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@Czaki Czaki released this 30 May 21:51
v0.15.0
21658ec
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0.15.0 - 2023-05-30

Bug Fixes

  • Print all exceptions instead of the latest one in exception dialog (#799)
  • Fix ROIExtractionResult __str__and __repr__ to use ROIExtractionResult not SegmentationResult (#810)
  • Fix code to address changes in the napari repository (#817)
  • Fix the problem with resize of multiline widgets (#832)
  • Fix tox configuration to run all required tests (#840)
  • Fix MSO step_limit description in GUI (#843)
  • Fix redefined-while-unusedimport code for python 3.9.7 (#844)
  • Fix warnings reported by Deepsource (#846)
  • Ensure that "ROI" layer is in the proper place for proper visualization (#856)
  • Fix tests of napari widgets (#862)
  • Fix build of the bundle for a new psygnal release (#863)
  • Fix minimal requirements pipeline (#877)
  • Fix bug with generation of form for the model with hidden field (#920)
  • Update pyinstaller configuration (#926)
  • Use text icon, not pixmap icon in colormap and labels list (#938)
  • Resolve warnings when testing custom save dialog. (#941)
  • Add padding zeros for component num when load Mask seg file to ROI GUI (#944)
  • Proper calculate bounds for watershed napari widget (#969)
  • Fix bug in the wrong order of axis saved in napari contribution (#972)

Dependency

  • [Automatic] Dependency upgrades (#824)
  • [Automatic] Dependency upgrades (#828)
  • [Automatic] Dependency upgrades: ipykernel, packaging (#838)
  • [Automatic] Dependency upgrades: imageio, ipykernel, napari, numpy, sentry (#850)
  • [Automatic] Dependency upgrades: imagecodecs, ipykernel, numpy, psygnal (#859)
  • [Automatic] Dependency upgrades: pydantic, pygments, xlsxwriter (#874)
  • [Automatic] Dependency upgrades: imageio, packaging, scipy, xlsxwriter (#878)
  • [Automatic] Dependency upgrades: ipykernel, requests, sentry, xlsxwriter (#884)
  • [Automatic] Dependency upgrades: h5py, imagecodecs, imageio, ipykernel, pandas, sentry, tifffile (#889)
  • [Automatic] Dependency upgrades: ipython, pyqt5 (#893)
  • [Automatic] Dependency upgrades: imageio, ipykernel, ipython, numpy, openpyxl, psygnal, pydantic, pyinstaller, pyqt5, scipy, sentry-sdk, tifffile, xlsxwriter (#897)
  • [Automatic] Dependency upgrades: imageio, psygnal (#905)
  • [Automatic] Dependency upgrades: ipython, magicgui, scipy, sentry-sdk, tifffile (#906)
  • [Automatic] Dependency upgrades: imagecodecs, imageio, ipykernel, openpyxl, pydantic, pyinstaller, qtawesome, qtconsole, sentry-sdk, tifffile, xlsxwriter (#908)
  • [Automatic] Dependency upgrades: imageio, ipykernel, ipython, pandas, psygnal, pydantic, pygments, pyinstaller, qtpy, sentry-sdk, tifffile (#917)

Documentation

  • Update README and project metadata (#805)

Features

  • Add PARTSEG_SENTRY_URL env variable support and basic documentation about error reporting (#802)
  • Allow to see underlying exception when show warning caused by exception (#829)
  • Add voxel size measurement and allow to overwrite voxel size in batch (#853)
  • Add alpha support for Qt6 (#866)
  • Add option to create projection alongside z-axis (#919)
  • Add napari image custom representation for better error report via sentry (#861)
  • Add import and export operation for labels and colormaps (#936)
  • Implement napari widgets for colormap and lables control (#935)
  • Add forget all button to multiple files widget (#942)
  • Do not abort processing whole mask segmentation project during exception on single component (#943)
  • Add distance based watersheed to flow methods (#915)
  • Add napari widgets for all group of algoritms (#958)
  • Add napari widget to copy lables along z-axis (#968)

