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Refactor prune_local #37

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Refactor prune_local #37

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In this PR:

  1. Renamed make_csrmatrix_noselfloop -> prune_local
  2. Renamed keep_all_local_dist -> do_prune_local, with the opposite meaning, i.e. do_prune_local = True is the same as keep_all_local_dist = False
  3. Added docstrings
  4. Added l2_std_factor as argument
  5. Removed unused discard_count
  6. Added tests for prune_local
  7. Renamed the following variables:
original new
distlist distances
row neighbors
updated_nn_ind updated_neighbors
updated_nn_weights updated_distances
ik index
rowi community_id
csr_graph csr_array
dist distance
keep_all_local_dist do_prune_local (opposite)

@ahill187
Merge pull request #1 from ahill187/fix-simplicial-set-embedding-bug
0278e06 
Fix simplicial set embedding bug
@ahill187
create a custom logger
54cfd50
@ahill187
replace all print statements with logging statements
891ae17
@ahill187
remove commented print statements
119a1af
@ahill187
Merge remote-tracking branch 'upstream/master'
7b87ff2
@ahill187
Merge pull request #8 from ahill187/logging
8e2749c 
Add logging
@ahill187
fix code line layout
3b770f6
@ahill187
remove unnecessary ==True and ==False
1a410f5
@ahill187
remove unnecessary dummy variables
6901748
@ahill187
remove unused variables
6aaae03
@ahill187
clean up comments
09b3ca6
@ahill187
make strings consistent
42a302e
@ahill187
make strings consistent
6f7a323
@ahill187
remove trailing whitespace
87d968a
@ahill187
update gitignore
7b87cd2
@ahill187
Merge branch 'code-cleanup' of https://github.com/ahill187/PARC into …
f7430a1 
…code-cleanup
@ahill187
rearrange run_toobig_PARC signature
966359f
@ahill187
Merge pull request #9 from ahill187/code-cleanup
fc4e249 
Code cleanup
@ahill187
move func_mode to utils
68042ac
@ahill187
add test for get_mode
8ac7a4e
@ahill187
modify get_mode docstring
b485cc7
@ahill187
Merge pull request #10 from ahill187/func-mode
61eb152 
`func_mode` -> `get_mode`
@ahill187
rename X_data, X_input, data -> x_data
dc99e66
@ahill187
rename true_label, true_labels -> y_data_true
56f4a9b
@ahill187
rename PARC_labels, labels -> y_data_pred
8c45f3d
@ahill187
rename PARC_labels_array -> y_data_pred_array
fe8ecc8
@ahill187
rename num_threads -> n_threads
7e6982d
@ahill187
rename N, n_cells, n_elements -> n_samples
571ce1a
@ahill187
rename small_pop -> small_community_size
af15b72
@ahill187
rename time_smallpop -> small_community_timeout
37fcf0f
@ahill187
rename run_PARC -> run_parc
3a21b6a
@ahill187
simplify find_partition logic
af0cf57
@ahill187
update logs
8d5a131
@ahill187
factor out get_leiden_partition
dab84ba
@ahill187
add tests for get_leiden_partition
63083bf
@ahill187
Merge pull request #14 from ahill187/get-leiden-partition
0fde470 
Factor out `get_leiden_partition`
@ahill187
rename knngraph_full to create_knn_graph
3a9a60a
@ahill187
clean up create_knn_graph
678fa34
@ahill187
rename k_umap -> knn
cb2b01d
@ahill187
set knn as argument
d323fa2
@ahill187
add tests for create_knn_graph
dc35c8e
@ahill187
rename graph -> csr_array
7ec52fc
@ahill187
Merge pull request #15 from ahill187/create-knn-graph
65434d8 
Refactor `knngraph_full` -> `create_knn_graph`
@ahill187
Rename make_csrmatrix_noselfloop -> prune_local
6ba48ef
@ahill187
rename keep_all_local_dist -> do_prune_local
7f1a2a3
@ahill187
remove unused discard_count
095a0b3
@ahill187
remove unnecessary comments
91fe748
@ahill187
rename distlist -> distances
8110841
@ahill187
add max_distance
b02b813
@ahill187
rename row -> neighbors
2bb3e68
@ahill187
rename updated_nn_ind -> updated_neighbors
0c3526d
@ahill187
rename updated_nn_weights -> updated_distances
c7bb875
@ahill187
rename ik -> index
54c1b08
@ahill187
rename rowi -> community_id
a90113e
@ahill187
rename csr_graph -> csr_array
1ed4b40
@ahill187
rename dist -> distance
0cfc2c2
@ahill187
clean up the prune_local function
73b5551
@ahill187
add l2_std_factor as argument to prune_local
8b58a53
@ahill187
add tests for prune_local
5bf9097
@ahill187 ahill187 mentioned this pull request Aug 13, 2024
Merged
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@ahill187