Merge pull request #96 from MunchLab/reviewer-edits

Reviewer edits

Author: yemeen

.github/pull_request_template.md

@@ -1,4 +1,7 @@
-<!--- Provide a general summary of your changes in the Title above -->
+# Pull Request
+
+## Summary
+<!--- Provide a brief summary of your changes -->
 
 ## Description
 <!--- Describe your changes in detail -->
@@ -17,11 +20,24 @@
 - [ ] Bug fix (non-breaking change which fixes an issue)
 - [ ] New feature (non-breaking change which adds functionality)
 - [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] Documentation update
+- [ ] Code refactoring
+- [ ] Performance improvement
+- [ ] Test improvement
 
 ## Checklist
 <!--- Go over all the following points, and put an `x` in all the boxes that apply. -->
 <!--- If you're unsure about any of these, don't hesitate to ask. We're here to help! -->
 - [ ] My code follows the code style of this project. (`make clean`)
-- [ ] I have incremented the version number in the `pyproject.toml` file.
-- [ ] I have added tests to cover my changes.
+- [ ] I have incremented the version number in the `pyproject.toml` file (if applicable).
+- [ ] I have added tests to cover my changes (if applicable).
 - [ ] All new and existing tests passed. (`make tests`)
+- [ ] I have updated the documentation (if applicable).
+- [ ] My changes generate no new warnings.
+- [ ] I have added any necessary new dependencies to `pyproject.toml`.
+
+## Additional Notes
+<!--- Add any additional notes, concerns, or questions for reviewers -->
+
+## Screenshots (if applicable)
+<!--- Add screenshots to help explain your changes if they are visual in nature -->

.github/workflows/compile-paper.yml

@@ -1,6 +1,6 @@
 on:
   push:
-    branches: [JOSS-Paper]
+    branches: [JOSS-Paper, reviewer-edits]
   workflow_dispatch:
 
 jobs:

.github/workflows/docs.yml

@@ -1,15 +1,12 @@
 name: Build and Deploy Docs
 on:
   push:
-    branches: [ "main" ]
+    branches: ["main"]
     paths:
-      - 'doc_source/**'
-      - 'src/ect/**'
+      - "doc_source/**"
+      - "src/ect/**"
   pull_request:
-    branches: [ "main" ]
-    paths:
-      - 'doc_source/**'
-      - 'src/ect/**'
+    branches: ["main"]
 
 jobs:
   docs:
@@ -20,36 +17,41 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-          
+
       - name: Install uv
         uses: astral-sh/setup-uv@v5
-        
+
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
           python-version-file: "pyproject.toml"
-          
+
       - name: Install system dependencies
         run: |
           sudo apt-get update
           sudo apt-get install -y pandoc
-          
+
       - name: Create venv and install dependencies
         run: |
           uv venv
           source .venv/bin/activate
           uv pip install -e .
-          uv pip install sphinx sphinx-rtd-theme nbsphinx autopep8 myst-parser
-          
+          uv pip install sphinx sphinx-rtd-theme nbsphinx autopep8 myst-parser ipykernel pandas
+
+      - name: Install python3 Jupyter kernel
+        run: |
+          source .venv/bin/activate
+          python -m ipykernel install --user --name python3 --display-name "Python 3"
+
       - name: Build documentation
         run: |
           source .venv/bin/activate
           make html
-          
+
       - name: Deploy to GitHub Pages
         if: github.event_name == 'push'
         uses: peaceiris/actions-gh-pages@v3
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./docs
-          force_orphan: true 
+          force_orphan: true

.gitignore

@@ -8,6 +8,9 @@ benchmarks/results/*
 src/ect/embed_graph.py
 src/ect/embed_cw.py
 
+.vscode
+docs_local
+
 .conda*
 .vscode/*