Changelog

0.10.1

17 April 2024

General Changes

  • Add check for overlapping points in neurites (Adrien Berchet - #151)

0.10.0

15 April 2024

New Features

  • Merge DetectErrors and PlotErrors and add a similar FinalCheck task (Adrien Berchet - #148)

Documentation Changes

  • Add Zenodo badge on the main page (#147) (Adrien Berchet - e23e232)

0.9.4

12 March 2024

New Features

  • Add sign flip in Orient (Alexis Arnaudon - #144)

Fixes

  • The add_soma() function should work with no root point (Adrien Berchet - #145)

0.9.3

15 February 2024

Fixes

  • Use absolute paths in the dataset created by the Initialize workflow (Adrien Berchet - #142)

0.9.2

12 February 2024

New Features

  • Make the FixZeroDiameters, Unravel and RepairNeurites steps skippable (Adrien Berchet - #135)

Documentation Changes

  • Make more clear that the dependency graphs are clickable (Adrien Berchet - #139)

  • Fix some more links (Adrien Berchet - #138)

  • Fix link to neuror.main.Repair (Adrien Berchet - #137)

CI Improvements

  • Add CodeCov token (Adrien Berchet - #136)

0.9.1

22 December 2023

New Features

  • Add nb_processes to MakeRelease and improve log level when using the CLI (Adrien Berchet - #131)

0.9.0

21 December 2023

Build

  • Bump MorphIO and fix tests accordingly (Adrien Berchet - #125)

New Features

  • Add logger entry to know which morphology could not be written in make_release (Adrien Berchet - #129)

Fixes

  • Handle any number of points in _add_soma and add a specific test (Adrien Berchet - #123)

  • Create contour soma properly (Adrien Berchet - #122)

0.8.1

15 November 2023

Fixes

  • Create the dataset before the metadata to not raise a useless warning (Adrien Berchet - #120)

0.8.0

1 November 2023

New Features

  • Smooth diameters for all population (Alexis Arnaudon - #117)

  • Improve Placeholders task (Adrien Berchet - #110)

Fixes

  • Some small doc/plot fixes (Alexis Arnaudon - #116)

  • Properly initialize logger (Adrien Berchet - #108)

  • Write morphologies with NRN order (Alexis Arnaudon - #104)

  • Fix axon stub for has_axon (Alexis Arnaudon - #103)

  • fix repair plotting (Alexis Arnaudon - #99)

Chores And Housekeeping

  • Apply Copier template (Adrien Berchet - #109)

Changes to Test Assests

  • Use monkeypatch fixture instead of os.chdir() (Adrien Berchet - #114)

  • Fix soma type in test_no_soma (Adrien Berchet - #105)

Tidying of Code eg Whitespace

  • Setup Ruff config (Adrien Berchet - #115)

0.7.0

22 May 2023

New Features

  • Change entry point from morphology_workflows to morphology-workflows (Adrien Berchet - #98)

Fixes

  • Compatibility with Pandas>=2 and urllib3>=2 (Adrien Berchet - #96)

Documentation Changes

  • Add link to the schema of the Repair params (Adrien Berchet - #91)

General Changes

  • Fix layers not int (Alexis Arnaudon - #92)

  • Use JSON schema from NeuroR.main.Repair and fix CLI command in docs (Adrien Berchet - #90)

0.6.1

27 March 2023

New Features

  • Update command and doc (Adrien Berchet - #88)

0.6.0

13 March 2023

New Features

  • Add helpers to create inputs (Adrien Berchet - #85)

Chores And Housekeeping

  • Bump Copier template (Adrien Berchet - #82)

CI Improvements

  • Do not export all test results as artifacts and fix dependency graphs in docs (Adrien Berchet - #84)

General Changes

  • Add propagation between workflows, fix MakeCollage and fix empty mtypes (Adrien Berchet - #83)

0.5.3

31 January 2023

Chores And Housekeeping

  • Add JSON schemas to ListParameters (Adrien Berchet - #79)

CI Improvements

  • Bump pre-commit hooks (Adrien Berchet - #80)

0.5.2

5 January 2023

Build

  • Bump Sphinx (Adrien Berchet - #77)

