Careamics

What's Changed
* Add code of conduct by jdeschamps in https://github.com/CAREamics/careamics/pull/330
* Chore(deps): Bump the python-packages group across 1 directory with 9 updates by dependabot in https://github.com/CAREamics/careamics/pull/329
* ci(pre-commit.ci): autoupdate by pre-commit-ci in https://github.com/CAREamics/careamics/pull/286
* chore: Better constraints for typer by jdeschamps in https://github.com/CAREamics/careamics/pull/332
* chore: Set `ruff` compatibility check to `py39` by jdeschamps in https://github.com/CAREamics/careamics/pull/331
* Fix: Mismatch between NumPy version used in mypy pre-commit and package dependencies. by melisande-c in https://github.com/CAREamics/careamics/pull/341
* ci(pre-commit.ci): autoupdate by pre-commit-ci in https://github.com/CAREamics/careamics/pull/338
* Chore(deps): Update psutil requirement from <=6.1 to <=6.1.1 by dependabot in https://github.com/CAREamics/careamics/pull/335
* Chore(deps): Update pytorch-lightning requirement from <=2.4,>=2.2 to >=2.2,<=2.5.0.post0 by dependabot in https://github.com/CAREamics/careamics/pull/336
* Chore(deps): Update pillow requirement from <=11.0.0 to <=11.1.0 by dependabot in https://github.com/CAREamics/careamics/pull/337
* Chore(deps): Update tifffile requirement from <=2024.12.12 to <=2025.1.10 by dependabot in https://github.com/CAREamics/careamics/pull/351
* refac: Algorithm specific configurations by jdeschamps in https://github.com/CAREamics/careamics/pull/344


**Full Changelog**: https://github.com/CAREamics/careamics/compare/v0.0.5...v0.0.6

What's Changed
* Update LVAE DataType list by veegalinova in https://github.com/CAREamics/careamics/pull/251
* 3D model by CatEek in https://github.com/CAREamics/careamics/pull/240
* ci(pre-commit.ci): autoupdate by pre-commit-ci in https://github.com/CAREamics/careamics/pull/250
* Feature: Predict to disk (outerloop implementation) by melisande-c in https://github.com/CAREamics/careamics/pull/253
* refac: modularized + cleaned the code for LVAE losses by federico-carrara in https://github.com/CAREamics/careamics/pull/255
* refac: reorganization of pydantic configs in LVAE model by federico-carrara in https://github.com/CAREamics/careamics/pull/256
* Fix(BMZ export): torchvision version; model validation by melisande-c in https://github.com/CAREamics/careamics/pull/257
* Fix: Enforce dataloader params to have shuffle=True by melisande-c in https://github.com/CAREamics/careamics/pull/259
* Performance test induced fixes by CatEek in https://github.com/CAREamics/careamics/pull/260
* ci(pre-commit.ci): autoupdate by pre-commit-ci in https://github.com/CAREamics/careamics/pull/262
* fix: Allow singleton channel in convenience functions by jdeschamps in https://github.com/CAREamics/careamics/pull/265
* feat: Add convenience function to read loss from CSVLogger by jdeschamps in https://github.com/CAREamics/careamics/pull/267
* Refac: Rename config file to careamics.yaml in BMZ export by melisande-c in https://github.com/CAREamics/careamics/pull/271
* Feature: Load model from BMZ using URL by melisande-c in https://github.com/CAREamics/careamics/pull/273
* feat: Enable prediction step during training by jdeschamps in https://github.com/CAREamics/careamics/pull/266
* refac: added possibility to pick `kl_restricted` loss & other loss-related refactoring by federico-carrara in https://github.com/CAREamics/careamics/pull/272
* A new enum for a new splitting task. by ashesh-0 in https://github.com/CAREamics/careamics/pull/270
* Fix(BMZ): Relax model output validation kwargs; extract weights and config file following new `spec` and `core` release by melisande-c in https://github.com/CAREamics/careamics/pull/279
* Fix(dependencies): Set bioimageio-core version greater than 0.7.0 by melisande-c in https://github.com/CAREamics/careamics/pull/280
* fix: fixed a bug in KL loss aggregation (LVAE) by federico-carrara in https://github.com/CAREamics/careamics/pull/277
* fix: ONNX exportability compatibity test and fix by nimiiit in https://github.com/CAREamics/careamics/pull/275
* refac: updated calibration code + moved it into a separate script by federico-carrara in https://github.com/CAREamics/careamics/pull/283
* MicroSplit: adding data type for a new dataset. by ashesh-0 in https://github.com/CAREamics/careamics/pull/284
* Feature: Add predict command to CLI by melisande-c in https://github.com/CAREamics/careamics/pull/281
* Noise models for paper notebooks by CatEek in https://github.com/CAREamics/careamics/pull/285
* Fix: fix device array handling in NoiseModels by CatEek in https://github.com/CAREamics/careamics/pull/288
* chore: Add templates by jdeschamps in https://github.com/CAREamics/careamics/pull/291
* Add dependabot and cap dependencies by jdeschamps in https://github.com/CAREamics/careamics/pull/287
* refac: optimize `WelfordStatistics` update and finalization by federico-carrara in https://github.com/CAREamics/careamics/pull/325
* Update BMZ README by jdeschamps in https://github.com/CAREamics/careamics/pull/322

