Use readonly morphio Morphology #979
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eleftherioszisis
commented
Feb 9, 2022
•
eleftherioszisis
commented
- Use exclusively morphio's readonly Morphology
- Morphology inheritance turned into composition
- Direct mutation removed
- Section booleaness removed as it is more confusing than useful
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It looks like there is no equality defined for readonly sections: def test_iter_sections_default():
ref = [s for n in POP.neurites for s in n.iter_sections()]
> assert (ref ==
[n for n in iter_sections(POP)])
E assert [Section(id=0...dren: 0>, ...] == [Section(id=0...dren: 0>, ...]
E At index 0 diff: Section(id=0, type=2, n_points=11)<parent: Section(id=None), nchildren: 2> != Section(id=0, type=2, n_points=11)<parent: Section(id=None), nchildren: 2>
E Use -v to get the full diff
tests/core/test_iter.py:103: AssertionError |
mgeplf
reviewed
Feb 11, 2022
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eleftherioszisis
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v4
Codecov Report
@@ Coverage Diff @@
## v4 #979 +/- ##
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Coverage ? 100.00%
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Files ? 36
Lines ? 2482
Branches ? 0
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Hits ? 2482
Misses ? 0
Partials ? 0 |
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it's fine most of our code have neurom<4 I think :P |
eleftherioszisis
commented
May 2, 2022
Comment on lines
-514
to
-517
| def __nonzero__(self): | ||
| """If has root node.""" | ||
| return bool(self.morphio_root_node) | ||
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@mgeplf you mentioned you don't agree with removing the section booleaness. Is this still true?
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no; I can see how it's confusing; one can check if there are children more explicitly.
eleftherioszisis
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Jun 7, 2022
Switch to using the morphio readonly morphology instead of mut Co-authored-by: Mike Gevaert <[email protected]>
eleftherioszisis
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May 14, 2024
* Mixed subtree processing (#981) * Refactor tests for test_mixed.py (#1027) * Remove deprecated modules and functions/classes & warnings (#1026, #1032) * Use readonly morphio Morphology by default (#979) * Morphology level radial distance features use the soma as reference point (#1030) * Expose subtree processing from the morph_stats api (#1034) * Remove pyXX prefix for lint, docs, and coverage (#1038) * Fix tutorials and add tutorial testenv (#1039) * Add isort for formatting/linting (#1040) * Add testing of example scripts (#1041) * Make documentation/docstrings testable (#1035) * Add black to neurom, format everything, and add to lint (#1042) * Fix load_morpholgies to always resolve paths (#1047) * allow Morphology objects to be either mut or immut (#1049) * Replace iter_* methods by properties in core objects and improve iter_segments (#1054) * Decouple Morphology constructor from io (#1120) * Move soma methods to functions (#1118)
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