0.5.1

22 December 2022

Chores And Housekeeping

  • Use optional params for region and mtype and improve default logger (Adrien Berchet - #75)

0.5.0

22 December 2022

New Features

  • Placeholders can be computed without metadata.csv file (Adrien Berchet - #72)

Fixes

  • Make the rerun parameter work with CLI (Adrien Berchet - #73)

0.4.2

13 December 2022

Chores And Housekeeping

  • Remove dead code in conf.py (Adrien Berchet - #68)

  • Bump AllenSDK and Sphinx and use proper optional parameters (Adrien Berchet - #67)

  • Fix language detection (Adrien Berchet - #64)

CI Improvements

  • Use tox 4 (Adrien Berchet - #70)

  • Apply Copier template (Adrien Berchet - #69)

General Changes

  • Update README.md (alex4200 - 53b70d4)

0.4.1

22 September 2022

Refactoring and Updates

  • Update from template (Adrien Berchet - #58)

  • Apply Copier template (Adrien Berchet - #57)

CI Improvements

  • Setup pre-commit and format the files accordingly (Adrien Berchet - #55)

  • Fix action to publish new releases on Pypi (Adrien Berchet - #54)

General Changes

  • Reconnect axons to soma (Alexis Arnaudon - #62)

  • Simpler smooth algorithm (Alexis Arnaudon - #56)

  • Add duplicate layers to releases (Alexis Arnaudon - #60)

  • Fail if spaces in morph name (Alexis Arnaudon - #59)

0.4.0

11 August 2022

Chores And Housekeeping

  • Set mtype_regex argument as optional (Adrien Berchet - #52)

Documentation Changes

  • Improve doc for the Fetch workflow (Adrien Berchet - #51)

  • Add the Placeholders workflow in the doc (Adrien Berchet - #49)

  • Improve instructions to create inputs (Adrien Berchet - #47)

General Changes

  • Remove warning from scipy (Adrien Berchet - #48)

  • Add workflow to compute placeholders (Adrien Berchet - #22)

CI Improvements

  • Use commitlint to check PR titles (#45) (Adrien Berchet - 4d9c3df)

0.3.2

1 July 2022

  • Improve test coverage (Adrien Berchet - #40)

  • Use luigi features moved from luigi-tools (Adrien Berchet - #42)

  • Fix task arguments in CLI and use new empty dependency graph feature of luigi-tools (Adrien Berchet - #41)

  • Improve MakeRelease and minor changes (Alexis Arnaudon - #11)

  • Constrain requirements for Jinja2 and Numpy (Adrien Berchet - #38)

0.3.1

17 June 2022

  • Ensure 0-length sections are always fixed, even if the min length is too small (Adrien Berchet - #35)

0.3.0

14 June 2022

  • Build and publish wheels (Adrien Berchet - #32)

  • Fix 0-length root sections in CheckNeurites task (arnaudon - #31)

  • Fix SSL certificate in example (Alexis Arnaudon - #23)

  • Fix optional imports (Adrien Berchet - #27)

  • Fetch morphologies workflow (Adrien Berchet - #20)

  • cleanup example (Alexis Arnaudon - #17)

  • Add link to the documentation into README.md (Adrien Berchet - #16)

  • Add banner to repo (alex4200 - #13)

  • Adding logo for Morphology-Workflows (alex4200 - #12)

  • Missed fix (#18) (Alexis Arnaudon - 3a9b56f)

  • Ensure axon stub (#26) (arnaudon - 7e7f750)

  • Updating copyright year (adietz - 9b662e5)

0.2.0

12 January 2022

  • Use the new input mechanism for DVF inputs (Adrien Berchet - #8)

0.1.3

20 December 2021

  • Use the SkippableMixin from DVF (Adrien Berchet - #1)

0.1.2

20 December 2021

  • Fix Pypi variable (Adrien Berchet - #3)

0.1.1

20 December 2021

  • Generate workflow images during sphinx build (Adrien Berchet - #2)

0.1.0

16 December 2021

  • Open source the Curate, Annotate and Repair workflows from the morphology-processing-workflow package (Adrien Berchet - ccd4854)