New Contributors
* nimiiit made their first contribution in https://github.com/CAREamics/careamics/pull/275

**Full Changelog**: https://github.com/CAREamics/careamics/compare/v0.0.4...v0.0.5

**Full Changelog**: https://github.com/CAREamics/careamics/compare/v0.0.4.1...v0.0.4.2

**Full Changelog**: https://github.com/CAREamics/careamics/compare/v0.0.4...v0.0.4.1

What's Changed
* feat: added ADAMAX optimizer among supported ones by federico-carrara in https://github.com/CAREamics/careamics/pull/227
* Remove old examples by CatEek in https://github.com/CAREamics/careamics/pull/228
* refac: removed noise model parameters from `LadderVAE` module by federico-carrara in https://github.com/CAREamics/careamics/pull/233
* fix: making range parameter mandatory in `psnr()` by federico-carrara in https://github.com/CAREamics/careamics/pull/236
* ci(pre-commit.ci): autoupdate by pre-commit-ci in https://github.com/CAREamics/careamics/pull/237
* fix: set upper Pydantic version to 2.8 by jdeschamps in https://github.com/CAREamics/careamics/pull/241
* refac: refactored serialization of arrays for noise model and likelihood configs by federico-carrara in https://github.com/CAREamics/careamics/pull/232
* fix: fixing various bugs to enable microSplit training by federico-carrara in https://github.com/CAREamics/careamics/pull/242
* Feature: Function that computes CAREamics `TileInformation` with `GridIndexManager` by melisande-c in https://github.com/CAREamics/careamics/pull/217
* Simplify `AlgorithmConfig` discrimination by jdeschamps in https://github.com/CAREamics/careamics/pull/222
* feat: added more metrics for evaluation of Splitting results by federico-carrara in https://github.com/CAREamics/careamics/pull/230
* Chore: Split test CIs into CAREamics official and LVAE by jdeschamps in https://github.com/CAREamics/careamics/pull/245
* Feature: Transform multiple arrays identically to `patch` and `target` by melisande-c in https://github.com/CAREamics/careamics/pull/238
* Added several params to training model by CatEek in https://github.com/CAREamics/careamics/pull/225
* bug fix (LC + noise set) by ashesh-0 in https://github.com/CAREamics/careamics/pull/246
* Feature: Update BMZ export by melisande-c in https://github.com/CAREamics/careamics/pull/248
* Add custom transforms to convenience functions, and other API improvement by jdeschamps in https://github.com/CAREamics/careamics/pull/239
* LVAE dataset: add MultiFileDset by veegalinova in https://github.com/CAREamics/careamics/pull/223
* Feature: CLI work in progress by melisande-c in https://github.com/CAREamics/careamics/pull/130
* Add stop training method by jdeschamps in https://github.com/CAREamics/careamics/pull/249

New Contributors
* ashesh-0 made their first contribution in https://github.com/CAREamics/careamics/pull/246

**Full Changelog**: https://github.com/CAREamics/careamics/compare/v0.0.3...v0.0.4

What's Changed
* Algorithm split by CatEek in https://github.com/CAREamics/careamics/pull/187
* Refactor: Noise Models by federico-carrara in https://github.com/CAREamics/careamics/pull/205
* Feature: LVAE prediction functions by melisande-c in https://github.com/CAREamics/careamics/pull/206
* General refactoring and testing of LVAE loss functions. by federico-carrara in https://github.com/CAREamics/careamics/pull/208
* Renaming pydantic models for noise models and likelihood to `SomethingConfig` by federico-carrara in https://github.com/CAREamics/careamics/pull/209
* Feature: Add tiling method from Disentangle repository by melisande-c in https://github.com/CAREamics/careamics/pull/207
* Fixing circular import error arising from importing `UNet` in `models/__init__.py` by federico-carrara in https://github.com/CAREamics/careamics/pull/213
* Masked percentage value upper limit by CatEek in https://github.com/CAREamics/careamics/pull/215
* docs: fix typos, and fix building of docs by tlambert03 in https://github.com/CAREamics/careamics/pull/214
* LVAE dataset: replace ml_config with pydantic by veegalinova in https://github.com/CAREamics/careamics/pull/212
* Feature: LVAE prediction compatible with CAREamics tiling pipeline by melisande-c in https://github.com/CAREamics/careamics/pull/211
* Fix: serialize data statistics as strings by jdeschamps in https://github.com/CAREamics/careamics/pull/197
* Update authors list by jdeschamps in https://github.com/CAREamics/careamics/pull/220
* Add custom algorithm to `FCNAlgorithmConfig` by jdeschamps in https://github.com/CAREamics/careamics/pull/221
* Noise model training by CatEek in https://github.com/CAREamics/careamics/pull/210
* Implemented `training_step` and `validation_step`, fixed all the configs needed to instantiate the lightning module by federico-carrara in https://github.com/CAREamics/careamics/pull/218

New Contributors
* tlambert03 made their first contribution in https://github.com/CAREamics/careamics/pull/214

**Full Changelog**: https://github.com/CAREamics/careamics/compare/v0.0.2...v0.0.3