Changelog¶

1.6.0 ¶

New Features¶

Add boundary context (Alexis Arnaudon - #9)

Fixes¶

Update to 3d angles and latest neurots (Alexis Arnaudon - #10)

General Changes¶

Update README.md (Alexis Arnaudon - 1dc1a45)

1.5.1 ¶

Chores And Housekeeping¶

Fix URLs and metadata and add license headers (Adrien Berchet - #5)

1.5.0 ¶

Fixes¶

OS fixing (Alexis Arnaudon - 39d7a9f)

General Changes¶

OS (arnaudon - 02cf9c9)
Update README.md (Alexis Arnaudon - df2d2c0)
Update README.md (Alexis Arnaudon - 70a5730)

1.4.0 ¶

Build¶

Bump NeuroTS and update the tests (Adrien Berchet - 66caf20)

New Features¶

Add support for empty population (Adrien Berchet - fb0c830)

1.3.1 ¶

Build¶

Freeze docutils version to be compatible with m2r2 (Adrien Berchet - 254da98)

Chores And Housekeeping¶

Ensure the morphology names are not considered as numbers (Adrien Berchet - b7af19a)

Documentation Changes¶

Remove deprecated example (Adrien Berchet - 10b4148)

1.3.0 ¶

New Features¶

Add morphology_producer column (Alexis Arnaudon - 6ec1f98)

Fixes¶

Allow for different region names between parameters and region_structure (Alexis Arnaudon - aad0232)

Chores And Housekeeping¶

Create empty columns before filling them (Adrien Berchet - c2cab98)
Configure dask-dataframe to be compatible with pyarrow (Adrien Berchet - 2652ee0)

Changes to Test Assests¶

Bump NeuroTS and update the tests (Adrien Berchet - ef6d3e3)

CI Improvements¶

Fix gitlab config (Adrien Berchet - f06d3f6)

1.2.9 ¶

Refactoring and Updates¶

Clean RegionMapper (Adrien Berchet - afc802d)

1.2.8 ¶

Performance Improvements¶

Significantly reduce memory consumption for atlas computations (Adrien Berchet - e50d1b0)

1.2.7 ¶

Performance Improvements¶

Dramatically reduce memory consumption when using MPI (Adrien Berchet - 38c50c1)

1.2.6 ¶

New Features¶

Add chunksize parameter (Adrien Berchet - 46444cc)

Performance Improvements¶

Remove serialization and simplify the code (Adrien Berchet - 6851a2f)

1.2.5 ¶

New Features¶

Improve logger for MPI (Adrien Berchet - 71c24fb)

1.2.4 ¶

Chores And Housekeeping¶

Add logger entries and ensure nb processes <= nb cells (Adrien Berchet - 95e2d00)
Use importlib instead of pkg_resources which is deprecated (Adrien Berchet - 7c4c5cc)

1.2.3 ¶

New Features¶

Add a logger entry for pip freeze (Adrien Berchet - d0d97b5)

1.2.2 ¶

New Features¶

Improve the ways dask can be configured (Adrien Berchet - 18130c0)

1.2.1 ¶

New Features¶

Update dask configuration and hide useless logger entries (Adrien Berchet - 50103f3)

CI Improvements¶

Increase MPI launch timeout setting (Adrien Berchet - 4dc542e)

1.2.0 ¶

New Features¶

Extent scaling for basals (Alexis Arnaudon - 93faecd)

Fixes¶

Update parameter schema for basal (Alexis Arnaudon - ce9c6b5)

Chores And Housekeeping¶

Remove some warnings (Adrien Berchet - 1267d7a)

1.1.4 ¶

New Features¶

The dask client is now initialized and closed only in the synthesize() method (Adrien Berchet - 9491081)

Fixes¶

Shutdown dask at the end of the computation (Adrien Berchet - 2b3175f)

CI Improvements¶

Run the py310-MPI job in CI (Adrien Berchet - 6b9e7b6)

1.1.3 ¶

New Features¶

Improve validation error messages (Adrien Berchet - d0063e5)

1.1.2 ¶

New Features¶

Handle no layers (Alexis Arnaudon - 2a0a366)

Fixes¶

Update test from NeuroTS changes (Alexis Arnaudon - 7e6443a)

1.1.1 ¶

1.1.0 ¶

New Features¶

Propagate mtypes from default region to all others (Adrien Berchet - 5813df4)
Add optional container finalize step (Alexis Arnaudon - 0ecdcae)

Fixes¶

Handle regions with parameters but no layer information (Adrien Berchet - 08aadd8)

1.0.1 ¶

Build¶

Relax constrain Numpy<1.25 (Adrien Berchet - 88d45f2)
Constrain Numpy<1.25 (Adrien Berchet - 319e3f2)

