Changelog¶

Fix for numpy>=1.24 and use more optional parameters (Adrien Berchet - 3b53020)
Update from copier template (Adrien Berchet - 50873ab)
Bump brainbuilder (Adrien Berchet - 9c3849f)
Fix lint (Adrien Berchet - f19a3a3)
Apply Copier template (Adrien Berchet - d6dcc09)
Add JSON schemas to ListParameter objects (Adrien Berchet - 03a48db)
Restrict brainbuilder to !=0.18.1 because of an issue with 56f304fe46a4d1c3ea14460eab735a20fc3ae056 (Adrien Berchet - 1433620)

Documentation Changes¶

Fix indent in lists (Adrien Berchet - 9815ee8)

Refactoring and Updates¶

Apply Copier template (Adrien Berchet - 61ee764)
Update from template (Adrien Berchet - 1cc8e4d)

CI Improvements¶

Bump pre-commit hooks and fix isort installation failure (Adrien Berchet - c9996c2)
Fix coverage for pytest-cov>=4 (Adrien Berchet - cf305d3)
Fix tests for new versions of Pandas and Sphinx (Adrien Berchet - ecd8dba)

General Changes¶

Use external file for custom parameters (Alexis Arnaudon - 4bcebcc)
Use NeuroCollage (Alexis Arnaudon - 5799ac7)
Use latest diameter-synthesis (Alexis Arnaudon - d0eaafd)
Export circuitconfig (Alexis Arnaudon - 44db085)
Fix substitution rule (Alexis Arnaudon - 5488996)

0.1.1 ¶

General Changes¶

Any region handling (v2) (Alexis Arnaudon - 3fd475a)
Trunk validation (Alexis Arnaudon - b0b407e)
Bump luigi-tools (Adrien Berchet - 9a19543)
Add commitlint on MR titles (Adrien Berchet - 0f1e9d4)
Fix doc generation (Adrien Berchet - daf066f)
Add multi-project trigger to ensure SynthDB is compatible with each new tag (Adrien Berchet - 15ec479)
Fix the multi-project trigger (Adrien Berchet - 95b95a3)

0.1.0 ¶

General Changes¶

Insitu validation (collage + extents plots) (arnaudon - d3e611d)
Use new versions of region-grower, TNS and diameter-synthesis (Adrien Berchet - 06257d7)
Use pytest template to improve tests and coverage reports (Adrien Berchet - 742eeed)
Bumped NeuroTS and diameter-synthesis versions (Adrien Berchet - 872f8ec)
Migrate from Gerrit to GitLab (Adrien Berchet - e14ecc1)
Fix vacuum example and use luigi-tools>=0.0.15 (Alexis Arnaudon - 041efbe)
cleanup vacuum example (Alexis Arnaudon - 6bacd19)
Update NeuroM dependency to 3.0.0 and update expected results (aleksei sanin - 2f8c447)
Use Gitlab registry in CI and remove several warnings (Adrien Berchet - ab8a526)
Drop support of py36 and py37 (Adrien Berchet - 62ed321)
Fix auto-release CI job (Adrien Berchet - 2e6eb0e)
Use Kubernetes runner (Adrien Berchet - 941d190)
Some minor fix (Alexis Arnaudon - 5d242a1)
Pin dependency versions in tests (Adrien Berchet - 593d67b)
Remove global-exclude from MANIFEST (Adrien Berchet - 17bd12b)

0.0.11 ¶

General Changes¶

Import morph-validator functions, fix the tests and fix dependencies (Adrien Berchet - c8d3fee)
Make choose_morphologies export scores (Adrien Berchet - 608b92f)
Use dir-diff-content, update to py38 and bump dependencies. (Adrien Berchet - a9be8db)
Black the code with line length of 100 (Adrien Berchet - f269215)
Pin versions before moving to region-grower >= 0.2 (Adrien Berchet - a2529e1)
Fix Py38 (Adrien Berchet - 3b93726)
density map tool (arnaudon - 8684580)
Fix compatibility with Py38 (Adrien Berchet - cd07dec)
Use workflow rendering functions that were transferred to luigi-tools (Adrien Berchet - fd582e5)
Use luigi-tools>=0.0.5 to automatically create parent directories of task targets (Adrien Berchet - fa9beab)
Create distributions for axon according to https://bbpcode.epfl.ch/code/#/c/52107 (Adrien Berchet - 8fa1ecc)
Update requirements (Adrien Berchet - 74a66b5)
Use importlib in setup.py instead of imp (Adrien Berchet - f6c43b3)
Merge “density map tool” (Alexis Arnaudon - 16af2e3)
Update tox to for py36 only for linting (Adrien Berchet - c44cb63)

0.0.10 ¶

General Changes¶

Use luigi-tools package (Adrien Berchet - 80d16ea)
Fix BuildAxonMorphologies to use worker from placement_algorithm (Adrien Berchet - 5cc05de)
Add methodology in the doc (Adrien Berchet - 63a8624)
Update changelog (Adrien Berchet - 0a368c0)
Use luigi-tools==0.0.3 (Adrien Berchet - 19b4a66)
Fix PlotPathDistanceFits for mtypes with no fit (Adrien Berchet - 5341bae)
Improve doc: add link to TNS doc (Adrien Berchet - e31dc56)

0.0.9 ¶

General Changes¶

Add a task to create annotation.json file (Adrien Berchet - d983444)
Fix parallelization in vacuum synthesis (Adrien Berchet - e2c68dc)
Minor doc updates (Adrien Berchet - 1b2e5f1)
Update morph-tool requirements (Adrien Berchet - 1d4d46e)

