TST: update tests for dev branch #143
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This introduces subtle differences from the current stable version of wsinfer.
These reference outputs were created using a patched version of 0.3.6 wsinfer. The patches involved padding the patches from large-image to be the expected patch size. Large image does not pad images by default, whereas openslide and tiffslide pad with black.
kaczmarj
added a commit
that referenced
this pull request
Jul 16, 2023
* use pytorch 2.0.0 as base image * install g++ * do not remove gcc * import torch to please jit compiler * move custom model impls to custom_models namespace * refactor to use wsinfer-zoo * run isort and then black * rm modeldefs + make modellib and patchlib public (no underscore) * do not use torch.compile on torchscript models * Fix/issue 131 (#133) * use tifffile in lieu of large_image * run isort * make outputs float or None * changes to please mypy * add newline at end of document * add openslide-python and tifffile to core deps * add back roi support and mps device caps * black formatting * rm unused file * add wsinfer-zoo to deps * predownload registry JSON + install system deps in early layer * scale step size and print info Fixes #135 * add patchlib presets to package data and rm modeldefs * set default step_size to None * only allow step-size=patch-size * allow custom step sizes * update mpp print logs to slide mpp * add tiff mpp via openslide * resize patches to prescribed patch size and spacing * add model config schema * add schemas to package data * fix error messages Replace `--model-name` with `--model`. * create OpenSlide obj in worker_init func Fixes #137 The OpenSlide object is no longer created in `__init__`. Previously the openslide object was shared across workers. Now each worker creates its own OpenSlide object. I hypothesize that this will allow multi-worker data loading on Windows. * handle num_workers=0 * ADD choice of backends (tiffslide or openslide) (#139) * replace openslide with tiffslide * patch zarr to avoid decoding tiles in duplicate This implements the change proposed in zarr-developers/zarr-python#1454 * rm openslide-python and add tiffslide * do not stitch because it imposes a performance penalty * ignore types in vis_params * add isort and tiffslide to dev deps * add NoBackendException * run isort * use wsinfer.wsi module instead of slide_utils and add tiffslide and openslide backends * use wsinfer.wsi.WSI as generic entrypoint for whole slides * replace PathType with "str | Path" * add logging and backend selection to cli * add "from __future__ import annotations" * TST: update tests for dev branch (#143) * begin to update tests * do not resize images prior to transform This introduces subtle differences from the current stable version of wsinfer. * fix for issue #125 * do not save slide path in model outputs csv * add test_cli_run_with_registered_models * add reference model outputs These reference outputs were created using a patched version of 0.3.6 wsinfer. The patches involved padding the patches from large-image to be the expected patch size. Large image does not pad images by default, whereas openslide and tiffslide pad with black. * skip jit tests and cli with custom config * deprecate python 3.7 * install openslide and tiffslide * remove WSIType object * remove dense grid creation fixes #138 * remove timm and custom models We will focus on using TorchScript models only. In the future, we can also look into using ONNX as a backend. fixes #140 * limit click versions to please mypy related to pallets/click#2558 * satisfy mypy * fix cli args for wsinfer run * fail loudly with dev pytorch + fix jit compile tests * fix test of issue 89 * move wsinfer imports to beginning of file * add test of mutually exclusive cli args * use -p shorthand for model-path * mark that we support typing * add py.typed to package data * run test-package on windows, macos, and linux * fix test of patching * install openslide differently on different systems * close the case statement * fix the way we install openslide on different envs * fix matrix.os test * get line length with python for cross-platform * test "wsinfer run" differently for unix and windows * fix windows test * fix path to csv * skip windows tests for now because tissue segmentation is different * run "wsinfer run" on windows but do not test file length * add test of local model with config
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Update the tests to reflect changes in the dev branch.