Modernize gh actions and pyproject

.github/dependabot.yml

@@ -0,0 +1,17 @@
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+# This configures updates via dependabot only for github actions.
+
+version: 2
+updates:
+- package-ecosystem: github-actions
+  directory: "/"
+  schedule:
+    interval: "monthly"
+  cooldown:
+    default-days: 5
+  groups:
+    github-actions:
+      patterns:
+        - "*"

.github/workflows/ci.yml

@@ -0,0 +1,57 @@
+name: Python package
+
+on:
+  push:
+    branches:
+    - master
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
+env:
+  PIP_DISABLE_PIP_VERSION_CHECK: "1"
+  PIP_PROGRESS_BAR: "off"
+
+permissions: {}
+
+jobs:
+  tests:
+    name: Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version:
+        - '3.9'
+        - '3.10'
+        - '3.11'
+        - '3.12'
+        - '3.13'
+        - '3.14'
+    steps:
+    - uses: actions/checkout@v6.0.1
+      with:
+        persist-credentials: false
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v6.1.0
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install package
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install .[dev]
+
+    - name: Run tests
+      run: |
+        python -m pytest
+
+    - name: Build Sphinx documentation
+      run: |
+        sphinx-build -b html --nitpicky --fail-on-warning --keep-going docs docs/_build/html

.github/workflows/pypi-publish.yml

@@ -0,0 +1,67 @@
+name: Publish Python Package
+# Publishes tO PyPI for releases created in GitHub UI
+# Note: For draft status, publishing is not triggered.
+# Builds a packages for new tags "v1.2.3" or "v1.2.3.something" on master
+
+on:
+  push:
+    tags:
+      # GitHub glob matching is limited [1]. So we can't define a pattern matching
+      # pep 440 version definition [N!]N(.N)*[{a|b|rc}N][.postN][.devN]
+      - 'v[0-9]+.[0-9]+.[0-9]+.?*'
+  release:
+    types: [published]
+
+permissions: {}
+
+jobs:
+  build:
+    name: Build Python 🐍 distributions 📦 for publishing
+    # Don't try to publish from forks
+    if: github.repository == 'NatLibFi/Skosify'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6.0.1
+        with:
+          persist-credentials: false
+
+      - name: Set up Python
+        uses: actions/setup-python@v6.1.0
+        with:
+          python-version: 3.13
+
+      - name: Install hatch
+        run: pipx install hatch
+
+      - name: Build source and wheel archives
+        run: hatch build
+
+      - name: Store built distribution
+        uses: actions/upload-artifact@v6.0.0
+        with:
+          name: distribution-files
+          path: dist/
+
+  pypi-publish:
+    name: Build and publish Python 🐍 package 📦 to PyPI and TestPyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi-release
+      url: https://pypi.org/p/skosify
+    permissions:
+      id-token: write  # this permission is mandatory for trusted publishing
+    steps:
+      - name: Download built distribution
+        uses: actions/download-artifact@v7.0.0
+        with:
+          name: distribution-files
+          path: dist
+
+      - name: Publish package 📦 to PyPI
+        if: github.event_name == 'release'
+        uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e  # v1.13.0
+        with:
+          verbose: true
+
+# [1] https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#filter-pattern-cheat-sheet

.gitignore

@@ -53,3 +53,5 @@ coverage.xml
 # Sphinx documentation
 docs/_build/
 
+# Autogenerated version file
+skosify/_version.py

Makefile

@@ -1,11 +1,11 @@
 .PHONY: test docs build
 
 test:
-	python setup.py test
+	pytest
 
 doc:
 	rm -rf docs/_build
 	$(MAKE) -C docs html
 
 build:
-	python setup.py bdist_wheel
+	hatch build

README.rst

@@ -1,7 +1,7 @@
 .. image:: https://badge.fury.io/py/skosify.svg
    :target: https://badge.fury.io/py/skosify.svg    
-.. image:: https://travis-ci.org/NatLibFi/Skosify.svg?branch=master
-   :target: https://travis-ci.org/NatLibFi/Skosify
+.. image:: https://github.com/NatLibFi/Skosify/workflows/CI/badge.svg
+   :target: https://github.com/NatLibFi/Skosify/actions
 .. image:: https://readthedocs.org/projects/skosify/badge/?version=latest
    :target: http://skosify.rtfd.io/ 
 .. image:: https://codecov.io/gh/NatLibFi/Skosify/branch/master/graph/badge.svg
@@ -18,12 +18,60 @@ the SKOS specification and related best practices.
 Installation
 ============
 
-Skosify requires Python 3.6+.
+Skosify requires Python 3.9+.
+
+If you only want to use the command line interface it is suggested to install
+with `uv tool <https://docs.astral.sh/uv/concepts/tools/>`_ 
+or `pipx <https://pypa.github.io/pipx/>`_. 
+Both simplify installing and managing python command line applications.
+
+.. code-block:: console
+
+    uv tool install skosify
+
+
+or
+
+.. code-block:: console
+
+    pipx install skosify
+
+
+Of course you also use pip to install as for any other Python package.
 
