Neurots

[3.3.2](https://github.com/BlueBrain/NeuroTS/compare/3.3.1..3.3.2)

> 4 May 2023

Fixes

- Raise clear errors for empty angles (Adrien Berchet - [65](https://github.com/BlueBrain/NeuroTS/pull/65))

General Changes

[3.3.1](https://github.com/BlueBrain/NeuroTS/compare/3.3.0..3.3.1)

> 13 March 2023

Fixes

- Convert apical_sections to new id (Alexis Arnaudon - [60](https://github.com/BlueBrain/NeuroTS/pull/60))

[3.3.0](https://github.com/BlueBrain/NeuroTS/compare/3.2.0..3.3.0)

> 13 March 2023

Build

- Use find_namespace_packages instead of find_packages (Adrien Berchet - [48](https://github.com/BlueBrain/NeuroTS/pull/48))

New Features

- new trunk generation algorithm (Alexis Arnaudon - [49](https://github.com/BlueBrain/NeuroTS/pull/49))
- Rework input validation process (Adrien Berchet - [52](https://github.com/BlueBrain/NeuroTS/pull/52))

Fixes

- Report errors in list properly (Adrien Berchet - [51](https://github.com/BlueBrain/NeuroTS/pull/51))

Chores And Housekeeping

- Apply Copier template (Adrien Berchet - [57](https://github.com/BlueBrain/NeuroTS/pull/57))
- Fix language detection (Adrien Berchet - [50](https://github.com/BlueBrain/NeuroTS/pull/50))

Refactoring and Updates

- Apply Copier template (Adrien Berchet - [46](https://github.com/BlueBrain/NeuroTS/pull/46))

CI Improvements

- Separate job for min_versions to speedup the CI (Adrien Berchet - [58](https://github.com/BlueBrain/NeuroTS/pull/58))
- Apply Copier template (Adrien Berchet - [55](https://github.com/BlueBrain/NeuroTS/pull/55))
- Test with minimal versions of dependencies (Adrien Berchet - [53](https://github.com/BlueBrain/NeuroTS/pull/53))

General Changes

- Use diameter-synthesis by default (Alexis Arnaudon - [47](https://github.com/BlueBrain/NeuroTS/pull/47))
- Fix schemas and tests (Adrien Berchet - [44](https://github.com/BlueBrain/NeuroTS/pull/44))

[3.2.0](https://github.com/BlueBrain/NeuroTS/compare/3.1.1..3.2.0)

> 26 August 2022

Documentation Changes

- Update DOI to the final article (Adrien Berchet - [32](https://github.com/BlueBrain/NeuroTS/pull/32))

CI Improvements

- Use codespellignorelines files for format job (Adrien Berchet - [41](https://github.com/BlueBrain/NeuroTS/pull/41))
- Publish wheels on Pypi (Adrien Berchet - [40](https://github.com/BlueBrain/NeuroTS/pull/40))
- Use commitlint to check PR titles (Adrien Berchet - [39](https://github.com/BlueBrain/NeuroTS/pull/39))
- Move black, codespell, isort, pycodestyle and pydocstyle from tox to pre-commit (Adrien Berchet - [29](https://github.com/BlueBrain/NeuroTS/pull/29))

General Changes

- Bar length warning under skip_validation (lidakanari - [43](https://github.com/BlueBrain/NeuroTS/pull/43))
- Compatibility of NeuriteType with NeuroM/MorphIO (Alexis Arnaudon - [42](https://github.com/BlueBrain/NeuroTS/pull/42))
- Update targeting/randomness to paper values (Alexis Arnaudon - [30](https://github.com/BlueBrain/NeuroTS/pull/30))
- Automatically build MyBinder docker image for each tag (Adrien Berchet - [28](https://github.com/BlueBrain/NeuroTS/pull/28))
- Update scipy requirement because of QHullError (Adrien Berchet - [27](https://github.com/BlueBrain/NeuroTS/pull/27))
- Fix warnings (Eleftherios Zisis - [25](https://github.com/BlueBrain/NeuroTS/pull/25))
- Update build-system (Eleftherios Zisis - [26](https://github.com/BlueBrain/NeuroTS/pull/26))
- Explicitely states where the examples and related data are located (Adrien Berchet - [24](https://github.com/BlueBrain/NeuroTS/pull/24))
- Remove useless installation of several packages in Github CI (Adrien Berchet - [23](https://github.com/BlueBrain/NeuroTS/pull/23))
- Setup MyBinder (Adrien Berchet - [22](https://github.com/BlueBrain/NeuroTS/pull/22))

