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Devel cleaning_cluster_population - #152

Merged

SimoneMartino98 merged 37 commits into

GMPavanLab:mainfrom

ChiaraLionello:devel-cleaning-cluster-pop

Feb 16, 2026

Merged

Devel cleaning_cluster_population#152
SimoneMartino98 merged 37 commits into
GMPavanLab:mainfrom
ChiaraLionello:devel-cleaning-cluster-pop

Commits on Jan 13, 2026
- Addition of a function that cleans cluster population for 2D labels.
  ChiaraLionello
  committed
  d2f4369
Commits on Jan 14, 2026
- cleaning_cluster_population now cleans also 3D labels.
  ChiaraLionello
  committed
  6cf5161
Commits on Jan 22, 2026
- Documentation added to cleaning_cluster_population.
  ChiaraLionello
  committed
  ff137be
- removed default for assigned_env.
  ChiaraLionello
  committed
  2314e3f
- better explained function doc.
  ChiaraLionello
  committed
  5e67c2c
- Now get_onion_analysis returns labels.
  ChiaraLionello
  committed
  86646a3
- Added excluded_env.
  ChiaraLionello
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  dcc2fea
- get_onion_analysis return list_of_labels.
  ChiaraLionello
  committed
  f78d066
- Added a warning for excluded_env.
  ChiaraLionello
  committed
  8d78027
- Added test for cleaning_cluster_population.
  ChiaraLionello
  committed
  f31af59
- mypy fixes.
  ChiaraLionello
  committed
  124167c
Commits on Jan 27, 2026
- Added warning function.
  ChiaraLionello
  committed
  178cfd3
- test_cluster uses np.array_equal.
  ChiaraLionello
  committed
  72db13d
Commits on Feb 3, 2026
- Merge branch 'GMPavanLab:main' into devel-cleaning-cluster-pop
  ChiaraLionello
  authored
  1f857db
Commits on Feb 5, 2026
- change default of logger auto_recording to false.
  ChiaraLionello
  committed
  4b8a45d
Commits on Feb 9, 2026
- fixed variable name in doctest.
  ChiaraLionello
  committed
  cb9149b
- changed format of labels in get_onion_analysis.
  ChiaraLionello
  committed
  d440983
- Added tutorial for cleaning_cluster_population in tips_and_tricks section.
  ChiaraLionello
  committed
  917b609
Commits on Feb 10, 2026
- Update docs/source/logs.rst.
  
  ChiaraLionello
  and
  SimoneMartino98
  authored
  89d45a4
- Merge branch 'GMPavanLab:main' into devel-cleaning-cluster-pop
  ChiaraLionello
  authored
  e11fd64
- Changed logo for tips and tricks tutorial section.
  ChiaraLionello
  committed
  3910ce6
Commits on Feb 11, 2026
- Small changes.
  ChiaraLionello
  committed
  2410328
- Updates tutorial section removing tips_and_tricks and dividing fundamentals from advanced topics.
  ChiaraLionello
  committed
  a50df17
- Small changes (typo).
  ChiaraLionello
  committed
  e6f2ff2
- changed check in dimensions and added elif.
  ChiaraLionello
  committed
  6d281cc
- reformatted file.
  ChiaraLionello
  committed
  a4dd2b6
Commits on Feb 12, 2026
- Better explenation of how to obtain cleaned_onion_output.
  ChiaraLionello
  committed
  856bd52
Commits on Feb 13, 2026
- Update docs/source/logs.rst
  ChiaraLionello
  authored
  8ad9263
- typo.
  ChiaraLionello
  committed
  cfad777
- All the import are in the first python code-block.
  ChiaraLionello
  committed
  7d42933
- Added explenation about the colors in cluster_population.png.
  ChiaraLionello
  committed
  6be5091
- Removed usless comment.
  ChiaraLionello
  committed
  258e6a4
- Added general path to load the trajectory.
  ChiaraLionello
  committed
  ee1b61f
- Added general path to load the trajectory.
  ChiaraLionello
  committed
  9dbc76e
Commits on Feb 16, 2026
- in the tutorials the path are consistent.
  ChiaraLionello
  committed
  b713ed7
- Updated citation to the paper.
  ChiaraLionello
  committed
  c438af9
- minor fixes.
  ChiaraLionello
  committed
  5baf6ea

Commits

Commits on Jan 13, 2026

Commits on Jan 14, 2026

Commits on Jan 22, 2026

Commits on Jan 27, 2026

Commits on Feb 3, 2026

Commits on Feb 5, 2026

Commits on Feb 9, 2026

Commits on Feb 10, 2026

Commits on Feb 11, 2026

Commits on Feb 12, 2026

Commits on Feb 13, 2026

Commits on Feb 16, 2026