CHANGELOG.md

Changelog

1.6.0

18 December 2024

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

7 November 2024

Chores And Housekeeping

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

1.5.0

7 November 2024

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

7 November 2024

Build

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

New Features

• Add support for empty population (Adrien Berchet - fb0c830)

1.3.1

7 November 2024

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

7 November 2024

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

7 November 2024

Refactoring and Updates

• Clean RegionMapper (Adrien Berchet - afc802d)

1.2.8

7 November 2024

Performance Improvements

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

1.2.7

7 November 2024

Performance Improvements

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

1.2.6

7 November 2024

New Features

• Add chunksize parameter (Adrien Berchet - 46444cc)

Performance Improvements

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

1.2.5

7 November 2024

New Features

• Improve logger for MPI (Adrien Berchet - 71c24fb)

1.2.4

7 November 2024

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

7 November 2024

New Features

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

1.2.2

7 November 2024

New Features

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

1.2.1

7 November 2024

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

7 November 2024

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

7 November 2024

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

7 November 2024

New Features

• Improve validation error messages (Adrien Berchet - d0063e5)

1.1.2

7 November 2024

New Features

• Handle no layers (Alexis Arnaudon - 2a0a366)

Fixes

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

1.1.1

7 November 2024

1.1.0

7 November 2024

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

7 November 2024

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

7 November 2024

New Features

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

CI Improvements

• Fix urllib3 requirement for Py38 (Adrien Berchet - ab6b680)

0.4.3

7 November 2024

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

7 November 2024

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

7 November 2024

General Changes

• NeuriteType compat with neurom (Alexis Arnaudon - 657d7cf)

0.4.0

7 November 2024

General Changes

• any regions handling (Alexis Arnaudon - acd8e97)

0.3.1

7 November 2024

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

7 November 2024

General Changes

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

0.2.4

7 November 2024

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

7 November 2024

General Changes

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

0.2.2

7 November 2024

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

7 November 2024

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

7 November 2024

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

7 November 2024

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

7 November 2024

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

7 November 2024

General Changes

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

0.1.8

7 November 2024

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

7 November 2024

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

7 November 2024

General Changes

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

0.1.5

7 November 2024

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

7 November 2024

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

7 November 2024

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

7 November 2024

General Changes

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

0.1.1

7 November 2024

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

7 November 2024

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

7 November 2024

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)