Upload to github

Author: Kaleb D Ruscitti

.gitignore

@@ -0,0 +1,3 @@
+.ipynb_checkpoints/*
+__pycache__/*
+mapperplayground.ipynb

DemoV0.1.ipynb

@@ -0,0 +1,53 @@
+## (Unclassified//OUO) Mapper' V.0.1 - June '24
+This is a mostly-working version of the mapper' code for generating graphs & sankey diagrams of timestamped data.
+Direct questions to Kaleb D. Ruscitti; ([email protected] before Aug 23 2024, or [email protected] afterthat).
+
+### Components
+There are three subcomponents
+1. `temporal_grapher` - this is the original code which implements mapper' and builds the graph object.
+2. `weighted fast_hdbscan` - HDBSCAN but the points are weighted; thanks Patsy Greenwood for writing this code :)
+3. `modified holoviews` - A copy of holoviews with the Sankey diagram code mangled to work with mass creation & destruction.
+
+### Conda Env
+The environment.yml file contains a dump of my conda env when I tested this code. 
+Stack overflow tells me that you can make a copy of the environment by running 
+`conda env create -f environment.yml`
+Worst case scenario you can just manually install all the usual packages. Just don't install holoviews or HDBSCAN to 
+avoid collisions.
+
+### Usage
+The file `DemoV0.1.ipynb` is a start-to-finish example of how to generate a Sankey diagram with this package.
+
+### Parameters
+Since temporal grapher is mostly undocumented, let me quickly mention a few choices you can make. 
+
+`HDBSCAN(min_cluster_size=n)`
+This is the usual HDBSCAN parameter, but now that the points are weighted, and the weights are strictly less than 1, you generally want to set this a bit lower than you might usually do.
+
+#### `tm.TemporalGraph()` parameters
+
+##### Checkpoints
+In mapper' there are no slices anymore. Slices have been replaced by checkpoints, which are single time points around
+which you wish to cluster. You can either pass tm.TemporalGraph() a list of checkpoints;  `checkpoints = arrayLike`
+or you can use the `N_checkpoints = int` and `slice_method = str` parameters to have it generate checkpoints for you.
+
+`slice-method` takes either 'time' or 'data'. The time option generates checkpoints evenly spaced in time, and the data
+option generates checkpoints evenly spaced in the number of data points.
+
+#### Temporal kernel parameters 
+The temporal kernel is used to give the points weight in time. You can pass a kernel function to tm.TemporalGraph
+`kernel=myFunc`. The default is `temporal_mapper.weighted_clusters.gaussian` which is a Gaussian kernel. If your kernel
+function takes parameters, you can pass `kernel_params = (param1, param2, ...)`
+
+If you want to recover original mapper, you can pass `kernel = temporal_mapper.weighted_clusters.square`. This has a 
+required parameter `kernel_params=(overlap,)` which is the amount of overlap between slices. If in doubt, set it = 1.
+
+The parameter `rate_sensitivity` can be any number >=0, or -1. This controls how sensitive the temporal kernel is to 
+changes in the temporal density of your data. This is an exponent factor; at the default setting (= 1.) points
+with double the temporal density will have a kernel that is half as wide. At sensitivity 2, double density gives 1/4 as 
+wide, and so on. The option -1 sets the scale to be logarithmic; 10x as dense = 1/2 as wide.
+
+### A note on the Holoviews code
+I'm not sure why, but sometimes when you try to plot the Sankey diagram it throws an error like `no plotting option Sankey`
+(I can't recreate it and I don't remember exactly what the error says). If this happens just reload the kernel and run 
+the code again top-down. Not sure what is causing this one.