Merge pull request #19 from GeoStat-Framework/refactor_2023

Refactor 2023

.git_archival.txt

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

.gitattributes

@@ -0,0 +1 @@
+.git_archival.txt  export-subst

.github/workflows/main.yml

@@ -16,50 +16,56 @@ 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
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install black 'pylint<3'
-          pip install --editable .
+          pip install --editable .[check]
 
       - name: black check
         run: |
           python -m black --check --diff --color .
 
+      - name: isort check
+        run: |
+          python -m isort --check --diff --color .
+
       - name: pylint check
         run: |
-          python -m pylint pentapy/
+          python -m pylint src/pentapy/
 
   build_wheels:
-    name: wheels on ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
+    name: wheels for ${{ matrix.cfg.os }} / ${{ matrix.cfg.arch }}
+    runs-on: ${{ matrix.cfg.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
+        cfg:
+        - { os: ubuntu-latest, arch: x86_64 }
+        - { os: ubuntu-latest, arch: i686 }
+        - { os: windows-latest, arch: AMD64 }
+        - { os: windows-latest, arch: x86 }
+        - { os: macos-latest, arch: x86_64 }
+        - { os: macos-latest, arch: arm64 }
+        - { os: macos-latest, arch: universal2 }
 
     steps:
       - uses: actions/checkout@v2
         with:
           fetch-depth: '0'
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v1.11.1.post1
+        uses: pypa/cibuildwheel@v2.12.1
         env:
-          CIBW_BUILD: cp36-* cp37-* cp38-* cp39-*
-          CIBW_TEST_EXTRAS: test
-          CIBW_TEST_COMMAND: pytest -v {project}/tests
+          CIBW_ARCHS: ${{ matrix.cfg.arch }}
         with:
           output-dir: dist
 
@@ -82,7 +88,7 @@ jobs:
           fetch-depth: '0'
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions\setup-python@v2
+        uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
 

.gitignore

@@ -87,9 +87,10 @@ celerybeat-schedule
 venv/
 ENV/
 
-# Spyder project settings
+# IDE project settings
 .spyderproject
 .spyproject
+.vscode
 
 # Rope project settings
 .ropeproject
@@ -113,4 +114,8 @@ info/
 paper/compile
 
 # setuptools_scm generated version files
-pentapy/_version.py
+src/pentapy/_version.py
+
+# generated docs
+docs/source/examples/
+docs/source/api/

CHANGELOG.md

@@ -3,6 +3,25 @@
 All notable changes to **pentapy** will be documented in this file.
 
 
+## [1.2.0] - 2023-04
+
+See [#19](https://github.com/GeoStat-Framework/pentapy/pull/19)
+
+### Enhancements
+- added support for python 3.10 and 3.11
+- add wheels for arm64 systems
+- created `solver.pxd` file to be able to cimport the solver module
+- added a `CITATION.bib` file
+
+### Changes
+- move to `src/` based package structure
+- dropped python 3.7 support
+- move meta-data to pyproject.toml
+- simplified documentation
+
+### Bugfixes
+- determine correct version when installing from archive
+
 ## [1.1.2] - 2021-07
 
 ### Changes
@@ -65,6 +84,7 @@ This is the first release of pentapy, a python toolbox for solving pentadiagonal
 The solver is implemented in cython, which makes it really fast.
 
 
+[1.2.0]: https://github.com/GeoStat-Framework/pentapy/compare/v1.1.2...v1.2.0
 [1.1.2]: https://github.com/GeoStat-Framework/pentapy/compare/v1.1.1...v1.1.2
 [1.1.1]: https://github.com/GeoStat-Framework/pentapy/compare/v1.1.0...v1.1.1
 [1.1.0]: https://github.com/GeoStat-Framework/pentapy/compare/v1.0.3...v1.1.0

