Add mmain and other major updates (#44)

* Move paths to a separate file

* Add mmain reader

* Add a verbosity flag

* Fix imports

* Fix bug

* Rename files

* Return ultimate parents

* Add script to generate mmain

* Remove mmain path

* edit path

* Add mmain path

* Change function name

* Rename function

* Turn off verbose

* Fix list requirement

* Edit init match paths

* Fix init pathing

* Edit paths docs

* Edit dumpdir name

* Rename path

* Fix split paths

* Remove unused import

* Add comment

* Update readme

* remove read mmain

* Rename haloatalogue

* Fix minor bugs

* Update nbs

* Add create directory option

* Move split jobs

* Move spliot jobs

* Remove splitting

* Add import

* Edit script

* Deeper split folder

* Fix paths bug

* Rename catalogue

* Rename Catalogue

* Add new clumpread

* Edit paths

* add knn paths

* Update commenting

* Update imports

* Add more conversions

* Update temp file

* Add a note

* Add catalogue

* Cooment

* Update TODO

* Update script

* add nb

* Update

* pep8

* edit paths & pep8

* Fix knn auto paths

* add paths docs

* Add auto and cross knn paths

* Add new paths

* Simplify tpcf reading

* pep8 patch

* update readme

* Update progress

* pep8

* pep8

* pep8

* pep8

* pep8

* pep8

* pep8

* pep8

* pep8

* pep8

* pep8

* pep8

* pep8

* pep8

* pep8

* Pep 8 and restructure

* add lambda spin

* add clump and halo

* add checks

* Edit halo profile fit

* Update gitignore

* backup script

README.md

@@ -2,8 +2,16 @@
 
 
 ##  Project Overlap
-- [ ] Calculate the overlap between all 101 IC realisations on DiRAC.
+- [x] Clean up the kNN paths in the summary.
+- [x] Clean up the 2PCF paths in the summary.
 
+- [ ] Sort out the splitting of individual clumps.
+- [ ] Update the fitting scripts to work for clumps and parent halos.
+- [ ] Calculated fitted quantities for clumps and parent halos and add them to the catalogues.
+- [ ] Update overlap scripts to work with summed parent halos.
+- [ ] Update the clustering scripts to work with clumps instead.
+
+- [ ] Calculate the overlap between all 101 IC realisations on DiRAC.
 
 
 ## Project Clustering
@@ -20,7 +28,7 @@
 - [x] For the cross-correlation try making the second field randoms.
 - [x] Clean up the reader code.
 - [x] Correct the crossing script.
-- [ ] Get started with the 2PCF calculation.
+- [x] Get started with the 2PCF calculation.
 
 ## Project Environmental Dependence
 - [ ] Add gradient and Hessian of the overdensity field.