0.0.8 ¶

General Changes¶

Simplify doc and improve its generation (Adrien Berchet - c73827d)
Add score matrix report (Adrien Berchet - 7d891ff)
Updates the way the neuronDB files are found. (arnaudon - 4a4269e)

0.0.7 ¶

General Changes¶

Improve doc (Adrien Berchet - a887fe8)
added creation of thickness mask for Isocortex (arnaudon - 1ab0730)
Add examples of configuration files into the doc (Adrien Berchet - 6c6e94d)

0.0.6 ¶

General Changes¶

Improve doc and tests (Adrien Berchet - 017ba53)

0.0.5 ¶

General Changes¶

Update changelog (Adrien Berchet - 8950c50)

0.0.4 ¶

General Changes¶

Fix CLI for synthesis-workflow and MorphVal (Adrien Berchet - a86eab5)

0.0.3 ¶

General Changes¶

Improve doc generation (Adrien Berchet - 66005e6)
Fix requirements (Adrien Berchet - 7d1591d)
Remove inheritance diagram from doc (Adrien Berchet - c4c951e)

0.0.1¶

General Changes¶

Add tests for the workflows and reorganize the code (Adrien Berchet - f1608c9)
Initial commit (Adrien Berchet - 480db73)
Add MorphVal library (Adrien Berchet - 3592568)
several things in that commit: (arnaudon - 2b5a492)
Reorganised the code ; Merged PlotMorphometrics and PlotVacuumMorphometrics tasks (Adrien Berchet - d212244)
Update apical rescaling (Adrien Berchet - 25733bd)
Fix morphval (Adrien Berchet - bd722fe)
collage update (arnaudon - 609fc39)
Improve mechanism for global parameters (Adrien Berchet - be274b3)
Fix axon choice and minor other cleanings (Adrien Berchet - 8af7b17)
Improve luigi tools (Adrien Berchet - e8eae3b)
generalise git clone task (arnaudon - d6dc669)
Fix logger and add logging of actual parameters after global variable processing (Adrien Berchet - 9984d60)
Fix CI (Adrien Berchet - 1a8ac95)
Improve validation configuration (Adrien Berchet - 75c7aa6)
Add CLI and rework logging (Adrien Berchet - eaa27b9)
Fix logger for region-grower (Adrien Berchet - a853dd5)
Add a new target class that add a prefix to its path (Adrien Berchet - 9be3c43)
Use specific targets to improve output directory tree (Adrien Berchet - 6ebdf5b)
Improved a few things (arnaudon - 3103154)
Clean vacuum workflow (Adrien Berchet - c7736c7)
Use absolute imports (Adrien Berchet - 7fc1c4d)
Use joblib everywhere instead of multiprocessing (Adrien Berchet - cc6c792)
Improve plot_collage (Adrien Berchet - 673282f)
Improve axon grafting (arnaudon - f095bed)
Make plots more robust ; Fix collage tasks (Adrien Berchet - a5fd59f)
small updates (arnaudon - 8156aaf)
Transform all luigi.tasks into WorkflowTask and improve outputs (Adrien Berchet - db706cc)
Add task to build a circuit MV3 file (Adrien Berchet - 4c19f80)
Add task to build a morphs_df file (Adrien Berchet - debf8a6)
Optimize test distribution among processes and pylint (Adrien Berchet - acd4962)
A None value for mtypes means that all mtypes are taken (Adrien Berchet - 8c92176)
Add task to checkout configuration from repository (Adrien Berchet - b26d226)
Add a test for luigi_tools.target_remove() (Adrien Berchet - c6d1286)
Improve parallel massively (arnaudon - 534cfdc)
Affine fit for path distance (arnaudon - 816e2ea)
Fix axon_morphs_base_dir extraction (Adrien Berchet - 65b4574)
Use luigi’s hook to log parameter values (Adrien Berchet - d82615a)
Add diametrizer in vacuum synthesis (Adrien Berchet - 123c36a)
Improve doc (Adrien Berchet - 73e5794)
Setup pytest and update requirements (Adrien Berchet - efe3ee1)
Improve Synthesize dependency of PlotScale (Adrien Berchet - 10d930b)
Make the PlotCollage task much faster (Adrien Berchet - cf27173)
Set requirements (Adrien Berchet - ed8c2b3)
Fix lint errors and add auto generation of version.py (Adrien Berchet - 1bb1a08)
Hide some warnings (Adrien Berchet - 80b55a8)
Optimize validation.get_layer_info() (Adrien Berchet - e47176b)
Optimize circuit slicing (Adrien Berchet - 8f2d7f2)
Fix create_axon_morphologies_tsv() (Adrien Berchet - 7813ece)
Use 2 processes for tests (Adrien Berchet - c4ddf19)
Merge “Improve parallel massively” (Alexis Arnaudon - 1a1b8fa)
Merge “Make the PlotCollage task much faster” (Alexis Arnaudon - 95676a1)
fix bug in task shuffle and atlas get_layers (arnaudon - f8060f6)
Minor fixes (Adrien Berchet - 31dddcb)
Merge “Add test for OutputLocalTarget with absolute path and prefix” (Adrien Berchet - 69ffe7e)
Add test for OutputLocalTarget with absolute path and prefix (Adrien Berchet - c18c368)
Merge “Add task to checkout configuration from repository” (Adrien Berchet - fcda863)
Cleaning warnings and add a new one when Parameters are set to None (Adrien Berchet - eb893e8)
Initial empty repository (Dries Verachtert - 99d6ae2)