Reviewer edits

.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/*
 

Makefile

@@ -28,6 +28,12 @@ html:
 	mkdir docs
 	sphinx-build -b html doc_source docs
 
+html-local:
+	# Running sphinx-build to build html files in a local docs folder
+	rm -rf docs_local
+	mkdir docs_local
+	sphinx-build -b html doc_source docs_local 
+
 benchmark:
 	python benchmarks/run_benchmarks.py
 

README.md

@@ -1,10 +1,16 @@
 # `ect`: A python package for computing the Euler Characteristic Transform
 
-Python computation tools for computing the Euler Characteristic Transform of embedded graphs. 
+Python computation tools for computing the Euler Characteristic Transform of embedded complexes. 
 
 ## Description
 
-Right now, the content includes stuff for doing ECT on graphs embedded in 2D. Eventually the goal is to get voxel versions, higher dimensional simplicial complexes, etc in here.
+The package provides fast tools for computing the Euler Characteristic Transform (ECT) on embedded cell complexes in any ambient dimension. You build a complex (vertices, edges, and optional higher‑dimensional cells), choose a set of directions and thresholds, and compute either the exact ECT or its smoothed/differentiable variants. Results come back as NumPy arrays with metadata, plotting helpers, and distance utilities, making it straightforward to visualize transforms and compare shapes. The core is implemented with NumPy and Numba, with optional validation of geometric and structural constraints when constructing complexes.
+
+- `EmbeddedComplex`: convert point clouds into complexes with vertices, edges, and higher‑dimensional cells with embedded coordinates.
+- `ECT`, `SECT`, `DECT` : ECT calculations along with the smooth and differentiable variants over sampled directions and transforms.
+- `Directions`: uniform, random, or custom directions (angles in 2D; vectors in any dimension)
+- Results as `ECTResult`: behaves like a NumPy array, with plotting and distance helpers
+- Optional geometric/structural validation when building complexes
 
 For more information on the ECT, see:
 
@@ -15,18 +21,14 @@ For more information on the ECT, see:
 ### Documentation and tutorials
 
 - The documentation is available at: [munchlab.github.io/ect](https://munchlab.github.io/ect/)
-- A tutorial jupyter notebook can be found [here](https://munchlab.github.io/ect/notebooks/Tutorial-ECT_for_embedded_graphs.html)
-
-### Dependencies
+- A tutorial jupyter notebook can be found [here](https://munchlab.github.io/ect/notebooks/Tutorial-EmbeddedComplex.html)
 
-- `networkx`
-- `numpy`
-- `matplotlib`
-- `numba`
 
 ### Installing
 
-The package can be installed using pip:
+Requires Python 3.10+.
+
+Install from PyPI:
 
 ```{bash}
 pip install ect
@@ -40,12 +42,35 @@ cd ect
 pip install .
 ```
 
+### Quickstart
+
+Compute an ECT for a simple embedded triangle and plot it.
+
+```python
+from ect import ECT, EmbeddedComplex
+
+G = EmbeddedComplex()
+G.add_node("a", [0.0, 0.0])
+G.add_node("b", [1.0, 0.0])
+G.add_node("c", [0.5, 0.8])
+G.add_edge("a", "b")
+G.add_edge("b", "c")
+G.add_edge("c", "a")
+
+ect = ECT(num_dirs=32, num_thresh=128)
+result = ect.calculate(G)
+result.plot()
+```
+
+
+
 ## Authors
 
 This code was written by [Liz Munch](https://elizabethmunch.com/) along with her research group and collaborators. People who have contributed to `ect` include:
 
 - [Sarah McGuire](https://www.sarah-mcguire.com/)
 - [Yemeen Ayub](https://yemeen.com/)
+- [Dan Chitwood](https://github.com/DanChitwood)
 
 ## License
 

doc_source/ECTResult.md

@@ -0,0 +1,9 @@
+# ECTResult
+
+`ECTResult` class provides a fast way to manipulate ECT matrices while also maintaining properties of being a numpy array.
+
+
+```{eval-rst}
+.. automodule:: ect.results
+   :members:
+```