CITATION.bib

@@ -0,0 +1,13 @@
+@Article{muller_pentapy_2019,
+AUTHOR = {M\"uller, Sebastian},
+TITLE = {pentapy: {A} {Python} toolbox for pentadiagonal linear systems},
+SHORTTITLE = {pentapy},
+JOURNAL = {Journal of Open Source Software},
+VOLUME = {4},
+YEAR = {2019},
+NUMBER = {42},
+PAGES = {1759},
+URL = {https://joss.theoj.org/papers/10.21105/joss.01759},
+DOI = {10.21105/joss.01759},
+ISSN = {2475-9066},
+}

LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2021 Sebastian Müller
+Copyright (c) 2023 Sebastian Müller
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

MANIFEST.in

@@ -1,7 +1,4 @@
-prune *
-graft tests
-recursive-include pentapy *.py *.pyx
-recursive-exclude pentapy *.c *.cpp
-include LICENSE README.md pyproject.toml setup.py setup.cfg
-exclude CHANGELOG.md CONTRIBUTING.md
-global-exclude __pycache__ *.py[cod] .*
+prune **
+recursive-include tests *.py
+recursive-include src/pentapy *.py *.pyx *.pxd
+include LICENSE README.md pyproject.toml setup.py

README.md

@@ -28,13 +28,7 @@ On Windows you can install [WinPython][winpy_link] to get Python and pip running
 
     pip install pentapy
 
-There are pre-built wheels for Linux, MacOS and Windows for most Python versions (2.7, 3.4-3.7).
-
-If your system is not supported and you want to have the Cython routines of
-pentapy installed, you have to provide a c-compiler and run:
-
-    pip install numpy cython
-    pip install pentapy
+There are pre-built wheels for Linux, MacOS and Windows for most Python versions.
 
 To get the scipy solvers running, you have to install scipy or you can use the
 following extra argument:
@@ -127,7 +121,7 @@ You can contact us via <[email protected]>.
 
 ## License
 
-[MIT][licence_link] © 2019 - 2021
+[MIT][licence_link] © 2019 - 2023
 
 [ref_link]: http://dx.doi.org/10.1155/2015/232456
 [pip_link]: https://pypi.org/project/pentapy

docs/source/_static/custom.css

@@ -0,0 +1,3 @@
+dl.py.property {
+    display: block !important;
+}

docs/source/_templates/autosummary/class.rst

@@ -0,0 +1,13 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :undoc-members:
+   :inherited-members:
+   :show-inheritance:
+
+.. raw:: latex
+
+    \clearpage

docs/source/_templates/autosummary/module.rst

@@ -0,0 +1,9 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ fullname }}
+
+.. automodule:: {{ fullname }}
+
+.. raw:: latex
+
+    \clearpage

docs/source/_templates/layout.html

@@ -1,21 +1,27 @@
 {% extends "!layout.html" %}
   {% block menu %}
-    <p class="link caption"><span class="link caption-text">Documentation</span></p>
-    {{ super() }}
-    <br />
-    <p class="link caption"><span class="link caption-text">pentapy Links</span></p>
-    <a href="https://github.com/GeoStat-Framework/pentapy">pentapy GitHub</a>
-    <a href="https://zenodo.org/record/2587215">pentapy Zenodo DOI</a>
-    <a href="https://pypi.org/project/pentapy/">pentapy PyPI</a>
-    <br />
-    <p class="link caption"><span class="link caption-text">GeoStat Framework</span></p>
-    <a href="https://geostat-framework.org">GeoStat Website</a>
-    <a href="https://github.com/GeoStat-Framework">GeoStat Github</a>
-    <a href="https://github.com/GeoStat-Examples">GeoStat Examples</a>
-    <a href="https://geostat-framework.readthedocs.io">GeoStat ReadTheDocs</a>
-    <a href="https://pypi.org/user/geostatframework/">GeoStat PyPI</a>
-    <br />
-    <br />
-    <a href="genindex.html">Index</a>
-    <a href="contents.html">Sitemap</a>
+  <p class="link caption"><span class="link caption-text">Documentation</span></p>
+  {{ super() }}
+  <br />
+  <p class="link caption"><span class="link caption-text">pentapy Links</span></p>
+  <ul>
+    <Li><a href="https://github.com/GeoStat-Framework/pentapy">pentapy GitHub</a></Li>
+    <a href="https://zenodo.org/record/2587215">pentapy Zenodo DOI</a></Li>
+    <a href="https://pypi.org/project/pentapy/">pentapy PyPI</a></Li>
+  </ul>
+  <br />
+  <p class="link caption"><span class="link caption-text">GeoStat Framework</span></p>
+  <ul>
+    <Li><a href="https://geostat-framework.org">GeoStat Website</a></Li>
+    <Li><a href="https://github.com/GeoStat-Framework">GeoStat Github</a></Li>
+    <Li><a href="https://github.com/GeoStat-Examples">GeoStat Examples</a></Li>
+    <Li><a href="https://geostat-framework.readthedocs.io">GeoStat ReadTheDocs</a></Li>
+    <Li><a href="https://pypi.org/user/geostatframework/">GeoStat PyPI</a></Li>
+  </ul>
+  <br />
+  <br />
+  <ul>
+    <Li><a href="{{ pathto('genindex') }}">Index</a></Li>
+    <Li><a href="{{ pathto(master_doc) }}">Sitemap</a></Li>
+  </ul>
   {% endblock %}