 .. code-block:: console
 
     pip install --upgrade skosify
 
+
+To help testing locally with multiple Python versions, a 
+`tox <https://tox.wiki/>`_ configuration file is provided (tox.ini).
+
+.. code-block:: console
+
+    uv tool install tox
+
+Execute `tox` in the root of the repo to run the full set of tests.
+Optionally just run specific environments, for example only Python 3.12:
+
+.. code-block:: console
+
+    tox -e py312
+
+The package can be built locally with any PEP517-conform build tool, for example 
+`build <https://pypi.org/project/build/>`_, 
+`uv build <https://docs.astral.sh/uv/concepts/build-backend/>`_
+or `hatch <https://pypi.org/project/hatch/>`_.
+Of course, you need to have the build tool installed. 
+For example, to use hatch as in gh-actions, run:
+
+.. code-block:: console
+
+    uvx hatch build
+
+This command uses `uvx <https://docs.astral.sh/uv/guides/tools/>`_
+to run hatch with out installing it permanently.
+
 Usage
 =====
 
@@ -79,6 +127,7 @@ Author and Contributors
 -  Jakob Voß
 -  Dan Michael O. Heggø
 -  Alex Kourijoki
+-  David Linke
 
 See also
 ========

docs/background.rst

@@ -20,10 +20,10 @@ Publications
 -  Osma Suominen and Christian Mader: Assessing and Improving the
    Quality of SKOS Vocabularies. Journal on Data Semantics, vol. 3, no.
    1, pp. 47-73, June, 2014
-   (`PDF <https://seco.cs.aalto.fi/publications/2014/suominen-mader-skosquality.pdf>`_)
+   (`PDF <https://seco.cs.aalto.fi/publications/2014/suominen-mader-skosquality.pdf>`__)
 
 -  Osma Suominen and Eero Hyvönen: Improving the Quality of SKOS
    Vocabularies with Skosify. Proceedings of the 18th International
    Conference on Knowledge Engineering and Knowledge Management (EKAW
    2012), Springer-Verlag, Galway, Ireland, October, 2012
-   (`PDF <https://seco.cs.aalto.fi/publications/2012/suominen-hyvonen-skosify-2012.pdf>`_)
+   (`PDF <https://seco.cs.aalto.fi/publications/2012/suominen-hyvonen-skosify-2012.pdf>`__)

docs/conf.py

@@ -1,12 +1,43 @@
-# -*- coding: utf-8 -*-
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+from importlib.metadata import version as pkg_version
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
 
 import os
 import sys
 sys.path.insert(0, os.path.abspath('../'))
 
-needs_sphinx = '1.1'
+# -- Project information -----------------------------------------------------
 
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.viewcode']
+# General information about the project.
+project = u'Skosify'
+title = u'Skosify Documentation'
+copyright = u'2017, Osma Suominen & Jakob Voß'
+author = u'Osma Suominen & Jakob Voß'
+# full version, including alpha/beta/rc tags
+release = pkg_version("skosify")
+# Short version
+version = ".".join(release.split(".")[:3])
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.viewcode',
+]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -20,20 +51,12 @@
 # The master toctree document.
 master_doc = 'index'
 
-# General information about the project.
-project = u'Skosify'
-title = u'Skosify Documentation'
-copyright = u'2017, Osma Suominen & Jakob Voß'
-author = u'Osma Suominen & Jakob Voß'
-version = '2.0.1'  # Use bumpversion to update
-release = version
-
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #
 # 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.
@@ -46,6 +69,8 @@
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
 
+# In --nitpick mode, ignore missing references to rdflib types
+nitpick_ignore = [('py:class', 'Graph')]
 
 # -- Options for HTML output ----------------------------------------------
 
@@ -79,7 +104,6 @@
     (master_doc, 'Skosify.tex', title, author, 'manual'),
 ]
 
-
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples
@@ -89,4 +113,6 @@
 ]
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3', None),
+}