Merge branch 'main' into dev

.github/workflows/doc.yml

@@ -0,0 +1,57 @@
+name: "Sphinx: Render docs"
+
+on: 
+  push:
+    branches:
+      - 'main'
+
+env:
+  GIT_USER_NAME: BattINFO Developers
+  GIT_USER_EMAIL: "BattINFO@big-map.org"
+
+jobs:
+
+  updatepages:
+
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v4 #Uses python install action from here: https://github.com/marketplace?type=actions
+      with:
+        python-version: '3.10'  # Replace with the desired Python version
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install Markdown==3.4.3 rdflib==6.3.2  # Add any other dependencies if needed
+        
+    - name: Render documentation from ttl
+      run: python sphinx/ttl_to_rst.py
+
+    - name: Build HTML
+      uses: ammaraskar/sphinx-action@master
+      with:
+        docs-folder: "sphinx/"
+        pre-build-command: "apt-get update -y; apt-get install -y pandoc"
+
+    - name: Upload artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: documentationHTML
+        path: sphinx/_build/html/
+
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v3
+      if: github.ref == 'refs/heads/main'
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: sphinx/_build/html
+
+

.github/workflows/doc.yml~

@@ -0,0 +1,65 @@
+name: "Sphinx: Render docs"
+
+on: 
+  push:
+    branches:
+      - 'master'
+
+env:
+  GIT_USER_NAME: BattINFO Developers
+  GIT_USER_EMAIL: "BattINFO@big-map.org"
+
+jobs:
+
+  updatepages:
+
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v4 #Uses python install action from here: https://github.com/marketplace?type=actions
+      with:
+        python-version: '3.10'  # Replace with the desired Python version
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install Markdown==3.4.3 rdflib==6.3.2  # Add any other dependencies if needed
+
+    - name: Render documentation from ttl
+      run: python sphinx/ttl_to_rst.py
+
+    - name: Build HTML
+      uses: ammaraskar/sphinx-action@master
+      with:
+        docs-folder: "sphinx/"
+
+    - name: Upload artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: documentationHTML
+        path: sphinx/_build/html/
+
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v3
+      if: github.ref == 'refs/heads/master'
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: sphinx/_build/html
+
+    - name: Commit updated documentation
+      run: |
+        cd ${GITHUB_WORKSPACE}
+        git config --global user.email "${GIT_USER_EMAIL}"
+        git config --global user.name "${GIT_USER_NAME}"
+        git config pull.rebase false
+        git add .
+        git commit --allow-empty -m "Automatic update of github pages"
+        git push origin master
+

chemicalsubstance.ttl

@@ -11,6 +11,7 @@
 @base <https://w3id.org/emmo/domain/chemicalsubstance/chemicalsubstance> .
 
 <https://w3id.org/emmo/domain/chemicalsubstance/chemicalsubstance> rdf:type owl:Ontology ;
+
                                                                     owl:versionIRI <https://w3id.org/emmo/domain/chemicalsubstance/0.3.0-beta/chemicalsubstance> ;
                                                                     owl:imports <http://emmo.info/emmo/1.0.0-beta5> ;
                                                                     dcterms:abstract "This ontology provides terms for chemical substances that can be referenced and re-used other resources."@en ;

sphinx/.gitignore

@@ -0,0 +1 @@
+_build

sphinx/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?= -v
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

sphinx/README.org

@@ -0,0 +1,47 @@
+#+TITLE: Documentation generation for BattInfo
+* Requirements
+** sphinx
+   installation instruction described [[https://www.sphinx-doc.org/en/master/usage/installation.html][here]]
+   #+begin_src
+     pip install sphinx
+   #+end_src
+** install sphinx pydata theme
+   https://pydata-sphinx-theme.readthedocs.io/en/latest/index.html
+   #+begin_src
+     pip install pydata-sphinx-theme
+   #+end_src
+** globabsubs extension
+   #+begin_src
+     pip install sphinxcontrib-globalsubs
+   #+end_src
+** autosectionlabel
+   - part of default distribution
+   - We use ~autosectionlabel_prefix_document = True~ which means that the internal link must be prefixed by the file
+     name and a semi-column, see [[https://www.sphinx-doc.org/en/master/usage/extensions/autosectionlabel.html][here]].
+
+* Workflow for editing
+
+  In the ~Documentation~ directory, run from terminal
+  #+BEGIN_SRC sh
+  make html
+  #+END_SRC
+
+  The command generates all the files for a static website and writes them in ~Documentation/_build/html~
+
+  All the files in this directory must then be copied to the ~BattInfo-doc~ [[https://github.com/BattMoTeam/BattMo-doc][repo]]. From there, make a *force* push. We do
+  not keep track of the history of the ouput files (html), but we of course keep track of the documentation source, directly in the
+  main repo ~BattInfo~.
+
+  The deployment of the webpage can be followed from the [[https://github.com/BattMoTeam/BattMo-doc/actions][github pages section]]
+
+  The result can be view at
+
+  https://battmoteam.github.io/Battinfo-doc/
+
+* Interesting Manuals
+** sphinx manual
+   https://www.sphinx-doc.org/en/master/contents.html
+** reStucturedText (rst) format
+   https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html
+* Configuration file
+  - ~conf.py~ see https://www.sphinx-doc.org/en/master/usage/configuration.html