New Features¶

Handles unknown regions (Alexis Arnaudon - dca11c6)

1.0.0 ¶

New Features¶

Support several regions at once (Alexis Arnaudon - 76cc9ab)

CI Improvements¶

Fix urllib3 requirement for Py38 (Adrien Berchet - ab6b680)

0.4.3 ¶

Chores And Housekeeping¶

Apply Copier template (Adrien Berchet - ab0da83)

CI Improvements¶

Setup min_versions job (Adrien Berchet - ee21db0)
Fix for tox>=4 (Adrien Berchet - a51546e)
Increase MPI timeout (Adrien Berchet - 7dd7635)

General Changes¶

Update to 3d_angle mode (Alexis Arnaudon - 8621e4e)
Fix f-string (Alexis Arnaudon - 0a21f7d)
Fix entry point (Alexis Arnaudon - 42f9a32)

0.4.2 ¶

Refactoring and Updates¶

Apply copier template (Adrien Berchet - 855c6dd)
Update from Copier template (Adrien Berchet - 61a741c)

Changes to Test Assests¶

Fix cluster creation to ignore missing Bokeh dependency (Adrien Berchet - 9b26479)

CI Improvements¶

Fix coverage for pytest-cov>=4 (Adrien Berchet - 30a8422)

0.4.1 ¶

General Changes¶

NeuriteType compat with neurom (Alexis Arnaudon - 657d7cf)

0.4.0 ¶

General Changes¶

any regions handling (Alexis Arnaudon - acd8e97)

0.3.1 ¶

General Changes¶

Update for NeuroTS >= 3.1 (Adrien Berchet - c236c7e)
rename tns into neurots (Alexis Arnaudon - db1f65b)
Drop support of py36 and py37 (Adrien Berchet - c368317)

0.3.0 ¶

General Changes¶

Update NeuroM dependency to 3.0.0 (Aleksei Sanin - 4115a3d)

0.2.4 ¶

General Changes¶

Use pytest template to improve reports and coverage (Adrien Berchet - e2b6cdb)
Fix changelog to be compatible with the auto-release CI job (Adrien Berchet - f9f3dda)
Migration from gerrit to GitLab (Adrien Berchet - acaf67b)
Fix retry for synthesize (Adrien Berchet - a83c40a)
Improve logger entries (Adrien Berchet - 3e9f426)
Update NeuroM requirement (Adrien Berchet - 5c54235)
Revert NeuroM requirement to <3 (Adrien Berchet - 9016ee3)
Improve bb5 constraint (Adrien Berchet - 5379c32)

0.2.3 ¶

General Changes¶

fix load filename with . (arnaudon - c366489)
update changelog (arnaudon - 5becc11)

0.2.2 ¶

General Changes¶

Use random number generator and use pickle to save debug infos (Adrien Berchet - ef54647)
Add skip_write option to not write synthesized morphologies (arnaudon - 7646c34)
Fix computation of max_ph in scale_default_barcode (Adrien Berchet - 6ca51ca)
fix duplicates in debug_infos (arnaudon - 7a5857e)

0.2.1 ¶

General Changes¶

small fixx (arnaudon - 2454ba9)
Revert “Force to update the CHANGELOG before each release” (Alexis Arnaudon - 958eba3)
Force to update the CHANGELOG before each release (Adrien Berchet - 6645e97)
update CHANGELOG (arnaudon - d1f0c75)
release 0.2.1 (arnaudon - d8d2f60)

0.2.0 ¶

General Changes¶

Add validation of diametrizer parameters, improve doc and fix formatting (Adrien Berchet - 4178013)
Refactor synthesis cli to use dask (with mpi) (Adrien Berchet - eb07813)
Import synthesize_morphologies from placement-algorithm (arnaudon - 3bf185f)
Improve coverage and use pytest (Adrien Berchet - 2e6371e)
Black the code (Adrien Berchet - 3ba33e3)
Make CLI more consistent and add debug data output (Adrien Berchet - a400abf)
depth_min parameter (arnaudon - 13c3417)
Test CI (Adrien Berchet - b7d3fa4)
Test CI (Adrien Berchet - ea01bee)
L3_TPC:B-> L3_TPC:C (arnaudon - 04e5548)

0.1.11 ¶

General Changes¶

Remove deprecated script [NSETM-730] (Benoît Coste - 6b7721f)
Use apical sections from TNS instead of apical points (Adrien Berchet - a136072)

