… the ID rather than the raw file ID to be consistent in meaning between MPI and non-MPI AHF versions. Also, remove spurious extra line in filename method.

…thin the file rather than the value in the ID column of the file. Now each handler defines a flad when this needs to occur

…m ones from MPI runs. Add a separate function to test this conversion specifically.

…the catalog of each halo. Include this in enumerate and iter_rows functions. Ensure that n_total is used to determine whether a halo satisfies min_halo_particles to ensure that ordering remains robust.

…catalog_id_offset

to these values. To remain consistent, children calculations will use only
the raw halo ID number with no offset applied

… ID numbers.

Fix the ID grp stat file reader to have catalog indices equal to the grp number
so that these values can be used to access halo catalog correctly via pynbody.

…nclude both finder_id and catalog_index as inputs

…utput_testing input handlers,

and Halo class functions

Fix tracker and phantom halo initialization to include a catalog_index input
Fix bh halo linking to now use catalog_index
update ahf trees test to use catalog_index

… statfile

-Update ahf_trees to use the raw finder_id values from tree data files
-Perform correct halo object initialization in manager.py
-If unset, make halo_number equal to the catalog index rather than finder_id
-Update crosslink to utilize catalog_index rather than finder_id
-Update property importer to expect correct number if outputs from stat file reader
-Update object cache to use catalog_index rather than finder_id

make sure that the adapted enumerate returns the expected default result structure

…r_id

with an additional argument in resolve

Include additional argument when dealing with timestep cache for Proxy Objects

…l particle

count (Gas + Stars + DM) rather than just dark matter

…x, finder_id, halo_number)

to provide backwards compatibility but are now deprecated

remove unneeded commented-out code

re-write docstrings for iter_rows_raw functions to actually reflect the
nature of the outputs.

… that

identifies halos by either finder_id or catalog_index separately. Include this change
in both the proxy object classes and property importer where appropriate.

make the AmigaIDLStatFile iter_rows_raw function more streamlined

and change all other variables and function names to be consistent with
this change where appropriate