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Rename and modify fit_predict#47

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ahill187 wants to merge 164 commits intoShobiStassen:masterfrom
ahill187:fit
Open

Rename and modify fit_predict#47
ahill187 wants to merge 164 commits intoShobiStassen:masterfrom
ahill187:fit

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@ahill187 ahill187 commented Nov 11, 2024

Description

In this PR:

  1. Renamed run_parc -> fit_predict.
  2. Allow x_data to be passed into fit_predict.
  3. Return y_data_pred from fit_predict.
  4. Add new attribute community_counts.

@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 added 30 commits August 13, 2024 12:56
@ahill187
update the docstrings
dc61bee
@ahill187
add tests for make_knn_struct
588d0ee
@ahill187
Merge pull request #19 from ahill187/refactor-knn-struct-2
f00473a 
Refactor `make_knn_struct`
@ahill187
fix small_community_size bug
5e8cec6
@ahill187
Merge pull request #20 from ahill187/small-community-size
6dffd7d 
Fix `small_community_size` bug
@ahill187
add tests for run_parc
63d5e1f
@ahill187
add pytest.ini
1e66c5b
@ahill187
fix & bug
fe2e2b1
@ahill187
add large_community_id
f44e4a5
@ahill187
update log messages
5390162
@ahill187
rearrange constructor to match order of attributes
78175a3
@ahill187
add tests_workflow
ab0bf8f
@ahill187
fix bugs in tests
59b7e2c
@ahill187
cancel tests if one fails
d1f960e
@ahill187
change default logging level to 25
fb3617f
@ahill187
Merge pull request #21 from ahill187/tests
119c664 
Tests
@ahill187
add x_data setter
60b484c
@ahill187
modify the y_data_true setter
0a1f3fa
@ahill187
add y_data_pred setter
acc585a
@ahill187
allow x_data to be passed in as pd.DataFrame
0cf4fd4
@ahill187
fix y_data_true setter
4419f67
@ahill187
Merge pull request #22 from ahill187/input-data-types
0c8f322 
Input data types
@ahill187
clean up setup.py
23510b3
@ahill187
add requirements.txt
b72c2f1
@ahill187
Merge pull request #23 from ahill187/requirements-setup
8862598 
`requirements.txt` and `setup.py`
@ahill187
rename run_parc -> fit_predict
8cf1d9b
@ahill187
refactor pop_list -> community_counts
580c3e8
@ahill187
convert logging message to info
4c89daf
@ahill187
add docstrings to fit_predict
01e44ca
@ahill187
move time_start to top
296e320
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@ahill187