🔖 Release 1.5.0#757

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shaneahmed merged 608 commits intomasterfrom pre-release

Dec 15, 2023

+37,182-25,466

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Commits on Aug 30, 2022

Commits on Sep 1, 2022

DEV: FIX Requirements Versions (#455 )

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DOC: JNB-RTD consistency for full-pipelines/slide-graph.ipynb (#425 )

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DOC: minor changes to 02-stain-normalization.ipynb (#466 )
DavidBAEpstein
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Commits on Sep 13, 2022

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Minor cnanges to 04-patch-extraction.ipynb (#468 )
DavidBAEpstein
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Commits on Sep 16, 2022

BUG: Fix the colorbar Bug with plt (#473 )
measty
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Commits on Sep 23, 2022

Commits on Sep 26, 2022

[skip ci] DOC: Update citation in README.md and CITATION.cff (#480 )

shaneahmed
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John-P
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Commits on Oct 7, 2022

DEV: Fix Circular import wsireader (#484 )

shaneahmed
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John-P
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Commits on Oct 10, 2022

[skip ci] DEV: Remove nbsphinx and replace it with myst-nb. (#454 )

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Commits on Oct 11, 2022

[pre-commit.ci] pre-commit autoupdate (#487 )
pre-commit-ci[bot]
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Commits on Oct 13, 2022

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BUG: Read TIFF Resolution Tags As A Fraction (#489 )

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Commits on Oct 18, 2022

ENH: Annotation Storage Additions For Visualization (#445 )

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Commits on Oct 20, 2022

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MANT: Refactor Parameterized Tests (#501 )

John-P
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pre-commit-ci[bot]
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Commits on Nov 14, 2022

NEW: Add NuClick architecture (#449 )

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Commits on Nov 17, 2022

ENH: Add Annotation Store Reader (#476 )

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Commits on Nov 22, 2022

🐳 DEV: Publishing Docker Images (#504 )
mostafajahanifar
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Commits on Nov 23, 2022

DEV: Update bump2version config (#511 )

shaneahmed
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John-P
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Commits on Nov 24, 2022

DEV: Update Dependencies (#498 )

shaneahmed
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John-P
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Commits on Nov 25, 2022

DEV: Fix Flake8 E800 for tests (#512 )

shaneahmed
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John-P
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Commits on Dec 6, 2022

Commits on Dec 9, 2022

✨ NEW: DFBR for Registering Images (#510 )

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Commits on Dec 14, 2022

DEV: Restrict shapely version to less than 2.0.0 (#520 )
shaneahmed
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Commits on Dec 19, 2022

📝 [skip ci] DOC: DFBR Jupyter Notebook revised (#494 )

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Commits on Dec 20, 2022

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Commits on Feb 16, 2023

🚑 BUG: Fix DICOMWSIReader metadata reading (#539 )

shaneahmed
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John-P
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Commits on Feb 17, 2023

🔖 REL: Release 1.3.2 (#542 )
shaneahmed
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Commits on Feb 20, 2023

💥 API: Change API for SCCNN input (#544 )
shaneahmed
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Commits on Feb 23, 2023

✅ TST: Fix Local Tests for Windows/Linux (#550 )

shaneahmed
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pre-commit-ci[bot]
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Commits on Feb 24, 2023

⬆️ DEP: Fix scipy deprecation (#547 )

shaneahmed
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adamshephard
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Commits on Mar 3, 2023

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Commits on Mar 10, 2023

🔧 DEV: Filter Logger Output to stdout and stderr (#557 )

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➖ DEP: Remove tox Dependency (#561 )

shaneahmed
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John-P
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Commits on Mar 13, 2023

Commits on Mar 16, 2023

📝 DOC: Improve Annotation Store Documentation + Fix Bug (#565 )

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Commits on Mar 17, 2023

🐛 BUG: Fix Level When Using DICOM read_region (#564 )

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Commits on Mar 20, 2023

🐛 BUG: Fix Docker Build for Ubuntu OS(s) (#569 )
mostafajahanifar
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Commits on Mar 23, 2023

📝 DOC: Improve Installation Instructions (#567 )

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Commits on Mar 24, 2023

🎨 Move Models to Top-Level Import (#574 )
shaneahmed
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Commits on Mar 27, 2023

🩹 BUG: Fix Parsing Missing Omero Version NGFF Metadata (#568 )

John-P
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shaneahmed
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Commits on Apr 3, 2023

➕ Add joblib as a dependency (#581 )
shaneahmed
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📌 Pin Pandas Version to >=2.0.0 (#583 )
shaneahmed
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Commits on Apr 11, 2023

🚨 Use logger Instead Of warnings for patchextraction.py (#589 )
shaneahmed
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Commits on Apr 12, 2023

✅ Add tests for lazy import (#591 )
shaneahmed
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Commits on Apr 14, 2023

Commits on Apr 17, 2023

[skip ci] 🐛 Fix Docstring and License Badge (#593 )
shaneahmed
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Commits on Apr 18, 2023

✨ Feature Engine for Multi-Task Segmenter (#424 )

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Commits on Apr 21, 2023

Commits on Apr 27, 2023

✏️ Fix Typo (#596 )
blaginin
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Commits on May 3, 2023

🐛 Fix MultiTaskSegmentor Example (#597 )

blaginin
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adamshephard
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⬆️ Upgrade numpy Dependency (#543 )
shaneahmed
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Commits on May 4, 2023

✨ ENH: Add Neighbourhood Querying Support To AnnotationStore (#540 )

