Update docs

README.md

@@ -15,7 +15,7 @@ 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)
+- A tutorial jupyter notebook can be found [here](https://munchlab.github.io/ect/notebooks/Tutorial-EmbeddedComplex.html)
 
 ### Dependencies
 

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:
+```

doc_source/contributing.rst

@@ -33,7 +33,7 @@ The `ect` package uses the Sphinx documentation system for generating documentat
 - First, include docstrings in the code which will be autogenerated into the documentation. When in doubt, write too much. 
 - Second, write documentation in the `doc_source` directory using the reStructuredText format. This package also supports writing files in markdown, although there are some issues when dealing with autogenerated content so it's a bit of a mix at the moment. Note that when the documentation is generated, everything in the `docs` folder is deleted and overwritten, so do not do your work in there, it will be lost!
 
-Assuming everything (TODO: Add install list) is set up correctly, you can generate the documentation by running the following command from the top level folder::
+Assuming everything is set up correctly (see the installation instructions in the main documentation), you can generate the documentation by running the following command from the top level folder::
 
     make html
 
@@ -93,10 +93,3 @@ If you would like to fix an issue and you are a contributor to the project, plea
 
 If you are not a contributor, you will need to fork the code and create a pull request from your fork.
 Note that all pull requests need to be approved by Liz Munch before they can be merged. 
-
-Conclusion
-----------
-
-- Acknowledgements
-- Future development plans
-- Contact information and support

doc_source/ect_on_graphs.md → doc_source/ect.md

@@ -1,4 +1,4 @@
-# ECT on Graphs
+# ECT
 
 ```{eval-rst}
 .. automodule:: ect.ect

doc_source/installation.rst

@@ -6,7 +6,7 @@ Prerequisites
 
 Before installing `ect`, make sure you have the following prerequisites:
 
-- Python (version 3.7 or higher)
+- Python (version 3.10 or higher)
 - Pip (Python package installer)
 
 Installing `ect`

doc_source/modules.rst

@@ -7,5 +7,6 @@ Table of Contents
 
    Embedded Complex <embed_complex.md>
    Validation System <validation.md>
-   ECT on graphs <ect_on_graphs.md>
+   ECT <ect.md>
+   ECTResult <ECTResult.md>
    Directions <directions.md>

src/ect/ect.py

@@ -10,19 +10,33 @@
 
 class ECT:
     """
-    A class to calculate the Euler Characteristic Transform (ECT) from an input :any:`EmbeddedComplex`.
+    A class to calculate the Euler Characteristic Transform (ECT) from an input :any:`EmbeddedComplex`,
+    using a set of directions to project the complex onto and thresholds to filter the projections.
 
-    The result is a matrix where entry ``M[i,j]`` is :math:`\chi(K_{a_i})` for the direction :math:`\omega_j` where :math:`a_i` is the ith entry in ``self.thresholds``, and :math:`\omega_j` is the ith entry in ``self.thetas``.
+    The result is a matrix where entry ``M[i,j]`` is :math:`\chi(K_{a_i})` for the direction :math:`\omega_j`
+    where :math:`a_i` is the ith entry in ``self.thresholds``, and :math:`\omega_j` is the jth entry in ``self.directions``.
 
     Attributes
-        num_dirs (int):
-            The number of directions to consider in the matrix.
-        num_thresh (int):
-            The number of thresholds to consider in the matrix.
-        directions (Directions):
-            The directions to consider for projection.
-        bound_radius (float):
-            Either ``None``, or a positive radius of the bounding circle.
+    ----------
+    num_dirs : int
+        The number of directions to consider in the matrix.
+    num_thresh : int
+        The number of thresholds to consider in the matrix.
+    directions : Directions
+        The directions to consider for projection.
+    bound_radius : float
+        Either ``None``, or a positive radius of the bounding circle.
+
+    Example:
+        >>> from ect import ECT, EmbeddedComplex
+        >>> from ect import EmbeddedGraph
+        >>> complex = EmbeddedComplex()
+        >>> complex.add_node(0, [0, 0])
+        >>> complex.add_node(1, [1, 0])
+        >>> complex.add_edge(0, 1)
+        >>> ect = ECT(num_dirs=10, num_thresh=10) # chooses 10 uniform directions and 10 thresholds
+        >>> result = ect.calculate(complex)
+        >>> result.plot()
     """
 
     def __init__(