Merge pull request #9 from Knowledge-Graph-Hub/rebuild2

Further adaptations to make this KG-centric

.github/workflows/build.yml

@@ -15,13 +15,16 @@ jobs:
     runs-on: ubuntu-latest
     container: obolibrary/odkfull:v1.2.30
     steps:
-      - uses: actions/checkout@master
+      - uses: actions/checkout@main
         with:
           persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
           fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+      - name: Install Poetry
+        run: |
+          pip install poetry
       - name: Create local changes
         run: |
-          python -m pip install -r requirements.txt
+          poetry install --no-interaction
           make
       - name: Commit files
         run: |
@@ -31,7 +34,7 @@ jobs:
       - name: Create Pull Request
         uses: peter-evans/create-pull-request@v3
         with:
-          commit-message: Update OBO foundry metadata
-          title: 'Update OBO foundry metadata'
+          commit-message: Update KG-Registry metadata
+          title: 'Update KG-Registry metadata'
           body: |
-            Recreates all OBO metadata.
+            Recreates all KG-Registry metadata.

Makefile

@@ -1,7 +1,7 @@
-# Makefile for OBOFoundry.github.io
+# Makefile for KG-Registry site
 #
 # This file contains commands for validating and generating
-# configuration files for the OBO Foundry website.
+# configuration files for the KG-Registry website.
 # The `util/` directory contains additional scripts
 # called from this Makefile.
 # It is intended to be run on a Unix system (Linux, Mac OS X)

_config.yml

@@ -1,13 +1,13 @@
-name: OBO Foundry
-title: The OBO Foundry
+name: KG-Registry
+title: The Knowledge Graph Registry
 markdown: kramdown
 highlighter: rouge
 baseurl: /
 imgurl: /images
-repo: https://github.com/OBOFoundry/OBOFoundry.github.io/
-repo_src: https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/
+repo: https://github.com/Knowledge-Graph-Hub/kg-registry
+repo_src: https://github.com/Knowledge-Graph-Hub/kg-registry/blob/main/
 author:
-  name: OBO Technical WG
+  name: KG-Hub, a team based at the Lawrence Berkeley National Laboratory
 plugins:
   - jekyll-sitemap
   - jekyll-feed

_config_header.yml

@@ -1,13 +1,13 @@
-name: OBO Foundry
-title: The OBO Foundry
+name: KG-Registry
+title: The Knowledge Graph Registry
 markdown: kramdown
 highlighter: rouge
 baseurl: /
 imgurl: /images
-repo: https://github.com/OBOFoundry/OBOFoundry.github.io/
-repo_src: https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/
+repo: https://github.com/Knowledge-Graph-Hub/kg-registry
+repo_src: https://github.com/Knowledge-Graph-Hub/kg-registry/blob/main/
 author:
-  name: OBO Technical WG
+  name: KG-Hub, a team based at the Lawrence Berkeley National Laboratory
 plugins:
   - jekyll-sitemap
   - jekyll-feed

_includes/footer.html

@@ -1,5 +1,5 @@
 <footer class="footer">
     <p class="small text-center text-muted">
-        © 2024 OBO Technical WG
+        KG-Registry
     </p>
 </footer>

_includes/header.html

@@ -3,7 +3,7 @@
         <a class="navbar-brand" href="/">
             <img src="/images/foundrylogo.png" alt="" style="max-height: 24px"
                  class="d-inline-block align-text-top">
-            OBO Foundry
+            KG-Registry
         </a>
         <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarSupportedContent"
                 aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
@@ -17,7 +17,6 @@
                         About
                     </a>
                     <ul class="dropdown-menu" aria-labelledby="navbarAboutDropdown">
-                        <li><a class="dropdown-item" href="/about-OBO-Foundry.html">About</a></li>
                         <li><a class="dropdown-item" href="/docs/COC.html">Code of Conduct</a></li>
                         <li><a class="dropdown-item" href="/resources">Resources</a></li>
                         <li>

index.html

@@ -1,19 +1,18 @@
 ---
 layout: default
-title: The OBO Foundry
+title: The Knowledge Graph Registry
 ---
 
 <div class="row">
     <h1 class="display-6">
-        NOT the OBO Foundry
+        KG-Registry
         <br/>
         <small class="text-muted">
-            Experimental aggregation of ontology-like resources.
+            Aggregation of Knowledge Graphs and their parts.
         </small>
     </h1>
 
-
-    <h4>NON OBO Resources</h4>
+    <h4>Graph Resources</h4>
 </div>
 
 <div class="row">

pyproject.toml

@@ -9,6 +9,13 @@ readme = "README.md"
 [tool.poetry.dependencies]
 python = "^3.9"
 linkml = "^1.8.5"
+pyyaml = "^6.0.2"
+jsonschema = "^4.23.0"
+sparqlwrapper = "^2.0.0"
+pyrsistent = "^0.20.0"
+python-frontmatter = "^1.1.0"
+yamllint = "^1.35.1"
+ruamel-yaml = "^0.18.10"
 
 [tool.poetry.dev-dependencies]
 pytest = ">=7.1.2"

src/obofoundry/cli.py

@@ -1,6 +1,7 @@
 """Command line interface for :mod:`obofoundry`.
 
-Why does this file exist, and why not put this in ``__main__``? You might be tempted to import things from ``__main__``
+Why does this file exist, and why not put this in ``__main__``?
+You might be tempted to import things from ``__main__``
 later, but that will cause problems--the code will get executed twice:
 
 - When you run ``python3 -m obofoundry`` python will execute``__main__.py`` as a script.