ Acknowledgments
 This research was supported by an ERC advanced Grant (no. 742545) and by the
 Alexander von Humboldt Professorship awarded to R. H. Baayen and by the
 University of Tübingen.
-

MANIFEST.in

@@ -1,4 +1,4 @@
-from setuptools import setup, Extension
+from setuptools import Extension
 from setuptools.command.build_ext import build_ext as _build_ext
 import sys
 
@@ -9,27 +9,11 @@ class build_ext(_build_ext):
     def finalize_options(self):
         _build_ext.finalize_options(self)
         # Prevent numpy from thinking it is still in its setup process:
-        __builtins__.__NUMPY_SETUP__ = False
+        #__builtins__.__NUMPY_SETUP__ = False
         import numpy
         self.include_dirs.append(numpy.get_include())
 
 
-pkg = __import__('pyndl')
-
-author =  pkg.__author__
-email = pkg.__author_email__
-
-version = pkg.__version__
-classifiers = pkg.__classifiers__
-
-description = pkg.__description__
-
-def load_requirements(fn):
-    """Read a requirements file and create a list that can be used in setup."""
-    with open(fn, 'r') as f:
-        return [x.rstrip() for x in list(f) if x and not x.startswith('#')]
-
-
 ndl_parallel = Extension("pyndl.ndl_parallel", ["pyndl/ndl_parallel.pyx"])
 ndl_openmp = Extension("pyndl.ndl_openmp", ["pyndl/ndl_openmp.pyx"],
                        extra_compile_args=['-fopenmp'], extra_link_args=['-fopenmp'])
@@ -46,30 +30,14 @@ def load_requirements(fn):
 elif sys.platform.startswith('darwin'):
     ext_modules = [ndl_parallel]  # skip openmp installation on macos for now
 
-setup(
-    name='pyndl',
-    version=version,
-    license='MIT',
-    description=description,
-    long_description=open('README.rst', encoding="utf-8").read(),
-    author=author,
-    author_email=email,
-    url='https://github.com/quantling/pyndl',
-    classifiers=classifiers,
-    platforms='Linux',
-    packages=['pyndl'],
-    setup_requires=['numpy', 'cython'],
-    install_requires=load_requirements('requirements.txt'),
-    extras_require={
-        'tests': [
-            'pylint',
-            'pytest',
-            'pycodestyle'],
-        'docs': [
-            'sphinx >= 1.4',
-            'sphinx_rtd_theme',
-            'numpydoc',
-            'easydev']},
-    ext_modules=ext_modules,
-    cmdclass={'build_ext': build_ext}
-)
+
+def build(setup_kwargs):
+    """
+    This function is mandatory in order to build the extensions.
+    """
+    setup_kwargs.update({
+        'ext_modules': ext_modules,
+        'cmdclass': {
+            'build_ext': build_ext
+        }
+    })

Makefile

@@ -0,0 +1,7 @@
+sphinx>=1.4
+sphinx_rtd_theme>=1.0.0
+notebook>=6.4.10
+seaborn>=0.11.2
+numpydoc>=1.2
+easydev>=0.9.35
+nbsphinx>=0.8.8

README.rst

@@ -7,8 +7,9 @@ Authors
 *pyndl* was mainly developed by
 `Konstantin Sering <https://github.com/derNarr>`_,
 `Marc Weitz <https://github.com/trybnetic>`_,
-`David-Elias Künstle <https://github.com/dekuenstle/>`_
-and `Lennart Schneider <https://github.com/sumny>`_. For the full list of
+`David-Elias Künstle <https://github.com/dekuenstle/>`_,
+`Lennart Schneider <https://github.com/sumny>`_ and
+`Elnaz Shafaei-Bajestan <https://github.com/elnazsh>`_. For the full list of
 contributors have a look at `Github's Contributor summary
 <https://github.com/quantling/pyndl/contributors>`_.