Speed up overlap (#27)

* Edit improt

* Simplify patch size calculation

* Add patch size percentiles

* Add various percentiles

* Remove  comment

* Update TODO

* Change to 95th percentile

* Add import

* Add KNN properties

* Add new matching initial condition

* Add import

* Remove import

* Add fast neighbours option

* Further edits to fast neighbours

* add imports

* add new overlap calculation and non-zero things

* Remove print

* Clean up code

* Fix small bug

* Remove comment

* Add run single cross match

* change values

* Edit hyperparams

* Add comment

* Add the argument parser

* Add new lagpatch calc

* New lagpatch calc

* Delete old patch definitions

* Make clump dumping once again optional

* Add lagpatch to the catalogue

* Edit print statement

* Fix small bug

* Remove init radius

* Change to lagpatch key

* Fix a small bug

* Fix little bug

README.md

@@ -3,10 +3,7 @@
 ## CSiBORG Matching
 
 ### TODO
-- [x] Implement CIC binning or an alternative scheme for nearby objects.
-- [x] Consistently locate region spanned by a single halo.
-- [x] Write a script to perform the matching on a node.
-- [x] Make a coarser grid for halos outside of the well resolved region.
+- [ ] Modify the call to tN
 
 ### Questions
 - What scaling of the search region? No reason for it to be a multiple of $R_{200c}$.