Biapy

Major:
- Add configuration file backward-compatibility
- Add `U-NeXt V2` model
- Actions added:
- Add `check_code_consistency.yml` action to test code consistency (every week)
- Add `upload_biapy_to_pypi.yml` to automatically create a PyPI package (when a new release is created)
- Add `create_release_container.yml` file to automatically create and update docker containers to Dockerhub (when a new release is created)

Minor:
- Update BMZ model creation and compatibility:
- Add cover creation and create `environment.yaml` to be packaged in the BMZ model
- Add `sigmoid` activation as BMZ postprocessing so we are more compatible
- Extract just the `pytorch_state_dict` from the checkpoint when creating BMZ package
- Save correct input/output (prediction) for BMZ package
- Move to `bioimageio.core==0.7.0`
- Change slightly the normalization so it can match the one done in BMZ

Bugs fixed:
- Fix BMZ model compatibility checks
- Update notebooks to avoid BMZ error when fields are `None`
- Fix bug on BMZ zip creation in the notebooks
- Fix missing letter `'S'` in configuration variable `'SIGNS`'.
- Disabling percentile clipping as that is not done by default in BMZ's `scale_range` normalization

**Full Changelog**: https://github.com/BiaPyX/BiaPy/compare/v3.5.5...v3.5.6

Major:
- Add backward compatibility loading checkpoint

Minor:
- Change `TEST.POST_PROCESSING.MEASURE_PROPERTIES.REMOVE_BY_PROPERTIES.STAT` to `TEST.POST_PROCESSING.MEASURE_PROPERTIES.REMOVE_BY_PROPERTIES.STATS`
- Only check lr scheduler when train in enabled

Bugs fixed:
- Fix a bug in DATA.FILTER_BY_IMAGE
- Update 3D_cell_detection_zarr_tutorial.yaml with new configuration

**Full Changelog**: https://github.com/BiaPyX/BiaPy/compare/v3.5.4...v3.5.5

Major:
- Add BMZ exportation through configuration

Minor:
- Set automatically BMZ path and change it to `PATHS.BMZ_EXPORT_PATH`

Bugs fixed:
- Fix minor bug when loading model checkpoint
- Fix small bug in semantic seg. multiclass jaccard calculation

**Full Changelog**: https://github.com/BiaPyX/BiaPy/compare/v3.5.3...v3.5.4

Major:
- Update BMZ model check to support more models and increase it's robustness.

Minor:
- Add class extraction for semantic seg. BMZ models.
- Adapt instance segmentation channels to a default value depending when loading BMZ models.
- Change `LOAD_MODEL_FROM_CHECKPOINT` default value to `True`.
- Increase UNETR building process robustness

Bugs fixed:
- Fix bug when filtering by entire images.
- Prevent top-5-accuracy when classes are less than 5 in classification workflow.
- Fix bug in single data generator used in classification and SSL workflows.
- Allow BMZ/Torchvision models override completely configuration with the variables they are imposing by making `update_dependencies()` config function more generic.
- Force entire image filtering when `DATA.EXTRACT_RANDOM_PATCH` is enabled.

**Full Changelog**: https://github.com/BiaPyX/BiaPy/compare/v3.5.2...v3.5.3

Major:
- Add `'resunet_se'` to I2I workflow
- Extend BMZ model support
- Remove `DATA.TRAIN.MINIMUM_FOREGROUND_PER`. Now for training, validation and test a sample filtering can be made with `DATA.TRAIN.FILTER_SAMPLES`, `DATA.VAL.FILTER_SAMPLES` and `DATA.TEST.FILTER_SAMPLES` respectively.

Minor:
- Add `MODEL.LOAD_MODEL_FROM_CHECKPOINT` variable
- `DATA.PREPROCESS.MEDIAN_BLUR.FOOTPRINT` changed to `DATA.PREPROCESS.MEDIAN_BLUR.KERNEL_SIZE`
- Add robust semantic mask check using `DATA.*.CHECK_DATA`
- Divide BMZ model check into two functions so they can be reused easily by the GUI
- Change BMZ COLLECTION_URL to a new version of it

Bugs fixed:
- Fix bug in detection workflow when predicting with Zarr/H5 by chunks
- Minor fix during instance training data creation using Zarr
- Correct minor errors during BMZ model import/export

**Full Changelog**: https://github.com/BiaPyX/BiaPy/compare/v3.5.1...v3.5.2

Major:
- Add GRN, ConvNeXtBlock_V2 and UpConvNeXtBlock_V2 blocks

Minor:
- Change `CENTRAL_POINT_DILATION` from int to list
- Add support for fixed_zero_mean_unit_variance preprocessing for BMZ models
- Adapt BMZ model check function to work properly with models in 0.4 and 0.5 version

Bugs fixed:
- Bug in instance segmentation using only `C` channel
- Correct tags in BMZ model creation
- Adapt BMZ model check function to work properly with models in 0.4 and 0.5 version

**Full Changelog**: https://github.com/BiaPyX/BiaPy/compare/v3.5.0...v3.5.1