[3.1.1](https://github.com/BlueBrain/NeuroTS/compare/3.1.0..3.1.1)

> 2 March 2022

General Changes

- Setup CodeCov (Adrien Berchet - [20](https://github.com/BlueBrain/NeuroTS/pull/20))

[3.1.0](https://github.com/BlueBrain/NeuroTS/compare/3.0.1..3.1.0)

> 1 March 2022

- Update README.md (alex4200 - [18](https://github.com/BlueBrain/NeuroTS/pull/18))
- Remove run time from gallery pages (Adrien Berchet - [17](https://github.com/BlueBrain/NeuroTS/pull/17))
- Make citation more clear and slightly improve coverage (Adrien Berchet - [16](https://github.com/BlueBrain/NeuroTS/pull/16))
- Update examples (lidakanari - [12](https://github.com/BlueBrain/NeuroTS/pull/12))
- Can pass parameters to the external diametrizer (Adrien Berchet - [13](https://github.com/BlueBrain/NeuroTS/pull/13))
- Update CONTRIBUTING.md (alex4200 - [11](https://github.com/BlueBrain/NeuroTS/pull/11))
- Improve readme file (lidakanari - [5](https://github.com/BlueBrain/NeuroTS/pull/5))
- default to use_morphio (Alexis Arnaudon - [10](https://github.com/BlueBrain/NeuroTS/pull/10))
- Fix banner in doc (alex4200 - [9](https://github.com/BlueBrain/NeuroTS/pull/9))
- Adding logo for NeuroTS (alex4200 - [8](https://github.com/BlueBrain/NeuroTS/pull/8))
- Add codespell in lint (Adrien Berchet - [7](https://github.com/BlueBrain/NeuroTS/pull/7))
- Improve installation section in README (Adrien Berchet - [4](https://github.com/BlueBrain/NeuroTS/pull/4))
- Fix tests/astrocyte/test_grower.py::test_grow__run test (Adrien Berchet - [6](https://github.com/BlueBrain/NeuroTS/pull/6))
- Change license and open the sources (Adrien Berchet - [1](https://github.com/BlueBrain/NeuroTS/pull/1))
- Fix distributions for trunk length feature (Adrien Berchet - [fd5235d](https://github.com/BlueBrain/NeuroTS/commit/fd5235d07e4faab523e7fd8fd18bdb34705e8a22))
- Take into account existing points when adding new trunks with no given orientation (Adrien Berchet - [14e11b2](https://github.com/BlueBrain/NeuroTS/commit/14e11b2095c71c902e1200f6bd4c0944c1ca7afa))
- Fix the parameter schema for the new orientation manager (Adrien Berchet - [a384c1c](https://github.com/BlueBrain/NeuroTS/commit/a384c1c1993a261a08cf46db2547f9cc9e55063f))

[3.0.1](https://github.com/BlueBrain/NeuroTS/compare/3.0.0..3.0.1)

> 14 October 2021

- Fix MANIFEST.in to package the JSON schemas (Adrien Berchet - [4c2d80c](https://github.com/BlueBrain/NeuroTS/commit/4c2d80cabe27a2e9faac81ca71abf83a3645b667))

[3.0.0](https://github.com/BlueBrain/NeuroTS/compare/2.5.0..3.0.0)

