Merge pull request #88 from MunchLab/drawing_improvements

Updating draw function, now has its own constrained layout generator rather than the old spring layout version.

Author: lizliz

Makefile

@@ -13,6 +13,15 @@ docs:
 	rsync -a docs/html/ docs/
 	rm -rf docs/html
 
+.PHONY: docs-execute
+docs-execute:
+	# Running sphinx-build and forcing nbsphinx to execute all notebooks.
+	rm -rf docs
+	mkdir -p docs
+	sphinx-build -M html doc_source docs -D nbsphinx_execute=always
+	rsync -a docs/html/ docs/
+	rm -rf docs/html
+
 install-editable:
 	@pip install -e .
 
@@ -41,6 +50,7 @@ help:
 	@echo "  make format              - Format code using black"
 	@echo "  make install-editable     - Install the package in editable mode for development"
 	@echo "  make docs                - Build the documentation in the docs/ folder"
+	@echo "  make docs-execute        - Build docs and execute all notebooks"
 	@echo "  make release             - Build the package for release"
 	@echo "  make tests               - Run the unit tests"
 	@echo "  make install-requirements- Install all dependencies from requirements.txt"

cereeberus/cereeberus/compute/computemapper.py

@@ -119,14 +119,14 @@ def __addedges(clusterpoints):
 # Does the Mapper Algorithm in order
 def computeMapper(pointcloud, lensfunction, cover, clusteralgorithm):
     """
-    Computes the mapper graph of an input function. 
-    
-    The point cloud should be given as a list of tuples or as a numpy array. 
-    
-    The lens function should be given as either a list of numbers with the same length as the number of points; or as a callable function where :math:`f(point) = \text{value}` so long as the function can be determined from the coordinate values of the point.    
-    
-    The cover should be given as a list of intervals. This can be done, for example, using the 'cereeberus.cover' function in this module, which takes in a minimum, maximum, number of covers, and percentage of overlap to create a cover. 
-    
+    Computes the mapper graph of an input function.
+
+    The point cloud should be given as a list of tuples or as a numpy array.
+
+    The lens function should be given as either a list of numbers with the same length as the number of points; or as a callable function where :math:`f(point) = \text{value}` so long as the function can be determined from the coordinate values of the point.
+
+    The cover should be given as a list of intervals. This can be done, for example, using the 'cereeberus.cover' function in this module, which takes in a minimum, maximum, number of covers, and percentage of overlap to create a cover.
+
     The clustering algorithm should be given as a callable that takes in a point cloud and outputs cluster labels (for example, `sklearn.cluster.DBSCAN(min_samples=2,eps=0.3).fit`).
 
     Parameters:
@@ -138,12 +138,12 @@ def computeMapper(pointcloud, lensfunction, cover, clusteralgorithm):
     Returns:
         A `MapperGraph` object representing the mapper graph of the input data and lens function.
     """
-    
-    lensfunctionoutput = __runlensfunction(lensfunction, pointcloud)                           
+
+    lensfunctionoutput = __runlensfunction(lensfunction, pointcloud)
     coveringsets = __createcoveringsets(lensfunctionoutput, cover)
     clusterpoints = __cluster(coveringsets, clusteralgorithm)
     outputgraph = __addedges(clusterpoints)
-    
+
     return outputgraph
 
 

cereeberus/cereeberus/compute/computereeb.py

@@ -79,8 +79,7 @@ def computeReeb(K: LowerStar, verbose=False):
     # A horizontal edge (both endpoints at the same height) must be processed
     # within one batch so it properly merges its endpoints into a single Reeb node.
     grouped = [
-        (filt, list(grp))
-        for filt, grp in _groupby(funcVals, key=lambda x: x[1])
+        (filt, list(grp)) for filt, grp in _groupby(funcVals, key=lambda x: x[1])
     ]
 
     R = ReebGraph()
@@ -101,9 +100,7 @@ def _dedup(lst):
 
     for group_idx, (filt, group_verts) in enumerate(grouped):
         now_min = filt
-        now_max = (
-            grouped[group_idx + 1][0] if group_idx + 1 < len(grouped) else np.inf
-        )
+        now_max = grouped[group_idx + 1][0] if group_idx + 1 < len(grouped) else np.inf
         vert_names = [v for v, _ in group_verts]
 
         if verbose:
@@ -183,9 +180,7 @@ def _dedup(lst):
             for e in edges_at_prev_level:
                 prev_comp = vert_to_component[e]
                 if any(
-                    is_face(prev_simp, simp)
-                    for simp in comp
-                    for prev_simp in prev_comp
+                    is_face(prev_simp, simp) for simp in comp for prev_simp in prev_comp
                 ):
                     R.add_edge(e, nextNodeName)
 
@@ -227,11 +222,8 @@ def _dedup(lst):
             for v in verts_at_level:
                 prev_comp = vert_to_component[v]
                 if any(
-                    is_face(simp, prev_simp)
-                    for simp in comp
-                    for prev_simp in prev_comp
+                    is_face(simp, prev_simp) for simp in comp for prev_simp in prev_comp
                 ):
                     R.add_edge(v, e_name)
 
     return R
-