Merge pull request #7 from GeoStat-Framework/modernize_packaging

Packaging: pep517/518 conform workflow with pyproject.toml

.github/workflows/main.yml

@@ -18,14 +18,40 @@ env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
+  source_check:
+    name: source check
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python 3.8
+        uses: actions\setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install black #pylint
+          pip install --editable .
+      - name: black check
+        run: |
+          python -m black --check .
+      # - name: pylint check
+      #   run: |
+      #     python -m pylint anaflow/
+
   build_sdist:
     name: sdist on ${{ matrix.os }} with py ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: [3.5, 3.6, 3.7, 3.8, 3.9]
+        python-version: [3.6, 3.7, 3.8, 3.9]
 
     steps:
       - uses: actions/checkout@v2
@@ -40,21 +66,18 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -U wheel
-          pip install -r requirements_setup.txt
-          pip install -r requirements.txt
-          pip install -r requirements_test.txt
-          pip install coveralls>=3.0.0
-
-      - name: Build sdist
-        run: |
-          python setup.py sdist --formats=gztar bdist_wheel -d dist
+          pip install build coveralls>=3.0.0
+          pip install --editable .[test]
 
       - name: Run tests
         run: |
           python -m pytest --cov anaflow --cov-report term-missing -v tests/
           python -m coveralls --service=github
 
+      - name: Build sdist
+        run: |
+          python -m build
+
       - uses: actions/upload-artifact@v2
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.9'
         with:
@@ -73,7 +96,7 @@ jobs:
       - name: Publish to Test PyPI
         # only if working on develop
         if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop'
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.test_pypi_password }}
@@ -83,7 +106,7 @@ jobs:
       - name: Publish to PyPI
         # only if tagged
         if: startsWith(github.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.pypi_password }}

.readthedocs.yml

@@ -0,0 +1,14 @@
+version: 2
+
+sphinx:
+  configuration: docs/source/conf.py
+
+formats: all
+
+python:
+  version: 3.7
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc

MANIFEST.in

@@ -1,9 +1,6 @@
-include README.md
-include MANIFEST.in
-include setup.py
-include setup.cfg
-recursive-include anaflow *.py
-recursive-include tests *.py
-recursive-include docs/source *
-include docs/Makefile docs/requirements.txt
-include LICENSE
+prune *
+graft anaflow
+graft tests
+
+include LICENSE README.md pyproject.toml setup.cfg
+global-exclude __pycache__ *.py[cod] .*

anaflow/flow/ext_grf_model.py

@@ -123,7 +123,7 @@ def ext_grf_steady(
     rate=-1e-4,
     h_ref=0.0,
     arg_dict=None,
-    **kwargs
+    **kwargs,
 ):
     """
     The extended "General radial flow" model for steady flow.

anaflow/tools/mean.py

@@ -192,7 +192,7 @@ def annular_amean(func, val_arr, ann_dim=2, arg_dict=None, **kwargs):
         f_inv=lambda x: x,
         ann_dim=ann_dim,
         arg_dict=arg_dict,
-        **kwargs
+        **kwargs,
     )
 
 
@@ -260,7 +260,7 @@ def annular_gmean(func, val_arr, ann_dim=2, arg_dict=None, **kwargs):
         f_inv=np.exp,
         ann_dim=ann_dim,
         arg_dict=arg_dict,
-        **kwargs
+        **kwargs,
     )
 
 
@@ -322,7 +322,7 @@ def annular_hmean(func, val_arr, ann_dim=2, arg_dict=None, **kwargs):
         f_inv=lambda x: 1.0 / x,
         ann_dim=ann_dim,
         arg_dict=arg_dict,
-        **kwargs
+        **kwargs,
     )
 
 
@@ -392,5 +392,5 @@ def annular_pmean(func, val_arr, p=2.0, ann_dim=2, arg_dict=None, **kwargs):
         f_inv=lambda x: np.power(x, 1.0 / p),
         ann_dim=ann_dim,
         arg_dict=arg_dict,
-        **kwargs
+        **kwargs,
     )

pyproject.toml

@@ -0,0 +1,65 @@
+[build-system]
+requires = [
+    "setuptools>=42",
+    "wheel",
+    "setuptools_scm[toml]>=3.5",
+]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+write_to = "anaflow/_version.py"
+write_to_template = "__version__ = '{version}'"
+local_scheme = "no-local-version"
+fallback_version = "0.0.0.dev0"
+
+[tool.black]
+exclude = """
+^/( ( examples ) /| anaflow/_version.py )
+"""
+line-length = 79
+target-version = [
+    "py36",
+    "py37",
+    "py38",
+]
+
+[tool.coverage]
+    [tool.coverage.run]
+    source = ["anaflow"]
+    omit = [
+        "*docs*",
+        "*examples*",
+        "*tests*",
+    ]
+
+    [tool.coverage.report]
+    exclude_lines = [
+        "pragma: no cover",
+        "if __name__ == '__main__':",
+        "def __repr__",
+        "def __str__",
+    ]
+
+[tool.pylint]
+    [tool.pylint.master]
+    extension-pkg-whitelist = [
+        "numpy",
+        "scipy",
+    ]
+    ignore = "_version.py"
+
+    [tool.pylint.message_control]
+    disable = [
+        "R0801",
+    ]
+
+    [tool.pylint.reports]
+    output-format = "colorized"
+
+    [tool.pylint.design]
+    max-args = 20
+    max-locals = 50
+    max-branches = 30
+    max-statements = 80
+    max-attributes = 25
+    max-public-methods = 75

setup.cfg

@@ -1,3 +1,67 @@
 [metadata]
-description-file = README.md
+name = anaflow
+description = AnaFlow - analytical solutions for the groundwater-flow equation.
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://github.com/GeoStat-Framework/AnaFlow
+author = Sebastian Mueller
+author_email = [email protected]
+maintainer = Sebastian Mueller
+maintainer_email = [email protected]
+license = MIT
 license_file = LICENSE
+platforms = any
+classifiers =
+    Development Status :: 5 - Production/Stable
+    Intended Audience :: Developers
+    Intended Audience :: End Users/Desktop
+    Intended Audience :: Science/Research
+    License :: OSI Approved :: MIT License
+    Natural Language :: English
+    Operating System :: MacOS
+    Operating System :: MacOS :: MacOS X
+    Operating System :: Microsoft
+    Operating System :: Microsoft :: Windows
+    Operating System :: POSIX
+    Operating System :: Unix
+    Programming Language :: Python
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3 :: Only
+    Programming Language :: Python :: 3.6
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Topic :: Scientific/Engineering
+    Topic :: Software Development
+    Topic :: Utilities
+project_urls =
+    Documentation = https://anaflow.readthedocs.io
+    Source = https://github.com/GeoStat-Framework/anaflow
+    Tracker = https://github.com/GeoStat-Framework/anaflow/issues
+    Changelog = https://github.com/GeoStat-Framework/anaflow/blob/develop/CHANGELOG.md
+    Conda-Forge = https://anaconda.org/conda-forge/anaflow
+
+[options]
+packages = find:
+install_requires =
+    numpy>=1.14.5,<2
+    pentapy>=1.1.0,<2
+    scipy>=1.1.0,<2
+python_requires = >=3.6
+zip_safe = False
+
+[options.packages.find]
+exclude =
+    tests*
+    docs*
+
+[options.extras_require]
+doc =
+    numpydoc>=1.1
+    sphinx>=3
+    sphinx-gallery>=0.8
+    sphinx-rtd-theme>=0.5
+test =
+    coverage[toml]>=5.2.1
+    pytest>=6.0
+    pytest-cov>=2.11.0