> 12 October 2021

- Black the code (Adrien Berchet - [59dd107](https://github.com/BlueBrain/NeuroTS/commit/59dd1072546baf55aa58c009812fbda1b747f0cc))
- Refactor and introduce orientation manager (Eleftherios Zisis - [b9bbeeb](https://github.com/BlueBrain/NeuroTS/commit/b9bbeeb3d7a335fedc63006b7d8c2d1e61e6a894))
- Use pytest (Adrien Berchet - [1a790fb](https://github.com/BlueBrain/NeuroTS/commit/1a790fba0d5a93e77c8be47c21d780d61029219b))
- Rename TNS into NeuroTS (Adrien Berchet - [bb08805](https://github.com/BlueBrain/NeuroTS/commit/bb088051517ecc1fdb4bc081471059d156ac0620))

[2.5.0](https://github.com/BlueBrain/NeuroTS/compare/2.4.5..2.5.0)

> 30 August 2021

- update NeuroM dependency to 3.0.0 (aleksei sanin - [68ed1f7](https://github.com/BlueBrain/NeuroTS/commit/68ed1f7a0cef2bb77503ff45eea38db18d944ba7))

[2.4.5](https://github.com/BlueBrain/NeuroTS/compare/2.4.4..2.4.5)

> 30 August 2021

- Improve extract_input.from_diameter.model (Adrien Berchet - [e324779](https://github.com/BlueBrain/NeuroTS/commit/e3247794dfe058a2dabd6990bc591b313ed1f2c7))
- Fix edge case for astrocyte target grower (Eleftherios Zisis - [9a06ea3](https://github.com/BlueBrain/NeuroTS/commit/9a06ea33bdf32c4330d90209b6e0924c7415fc39))
- prepare release 2.4.5 (aleksei sanin - [a94e5a5](https://github.com/BlueBrain/NeuroTS/commit/a94e5a568672e896a2dabbb93c6db650371f118d))
- Use random generator in morphmath.bifurcation.random() (Adrien Berchet - [c955380](https://github.com/BlueBrain/NeuroTS/commit/c955380fe75b1843bbe38c2ae0ce45d3c873bea7))

[2.4.4](https://github.com/BlueBrain/NeuroTS/compare/2.4.3..2.4.4)

> 7 June 2021

- Update NeuroM requirements (Adrien Berchet - [6a56e55](https://github.com/BlueBrain/NeuroTS/commit/6a56e55bc2044da7ef047134bdf8d44bd7eb969e))
- Fix for NeuroM>=2.2 (Adrien Berchet - [6318a26](https://github.com/BlueBrain/NeuroTS/commit/6318a26aac1e6de984f8b4474b6292326181e95a))

[2.4.3](https://github.com/BlueBrain/NeuroTS/compare/2.4.2..2.4.3)

> 2 June 2021

- Make astrocyte grower RandomState rng consistent with global (Eleftherios Zisis - [fa69154](https://github.com/BlueBrain/NeuroTS/commit/fa69154373018069461534a9e0b579510a0b20ed))

[2.4.2](https://github.com/BlueBrain/NeuroTS/compare/2.4.1..2.4.2)

> 6 May 2021

- Merge "Use an instance of a numpy random generator instead of global numpy.random" (Alexis Arnaudon - [754d697](https://github.com/BlueBrain/NeuroTS/commit/754d697ce8551595f1668ae3c524e8a73822575f))
- Use an instance of a numpy random generator instead of global numpy.random (Adrien Berchet - [2cbcfe0](https://github.com/BlueBrain/NeuroTS/commit/2cbcfe018abaa158ac16a3ca1c3f17ee424c8db4))

[2.4.1](https://github.com/BlueBrain/NeuroTS/compare/2.4.0..2.4.1)

> 5 May 2021

- Improve JSON schemas and add them in the documentation (Adrien Berchet - [1760dee](https://github.com/BlueBrain/NeuroTS/commit/1760dee7e743984dd6642085432eacc78c08c72c))

[2.4.0](https://github.com/BlueBrain/NeuroTS/compare/2.3.3..2.4.0)

