Adds many tests

This release adds many tests, including of the wsinfer run command.

What's Changed

• Minor fixes by @kaczmarj in #46
• ENH: use yaml config files to define models by @kaczmarj in #48

Full Changelog: v0.3.0...v0.3.1

Hello wsinfer command line

This release introduces the wsinfer command line, with subcommands to run model inference and to convert model outputs to other formats.

What's Changed

• update model-specific docker image versions + fix _in_container + make --model required by @kaczmarj in #40
• ENH: rename the cli to wsinfer by @kaczmarj in #42
• ADD: 'wsinfer list' command by @kaczmarj in #44
• ADD: pytest tests and run in CI by @kaczmarj in #45

Full Changelog: v0.2.1...v0.3.0

Version 0.2.1

This version fixes the conversion to SBU BMI format. Now the user needs to point to the results directory and the slides directory, and the conversion is done automatically.

What's Changed

• add table of available models to readme by @kaczmarj in #35
• FIX: conversion script to make SBU BMI output format by @kaczmarj in #37

Full Changelog: v0.2.0...v0.2.1

Version 0.2.0

We now have models for the detection of the following:

• tumor infiltrating lymphocytes (pancancer)
• breast cancer
• lung adenocarcinoma
• pancreatic cancer
• prostate cancer

What's Changed

• FIX mpp for TCGA BRCA v1 models by @kaczmarj in #19
• ADD: TILs inceptionv4 + docker images for apps by @kaczmarj in #21
• FIX: skip slides without spacing information by @kaczmarj in #22
• skip slides with missing patch hdf5 files by @kaczmarj in #25
• ENH: convert directory of CSVs to GeoJSON by @kaczmarj in #26
• ADD: resnet34 models for LUAD and PRAD by @kaczmarj in #27
• FIX: disable tilesource tile cache by @kaczmarj in #28
• ADD: paad model by @kaczmarj in #29
• ADD: docker apps by @kaczmarj in #30
• FIX: make downloaded models readable by all users by @kaczmarj in #31

Full Changelog: v0.1.0...v0.2.0

Version 0.1.0

This is the first release of the pipeline. It includes model weights for TCGA-BRCA tumor classification (tumor versus no tumor).

What's Changed

• add GPL license by @kaczmarj in #1
• Make this a package by @kaczmarj in #3
• ADD: click command line interface by @kaczmarj in #4
• ADD examples by @kaczmarj in #5
• add ci github workflow by @kaczmarj in #7
• use --find-links for pip install by @kaczmarj in #8
• Add: model weight urls by @kaczmarj in #10
• instantiate inceptionv4 from scratch (then load state) by @kaczmarj in #11
• add conversion script to sbu bmi + support multires tiff + add dense grid prediction by @kaczmarj in #12

New Contributors

• @kaczmarj made their first contribution in #1

Full Changelog: https://github.com/kaczmarj/patch-classification-pipeline/commits/v0.1.0