0.1.10 ¶

General Changes¶

Merge “raise RegionGrowerError for bad scaling” (Benoît Coste - 94bca89)
fix issue in max y extend with orientation (arnaudon - 63d4e0d)
Fix atlas mock (Adrien Berchet - 3d14899)
raise RegionGrowerError for bad scaling (arnaudon - 1d412c5)

0.1.9 ¶

General Changes¶

Add scale logging for validation purpose (Adrien Berchet - 31b62c2)

0.1.8 ¶

General Changes¶

Refactor of neurite scaling (arnaudon - 54e5988)
Use brainbuilder in atlas_mock for tests (arnaudon - d5ca1b9)
Add specific parameters validation (Adrien Berchet - 940f67b)
Rescale apical points to be consistent with the actual apical neurite points (Adrien Berchet - 4344ed6)
Call TNS validator in Context::verify (Benoît Coste - 924d16c)

0.1.7 ¶

General Changes¶

Set neurite_types for each mtypes independently. (arnaudon - d856397)
Fix bug that prevent TNS validation from passing (Benoît Coste - 03cabac)
Bump to version 0.1.7 (Benoît Coste - db803df)

0.1.6 ¶

General Changes¶

Refactor atlas handling (arnaudon - c40b36b)
simplest scaling from atlas (arnaudon - 94f3182)
Bump v0.1.6 (Benoît Coste - 2a28273)

0.1.5 ¶

General Changes¶

cli update (.dat, 2 functions, allow for external tmd_parameters) (arnaudon - 81e0fa1)
updated dependency + fix tests (arnaudon - 5dacd2f)
Sphinx does warning as error (Benoît Coste - 98dc360)
Bump version to 0.1.5 (Benoît Coste - d2656f9)

0.1.4 ¶

General Changes¶

Return the result of synthesize() in a SynthesisResult object (Benoît Coste - 2898424)
Bump version to 0.1.4 (Benoît Coste - 3a51c3d)

0.1.3 ¶

General Changes¶

can use external dimetrizer (diameter-synthesis) (Alexis Arnaudon - 5303922)
tns v2 compatibility (Alexis Arnaudon - 1893032)
SpaceContext.synthesize() also return metadata (Benoît Coste - 6a9176e)
Fix mtype substitution (kanari - caa0cd4)
Bump version to v0.1.3 (Benoît Coste - e02fc69)

0.1.2 ¶

General Changes¶

Fix orientation bug caused by shallow copy (Benoît Coste - 5085152)
Bump version (Benoît Coste - 35ab1bd)

0.1.1 ¶

General Changes¶

Update script to incorporate diameter parameters into distribs (Benoît Coste - 694107a)
Add ‘method’ in distrib if missing (Benoît Coste - ab7ada5)
Release region-grower==0.1.1 (Arseny V. Povolotsky - 98f593e)

0.1.0 ¶

General Changes¶

Add flag to synthesized centered at 0 or not (Benoît Coste - e5cf79a)
Add diametrization process (Benoît Coste - b4fdd67)
Fix grow in space example (Benoît Coste - 037ca8a)
Grow cells accounting for space. (kanari - b2cb80b)
Experimental script to decompose cells into directories according to mtypes based on xml input (kanari - 2c213b4)
Introduced SpaceContext.verify() method (Arseny V. Povolotsky - 53b5896)
Update generation of distribution files (Benoît Coste - 85f7150)
Release region-grower==0.1.0 (Arseny V. Povolotsky - d33f201)

0.0.2¶

General Changes¶

Release region-grower==0.0.2 (Arseny V. Povolotsky - 5e486e2)
Merge “Revised the script for extracting distributions” (Arseniy Povolotskiy - 934c1e2)
Automatic generation of mtype parameters (kanari - 30114ce)
Fix parameter generation errors (kanari - a338948)
First commit (Benoît Coste - ece67b3)
Conform API to circuit building pipeline specification (Benoît Coste - 0058142)
Enable tox (Benoît Coste - 9b17658)
Revised the script for extracting distributions (Arseny V. Povolotsky - e11d831)
Add code to extract distributions; includes necessary hacks (kanari - 9ae8100)
Fixed setup.py (Arseny V. Povolotsky - a4cc76d)
Adding validation file (Benoît Coste - 2284af0)
Use Atlas and cells instead of circuit config (kanari - 9ca48fe)
Fix parameter definition for interneurons (kanari - 1e2758d)
Changed SpaceContext construction arguments (Arseny V. Povolotsky - 7b0b9b5)
Make mayavi dependency optional (kanari - 2f873e3)
Release region-grower==0.0.1 (Arseny V. Povolotsky - 062e8c4)
Remove dependency from bluepy (kanari - 7a090ff)
Initial empty repository (Dries Verachtert - 3e25b6f)