merge from main

.bumpversion.cfg

@@ -3,6 +3,8 @@ current_version = 0.3.6
 commit = True
 tag = False
 
-[bumpversion:file:setup.py]
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
 
 [bumpversion:file:CITATION.cff]

.github/workflows/deploy.yml

@@ -16,15 +16,12 @@ jobs:
       with:
         python-version: "3.10"
 
-    - name: Install dependencies
+    - name: Install build dependencies
       run: >-
-        python -m pip install --user --upgrade setuptools wheel
-    - name: Convert dependencies
+        python -m pip install --upgrade build
+    - name: Build distribution
       run: >-
-        sed -i 's/==/>=/g' setup.py; cat setup.py
-    - name: Build
-      run: >-
-        python setup.py sdist bdist_wheel
+        python -m build
     - name: Publish distribution 📦 to PyPI
       if: startsWith(github.event.ref, 'refs/tags') || github.event_name == 'release'
       uses: pypa/gh-action-pypi-publish@master

.github/workflows/testing.yml

@@ -29,8 +29,7 @@ jobs:
         pip install -e .
         pip install pytest
         pip install pytest-cov
-        #pytest tests/
-        pytest --cov-report=xml --cov=atomrdf tests/    
+        pytest --cov-report=xml --cov=tools4rdf tests/    
 
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v4.0.1

CITATION.cff

@@ -13,10 +13,22 @@ authors:
   family-names: Azocar Guzman
   affiliation: Institute for Advanced Simulations – Materials Data Science and Informatics (IAS-9), Forschungszentrum Jülich GmbH
   orcid: 'https://orcid.org/0000-0001-7564-7990'
-#date-released: '2024-02-15'
-#doi: 10.5281/zenodo.8146527
-#url: 'https://atomrdf.pyscal.org'
+- given-names: Osamu
+  family-names: Waseda
+  affiliation: Max Planck Institute for Sustainable Materials, Düsseldorf, Germany
+  orcid: 'https://orcid.org/0000-0002-1677-4057'
+- given-names: Stefan
+  family-names: Sandfeld
+  affiliation: Institute for Advanced Simulations – Materials Data Science and Informatics (IAS-9), Forschungszentrum Jülich GmbH, Jülich, Germany
+  orcid: 'https://orcid.org/0000-0001-9560-4728'
+- given-names: Tilmann
+  family-names: Hickel
+  affiliation: Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
+  orcid: 'https://orcid.org/0000-0003-0698-4891'
+#date-released: 
+#doi: 
+url: 'https://tools4rdf.readthedocs.io/en/latest/'
 license: "MIT"
-repository-code: https://github.com/codo/tools4RDF
+repository-code: https://github.com/OCDO/tools4RDF
 type: software
 version: 0.3.6

README.md

@@ -1,4 +1,5 @@
-## 🧰 tools4RDF
+
+![logo](docs/source/_static/logo.png "logo")
 
 **tools4RDF** is a Python toolkit for working with RDF data, SPARQL queries, and semantic networks. 
 

_config.yml

@@ -1,7 +1,7 @@
 # Book settings
 # Learn more at https://jupyterbook.org/customize/config.html
 
-title: "atomrdf"
+title: "tools4RDF"
 #author: The Jupyter Book Community
 logo: docs/source/_static/logo.png
 
@@ -19,7 +19,7 @@ latex:
 
 # Information about where the book exists on the web
 repository:
-  url: https://github.com/pyscal/atomrdf
+  url: https://github.com/OCDO/tools4RDF/
   path_to_book: book
   branch: main
 

environment-docs.yml

@@ -10,4 +10,4 @@ dependencies:
   - python-graphviz
   - networkx
   - pandas
-  - jupyter-book
+  - jupyter-book =1.0.4

index.ipynb

@@ -13,7 +13,7 @@
    "id": "a123db1c",
    "metadata": {},
    "source": [
-    "`tools4RDF` is a Python toolkit designed to simplify working with RDF data, ontologies, and knowledge graphs. It provides user-friendly utilities for creating, manipulating, querying, and visualizing RDF data, making it easier to integrate semantic web technologies into your research and applications.\n",
+    "`tools4RDF` is a Python toolkit designed to simplify working with RDF data, ontologies, and knowledge graphs. It provides user-friendly utilities for creating, manipulating, querying, and visualizing RDF data, making it easier to integrate semantic web technologies into research and applications, particularly for domain scientists and developers without deep RDF expertise.\n",
     "\n",
     "It is built on top of rdflib, and a primary function is the automated creation of SPARQL queries through an autocompleted programmatic interface.\n",
     "\n",
@@ -53,7 +53,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "onto = OntologyNetwork('http://xmlns.com/foaf/0.1/')"
+    "# via XMLNS (recommended)\n",
+    "onto = OntologyNetwork('http://xmlns.com/foaf/0.1/')\n",
+    "\n",
+    "# if XMLNS fails\n",
+    "# onto = OntologyNetwork(\"https://raw.githubusercontent.com/SPAROntologies/foaf/master/docs/current/foaf.xml\")"
    ]
   },
   {
@@ -347,7 +351,7 @@
     "- Read and parse ontologies\n",
     "- Combine ontologies programatically and connect them\n",
     "\n",
-    "For more examples, please check [here](add link)\n"
+    "For more examples, please check [here](https://tools4rdf.readthedocs.io/en/latest/docs/examples.html)"
    ]
   }
  ],

pyproject.toml

@@ -0,0 +1,86 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "tools4rdf"
+version = "0.3.6"
+description = "python tool for working with ontologies and data models"
+readme = "README.md"
+requires-python = ">=3.8"
+license = {text = "MIT"}
+authors = [
+    {name = "Abril Azocar Guzman", email = "sarath.menon@pyscal.org"},
+    {name = "Sarath Menon", email = "sarath.menon@pyscal.org"}
+]
+maintainers = [
+    {name = "Sarath Menon", email = "sarath.menon@pyscal.org"}
+]
+keywords = ["ontology", "rdf", "sparql", "semantic-web", "knowledge-graph"]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering",
+]
+dependencies = [
+    "numpy",
+    "rdflib",
+    "pyyaml",
+    "graphviz",
+    "networkx",
+    "pandas",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=7.0",
+    "pytest-cov",
+]
+docs = [
+    "sphinx",
+    "sphinx-rtd-theme",
+]
+
+[project.urls]
+Homepage = "https://pyscal.org"
+Documentation = "https://pyscal.org"
+Repository = "https://github.com/ocdo/tools4rdf"
+Download = "https://github.com/ocdo/tools4rdf"
+
+[tool.setuptools]
+zip-safe = false
+include-package-data = true
+
+[tool.setuptools.packages.find]
+include = ["tools4rdf*"]
+
+[tool.setuptools.package-data]
+tools4rdf = ["data/*.owl", "data/*.rdf", "data/*.ttl"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+addopts = "-v --strict-markers"
+
+[tool.coverage.run]
+source = ["tools4rdf"]
+omit = ["*/tests/*", "*/test_*.py"]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "def __repr__",
+    "raise AssertionError",
+    "raise NotImplementedError",
+    "if __name__ == .__main__.:",
+    "if TYPE_CHECKING:",
+]