kNN-CDF implementation (#34)

* Rewrite doc

* add kNN

* edit loading of samples with no init

* Add verbosity flag

* add KNN submission script

* do not make peaked cdf by default

* Add submit script

* stop ignore sh

* Add mass thresholding

* Edit gitignore

* edits

* Space points in logspace

* Calculate for all ICs

* Update TODO

* Add dtype support

* Update readme

* Update nb

README.md

@@ -1,24 +1,16 @@
-# CSiBORGTools
+# CSiBORG Analysis
 
 
-### Questions
-- How well can observed clusters be matched to CSiBORG? Do their masses agree?
-- Is the number of clusters in CSiBORG consistent?
+##  Project Overlap
+- [ ] Calculate the overlap between all 101 IC realisations on DiRAC.
 
-## CSiBORG Galaxy Environmental Dependence
 
-### TODO
+
+## Project Clustering
+- [ ] Add uncertainty to the kNN-CDF autocorrelation.
+- [ ] Add the joint kNN-CDF calculation.
+- [ ] Make kNN-CDF more memory friendly if generating many randoms.
+
+
+## Project Environmental Dependence
 - [ ] Add gradient and Hessian of the overdensity field.
-
-
-### Questions
-- Environmental dependence of:
-  - $M_*$, colour and SFR.
-  - Galaxy alignment.
-  - HI content.
-
-- Fields to calculate:
-    1. Overdensity field $\delta$
-    2. Gradient and Hessian of $\delta$
-    3. Gravitational field $\Phi$
-    4. Gradient and Hessian of $\Phi$