Releases | Open Source Science

https://github.com/bluebrain/neurom - v3.2.8

What's Changed

Replace pkg_resources with importlib in docs by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/1104
fix sdist so pypi upload can happen by @mgeplf in https://github.com/BlueBrain/NeuroM/pull/1105
github action: fix var name for sdist upload by @mgeplf in https://github.com/BlueBrain/NeuroM/pull/1106
fix location of readme, update links for badges and banner by @mgeplf in https://github.com/BlueBrain/NeuroM/pull/1107

Full Changelog: https://github.com/BlueBrain/NeuroM/compare/v3.2.7...v3.2.8

- Python
Published by mgeplf over 2 years ago

https://github.com/bluebrain/neurom - v3.2.7

What's Changed

update contributors to match git logs by @mgeplf in https://github.com/BlueBrain/NeuroM/pull/1100
do not use master for github actions by @mgeplf in https://github.com/BlueBrain/NeuroM/pull/1101

Full Changelog: https://github.com/BlueBrain/NeuroM/compare/v3.2.6...v3.2.7

- Python
Published by mgeplf over 2 years ago

https://github.com/bluebrain/neurom - v3.2.6

What's Changed

update soma for new morphio 3.3.7 error by @mgeplf in https://github.com/BlueBrain/NeuroM/pull/1089
modernize to pyproject.toml by @mgeplf in https://github.com/BlueBrain/NeuroM/pull/1088
fix examples after move to v3 by @mgeplf in https://github.com/BlueBrain/NeuroM/pull/1091
Remove pyXX prefix for lint, docs, and coverage by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/1092
Fix warnings in tests by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/1093
Add proper spacing in morph_stats docstring config path by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/1094
Fix tutorial & add tutorial testing by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/1095
Add testing of example scripts (#1041) by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/1096
Add testing for python3.12 by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/1098
try updating .zenodo.json by @mgeplf in https://github.com/BlueBrain/NeuroM/pull/1099

Full Changelog: https://github.com/BlueBrain/NeuroM/compare/v3.2.5...v3.2.6

- Python
Published by mgeplf over 2 years ago

https://github.com/bluebrain/neurom - Release 3.2.5

What's Changed

Remove shebang lines by @musicinmybrain in https://github.com/BlueBrain/NeuroM/pull/1083
Replace PyPI mock test dependency with unittest.mock by @musicinmybrain in https://github.com/BlueBrain/NeuroM/pull/1084
Add Zenodo author list by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/1086
Set readthedocs python to a version we know we have morphio wheels for by @mgeplf in https://github.com/BlueBrain/NeuroM/pull/1087

New Contributors

@musicinmybrain made their first contribution in https://github.com/BlueBrain/NeuroM/pull/1083

Full Changelog: https://github.com/BlueBrain/NeuroM/compare/v3.2.4...v3.2.5

- Python
Published by eleftherioszisis over 2 years ago

https://github.com/bluebrain/neurom - Release 3.2.4

What's Changed

Fix Rectangle kwarg error due to matplotlib==3.8 by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/1082

Full Changelog: https://github.com/BlueBrain/NeuroM/compare/v3.2.3...v3.2.4

- Python
Published by eleftherioszisis almost 3 years ago

https://github.com/bluebrain/neurom - Release 3.2.3

What's Changed

Remove duplicated deps jinja, sphinx by @stefanoantonel in https://github.com/BlueBrain/NeuroM/pull/1043
Remove single point contour somas in h5 and asc tests by @mgeplf in https://github.com/BlueBrain/NeuroM/pull/1045
Check that soma is not empty when features need it by @adrien-berchet in https://github.com/BlueBrain/NeuroM/pull/1073
Keep in sync with morphio 3.3.6, and the new SWC types that are avail… by @mgeplf in https://github.com/BlueBrain/NeuroM/pull/1075
Can pass List[Population] args to neurom.app.morphstats.extractdataframe by @adrien-berchet in https://github.com/BlueBrain/NeuroM/pull/1076
Fix neurom.app.morphstats.extractdataframe for Population objects with several workers by @adrien-berchet in https://github.com/BlueBrain/NeuroM/pull/1080

New Contributors

@stefanoantonel made their first contribution in https://github.com/BlueBrain/NeuroM/pull/1043

Full Changelog: https://github.com/BlueBrain/NeuroM/compare/v3.2.0...v3.2.3

- Python
Published by eleftherioszisis almost 3 years ago

https://github.com/bluebrain/neurom - v3.2.2

What's Changed

Fix QhullError warning by @GianlucaFicarelli in https://github.com/BlueBrain/NeuroM/pull/1063

New Contributors

@GianlucaFicarelli made their first contribution in https://github.com/BlueBrain/NeuroM/pull/1063

Full Changelog: https://github.com/BlueBrain/NeuroM/compare/v3.2.1...v3.2.2

- Python
Published by GianlucaFicarelli almost 4 years ago

https://github.com/bluebrain/neurom - v3.2.1

What's Changed

Remove duplicated deps jinja, sphinx by @stefanoantonel in https://github.com/BlueBrain/NeuroM/pull/1043
Remove single point contour somas in h5 and asc tests by @mgeplf in https://github.com/BlueBrain/NeuroM/pull/1045
Fix view cli by @arnaudon in https://github.com/BlueBrain/NeuroM/pull/1051
Fix coverage by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/1056
Fix: extract_stats could not work on single neurite by @adrien-berchet in https://github.com/BlueBrain/NeuroM/pull/1060
Fix language detection by @adrien-berchet in https://github.com/BlueBrain/NeuroM/pull/1058

New Contributors

@stefanoantonel made their first contribution in https://github.com/BlueBrain/NeuroM/pull/1043

Full Changelog: https://github.com/BlueBrain/NeuroM/compare/v3.2.0...v3.2.1

- Python
Published by adrien-berchet almost 4 years ago

https://github.com/bluebrain/neurom - v3.2.0

What's Changed

Deprecate python3.6 by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/976
Add trunkanglesintertypes feature and make trunkangles more generic by @adrien-berchet in https://github.com/BlueBrain/NeuroM/pull/965
Remove dynamic test creation of makemonotonic and makeflat by @mgeplf in https://github.com/BlueBrain/NeuroM/pull/980
Use soma center in sholl_frequency distance calculation by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/989
Fix the trunkoriginradii feature by @adrien-berchet in https://github.com/BlueBrain/NeuroM/pull/986
Fix sholl_frequency if neurite_type is not available by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/990
Make output file in morph_check mandatory by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/992
Fix doc of neurom.core.morphology.Neurite.iter_sections method by @adrien-berchet in https://github.com/BlueBrain/NeuroM/pull/994
Add volume density at the morphology level by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/996
Remove duplicate points in principaldirectionextents by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/999
Fix partition_asymmetry Uylings to not throw for bifurcations with leaves by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/1001
Make deprecation warnings respect pre-existing warnings configuration by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/1002
Standardize flatten iterator recipe by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/1003
Generalize partition asymmetry by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/1006
Fix principal direction extent calculation by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/1008
Implement new shape related features (placeholder features) by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/1013
Update neurom.features.get docstring with available builtin features by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/1016
Sort principal direction extents in descending order by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/1017
Return nan if no points found in shape features by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/1018
Fix: kwargs are unnecessarily updated in extract_stats by @adrien-berchet in https://github.com/BlueBrain/NeuroM/pull/1020
Allow using lists of kwargs in morph_stats features by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/1021
Implement new feature of length above soma by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/1023
Exit early if no points, to avoid hull warning by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/1024

Full Changelog: https://github.com/BlueBrain/NeuroM/compare/v3.1.0...v3.2.0

- Python
Published by eleftherioszisis about 4 years ago

https://github.com/bluebrain/neurom - v3.1.0

What's Changed

Add new features totalwidth, totalheight and total_depth by @eleftherioszisis in https://github.com/BlueBrain/NeuroM/pull/974

Full Changelog: https://github.com/BlueBrain/NeuroM/compare/v3.0.2...v3.1.0

- Python
Published by eleftherioszisis over 4 years ago

https://github.com/bluebrain/neurom - v3.0.2

What's Changed

Add example astrocyte analysis notebook. by @pgetta in https://github.com/BlueBrain/NeuroM/pull/957
fix readthedocs build by @asanin-epfl in https://github.com/BlueBrain/NeuroM/pull/958
Update example astrocyte analysis notebook by @pgetta in https://github.com/BlueBrain/NeuroM/pull/959
Clean up the output when creating figures in example astrocyte analysis notebook by @pgetta in https://github.com/BlueBrain/NeuroM/pull/960
fix the link to the migration doc by @asanin-epfl in https://github.com/BlueBrain/NeuroM/pull/961
Improve astrocyte analysis notebook by @pgetta in https://github.com/BlueBrain/NeuroM/pull/962
Fix typo in astrocyte analysis notebook by @pgetta in https://github.com/BlueBrain/NeuroM/pull/963
fix raw option in morph_stat by @arnaudon in https://github.com/BlueBrain/NeuroM/pull/964
Delete all requirements txt files and update documentation accordingly by @asanin-epfl in https://github.com/BlueBrain/NeuroM/pull/967
replace outdated requirements_docs with docs extras by @asanin-epfl in https://github.com/BlueBrain/NeuroM/pull/968
Add jupyterlab-plotly extension to MyBinder postBuild by @pgetta in https://github.com/BlueBrain/NeuroM/pull/970
unifurcation check by @arnaudon in https://github.com/BlueBrain/NeuroM/pull/972

New Contributors

@pgetta made their first contribution in https://github.com/BlueBrain/NeuroM/pull/957

Full Changelog: https://github.com/BlueBrain/NeuroM/compare/v3.0.1...v3.0.2

- Python
Published by eleftherioszisis over 4 years ago

https://github.com/bluebrain/neurom - v3.0.1

Ensure anglebetweenvectors() always return 0 when the vectors are equal (#955)
Add method to Soma class to check wether it overlaps a point or not (#956)

- Python
Published by asanin-epfl almost 5 years ago

https://github.com/bluebrain/neurom - v3.0.0

rename neuron to morphology
refactor features
refactor viewer
allow pass arguments to neurom stats

See CHANGELOG.rst for more details on changes.

- Python
Published by asanin-epfl almost 5 years ago

https://github.com/bluebrain/neurom - Fix 'sholl_frequency' feature for a neuron population

better comments to Population (#938)
fix _neuron_population for 'sholl_frequency' feature over a neuron population (#944)
use a tuple for subplot default value in view.common.get_figure (#946)

- Python
Published by asanin-epfl about 5 years ago

https://github.com/bluebrain/neurom - Remove `NeuriteType.all` from `NEURITES`

Use MorphIO specification for definitions doc page (#925)
Introduce a new method to calculate partition asymmetry by Uylings (#930)
document NEURITES (#932)
Follow the same rules of morphology validation as MorphIO (#934)
Remove the cli command neurom features (#933)
remove NeuriteType.all from NEURITES (#931)

- Python
Published by asanin-epfl about 5 years ago

https://github.com/bluebrain/neurom - Fix 'section_path_lengths' feature for Population (#927)

- Python
Published by asanin-epfl about 5 years ago

https://github.com/bluebrain/neurom -

Optimize Sholl analysis code (#905, #919)
Update documentation (#899, #907, #908, #911, #923, #917)
Include neuron filename extension into its name (#909)
Extend tree_type_checker to accept a single tuple as an argument. Additionally validate function's arguments (#912, #914)
fix test data path in examples (#916)
move 'total_length' feature to neuronfunc (#924)
Don't force loading of neurons into memory (#922)

- Python
Published by asanin-epfl about 5 years ago

https://github.com/bluebrain/neurom - Morphologies without soma

allow for morphologies without soma (#900)

- Python
Published by asanin-epfl about 5 years ago

https://github.com/bluebrain/neurom - Fix custom neurite bug (introduce all custom neurites from MorphIO)

clean imports (keep backward compatibility) (#898)
import plotly locally as it is an extra dependency (#901)
Account for all custom neurite types in NeuriteType (#902)
less pylint disables (#903)

- Python
Published by asanin-epfl about 5 years ago

https://github.com/bluebrain/neurom - Single cli entry under `neurom`

Add push to codecov and run ci on master push (#895)
Update LICENSE.txt (#896)
nose to pytest, move all tests to 'tests' folder (#892)
Code cleaning of 'apps' package (#888)
Fix notebooks (#897)

- Python
Published by asanin-epfl over 5 years ago

https://github.com/bluebrain/neurom - NeuroM 2.0.1

Fix pypi version publishing (#893)

- Python
Published by asanin-epfl over 5 years ago

https://github.com/bluebrain/neurom - NeuroM 2.0

Use MorphIO for reading/writing morphologies.

For the full list of changes see https://neurom.readthedocs.io/en/latest/migration_v2.html

- Python
Published by asanin-epfl over 5 years ago

https://github.com/bluebrain/neurom -

- Python
Published by asanin-epfl over 5 years ago

https://github.com/bluebrain/neurom - Stop supporting h5v2

- Python
Published by wizmer over 5 years ago

https://github.com/bluebrain/neurom - Change shape of dataframe of `extract_dataframe` in morph_stats (#874)

- Python
Published by wizmer over 5 years ago

https://github.com/bluebrain/neurom - Change the shape of the output DataFrame of `extract_dataframe` (#862)

- Python
Published by wizmer over 5 years ago

https://github.com/bluebrain/neurom - Drop the fst/ deprecated folder

- Python
Published by wizmer over 5 years ago

https://github.com/bluebrain/neurom - Pin h5py < 3.0.0

- Python
Published by wizmer over 5 years ago

https://github.com/bluebrain/neurom - Fix newer pylint constraints (#851)

- Python
Published by wizmer over 5 years ago

https://github.com/bluebrain/neurom - add multiprocessing to morph_stat.extract_dataframe

- Python
Published by wizmer almost 6 years ago

https://github.com/bluebrain/neurom - New function extract_dataframe that extract morphometrics as a dataframe

- Python
Published by wizmer about 6 years ago

https://github.com/bluebrain/neurom - Drop python 2 support

- Python
Published by wizmer about 6 years ago

https://github.com/bluebrain/neurom - morph_stat can now extract all features with the '-f' flag (#817)

- Python
Published by wizmer over 6 years ago

https://github.com/bluebrain/neurom - All checks should return list of points (#807)

- Python
Published by wizmer over 6 years ago

https://github.com/bluebrain/neurom - features are now part of the `neurom.features` sub-package

- Python
Published by wizmer over 6 years ago

https://github.com/bluebrain/neurom - Plotly drawer also accepts neurites

Plotly drawer also accepts neurites (#797)
Cast load_data 'handle' arg as string (#801)
faster path_distance computation (~2x) (#791)
The section color is chosen section by section (#787)
Reconcile mut_morphio and master a bit more (#794)

- Python
Published by wizmer over 6 years ago

https://github.com/bluebrain/neurom - segment_areas and segment_path_lengths features

Adding 2 features: segmentareas and segmentpath_lengths (#789)
Suppress warnings from Tox output (#788)

- Python
Published by wizmer over 6 years ago

https://github.com/bluebrain/neurom - Release v1.4.15

Fix wrong import in plotly tutorial: #765 (#767) Fix strahler.swc (#769) Add PyPi classifiers in setup.py (#764) Fix enum34 incompatibility with Python 3.6 (#771) adding a banner to NeuroM readme (#774) adding license badge (#775) Refactor dendrogram (#780) Add soma_volumes feature per soma type (#778)

- Python
Published by asanin-epfl over 6 years ago

https://github.com/bluebrain/neurom - Release v1.4.14

Add hasnorootnodejumps check (#760) Fix broken IDs in reversedNRNneuriteorder.swc (#759) Fix test file with wrong section types (#758) Do not depends on addchild in tests (#756) Bump scipy dependency (#757) readthedocs: use site packages, when possible (#754) wheel is required in pyproject.toml (#753) readthedocs: add enum to install (#752) reduce pyproject.toml deps (#751) readthedocs: use python 2 (#750) readthedocs: make sure the package gets installed (#749) pin sphinx so it creates docs (#748) Unpin plotly (#745) Fix soma position on 2d plot (#744) Update documentation (#737) Skip spines (#738) reduce error messages like: 'No handlers could be found for logger' (#734)

- Python
Published by wizmer almost 7 years ago

https://github.com/bluebrain/neurom - Fix ASC first point and dendrogram with neurites

Last soma point is no longer first neurite point in ASC
Dendrogram now works when called with a neurite

- Python
Published by wizmer over 7 years ago

https://github.com/bluebrain/neurom - Remove Numpy version upper bound

And switch and linting is now done with Python 3.6 in Travis

- Python
Published by wizmer over 7 years ago

https://github.com/bluebrain/neurom - morph_stats and morph_checks print their default config url

When morphstats and morphchecks are called without specifying a config, the default one which is hard-coded is used. This commit puts the default config in a yaml file and the url is displayed when used. Benefits: 1) People can see what's in the default config 2) It can serve as an example when you have no idea how morph_check/stat work.

- Python
Published by wizmer over 7 years ago

https://github.com/bluebrain/neurom - Remove distutils markers

- Python
Published by wizmer almost 8 years ago

https://github.com/bluebrain/neurom - Release v1.4.9

Changes: - Require 'enum34' only for Python<3.4 - Create plotly module - Specify morph_stats example config path in help - Fix: Section type constants are shown as integers #697 - 3-points contours are not longer interpreted as SomaThreePoint

- Python
Published by wizmer almost 8 years ago

https://github.com/bluebrain/neurom - v1.4.8

Unpin h5py dependency

- Python
Published by mgeplf about 8 years ago

https://github.com/bluebrain/neurom - Synthesis stats

Adds new statistics useful for the morphology synthesis Cf. PR #689

- Python
Published by wizmer about 8 years ago

https://github.com/bluebrain/neurom - Release v1.4.6

add strahler order
documentation fixes
remove testing of python 2.6

- Python
Published by mgeplf over 8 years ago

https://github.com/bluebrain/neurom - Instance-scope memoizer

Fix a memory leak occuring as the memoizer was never releasing memory when neurons where deleted.

- Python
Published by wizmer over 8 years ago

https://github.com/bluebrain/neurom - Has no narrow dendritic section check

Fixed spelling in the code
Added a new check: hasnonarrowdendriticsection
Changed annotate function signature

- Python
Published by wizmer over 8 years ago

https://github.com/bluebrain/neurom - MUK-like annotations for Neurolucida morphologies

Annotate app
Cut plane detection app
Scholl analysis app

- Python
Published by wizmer over 8 years ago