> 4 May 2021

- Compat for NeuroM==2.1.1 (Adrien Berchet - [eeeb2da](https://github.com/BlueBrain/NeuroTS/commit/eeeb2dab8b1785947f57e77e287a7f0647f95c95))
- Pass the context to the modify function (Adrien Berchet - [015dbf8](https://github.com/BlueBrain/NeuroTS/commit/015dbf8ef9976870da89ce675fea57d41bb8b797))

[2.3.3](https://github.com/BlueBrain/NeuroTS/compare/2.3.2..2.3.3)

> 19 April 2021

- fix test for neuromv2 (arnaudon - [f0e87d7](https://github.com/BlueBrain/NeuroTS/commit/f0e87d72c538b56a47b548bee0f2d5b6337e408f))
- Tree -> Section (arnaudon - [3654e87](https://github.com/BlueBrain/NeuroTS/commit/3654e87a8e1ca34a82d90b8f15b6bbf0a914e300))

[2.3.2](https://github.com/BlueBrain/NeuroTS/compare/2.3.1..2.3.2)

> 18 March 2021

- bump morphio (arnaudon - [241bcf9](https://github.com/BlueBrain/NeuroTS/commit/241bcf9cde194b5434d6e649d3ca96c99ec5f391))
- bump version (arnaudon - [7ea8e40](https://github.com/BlueBrain/NeuroTS/commit/7ea8e40334987f5805313c6c35db8e4c8a5de4c0))

[2.3.1](https://github.com/BlueBrain/NeuroTS/compare/2.3.0..2.3.1)

> 16 March 2021

- Add absolute distribution to trunk orientation (Adrien Berchet - [09fa4d8](https://github.com/BlueBrain/NeuroTS/commit/09fa4d83454838033fafb822b84134bd6f9c5ff5))
- Add grower for axon trunks (Adrien Berchet - [986d275](https://github.com/BlueBrain/NeuroTS/commit/986d2759bd6b077678b038043afb3a980471827f))
- Can now diametrize only a subset of neurite types (Adrien Berchet - [50532f7](https://github.com/BlueBrain/NeuroTS/commit/50532f7dc6c490e453b677c173016f2228817536))
- bump version (arnaudon - [a67972b](https://github.com/BlueBrain/NeuroTS/commit/a67972be3eae919c0aa5b7fe5e7d6060f52f631f))
- remove enum-compat (arnaudon - [e22e5de](https://github.com/BlueBrain/NeuroTS/commit/e22e5de5a2c394841844775c7105a2d36ba83d2a))

[2.3.0](https://github.com/BlueBrain/NeuroTS/compare/2.2.9..2.3.0)

> 12 January 2021

- Improve test coverage and minor cleaning (Adrien Berchet - [1e1f43e](https://github.com/BlueBrain/NeuroTS/commit/1e1f43ee87628119e1da6820f2d643fa1cfce828))
- Store the ID of section containing the apical point (Adrien Berchet - [16cc1ab](https://github.com/BlueBrain/NeuroTS/commit/16cc1ab80ef1db9227df716993c05ca7986ed576))
- Store apical section IDs into the diametrizer parameters (Adrien Berchet - [277b78b](https://github.com/BlueBrain/NeuroTS/commit/277b78b06dbc599377f47637b16cda61f7e3b1b5))

[2.2.9](https://github.com/BlueBrain/NeuroTS/compare/2.2.8..2.2.9)

> 9 December 2020

[2.2.8](https://github.com/BlueBrain/NeuroTS/compare/2.2.7..2.2.8)

> 9 December 2020

- Add doc generation (Adrien Berchet - [0852d7c](https://github.com/BlueBrain/NeuroTS/commit/0852d7c89f74b4c95da015a0ad9f0555f1639e62))
- Improve doc (Adrien Berchet - [b1e86be](https://github.com/BlueBrain/NeuroTS/commit/b1e86be33535568314c7f388f5fa942846d6f705))

[2.2.7](https://github.com/BlueBrain/NeuroTS/compare/2.2.6..2.2.7)

> 4 November 2020

- Compute persistence length correctly (kanari - [86fe018](https://github.com/BlueBrain/NeuroTS/commit/86fe018bf799b3295db5f50d41220aaebbdc20b6))