18 December 2024
- Fix commands given in the examples (Adrien Berchet - #11)
11 November 2024
- Fix RTD config (Adrien Berchet - #6)
11 November 2024
- Fix RTD config (Adrien Berchet - #4)
11 November 2024
- Fix OS (Alexis Arnaudon - #1)
- (dependabot) Bump mikepenz/action-junit-report from 4 to 5 (Alexis Arnaudon - #2)
- Bump NeuroTS and fix tests accordingly (Adrien Berchet - 93da345)
- Bump neurocollage (Adrien Berchet - 49daf8f)
- Bump region-grower (Adrien Berchet - a2d1690)
- Drop support for Python 3.8 (Adrien Berchet - c23be04)
- Bump Brainbuilder and NeuroCollage (Adrien Berchet - a52e8da)
- Freeze docutils version to be compatible with m2r2 (Adrien Berchet - 2c3f737)
- Rework plot Violin features for Pandas>=2.2 (Adrien Berchet - 602c862)
- Fix lint (Adrien Berchet - 2c22e09)
- Bump dir-content-diff (Adrien Berchet - f62d9bb)
- Update PyLint config (Adrien Berchet - 8b0991a)
- Bump NeuroTS and update the tests (Adrien Berchet - ccf8708)
- OS (arnaudon - fd4ae3e)
- Update README.rst (Alexis Arnaudon - 447f47e)
- Update README.rst (Alexis Arnaudon - d069c8d)
8 November 2024
- (deps) Relax NeuroTS and region-grower versions (Adrien Berchet - a40edb4)
- Bump region-grower (Adrien Berchet - 4c0914a)
- Relax matplotlib version (Adrien Berchet - 113fc62)
- Add boundary thickness mask (Alexis Arnaudon - 967cdcb)
- Extent scaling for basals (Alexis Arnaudon - e1def8a)
- Use default diametrizer (Alexis Arnaudon - a854099)
- Use cell_composition for nrrd density filenames (Alexis Arnaudon - 33fac21)
8 November 2024
- (deps) Constrain NeuroTS and region-grower versions (Adrien Berchet - 31e9f97)
- Add -dgdpi for workflow diagram and --version and fix logger (Adrien Berchet - b96264c)
- Raise an exception when the morphologies extracted from the NeuronDB file can not be found (Adrien Berchet - 570c0eb)
- Apply Copier template (Adrien Berchet - 3c493f5)
- Fix doc for optional parameters (Adrien Berchet - 2177b44)
8 November 2024
- Update examples for tutorial (Alexis Arnaudon - 37f7dc0)
8 November 2024
- Add region support (Alexis Arnaudon - 506be99)
8 November 2024
- Set max version for region-grower (Adrien Berchet - b11e682)
- Axon fixing (Alexis Arnaudon - fd5b184)
- Fix circuit place seed (Alexis Arnaudon - be61217)
8 November 2024
- Use 3d_angles and simpler diametrizer by default (Alexis Arnaudon - 14d6a2d)
- 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)
- Fix indent in lists (Adrien Berchet - 9815ee8)
- 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)
- 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)
8 November 2024
- 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)
8 November 2024
- 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)
8 November 2024
- 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)
8 November 2024
- 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)
8 November 2024
- 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)
8 November 2024
- 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)
8 November 2024
- 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)
8 November 2024
- Improve doc and tests (Adrien Berchet - 017ba53)
8 November 2024
- Update changelog (Adrien Berchet - 8950c50)
8 November 2024
- Fix CLI for synthesis-workflow and MorphVal (Adrien Berchet - a86eab5)
8 November 2024
- Improve doc generation (Adrien Berchet - 66005e6)
- Fix requirements (Adrien Berchet - 7d1591d)
- Remove inheritance diagram from doc (Adrien Berchet - c4c951e)
8 November 2024
- 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)