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Changelog

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

0.2.0 - 2025-02-05

Compare with first commit

Features

  • made optional params Optional in Pydantic definition (01b060d by mgrapotte).

Bug Fixes

  • added to gitignore. (c2f6c03 by mgrapotte).
  • sometimes tuning reports no best trial found (daf30f2 by mgrapotte).
  • added extra tests. (503048a by mgrapotte).
  • tune should output results (e0ee5a3 by mgrapotte).
  • added error checking for checking that output of tune is not None (d9e1bd5 by mgrapotte).
  • fixed bad arg definition. (ddcc969 by mgrapotte).
  • fix documentation error in check_model (7af84d0 by mgrapotte).
  • fixed pytest not closing files and moved ray init outside of check_model. (15a92de by mgrapotte).
  • run make format (f8dcaf6 by mgrapotte).
  • ran make format (58cc43c by mgrapotte).
  • added comments and ran make format (200e30a by mgrapotte).
  • added debug section for checking tensor shapes and make format (748b887 by mgrapotte).
  • fix linting issues (6ea4bb0 by mgrapotte).
  • run make format (4256e88 by mgrapotte).
  • correct tensor shapes. - stack during forward was not well executed - target shape was incorrect (b37f099 by mgrapotte).
  • make format (189aab7 by mgrapotte).
  • current implementation was considering everything as a slice. (539089d by mgrapotte).
  • pass data refs through config instead of function def (fe76db1 by mgrapotte).
  • replace bad model_param keyword with network_params in config (476b322 by mgrapotte).
  • fixed arg issue (86cd582 by mgrapotte).
  • fixed data init to be within the trainable setup, this prevents from passing data through ray object store (3e83e8b by mgrapotte).
  • fix issue where raytune was not shutting down properly (74c1944 by mgrapotte).
  • make format (789591f by mgrapotte).
  • add init.py to make linter happy (01bf0bf by mgrapotte).
  • fixed issues in raytune_learner (45e3292 by mgrapotte).
  • fixed import error. (15f809f by mgrapotte).
  • main was calling args.json instead of args.yaml (b5265b5 by mgrapotte).
  • fix imports in raytune_learner (5bf0481 by mgrapotte).
  • resolve merge conflicts (5e6faa0 by mgrapotte).
  • added mode field to custom parameter class (8f8cd06 by mgrapotte).
  • added arbitrary_type support for Domain (72e692e by mgrapotte).
  • changed order of validator to output better error messages (39f1d0c by mgrapotte).
  • modified gpu test config to accomodate for new Pydantic format (97158b5 by mgrapotte).
  • fixed linting by adding punctuation to main docstring (c075a12 by mgrapotte).
  • model_ is a pydantic protected namespace, replaced by network_ (d94df0a by mgrapotte).

Code Refactoring

  • removed analysis default as it was outdated (3833486 by mgrapotte).
  • use ray grid instead of dict. (6f6471e by mgrapotte).
  • added error detection for tuning parsing. (31f833c by mgrapotte).
  • refactored tuning cli to comply with current implementations. (8d627ed by mgrapotte).
  • refactored check_model cli (ac60446 by mgrapotte).
  • removed unused launch utils. (4e4519d by mgrapotte).
  • fixed import to use refactored classes and removed unused flag with current paradigm (f014373 by mgrapotte).
  • removed check_ressources function (088f85c by mgrapotte).
  • explicit declaration of RunConfig (d2ceca8 by mgrapotte).
  • refactored TuneConfig creation (47061ce by mgrapotte).
  • now takes as input the seed instead of loading it from the config (270f068 by mgrapotte).
  • now takes as input the model config directly instead of path (1868e71 by mgrapotte).
  • run make format (07ca1c6 by mgrapotte).
  • removed ressource allocation specifics since ray cluster will be initialized outside of the python script (7fb60d0 by mgrapotte).
  • modified model_schema to output pydantic class instead of dumped model (d0f6d07 by mgrapotte).
  • YamlConfigLoader now fully depends on pydantic class (4931f3b by mgrapotte).
  • class YamlRayConfigLoader should properly use Pydantic classes (7241179 by mgrapotte). todo: Pydantic class does not yet use TunableParameters, YamlRayConfigLoader should be adapted for this (mostly the convert to ray method)
  • moved validation from space_selector to pydantic (5bc0008 by mgrapotte).
  • adding a pydantic class for dealing with tunable parameters (9213522 by mgrapotte).
  • reverted changes for adding raytune objects in yaml config. (660fdc3 by mgrapotte).
  • added Pydantic classes for parsing model yaml (6ee91ea by mgrapotte).
  • have model yaml take ray search space directly (1ee47aa by mgrapotte).
  • improve TransformLoader initialization and organization (94ca92b by mgrapotte).
  • implement initial manager classes for dataset handling (f27101d by mgrapotte).

