BIG-MAP · jsimonclark · Mar 12, 2024 · Mar 2, 2022 · Mar 2, 2022 · Jul 22, 2022
diff --git a/.github/workflows/ci_tests.yml b/.github/workflows/ci_tests.yml
@@ -14,7 +14,7 @@ jobs:
     - name: Set up Python 3.7
       uses: actions/setup-python@v5
       with:
-        python-version: 3.7
+        python-version: '3.7'
 
     - name: Install EMMOntoPy
       run: |
@@ -29,5 +29,3 @@ jobs:
           --skip test_quantity_dimension \
           --configfile=.github/utils/emmocheck_config.yml \
           battinfo.ttl
-
-
diff --git a/.github/workflows/doc.yml b/.github/workflows/doc.yml
@@ -4,34 +4,36 @@ on:
   push:
     branches:
       - 'master'
-
+  pull_request:
+
 env:
   GIT_USER_NAME: BattINFO Developers
   GIT_USER_EMAIL: "[email protected]"
-    
+
 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@v5 #Uses python install action from here: https://github.com/marketplace?type=actions
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.10'  # Replace with the desired Python version
+        python-version: '3.10'
 
     - 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
-
+        pip install -U setuptools wheel
+        pip install -r requirements_docs.txt
+
     - name: Render documentation from ttl
       run: python sphinx/ttl_to_rst.py
 
@@ -40,17 +42,19 @@ jobs:
       with:
         docs-folder: "sphinx/"
         pre-build-command: "apt-get update -y; apt-get install -y pandoc"
-
+
+    # Still upload built documentation as an artifact if not deploying
+    # This is to provide the opportunity to download the built documentation
     - name: Upload artifacts
       uses: actions/upload-artifact@v4
       with:
         name: documentationHTML
         path: sphinx/_build/html/
-
+
+    # Only deploy if pushing to 'master'
     - name: Deploy
       uses: peaceiris/actions-gh-pages@v3
-      if: github.ref == 'refs/heads/master'
+      if: github.ref == 'refs/heads/master' && github.event_name == 'push'
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: sphinx/_build/html
-
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,6 @@
+# Python
+__pycache__
+*.py[cod]
+
+# Documentation
+site
diff --git a/docs/about.html b/docs/about.html
@@ -8,7 +8,7 @@
                 <link rel="icon" type="image/x-icon" href="./assets/favicon.ico">
         </head>  
         <body>      
-        
+
         <div class="banner">
             <a href="index.html">
                 <img src="./assets/banner.jpg" alt="Banner Image">
@@ -41,4 +41,3 @@ <h3>Aknowledgements</h3>
 <p>This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 957189.</p>
             </body>
         </html>
-
diff --git a/docs/assets/about.md b/docs/assets/about.md
@@ -1,12 +1,12 @@
 # About BattINFO
-The BattINFO Ontology has been developed as part of the [BIG-MAP](http://www.big-map.eu/) project, in an effort to deliver a digital resource the battery community 
-to facilitate the implementation of FAIR data standards.
 
-### License
+The BattINFO Ontology has been developed as part of the [BIG-MAP](http://www.big-map.eu/) project, in an effort to deliver a digital resource the battery community to facilitate the implementation of FAIR data standards.
+
+## License
 
 The Battery Interface 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).
 
-### Contributors
+## Contributors
 
 - Simon Clark, SINTEF, Norway
 - Jesper Friis, SINTEF, Norway
@@ -24,6 +24,6 @@ The Battery Interface Domain Ontology is released under the [Creative Commons At
 - Inga Gudem Ringdalen, SINTEF, Norway
 - Emanuele Farhi, SOLEIL synchrotron, France
 
+## Aknowledgements
 
-### Aknowledgements
 This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 957189.
diff --git a/docs/assets/contribute.md b/docs/assets/contribute.md
@@ -1,15 +1,20 @@
 # Contributing to BattINFO
+
 There are two ways you can contribute to BattINFO.
-### Suggest minor changes on existing elements
-Create a [Feature request in a Github Issue](https://docs.github.com/en/issues/tracking-your-work-with-issues/creating-an-issue) to suggest edits to names, defintions, references on existing classes and properties. 
-### Propose additions/deletion of elements
+
+## Suggest minor changes on existing elements
+
+Create a [Feature request in a Github Issue](https://docs.github.com/en/issues/tracking-your-work-with-issues/creating-an-issue) to suggest edits to names, defintions, references on existing classes and properties.
+
+## Propose additions/deletion of elements
+
 > **_NOTE:_**  We recommend contacting some of BattINFO contributors in advance to discuss which additions deletions you wish to make.  
 