docs/source/package.rst → docs/source/api.rst

@@ -7,9 +7,3 @@ pentapy API
 .. raw:: latex
 
     \clearpage
-
-.. toctree::
-   :hidden:
-
-   core.rst
-   tools.rst

docs/source/conf.py

@@ -1,6 +1,3 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-#
 # GeoStatTools documentation build configuration file, created by
 # sphinx-quickstart on Fri Jan  5 14:20:43 2018.
 #
@@ -56,7 +53,7 @@ def setup(app):
     "sphinx.ext.doctest",
     "sphinx.ext.intersphinx",
     "sphinx.ext.coverage",
-    "sphinx.ext.imgmath",
+    "sphinx.ext.mathjax",
     "sphinx.ext.ifconfig",
     "sphinx.ext.viewcode",
     "sphinx.ext.autosummary",
@@ -77,7 +74,10 @@ def setup(app):
 # Notes in boxes
 napoleon_use_admonition_for_notes = True
 # Attributes like parameters
-# napoleon_use_ivar = True
+napoleon_use_ivar = True
+# keep "Other Parameters" section
+# https://github.com/sphinx-doc/sphinx/issues/10330
+napoleon_use_param = False
 # this is a nice class-doc layout
 numpydoc_show_class_members = True
 # class members have no separate file, so they are not in a toctree
@@ -118,7 +118,7 @@ def setup(app):
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -150,14 +150,18 @@ def setup(app):
     # Toc options
     "collapse_navigation": False,
     "sticky_navigation": True,
-    "navigation_depth": 4,
+    "navigation_depth": 6,
     "includehidden": True,
     "titles_only": False,
 }
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-# html_static_path = ['_static']
+html_static_path = ["_static"]
+
+# These paths are either relative to html_static_path
+# or fully qualified paths (eg. https://...)
+html_css_files = ["custom.css"]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -243,7 +247,6 @@ def setup(app):
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
-    "Python 3.6": ("https://docs.python.org/3.6", None),
     "Python": ("https://docs.python.org/", None),
     "NumPy": ("http://docs.scipy.org/doc/numpy/", None),
     "Sphinx": ("http://www.sphinx-doc.org/en/stable/", None),

docs/source/contents.rst

@@ -4,9 +4,9 @@ Contents
 
 .. toctree::
    :includehidden:
-   :maxdepth: 3
+   :maxdepth: 6
 
    index
    examples/index
-   package
+   api
    changelog

docs/source/index.rst

@@ -21,15 +21,7 @@ Python and pip running.
 
     pip install pentapy
 
-There are pre-built wheels for Linux, MacOS and Windows for most Python versions (2.7, 3.4-3.7).
-
-If your system is not supported and you want to have the Cython routines of
-pentapy installed, you have to provide a c-compiler and run:
-
-.. code-block:: none
-
-    pip install numpy cython
-    pip install pentapy
+There are pre-built wheels for Linux, MacOS and Windows for most Python versions.
 
 To get the scipy solvers running, you have to install scipy or you can use the
 extra argument: