Changelog

2.4.0

21 November 2023

Build

• Drop support for Python 3.7 (Adrien Berchet - #84)

Chores And Housekeeping

• Remove some warnings (Adrien Berchet - #86)

General Changes

• Plot improvements (lidakanari - #76)

v2.3.1

16 May 2023

New Features

• Files with upper-case extensions can be loaded (Adrien Berchet - #78)

v2.3.0

28 April 2023

Chores And Housekeeping

• Update from Copier template (Adrien Berchet - #73)

• Fix license detection (Adrien Berchet - #59)

• Fix citation section and add CITATION.cff file (Adrien Berchet - #58)

• Fix pylint config (Adrien Berchet - #57)

Documentation Changes

• Fix RTD (Adrien Berchet - #56)

Refactoring and Updates

• Make (x/y)lims and (x/y)lim consistent in plot functions (Adrien Berchet - #69)

• Apply copier template (Adrien Berchet - #55)

Tidying of Code eg Whitespace

• Handle default kwargs (Adrien Berchet - #67)

CI Improvements

• Use Py37 with precommit (Adrien Berchet - #72)

• Fix title in commitlint job (Adrien Berchet - #70)

• Store tests results as artifacts (Adrien Berchet - #66)

• Fix tests, bump Github actions and add get_by_name method to Population (Adrien Berchet - #64)

• Fix action to publish new releases on Pypi (Adrien Berchet - #53)

General Changes

• Add new plotting functions to create overview figures for papers (lidakanari - #63)

• Fix load_population to be able to load single files and to raise a proper exception (Adrien Berchet - #54)

v2.2.0

22 August 2022

General Changes

• Update to dendrite types (Alexis Arnaudon - #52)

• Updated copyright year in several files (alex4200 - #51)

v2.1.0

9 March 2022

• Add trunk length feature (Adrien Berchet - #44)

• Use points instead of diameters for MorphIO conversion (Adrien Berchet - #47)

• Add missed coverage (Eleftherios Zisis - #49)

• Refactor tests to use pytest & remove warnings (Eleftherios Zisis - #48)

• Improve perf of find_apical_point_distance_smoothed (Adrien Berchet - #46)

• Add tracking of points for bars (lidakanari - #43)

• Fix license (Adrien Berchet - #42)

v2.0.11

18 March 2021

• bump morphio version (Alexis Arnaudon - #41)

v2.0.10

16 March 2021

• remove enum compat (Alexis Arnaudon - #40)

• Move morphio loader to io module (lidakanari - #38)

• Convert morphio Morphology to tmd Neuron (Eleftherios Zisis - #37)

• Refactor Topology methods (Eleftherios Zisis - #36)

• Create run-tox.yml (Alexis Arnaudon - #34)

• Create publish-sdist.yml (Alexis Arnaudon - #35)

• lint fixes + improvement of some older code (Alexis Arnaudon - #32)

v2.0.9

27 April 2020

• new_axes=False + soma outline fix (Alexis Arnaudon - #30)

v2.0.8

20 March 2020

• Add apical point function (lidakanari - #29)

v2.0.7

11 February 2020

• Update version to fix release (lidakanari - #27)

• version = 2.0.6 (kanari - 8adba8d)

v2.0.6

11 February 2020

• check if .asc files as input (Alexis Arnaudon - #24)

• Update enum (kanari - 795a277)

• automate version update with releases (kanari - ceb7437)

v2.0.5

17 January 2020

• Version increase (lidakanari - #23)

• Improve apical point definition (lidakanari - #22)

• Move all tests in a single directory (Benoit Coste - #19)

• Fix path distances consistency (lidakanari - #15)

• Updated Tutorial.txt (lidakanari - #12)

• Generalize population loader to accept list of files as input (lidakanari - #6)

• Activate tox envs (Benoît Coste - 3774d12)

• Fixes for review (kanari - 433470e)

• Fix tests, activate tests for p27, pylint, pep8 (kanari - 7d4f427)

• This doesn’t work (kanari - 010e53c)

• Fix xrange for python 3 (kanari - 202354a)

• Update Tutorial.txt (lidakanari - 530ed57)

• Changed get_ph_diagram to get_persistence_diagram (Stanislav Schmidt - 8d8c952)

v2.0.4

3 March 2019

• Fix incopatibility with python3 (lidakanari - #11)

• Deploy on each commit (Eleftherios Zisis - #9)

• Implementation of closest barcode function (Eleftherios Zisis - 076ba9e)

• review corrections (Eleftherios Zisis - ea9c93c)

• Minor corrections (kanari - 23d9dd2)