 We recoommend using the [forking workflow](https://www.atlassian.com/git/tutorials/comparing-workflows/forking-workflow) to contribute additions/deletions. Fork this repository, clone the fork on you local PC, create your branch based on the existing ```dev``` branch (e.g. ```dev_john_doe```) and work on the editions in you local copy. You can edit ontologes in two main ways. One is programmatically, using for instance [EMMOntoPy](https://github.com/emmo-repo/EMMOntoPy). The second and more common is using the interface provided by the Protege software. In case of the latter, [install Protege](https://protege.stanford.edu/) and use it to open the ontology file you wish to edit. Before adding elements, ensure Protege is configured to create IRIs in the right format:  
+
 * Open Protégé
 * Go to File/Open and load the ontology file you wish to modify
 * Go to File/Preferences and there go to the New Entities Tab
 * Ensure you have configured the preferences with the correct IRI prefixes.
-
 * Once you have made your changes, commit them to your fork and [create a pull request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request).
-* We will merge the request after assessing it.
+* We will merge the request after assessing it.
diff --git a/docs/assets/index.md b/docs/assets/index.md
@@ -1,17 +1,11 @@
+# BattINFO
 
 | [**About**](./about.html) | [**Contribute**](./contribute.html) | [![BattINFO Github](https://badgen.net/badge/icon/github?icon=github&label)](https://github.com/BIG-MAP/BattINFO)
 
-
-The **Batt**ery **IN**ter**F**ace **O**ntology is a digital resource to support interoperability of battery data.   
+The **Batt**ery **IN**ter**F**ace **O**ntology is a digital resource to support interoperability of battery data.
 
 BattINFO consists of a list of entities representing concepts used in batteries and electrochemistry. Each entity has a unique identifier (IRI) and is annotated with additional information, such as its preferred name ("prefLabel"), alternative names, definition, references, etc. As users link their research resources to BattINFO entities, they are effectively describing their resource using a common vocabulary. Resources can be datasets, documents, persons, organizations, equipment, samples... anything linked to the common vocabulary described in BattINFO, becomes part of an ecosystem of Findable resources.
 
 Here you can find the entities described in BattINFO, classified in two domains.
 
-
 [**Battery Domain**](http://emmo.info/battery) | [**Electrochemistry Domain**](http://emmo.info/electrochemistry)  
-
-
-
-
-
diff --git a/docs/contribute.html b/docs/contribute.html
@@ -8,7 +8,7 @@
                 <link rel="icon" type="image/x-icon" href="./assets/favicon.ico">
         </head>  
         <body>      
-        
+
         <div class="banner">
             <a href="index.html">
                 <img src="./assets/banner.jpg" alt="Banner Image">
@@ -33,4 +33,3 @@ <h3>Propose additions/deletion of elements</h3>
 </ul>
             </body>
         </html>
-
diff --git a/docs/index.html b/docs/index.html
@@ -8,7 +8,7 @@
                 <link rel="icon" type="image/x-icon" href="./assets/favicon.ico">
         </head>  
         <body>      
-        
+
         <div class="banner">
             <a href="index.html">
                 <img src="./assets/banner.jpg" alt="Banner Image">
@@ -21,4 +21,3 @@
 <p><a href="http://emmo.info/battery"><strong>Battery Domain</strong></a> | <a href="http://emmo.info/electrochemistry"><strong>Electrochemistry Domain</strong></a>  </p>
             </body>
         </html>
-
diff --git a/docs/scripts/__pycache__/html_styling.cpython-310.pyc b/docs/scripts/__pycache__/html_styling.cpython-310.pyc
diff --git a/docs/scripts/__pycache__/md_to_html.cpython-310.pyc b/docs/scripts/__pycache__/md_to_html.cpython-310.pyc
diff --git a/docs/scripts/__pycache__/ttl_to_html.cpython-310.pyc b/docs/scripts/__pycache__/ttl_to_html.cpython-310.pyc
diff --git a/docs/scripts/__pycache__/ttl_to_md.cpython-310.pyc b/docs/scripts/__pycache__/ttl_to_md.cpython-310.pyc
diff --git a/docs/scripts/md_to_html.py b/docs/scripts/md_to_html.py
@@ -24,7 +24,7 @@ def render_html_top() -> str:
             </a>
         </div>
         '''
-    
+
     return top_html + banner
 
 ########## RENDER HTML BOTTOM ################
@@ -39,7 +39,7 @@ def render_html_bottom() -> str:
 ########## LOAD MD INTO HTML  ################
 
 def load_md_into_html(path:str)-> str:
-    
+
     with open(path, 'r', encoding="utf-8") as file:
         markdown_text = file.read()
 

diff --git a/requirements.txt b/requirements.txt
@@ -1,2 +1,2 @@
-EMMOntoPy>=0.1.3,<1
-semver>=2.13.0,<3
+EMMOntoPy>=0.7.1,<1
+semver>=3.0.2,<4
diff --git a/requirements_docs.txt b/requirements_docs.txt
@@ -0,0 +1 @@
+rdflib==6.3.2