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🐛 Fix pixman incompatibility error on Colab (#601 )
shaneahmed
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Commits on May 9, 2023

[skip ci] 🩹 Update notebooks for Google Colab runs (#604 )
shaneahmed
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Commits on May 19, 2023

♻️ High Level misc functions Import (#606 )
shaneahmed
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Commits on May 23, 2023

Update README.md (#613 )
John-P
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Commits on May 26, 2023

♻️ Refactor Resolution and Units (#598 )
blaginin
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♻️ High Level engines Import (#607 )

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Commits on Jun 9, 2023

✨ File Magic Detection & NGFF SQLite3 Support (#616 )
John-P
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Commits on Jun 16, 2023

♻️ Replace deprecated input pretrained with weights (#621 )

shaneahmed
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measty
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Commits on Jun 22, 2023

[pre-commit.ci] pre-commit autoupdate (#515 )

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Commits on Jun 23, 2023

🗑️ Remove shapely.speedups (#622 )

shaneahmed
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measty
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🐛 Fix Errors in the slidegraph Example Notebook (#608 )

measty
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shaneahmed
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Commits on Jul 1, 2023

✅ Reduce run time for Mapde test (#627 )
shaneahmed
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📝 Fix docstrings (#624 )

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Commits on Jul 18, 2023

[pre-commit.ci] pre-commit autoupdate (#642 )
pre-commit-ci[bot]
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Commits on Jul 19, 2023

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🚨 Fix linter errors in line with #625 (#647 )

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Commits on Jul 22, 2023

🚨 Fix Linter Error in cli, annotation and visualization (#648 )

shaneahmed
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measty
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🚨 Fix Linter Error in tools, utils and pre-commit (#649 )

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🚨 Replace ruff with flake8 using basic settings (#650 )

shaneahmed
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John-P
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✨ Feature: wkb Decoding via numpy (#632 )

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🚨 Add bugbear. pep8-naming, flake8-commas, flake8-print, mccabe, pycodestyle-Error and pyupgrade Checks (#652 )

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🚨 Add Perflint, flake8-simplify, flake8-raise, flake8-implicit-str-concat, flake8-fixme, pandas-vet (#653 )

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✨ Use ruff for Linting (#625 )

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Commits on Jul 23, 2023

🚨 Add "NPY" NumPy-specific rules Checks (#654 )
shaneahmed
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🚨 Fix ANN201 Errors in tests (#683 )
shaneahmed
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Commits on Aug 7, 2023

🚨 Add flake8-boolean-trap Checks (#686 )
shaneahmed
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Commits on Aug 8, 2023

🚨 Add flake8-bandit Checks (#687 )
shaneahmed
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Commits on Aug 11, 2023

🚨 Add pylint Checks (#691 )

shaneahmed
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pre-commit-ci[bot]
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🐛 Fix prealignment Function (#693 )

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Commits on Aug 14, 2023

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🚨 Fix flake8-annotations Checks in models (#702 )
shaneahmed
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Commits on Aug 29, 2023

Commits on Aug 30, 2023

🚨 Add flake8-annotations to All Except tiatoolbox/annotations (#707 )
shaneahmed
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Commits on Sep 1, 2023

🐛 Add IOConfig for NuClick in pretrained_model.yaml (#709 )
mostafajahanifar
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Commits on Sep 13, 2023

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[pre-commit.ci] pre-commit autoupdate (#714 )
pre-commit-ci[bot]
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Commits on Sep 22, 2023

🚨 Fix flake8-annotation Linter Errors (#713 )

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Commits on Sep 26, 2023

Commits on Oct 3, 2023

[pre-commit.ci] pre-commit autoupdate (#717 )
pre-commit-ci[bot]
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Commits on Oct 6, 2023

⬆️ Update torch dependency (#719 )
shaneahmed
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Commits on Oct 10, 2023

[pre-commit.ci] pre-commit autoupdate (#720 )
pre-commit-ci[bot]
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Commits on Oct 13, 2023

❇️ Add Convert patches Output to AnnotationStore (#718 )

measty
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shaneahmed
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Commits on Oct 19, 2023

🚧 Add Type Checking using mypy (#723 )

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Commits on Oct 23, 2023

🔨 Add mypy Checks to exceptions.py (#725 )
shaneahmed
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Commits on Oct 31, 2023

[pre-commit.ci] pre-commit autoupdate (#730 )
pre-commit-ci[bot]
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Commits on Nov 3, 2023

♻️ Add typehints for dataset_abc.py (#726 )

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🔨 Add typing.py and env_detection.py to mypy Type Check (#731 )
Jiaqi-Lv
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[pre-commit.ci] pre-commit autoupdate (#741 )
pre-commit-ci[bot]
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Commits on Nov 22, 2023

✨ Add Support for QuPath Annotation Imports (#721 )

measty
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shaneahmed
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🔨 Add mypy Checks (#740 )

Jiaqi-Lv
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shaneahmed
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Commits on Nov 29, 2023

🔨 Add utils/misc.py to mypy (#744 )

Jiaqi-Lv
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shaneahmed
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Commits on Nov 30, 2023

📌 Update dependency link for pytorch cuda version (#746 )
shaneahmed
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Commits on Dec 8, 2023

🐛 Return masks instead of [mask] (#748 )
Abdol
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Commits on Dec 12, 2023

[pre-commit.ci] pre-commit autoupdate (#754 )
pre-commit-ci[bot]
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Commits on Dec 15, 2023