• lint corrections (Eleftherios Zisis - 3903168)

• Docstring clarification (Eleftherios Zisis - c2955ff)

• removed commented code (Eleftherios Zisis - bfc3494)

• import view should be import tmd.view as view (Oren Amsalem - 3f9a04d)

• Revert deploy on each commit (Benoît Coste - c3e41f8)

v2.0.3

16 January 2019

• Test fix Jenkins (Benoit Coste - #2)

• Add Travis and Pypi integration (Benoit Coste - #1)

• Cleaning up code (kanari - 7705675)

• Fix remaining pylint, pep8 issues (kanari - 8d809c3)

• Further cleaning and removing unused functions (kanari - 5da070b)

• Add basic functionality (kanari - 6f3af7c)

• Minor modifications to basic functionality. Improve visualization. (kanari - a5c52de)

• Add appropriate license for open sourcing (Lida Kanari - b9b3776)

• Fixing final pylinting issues; (kanari - e5dfc6e)

• Correct pep8 (kanari - 56dca21)

• Optimize path_distance computation: use path_distances_2 (kanari - b42c5de)

• Add pypi integration (Benoît Coste - 6ef1ff4)

• Add apical point definition (kanari - 58b8b3c)

• Cleaning up and README update (Lida Kanari - 7975fe2)

• Readme corrections (Lida Kanari - b702757)

• Update README.md (lidakanari - 8996afc)

• Update README.md (lidakanari - f3a01ea)

• Update README.md (lidakanari - f4aee95)

• tmd/Topology/transformations.py (kanari - bfccd1b)

• Make viewers optional (kanari - 8a87f84)

• Minor corrections (kanari - 2f0dc5b)

• More attempts on readme (Lida Kanari - 051af30)

• Update Travis secret (Benoît Coste - ffc1cff)

• Fix minor issue with apical distance definition” (kanari - 04f5dfa)

• missing _neuron in load command (nadavyayon - 50a1584)

• Update README.md (lidakanari - b6e0ea8)

• Bump version (Benoît Coste - 7fb11db)

• fix docs (Benoît Coste - 159ad93)

• Update README.md (lidakanari - 3bb4534)

• Update README.md (lidakanari - 8cc1bfa)

• Rename LICENSE.txt to LICENSE.md (lidakanari - 22757f6)

• More attempts on readme (Lida Kanari - bf1f36c)

• Transfer Readme file (Lida Kanari - 1102051)

• Merge “Bump version” (Lida Kanari - 87b66a7)

• Merge “fix docs” (Lida Kanari - 11e00a2)

• Migrating code from bitbucket (Lida Kanari - 01be170)

• Add Tox file (Benoit Coste - 69333fb)

• Cleaning up code to simplify applications (kanari - 2f8a80b)

• Add examples and minor changes (kanari - ab560ae)

• Clean up pep n pylint errors (Lida Kanari - 7e9f6b8)

• Add matching with munkress (kanari - 2dbe26b)

• Improvements and new plots (kanari - f3e34ad)

• Commit statistics as examples (kanari - f9cca06)

• Simplify matchings (kanari - 544e6fd)

• Add example to classify one cell against a population of cells (kanari - e878a91)

• Average PI (kanari - 273b92b)

• Add simple doc and remove unnecessary directories (Lida Kanari - df48cc6)

• Minor corrections (Lida Kanari - 823df3d)

• Add polar plots code and example (kanari - 942fce0)

• Add version number in TMD installation (Benoit Coste - c414aa2)

• Update viewers (Lida Kanari - d5ad47a)

• Correct plotting functions (Lida Kanari - 5cf0b10)

• Update matching options (Lida Kanari - d4d6cb3)

• Add properties to Neuron, Population (Lida Kanari - 5380fd9)

• Change the neurite_types inside a population to make consistent with neuron types (kanari - 57b7e70)

• Add examples and view (kanari - 8178c8e)

• Minor updates on viewers (Lida Kanari - 4230592)

• Improve matching (kanari - d9463f3)

• Minor plotting improvements (Lida Kanari - ef3d5c0)

• Replace pep8 (Lida Kanari - 8ea0ccc)

• Allow optional definition of soma type (kanari - f4cd02d)

• Minor simplification (Lida Kanari - 1252b86)

• Fix fail error message in population loader (kanari - 353f767)

• Update makefile (Lida Kanari - dd502e3)

• Fix error in previous commit (Lida Kanari - ccb6db1)

• Data to check in h5 format (Lida Kanari - a724985)

• Initial empty repository (Julien Francioli - 3ce483e)