3d trunk angles #49

arnaudon · 2022-09-12T08:10:31Z

No description provided.

neurots/extract_input/input_distributions.py

neurots/extract_input/input_parameters.py

neurots/generate/grower.py

neurots/generate/orientations.py

neurots/schemas/distributions.json

arnaudon · 2022-09-14T13:14:49Z

@lidakanari @adrien-berchet , I've clean up the main code, once we agree on it, I'll clean up the schema/tests so we can merge. I'm done with it for now.

neurots/extract_input/from_neurom.py

docs/source/conf.py

neurots/extract_input/from_neurom.py

neurots/generate/orientations.py

neurots/generate/grower.py

neurots/extract_input/from_neurom.py

neurots/extract_input/input_distributions.py

neurots/generate/orientations.py

neurots/extract_input/from_neurom.py

neurots/generate/orientations.py

neurots/generate/grower.py

arnaudon · 2022-09-19T14:23:39Z

@lidakanari , I wait on your green light to start cleaning up test/schemas

neurots/generate/grower.py

neurots/extract_input/from_neurom.py

neurots/extract_input/input_parameters.py

neurots/generate/orientations.py

codecov · 2022-09-26T12:49:25Z

Codecov Report

Merging #49 (c18688a) into main (01c941f) will increase coverage by 0.11%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main      #49      +/-   ##
==========================================
+ Coverage   97.44%   97.56%   +0.11%     
==========================================
  Files          38       39       +1     
  Lines        1954     2132     +178     
  Branches      288      324      +36     
==========================================
+ Hits         1904     2080     +176     
- Misses         34       35       +1     
- Partials       16       17       +1

Flag	Coverage Δ
pytest	`97.56% <100.00%> (+0.11%)`	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
neurots/astrocyte/grower.py	`75.86% <ø> (ø)`
neurots/astrocyte/tree.py	`100.00% <ø> (ø)`
neurots/extract_input/input_distributions.py	`100.00% <ø> (ø)`
neurots/extract_input/input_parameters.py	`97.43% <ø> (ø)`
neurots/generate/algorithms/tmdgrower.py	`99.24% <ø> (-0.02%)`	⬇️
neurots/generate/tree.py	`98.90% <ø> (-0.02%)`	⬇️
neurots/extract_input/from_neurom.py	`96.49% <100.00%> (-3.51%)`	⬇️
neurots/generate/grower.py	`100.00% <100.00%> (ø)`
neurots/generate/orientations.py	`100.00% <100.00%> (ø)`
neurots/morphmath/sample.py	`100.00% <100.00%> (ø)`
... and 5 more

Co-authored-by: Adrien Berchet <adrien.berchet@gmail.com>

arnaudon · 2023-02-13T15:32:35Z

Finally! I can't spot what is not covered, maybe codecov needs some time to be up to date.

arnaudon · 2023-02-16T13:44:45Z

ALL GREEEEN!!!!!!

adrien-berchet · 2023-02-16T14:00:36Z

ALL GREEEEN!!!!!!

Yay 🥳

neurots/schemas/distributions.json

neurots/schemas/parameters.json

Co-authored-by: Adrien Berchet <adrien.berchet@epfl.ch>

neurots/schemas/parameters.json

adrien-berchet

LGTM!

lidakanari · 2023-03-13T08:47:22Z

Finally double checking and all is good from my side to merge this one. @eleftherioszisis if you want to check for astrocytes please provide feedback for this, otherwise we are ok to merge this one.

arnaudon · 2023-03-13T09:40:12Z

great thanks! I'll then make a minor release of neurots, so we can merge the dependencies

arnaudon force-pushed the trunk_angles_rebase branch 2 times, most recently from 09832c3 to c7b6b59 Compare September 13, 2022 15:23

arnaudon requested a review from lidakanari September 13, 2022 15:23

arnaudon marked this pull request as ready for review September 13, 2022 15:24

lidakanari reviewed Sep 14, 2022

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arnaudon changed the title ~~Trunk angles rebase~~ 3d trunk angles Sep 14, 2022

arnaudon force-pushed the trunk_angles_rebase branch 2 times, most recently from 30e23cc to 723e9cf Compare September 14, 2022 11:38

arnaudon marked this pull request as draft September 14, 2022 12:41

arnaudon self-assigned this Sep 14, 2022

arnaudon marked this pull request as ready for review September 14, 2022 13:14

arnaudon requested a review from adrien-berchet September 14, 2022 13:14

adrien-berchet reviewed Sep 14, 2022

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arnaudon commented Sep 14, 2022

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eleftherioszisis reviewed Sep 16, 2022

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eleftherioszisis reviewed Sep 19, 2022

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lidakanari requested changes Sep 23, 2022

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adrien-berchet mentioned this pull request Oct 7, 2022

Feat: Rework input validation process #52

Merged

arnaudon and others added 8 commits February 8, 2023 09:28

Feat: New trunk angle implementation (squashed)

54b8d98

Test: Fix function comparison

121c015

Update neurots/generate/soma.py

b158d1b

Co-authored-by: Adrien Berchet <adrien.berchet@gmail.com>

Update neurots/extract_input/from_neurom.py

15c8560

Co-authored-by: Adrien Berchet <adrien.berchet@gmail.com>

Update neurots/extract_input/from_neurom.py

2dfd926

Co-authored-by: Adrien Berchet <adrien.berchet@gmail.com>

Update neurots/extract_input/from_neurom.py

bc469f3

Co-authored-by: Adrien Berchet <adrien.berchet@gmail.com>

Update neurots/extract_input/input_parameters.py

bec41a6

Co-authored-by: Adrien Berchet <adrien.berchet@gmail.com>

Update neurots/extract_input/input_parameters.py

6c10d37

Co-authored-by: Adrien Berchet <adrien.berchet@gmail.com>

arnaudon added 3 commits February 13, 2023 15:24

fix hook

19f87ec

daaaah

0fa6f3f

format

48b4645

adrien-berchet and others added 5 commits February 16, 2023 12:53

Merge branch 'main' into trunk_angles_rebase

7669c4e

fix check_3d

486060f

fixt

ad8e4fc

improve cov

9ed97ed

improve cov

e773c58

adrien-berchet reviewed Feb 22, 2023

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arnaudon and others added 5 commits March 3, 2023 07:52

Update neurots/schemas/parameters.json

7b02853

Co-authored-by: Adrien Berchet <adrien.berchet@epfl.ch>

fix schema

ceb1092

Fix description and indent in schema

047c51b

use mean/std instead of tuple

5cff823

merge

e2b96c4

adrien-berchet reviewed Mar 3, 2023

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arnaudon added 5 commits March 3, 2023 12:19

fix test file

891d126

fix

7f72220

bump numpy

cbd9178

lint

b6aedaf

improve schema

8deae28

adrien-berchet approved these changes Mar 3, 2023

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fix docstring

c18688a

lidakanari approved these changes Mar 13, 2023

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arnaudon merged commit 912320d into main Mar 13, 2023

arnaudon deleted the trunk_angles_rebase branch March 13, 2023 09:40

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3d trunk angles #49

3d trunk angles #49

arnaudon commented Sep 12, 2022

arnaudon commented Sep 14, 2022

arnaudon commented Sep 19, 2022

codecov bot commented Sep 26, 2022 •

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lidakanari commented Mar 13, 2023

arnaudon commented Mar 13, 2023

3d trunk angles #49

3d trunk angles #49

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lidakanari commented Mar 13, 2023

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