0.2.1 - 2025-02-05

Compare with 0.2.0

0.2.2 - 2025-02-05

Compare with 0.2.1

Bug Fixes

  • remove deprecated tests from analysis types. (1dc4ed9 by mgrapotte).
  • removed deprecated types from analysis in init.py. (7a7390f by mgrapotte).
  • added split-yaml removed deprecated split json and run analysis-default. (ddd9c9f by mgrapotte).

Code Refactoring

  • removed analysis cli since it is deprecated. (e2f44cf by mgrapotte).

0.2.3 - 2025-02-07

Compare with 0.2.2

Bug Fixes

  • src.stimulus.data -> stimulus.data. (b04546c by mgrapotte).
  • src.stimulus.utils -> stimulus.utils. (55d1fed by mgrapotte).

0.2.4 - 2025-02-07

Compare with 0.2.3

Bug Fixes

  • test were failing, made format to fix it. (19dce1f by mgrapotte).

0.2.5 - 2025-02-12

Compare with 0.2.4

Features

  • removed test results from git push. (3f3f516 by mgrapotte).
  • added dockerfiles. (c18489f by mgrapotte).

Bug Fixes

  • fixed duplicate in ruff config. (eb9d3bf by mgrapotte).
  • update ruff config to ignore shadowing python typing. (55d33be by mgrapotte).
  • renamed dockerfiles directory as it was causing ci to crash. (6c19df4 by mgrapotte).
  • ray init needs to be called in the run command otherwise ray cluster is not found. (c9526d6 by mgrapotte).
  • ray init needs to be called in the run command, otherwise ray cluster is not found. (4ebd495 by mgrapotte).

0.3.0 - 2025-03-18

Compare with 0.2.6

Features

  • get device can now return mps backend objecs. (afd4e30 by mathysgrapotte).
  • config parser now also responsible for dealing with suggesting parameters. (be51083 by mgrapotte).
  • now supports variable lists in search space definition. (ff5e0b8 by mgrapotte).
  • added extra test znf data. (ab15e5e by mgrapotte).
  • added support for stimulus-split-yaml-split and stimulus-split-yaml-transform. (d85f6e0 by mgrapotte).

Bug Fixes

  • fixed a bug where predict was not transfering the batch to the device (when device is not CPU). (1fa3e44 by mathysgrapotte).
  • polars.vstack is deprecated, replaced by pl.concat. (989a1fd by mgrapotte).
  • data handlers was calling the transform method instead of transform_all and passing a pl.series instead of a list. (8463e90 by mgrapotte).
  • tests should now use temp_paths. (5368518 by mathysgrapotte).
  • fix issue where spearmanr would cause a warning when labels/predictions would be constant, now outputs 0.0 correlation. (ecd9799 by mgrapotte).
  • add option in case of divide by zero which disables warnings. (ddef6f5 by mgrapotte).
  • fix importlib import errors. (af20925 by mgrapotte).
  • added importlib_metadata dependencies. (57d1e35 by mgrapotte).
  • teardown is now a fixture with autouse set to true. (414f315 by mgrapotte).
  • redundant teardown. (7991a57 by mgrapotte).
  • made teardown redundant. CI was failing because test is exectuting in parralel, CI workers do not share fixture state, so teardown was not called in all tests. (853a0a2 by mgrapotte).
  • updated ray version since ray 2.43 introduces breaking changes. (dd0975f by mgrapotte).
  • fix ray not shutting down properly in the tests. (6b58655 by mgrapotte).
  • removed minor bugs. (2493bfb by mgrapotte).
  • now path can be given as intended to shuffle-csv. (2fe4a0c by mgrapotte).
  • fix linting (dfb7fca by mgrapotte).
  • change -j flag to -y flag (48b7ea9 by V-E-D).
  • fix linting issues. (7c2dd2a by mgrapotte).
  • running make format. (736d6fc by mgrapotte).

Code Refactoring

  • added extra yaml subconfigs. (11d2405 by mgrapotte).
  • added ibis test files. (0401fac by mgrapotte).
  • removing non-conclusive test files. (bb5a4f7 by mgrapotte).
  • udpate check_model and tests. (59ae38a by mgrapotte).
  • removed test_model_yaml since it has been moved to learner/interface. (4b5423b by mgrapotte).
  • changed typing to follow optuna refactor. (eed338d by mgrapotte).
  • tuning cli now up to date with optuna refactor. (6d8c431 by mgrapotte).
  • removed tune related in tests. (a937370 by mgrapotte).
  • removed tune related in src. (da28b82 by mgrapotte).
  • finished optuna_tune. (234856b by mgrapotte).
  • implemented optuna support, inital commit. (173d54f by mgrapotte).
  • made dir paths shorter. (4f33101 by mgrapotte).
  • tuning adapted to the new paradigm. (7b6ed78 by mgrapotte).
  • added tuning cli refactoring. (6a371be by mgrapotte).
  • refactored transform_csv to use click. (806b9b6 by mathysgrapotte).
  • Change split_transforms to the new format (ec3784b by itrujnara).
  • added refactoring for split_csv cli. (92558c0 by mathysgrapotte).
  • updated shuffle_csv to the new paradigm. (e6a0e23 by mgrapotte).
  • added refactoring for check-model cli. (09044c7 by mgrapotte).
  • added main cli. (01d4532 by mgrapotte).
  • gets a torchdataset as input. (973e6f6 by mgrapotte).
  • moved raytune_learner to new paradigm. (3efda09 by mgrapotte).
  • fix typing accross codebase. (ce0d5d4 by mgrapotte).
  • removed test_data_yaml. (e3951f9 by mgrapotte).
  • changed import paths and removed unused fixture. (8150042 by mgrapotte).
  • removed test_experiment. (dcb2c80 by mgrapotte).
  • made data_handlers more explicit and added extra function to parse various configs. (bdac5e4 by mgrapotte).
  • added tests for config loading interface. (3c4e9b4 by mgrapotte).
  • removed duplicate files. (21bc026 by mgrapotte).
  • refactored tests for data_handlers. (6ffcf12 by mgrapotte).
  • adapted TorchDataset to new paradigm. (f3f13b6 by mgrapotte).
  • removed handlertorched and happend it to data_handlers. (377e72e by mgrapotte).
  • removed loader and manager logic. (dbae19b by mgrapotte).
  • added the interface module. (90f4bb1 by mgrapotte).
  • data_config interface in a single module. (34049d0 by mgrapotte).
  • added boilerplate code for instantiating encoders splitters and transforms. (fea0b87 by mgrapotte).
  • added parse_config function signature. (6a6d21a by mgrapotte).
  • changed filenames to have more consistant naming conventions. (576885e by mgrapotte).
  • renamed to model_file_interface. (47026f8 by mgrapotte).
  • renamed data_config_parsing to data_config_splitting. (14daba8 by mgrapotte).
  • splitted yaml_data_schema and data_config_parsing. (c1df9cf by mgrapotte).
  • renamed yaml_data into yaml_data_schema for consistency. (dbca1d5 by mgrapotte).
  • made dumper cleaner. (8802c12 by mgrapotte).
  • removed check_yaml, redundancy with pydantic functions. (e76d246 by mgrapotte).