Installation + Context Managment + Unit testing Improved (#188)

* fix: fix ext when processing ome.tiff imgs

* feat: simplify installation + trident doctor to check packages

* docs: simplify installation

* feat: better gitignore

* fix: doctor checks all encoders

* feat: cleaner wsi converter

* feat: mag can be non-integer

* fix: clean converter

* feat: support for otsu thresh for tissue vs bg seg

* fix: make otsu faster

* fix: add otsu file

* test: increase unit test coverage

* docs: link to details

* feat: extended python support

* version: bump to 0.2.4

* docs: update explanations

* feat: simplify concept of lazy init

* fix: set skimage version

* tests: separate fast from slow unit tests

* fix: empty coords

* feat: increase ci coverage

* fix: avoid decorator forcing gpu seg

Bump version from 0.2.1 to 0.2.3 (#179)

minor bug fixes + support for slide semantic segmentation + minor imp…

…rovements (#132)

* bug fix, default argument for segment_tissue throws an exception

* add num_workers arg to segment_tissue

* bug fix, display mpp for patcher vis if magnification is None

* don t install heavy libraries by default

* add ability to create WSIPatcher from CLAM type coordinates

* fix from_legacy_coords

* add coords_only arg to from_legacy

* add pil argument to from_legacy_coords

* pass slide_path as positional argument in CuCIMWSI, ImageWSI + fix src_pixel_size exception WSIPatcher

* add semantic segmentation inference

* add semantic segmentation inference

* test

* add forward_kwargs and create save_coords_h5

* cleanup before PR

* fix parameter propagation from ImageWSI to WSI

* cleanup before PR

* add README newline

* remove forward_kwargs

* remove get_channels

* fix: set correct wsi path in processor unit test

---------

Co-authored-by: Richard Chen <richen1939@gmail.com>
Co-authored-by: guillaumejaume <gjaume@bwh.harvard.edu>

Merge pull request #126 from mahmoodlab/fix_tutorial3

hot fix: do NOT freeze ABMIL for training from scratch

Merge pull request #101 from mahmoodlab/tong

v0.2.0: New caching for very large-scaling processing + devops optimization

Merge pull request #79 from mahmoodlab/docs

Add readthedoc documentation to Trident

Merge pull request #62 from mahmoodlab/image_readers

Image readers

Merge pull request #13 from mahmoodlab/convert

feat: image converter

Merge pull request #2 from mahmoodlab/more_models

Support for additional patch encoders

Merge pull request #7 from mahmoodlab/more_segmenters

Tissue vs Background segmentation