sphinx/_static/css/custom.css

@@ -0,0 +1,34 @@
+td.element-table-key, td.element-table-value {
+    vertical-align: top;
+}
+
+td.element-table-key {
+    text-align: right;
+    padding-right: 2mm;
+    width: 20%;
+}
+
+span.element-table-key {
+    font-weight: bold;
+}
+
+table.element-table {
+    width: 100%;
+    text-align: left;
+}
+
+html table.element-table tr:nth-child(odd) td{
+   background-color: Gainsboro;
+}
+
+table.element-table tr:nth-child(even) td{
+   background-color: GhostWhite;
+}
+
+html[data-theme=dark] table.element-table tr:nth-child(odd) td{
+   background-color: black;
+}
+
+html[data-theme=dark] table.element-table tr:nth-child(even) td{
+   background-color: black;
+}

sphinx/about.rst

@@ -0,0 +1,107 @@
+.. toctree::
+   :hidden:
+
+   example_person_jsonld_nb.ipynb
+
+
+Chemical Substance Domain Ontology
+==================================
+
+Overview
+--------
+
+The Chemical Substance Domain Ontology is a specialized ontology
+designed to provide persistent machine-readable identifiers for chemical
+substances within the broader context of the Elementary Multiperspective
+Materials Ontology (EMMO). It plays a crucial role in enhancing the
+semantic representation of chemical entities and their relationships
+within materials science and related domains.
+
+Integration with EMMO
+~~~~~~~~~~~~~~~~~~~~~
+
+The primary purpose of the Chemical Substance Domain Ontology is to
+seamlessly integrate chemical substances into the EMMO ontology
+ecosystem. EMMO serves as the top-level ontology for materials science
+and modeling, providing a standardized framework for describing
+materials, processes, and phenomena. By establishing a domain ontology
+for chemical substances, we bridge the gap between materials modeling
+and chemistry, ensuring consistent and interoperable knowledge
+representation.
+
+Persistent Identifiers
+~~~~~~~~~~~~~~~~~~~~~~
+
+This ontology assigns persistent machine-readable identifiers to
+chemical substances. These identifiers are essential for accurate
+referencing and linking of chemical data, ensuring data consistency, and
+facilitating data exchange and interoperability among various tools and
+systems. It includes annotations to other sources of information
+including `PubChem <https://pubchem.ncbi.nlm.nih.gov/>`__ and
+`Wikidata <https://www.wikidata.org/>`__.
+
+Standardized Nomenclature
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The ontology includes standardized nomenclature for chemical substances,
+relying on `IUPAC <https://iupac.org/what-we-do/nomenclature/>`__
+recommendations for naming coneventions. IUPAC is the
+universally-recognized authority on chemical nomenclature and
+terminology. This consistency in naming conventions enhances
+collaboration and data sharing.
+
+Key Features
+------------
+
+-  Seamless integration with the EMMO ontology.
+-  Provides persistent machine-readable identifiers for chemical
+   substances.
+-  Standardized nomenclature for chemical entities.
+-  Facilitates data exchange and interoperability within the EMMO
+   ecosystem.
+
+Usage
+-----
+
+Researchers, domain experts, and developers within the materials science
+and chemistry communities can utilize the Chemical Substance Domain
+Ontology for various purposes, including:
+
+-  Incorporating consistent and standardized chemical substance
+   information into their modeling and simulation activities.
+-  Enhancing data interoperability between materials modeling tools,
+   databases, and platforms.
+-  Supporting research projects that require precise and standardized
+   chemical entity representation.
+-  Building applications, databases, or knowledge graphs that leverage
+   EMMO and require chemical substance information.
+
+Contributing
+------------
+
+We welcome contributions from the community to enhance and expand the
+Chemical Substance Domain Ontology. If you have suggestions,
+improvements, or additional chemical substance information to
+contribute, please refer to our :ref:`contributing guidelins<contribute:Contributing to the ontology>`.
+
+Acknowledgements
+----------------
+
+This project has received support from European Unition research and
+innovation programs, under grant agreement numbers:
+
+-  957189 - `BIG-MAP <http://www.big-map.eu/>`__
+
+License
+-------
+
+The Chemical Substance Domain Ontology is released under the `Creative
+Commons Attribution 4.0
+International <https://creativecommons.org/licenses/by/4.0/legalcode>`__
+license (CC BY 4.0).
+
+Please cite this content using the following DOI:
+`10.5281/zenodo.10254978 <https://zenodo.org/doi/10.5281/zenodo.10254978>`__
+
+.. |DOI| image:: https://zenodo.org/badge/697870611.svg
+   :target: https://zenodo.org/doi/10.5281/zenodo.10254978