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V4 #1111

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merged 43 commits into from
May 14, 2024
Merged

V4 #1111

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57b634d
Mixed subtree processing (#981)
mgeplf Apr 25, 2022
9a12f38
Refactor tests for test_mixed.py (#1027)
eleftherioszisis Apr 27, 2022
82ceb48
Remove deprecations (#1026)
eleftherioszisis Apr 27, 2022
ef56cbc
Fix type order of acD warning (#1031)
eleftherioszisis May 2, 2022
d66d037
Use readonly morphio Morphology (#979)
eleftherioszisis May 3, 2022
f6451f6
Remove deprecated viewer module (#1032)
eleftherioszisis May 3, 2022
580bd1a
Morphology level radial distance features use the soma as reference p…
eleftherioszisis May 9, 2022
006cafc
Remove deprecated bifurcationfunc (#1033)
eleftherioszisis May 9, 2022
5901eb2
Expose subtree processing from the morph_stats api (#1034)
eleftherioszisis May 12, 2022
8ac8eac
Remove pyXX prefix for lint, docs, and coverage (#1038)
eleftherioszisis May 18, 2022
d68d656
Fix tutorials and add tutorial testenv (#1039)
eleftherioszisis May 19, 2022
ed338f3
Add isort for formatting/linting (#1040)
eleftherioszisis May 20, 2022
0f3b8d0
Add testing of example scripts (#1041)
eleftherioszisis May 24, 2022
08270b2
Update v4 with latest master (#1044)
eleftherioszisis May 31, 2022
367544e
Make documentation/docstrings testable (#1035)
eleftherioszisis Jun 7, 2022
94f79e5
Add black to neurom, format everything, and add to lint (#1042)
eleftherioszisis Jun 7, 2022
2ff9737
Fix load_morpholgies to always resolve paths (#1047)
eleftherioszisis Jun 16, 2022
18871f2
Fix QhullError warning (#1048)
eleftherioszisis Jun 17, 2022
41ec17f
allow Morphology objects to be either mut or immut (#1049)
mgeplf Jul 8, 2022
8bddfc9
Sync with master (#1055)
eleftherioszisis Sep 20, 2022
45ae28b
Feat: Ensure all features return built-in types (#1064)
adrien-berchet Oct 10, 2022
77dcaff
Load mixed expected results from json (#1070)
eleftherioszisis Mar 17, 2023
1a5453e
Proposal for v4 composite types (#1071)
adrien-berchet Jul 6, 2023
e2101dc
Merge remote-tracking branch 'origin/master' into v4
eleftherioszisis Jan 24, 2024
28f0d67
Merge remote-tracking branch 'origin/master' into v4
mgeplf Apr 4, 2024
6462553
Fix pytest-cov for py311 & py312
eleftherioszisis Apr 5, 2024
556d848
Remove NeuriteType register/unregister
eleftherioszisis Apr 5, 2024
f4ad9a8
Fix docs
eleftherioszisis Apr 5, 2024
4d28b17
Fix CHANGELOG.rst docs issue
eleftherioszisis Apr 5, 2024
38aa876
Remove unused imports
eleftherioszisis Apr 5, 2024
35d2b10
Update docs
eleftherioszisis Apr 8, 2024
c8f66ca
Remove comma
eleftherioszisis Apr 8, 2024
6bdf13f
Update doc
eleftherioszisis Apr 9, 2024
69a0073
Update CHANGELOG.rst
eleftherioszisis Apr 9, 2024
c8c1ea7
Format long lists in tests (#1057)
adrien-berchet Apr 16, 2024
4672c78
Fix NeuriteType for Python 3.12.3 (#1116)
adrien-berchet Apr 17, 2024
90224b1
Replace iter_* methods by properties in core objects and improve iter…
adrien-berchet Apr 18, 2024
985a4dd
Add __version__ attribute (#1117)
adrien-berchet Apr 23, 2024
98b5326
Decouple Morphology constructor from io (#1120)
eleftherioszisis Apr 25, 2024
8ad258b
Move soma methods to functions (#1118)
eleftherioszisis May 2, 2024
18670a6
Add note for radial distances in migration guides
eleftherioszisis May 3, 2024
5237448
Merge master
eleftherioszisis May 14, 2024
ab906d1
Fix
eleftherioszisis May 14, 2024
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18 changes: 18 additions & 0 deletions CHANGELOG.rst
Original file line number Diff line number Diff line change
@@ -1,6 +1,24 @@
Changelog
=========

Version 4.0.0
-------------

- Morphology class accepts only morphio objects, not files anymore. (#1120)
- Replace ``iter_*`` methods by properties in core objects and improve ``iter_segments``. (#1054)
- NeuriteType extended to allow mixed type declarations as tuple of ints. (#1071)
- All features return built-in types (#1064)
- Morphology class also allows mutable morphio objects to be passed explicitly. (#1049)
- Morphology class uses morphio immutable class by composition, istead of inheritance. (#979)
- Morphology level radial distance features use the somata as reference point. (#1030)
- Make ``neurom.core.Population`` resolve paths. Symlinks are not resolved. (#1047)
- Mixed subtree processing can be used in morph_stats app via the use_subtrees flag. (#1034)
- ``neurom.view.[plot_tree|plot_tree3d|plot_soma|plot_soma3D]`` were hidden from the
neurom.view module. They can still be imported from neurom.view.matplotlib_impl. (#1032)
- Mixed subtree processing. (#981)
- Deprecated modules and classes were removed. (#1026)


Version 3.2.3
-------------

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220 changes: 0 additions & 220 deletions doc/Makefile

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2 changes: 0 additions & 2 deletions doc/clean.sh

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