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CHANGELOG.md

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paquo changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Unreleased

0.8.2 - 2024-12-19

Fixes

  • exclude jpype==1.5.1 (see: #122)

0.8.1 - 2024-07-21

Fixes

  • paquo get_qupath now downloads the correct QuPath on Mac arm64

0.8.0 - 2024-06-02

Added

  • added support for PathCellObjects
  • added .cells and .tiles attributes to hierarchy

Fixed

  • fixed QuPath=0.5.1 download via get_qupath

0.7.2 - 2024-02-22

Fixed

  • fixed QuPath=0.5.0 download via get_qupath

Changed

  • ci: test against QuPath=0.5.0

0.7.1 - 2023-08-05

Fixed

  • prevent warning in ome conversion with pydantic>=2
  • speedup hierarchy loading in readonly mode
  • fix import of geojson tile objects

0.7.0 - 2023-06-16

Changed

  • drop Python=3.7 support

Added

  • paquo: support for newer ome-types

Fixed

  • paquo: fixed deprecation warnings on py311

0.6.1 - 2023-03-01

Fixed

  • paquo: fix saving manually updated measurements
  • paquo: prevent deprecation warnings with QuPath>=0.4.0
  • paquo: prevent deprecation warnings with shapely>=2

0.6.0 - 2022-11-21

Fixed

  • paquo: support windows network share URIs
  • paquo: add all available scenes of image in add_image

Added

  • paquo: support snapshot versions of QuPath for testing newer upstream compatibility
  • paquo: allow user to provide path to JVM to support Apple M1 hardware
  • paquo: add remove_image method to QuPathProject

Changed

  • paquo: simplify ImageProvider and deprecate SimpleImageProvider
  • ci: install paquo via pip to speedup workflows
  • ci: test against python 3.11

0.5.1 - 2022-07-15

Fixed

  • paquo: env var configuration now works via PAQUO_ and PAQUO__ prefix

0.5.0 - 2022-04-05

Fixed

  • cli: startup time improved
  • docs: fix configuration section (double underscore for prefix PAQUO__)
  • paquo.java: prevent emitting a QuPath logging message on import
  • paquo: reduce cli startup time by lazy importing settings
  • cli: fixed help display if terminal doesn't support unicode

Added

  • cli: add get_qupath command for downloading specific QuPaths

Changed

  • paquo: drop Python=3.6 support

0.4.2 - 2022-01-10

Added

  • paquo: support QuPath v0.2.0 (a83d8a2)

Fixed

  • paquo._config: fixed searchtree to allow local override
  • tests: fixed jpype test when run in conda env with external QuPath

Changed

  • paquo: multiple typing improvements and minor fixes

0.4.1 - 2022-01-05

Added

  • paquo: emit warning on windows when MicrosoftStore Python is detected

Fixed

  • paquo: fixed EXCEPTION_ACCESS_VIOLATION on Windows with QuPath versions 0.3.x
  • paquo: removed distutils.version usage to silence warnings on py39+ (pep632)

0.4.0 - 2021-08-25

Added

  • paquo: support qupath version 0.3.0-rc1
  • paquo.hierarchy: no_autoflush context manager for speeding up adding many path objects
  • paquo.projects: support try_relative in update_image_paths
  • cli: allow providing both --annotations and --annotations-cmd
  • paquo.hierarchy: support conversion to ome xml
  • docs: quickstart example for loading detection measurements as pd.DataFrame (@nickdelgrosso)

Changed

  • paquo._base: remove QuPathBase base class

Fixed

  • paquo.hierarchy: improved update_class_path speed
  • paquo.hierarchy: support slicing for annotation and detection proxies
  • paquo.hierarchy: fixed proxy issue after load_geosjon
  • paquo.projects: speedup add_image for large projects

0.3.1 - 2021-04-02

Fixed

  • paquo: changing annotations in a hierarchy now propagates to is_changed

0.3.0 - 2021-03-29

Added

  • cli: added qpzip subcommand that allows opening zipped QuPath projects
  • cli: added quickview subcommand for opening qupath with a specific image
  • cli: quickview subcommand support loading annotations
  • extras: added an example for an osx app shim allowing paquo to be used as an OSX app

Changed

  • switched conda env to conda-devenv
  • changed repr style of paquo classes
  • conda env doesn't use defaults anymore

Fixed

  • paquo._logging: paquo doesn't call basicConfig anymore
  • paquo: fixed java logging redirection in images and projects
  • paquo: hierarchy now skips broken annotations
  • paquo: hierarchy annotation loading speedup
  • mypy: fixes

0.2.0 - 2020-08-21

Added

  • more verbose logging when saving project data

Changed

  • updated the docs

Fixed

  • parse windows network share URIs correctly

0.1.1 - 2020-08-12

Added

  • added verbose repr's for improved ipython notebook display

Fixed

  • excluded broken dynaconf==3.1.0
  • QuPathProject.add_image is now calling QuPathProject.save

0.1.0 - 2020-08-12

Added

  • initial release of paquo