Add basic package structure

.coveragerc

@@ -0,0 +1,14 @@
+[run]
+cover_pylib = false
+omit =
+    */site-packages/*
+    */tests/*
+
+[report]
+exclude_lines =
+    pragma: no cover
+    def __repr__
+    RuntimeError
+    NotImplementedError
+    FileNotFoundError
+    ImportError

.flake8

@@ -0,0 +1,5 @@
+[flake8]
+max-line-length = 127
+exclude = .git,__pycache__,doc/,docs/,build/,dist/,archive/
+per-file-ignores =
+  __init__.py:F401

.github/workflows/python-package.yml

@@ -23,20 +23,19 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+    - name: Install package with dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 pytest pytest-cov
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install -e .[bridge, tests, docs]
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        flake8 . --count --exit-zero --max-complexity=10 --statistics
     - name: Test with pytest and measure coverage
       run: |
-        pytest --cov=./ --cov-report=xml
+        pytest --cov --cov-report=xml
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v1
       with:

.mypy.ini

@@ -0,0 +1,6 @@
+[mypy]
+ignore_missing_imports = True
+strict_optional = False
+allow_redefinition = True
+show_error_context = False
+show_column_numbers = True

ordcomp/__init__.py

@@ -0,0 +1,3 @@
+from ._version import __version__
+
+__all__ = ['__version__']

ordcomp/_version.py

@@ -0,0 +1 @@
+__version__ = "0.0.0"

pyproject.toml

@@ -0,0 +1,5 @@
+[build-system]
+requires = ["setuptools", "wheel"]
+
+[tool.pytest.ini_options]
+addopts = "--doctest-modules -ra -v"

setup.cfg

@@ -0,0 +1,51 @@
+# Static configuration of the distribution package, as defined by setuptools
+[metadata]
+name = ordcomp
+description = Machine Learning Toolkit for Ordinal Comparison in Python.
+long_description = file: README.md, LICENSE
+author = 'David-Elias Künstle'
+author_email = 'david-elias dot kuenstle at uni-tuebingen dot de'
+url = 'https://github.com/dekuenstle/ordcomp'
+classifierts =
+    Development Status :: 1 - Planning
+    Environment :: GPU :: NVIDIA CUDA
+    Intended Audience :: Science/Research
+    Intended Audience :: Developers
+    License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)
+    Programming Language :: Python
+    Topic :: Software Development
+    Topic :: Scientific/Engineering
+    Operating System :: Microsoft :: Windows
+    Operating System :: POSIX
+    Operating System :: Unix
+    Operating System :: MacOS
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Typing :: Typed
+description-file = README.md
+license_files = LICENSE
+
+[options]
+python_requires = >=3.7
+packages = find:
+zip_safe = False
+install_requires =
+    numpy
+    scipy
+    scikit-learn
+
+[options.extras_require]
+bridge =
+    rpy2
+    oct2py
+tests =
+    pytest
+    pytest-cov
+    flake8
+    mypy
+docs =
+    sphinx
+    sphinx-gallery
+    sphinx_rtd_theme
+    numpydoc
+    matplotlib

setup.py

@@ -0,0 +1,13 @@
+#! /usr/bin/env python
+""" Dynamic configuration of distribution package. """
+
+import os
+
+from setuptools import find_packages, setup
+
+# get __version__ from _version.py
+ver_file = os.path.join('ordcomp', '_version.py')
+with open(ver_file) as f:
+    exec(f.read())
+
+setup(version=__version__)