Miscellaneous Tasks

  • Improve ruff configuration, remove isort (#815)
  • Use fail_on_no_env feature from tox-gh-actions (#842)
  • Add python 3.11 to list of supported versions (#867)
  • Disable python 3.11 test because of timeout (#870)
  • Bump ruff to 0.0.218, remove flake8 from pre-commit (#880)
  • Replace GabrielBB/xvfb-action@v1 by aganders3/headless-gui, part 2 (#887)
  • Better minimal requirements test (#888)
  • Improve regexp for proper generate list of packages in update report (#894)
  • Add check for PR title (#933)
  • Migrate from nme to local_migrator (#951)

Refactor

  • Simplify and refactor github workflows. (#864)
  • Better load Mask project in Roi Analysis (#921)
  • Use more descriptive names in pylint: disable (#922)
  • Remove pkg_resources usage as it is deprecated (#967)
  • Convert napari plugin to npe2 (#966)

Security

  • Bump peter-evans/create-pull-request from 4 to 5 (#928)

Styling

  • Change default theme to dark, remove blinking windows on startup. (#809)

Testing

  • [Automatic] Dependency upgrades: packaging, pyinstaller, pyopengl-accelerate, tifffile, xlsxwriter (#932)
  • [Automatic] Constraints upgrades: fonticon-fontawesome6, imageio, numpy, partsegcore-compiled-backend, pygments, sentry-sdk (#937)
  • [Automatic] Constraints upgrades: imageio, ipython, pandas, requests, sentry-sdk (#948)
  • [Automatic] Constraints upgrades: ipython, nme, qtconsole, requests, sentry-sdk (#955)
  • [Automatic] Constraints upgrades: ipykernel, local-migrator, pyinstaller, sentry-sdk, sympy (#957)
  • [Automatic] Constraints upgrades: sentry-sdk, xlsxwriter (#959)
  • [Automatic] Constraints upgrades: requests (#961)

Ci

  • Update codecov configuration to wait on two reports before post information (#934)
  • [pre-commit.ci] pre-commit autoupdate (#945)
  • [pre-commit.ci] pre-commit autoupdate (#956)
  • [pre-commit.ci] pre-commit autoupdate (#964)

Changes:

  • 21658ec docs: Create release notes for PartSeg 0.15.0 (#971)
  • 5a2957f fix: Fix bug in the wrong order of axis saved in napari contribution (#972)
  • 2e2a0c0 test: [Automatic] Constraints upgrades: imageio, pandas, pydantic, pyopengl-accelerate, sentry-sdk, xlsxwriter (#970)
  • ab50a72 feat: add napari widget to copy lables along z-axis (#968)
  • bc9479d fix: Proper calculate bounds for watershed napari widget (#969)
  • ce309a7 refactor: Convert napari plugin to npe2 (#966)
  • cd9ba1f refactor: Remove pkg_resources usage as it is deprecated (#967)
  • 7c17dd1 feat: Add napari widgets for all group of algoritms (#958)
  • ff3be38 ci: [pre-commit.ci] pre-commit autoupdate (#964)
  • 8d5c79f test: [Automatic] Constraints upgrades: requests (#961)
See More
  • dbd57dd test: [Automatic] Constraints upgrades: sentry-sdk, xlsxwriter (#959)
  • d62fcc4 feat: Add distance based watersheed to flow methods (#915)
  • 74cb89a feat: Do not abort processing whole mask segmentation project during exception on single component (#943)
  • 19d82a3 test: [Automatic] Constraints upgrades: ipykernel, local-migrator, pyinstaller, sentry-sdk, sympy (#957)
  • 0f4ae26 ci: [pre-commit.ci] pre-commit autoupdate (#956)
  • 9f5780a chore: Migrate from nme to local_migrator (#951)
  • 3c39384 test: [Automatic] Constraints upgrades: ipython, nme, qtconsole, requests, sentry-sdk (#955)
  • f436158 test: [Automatic] Constraints upgrades: imageio, ipython, pandas, requests, sentry-sdk (#948)
  • 13e6d12 ci: [pre-commit.ci] pre-commit autoupdate (#945)
  • 17eb812 test: [Automatic] Constraints upgrades: fonticon-fontawesome6, imageio, numpy, partsegcore-compiled-backend, pygments, sentry-sdk (#937)
  • ba6d87e fix: Add padding zeros for component num when load Mask seg file to ROI GUI (#944)
  • 1929ad8 fix: Resolve warnings when testing custom save dialog. (#941)
  • 962ef52 feat: Add forget all button to multiple files widget (#942)
  • 0369b34 feat: Implement napari widgets for colormap and lables control (#935)
  • b2ccddd fix: Use text icon, not pixmap icon in colormap and labels list (#938)
  • 44ce9df feat: Add import and export operation for labels and colormaps (#936)
  • ad6bda2 test: [Automatic] Dependency upgrades: packaging, pyinstaller, pyopengl-accelerate, tifffile, xlsxwriter (#932)
  • cee4aa6 ci: Update codecov configuration to wait on two reports before post information (#934)
  • 8663c39 chore: Add check for PR title (#933)
  • f732d24 dep: [Automatic] Dependency upgrades: imageio, ipykernel, ipython, pandas, psygnal, pydantic, pygments, pyinstaller, qtpy, sentry-sdk, tifffile (#917)
  • 6b5f2ef Protect from saving when mask or segmentation is absent (#931)
  • 1d1eb8e build(deps): bump peter-evans/create-pull-request from 4 to 5 (#928) [ evans/create-pull-request#1170, evans/create-pull-request#1792, evans/create-pull-request#1610, evans/create-pull-request#1324, evans/create-pull-request#1318, #1792, #1803, #1801, #1802, #1800, #1799, #1768, #1767, #1766, #1765 ]
  • 19964a7 [pre-commit.ci] pre-commit autoupdate (#929)
  • da0fe91 Add constrains file for tests (#930)
  • bd8db2c fix: Update pyinstaller configuration (#926)
  • 57d32f9 [pre-commit.ci] pre-commit autoupdate (#925)
  • 9a73991 Pin pydantic in test (#924)
  • 52721d8 refactor: use more descriptive names in pylint: disable (#922)
  • 12ae2a8 refactor: Better load Mask project in Roi Analysis (#921)
  • 9881c84 feat: Add napari image custom representation for better error report via sentry (#861)
  • 2017dd5 bugfix: fix bug with generation of form for model with hidden field (#920)
  • 7fd9822 feat: Add option to create projection alongside z-axis (#919)
  • 27f662e [pre-commit.ci] pre-commit autoupdate (#918)
  • 7239fef Add more ruff rules, fix pointed problems, add tests (#910)
  • d9c33f4 dep: [Automatic] Dependency upgrades: imagecodecs, imageio, ipykernel, openpyxl, pydantic, pyinstaller, qtawesome, qtconsole, sentry-sdk, tifffile, xlsxwriter (#908)
  • d968cc7 Use tox-min-req (#912)
  • f13f7b3 [pre-commit.ci] pre-commit autoupdate (#907)
  • dfbd471 dep: [Automatic] Dependency upgrades: ipython, magicgui, scipy, sentry-sdk, tifffile (#906)
  • c168cb0 [pre-commit.ci] pre-commit autoupdate (#902)
  • 86e97b0 dep: [Automatic] Dependency upgrades: imageio, psygnal (#905)
  • 65dbe03 dep: [Automatic] Dependency upgrades: imageio, ipykernel, ipython, numpy, openpyxl, psygnal, pydantic, pyinstaller, pyqt5, scipy, sentry-sdk, tifffile, xlsxwriter (#897)
  • cffbfbe [pre-commit.ci] pre-commit autoupdate (#898)
  • 174e479 Fix conda tests (#899)
  • 1a25c68 [pre-commit.ci] pre-commit autoupdate (#896)
  • 3c28c72 dep: [Automatic] Dependency upgrades: ipython, pyqt5 (#893)
  • ed3bc56 chore: Improve regexp for proper generate list of packages in update report (#894)
  • d19e40c [pre-commit.ci] pre-commit autoupdate (#890)
  • f26b4ff dep: [Automatic] Dependency upgrades: h5py, imagecodecs, imageio, ipykernel, pandas, sentry, tifffile (#889)
  • 5720c3f chore: Better minimal requirements test (#888)
  • 0ea52e8 chore: replace GabrielBB/xvfb-action@v1 by aganders3/headless-gui, part 2 (#887)
  • 4780553 [pre-commit.ci] pre-commit autoupdate (#886)
  • 3449dc2 switch from GabrielBB/xvfb-action to aganders3/headless-gui (#885)
  • bde0a5f dep: [Automatic] Dependency upgrades: ipykernel, requests, sentry, xlsxwriter (#884)
  • 59318b3 Update pre-commit hooks (#883)
  • 3f8f3bc chore: Bump ruff to 0.0.218, remove flake8 from pre-commit (#880)
  • 449ad26 dep: [Automatic] Dependency upgrades: imageio, packaging, scipy, xlsxwriter (#878)
  • 736379c fix: Fix minimal requirments pipeline (#877)
  • cf8abdf [pre-commit.ci] pre-commit autoupdate (#875)
  • c7fea13 dep: [Automatic] Dependency upgrades: pydantic, pygments, xlsxwriter (#874)
  • 36354f6 Update ruff configuration to use more rules (#871)
  • 9ba36aa chore: disable python 3.11 test because of timeout (#870)
  • 0142473 Fix badges in readme (#868)
  • f3430b5 chore: Add python 3.11 to list of supported versions (#867)
  • 9478288 feat: Add alpha support for Qt6 (#866)
  • 3c9373e refactor: Simplify and refactor github workflows. (#864)
  • 210f8af [pre-commit.ci] pre-commit autoupdate (#851)
  • 53cefac dep: [Automatic] Dependency upgrades: imagecodecs, ipykernel, numpy, psygnal (#859)
  • c20afde fix: Fix build of bundle for a new psygnal release (#863)
  • 50b510a fix: Fix tests of napari widgets (#862)
  • 2c96907 fix: ensure that "ROI" layer is in proper place for proper visualization (#856)
  • 0b6c67c Update ruff version and configuration (#855)
  • 0ad7498 feat: Add voxel size measurement and allow to overwritte voxel size in batch (#853)
  • 3544472 dep: [Automatic] Dependency upgrades: imageio, ipykernel, napari, numpy, sentry (#850)
  • f611424 Create codeql-analysis.yml (#420)
  • 31a568b fix: Fix warnings reported by Deepsource (#846)
  • dc92c8e fix: fix redefined-while-unusedimport code for python 3.9.7 (#844)
  • 2f8a2f9 fix: Fix MSO step_limit description in GUI (#843)
  • 9249e0e chore: Use fail_on_no_env feature from tox-gh-actions (#842)
  • c55659f fix: Fix tox configuration to run all required tests (#840)
  • bb0d188 [pre-commit.ci] pre-commit autoupdate (#839)
  • fadc4f8 dep: [Automatic] Dependency upgrades: ipykernel, packaging (#838)
  • 7c4081d Show which packages are updated by automatic vorkflow (#837)
  • 36f2869 fix: Fix problem with resize of multiline widgets (#832)
  • 66b27e5 feat: Allow to see underlaing exception when show warning caused by exception (#829)
  • e8a1c1d Update installation instruction. (#831)
  • cab4674 [pre-commit.ci] pre-commit autoupdate (#830)
  • 4841a1f dep: [Automatic] Dependency upgrades (#828)
  • fd6839a Add option to insert hline in algorithm description (#825)
  • 1795f1e dep: [Automatic] Dependency upgrades (#824)
  • 4a34afd Fix creating update dependencies workflow (#819)
  • c075137 fix: Fix code to addres changes in napari repository (#817)
  • e16ae7d chore: Improve ruff configuration, remove isort (#815)
  • c4dda87 [pre-commit.ci] pre-commit autoupdate (#812)
  • 1dcaa3c Automated dependency upgrades (#811)
  • 605cdb5 Add Upgrade & Open Pull Request Workflow (#699)
  • 318bdef fix: Fix ROIExtractionResult __str__and __repr__ to use ROIExtractionResult not SegmentationResult (#810)
  • 2ccb744 style: Change default theme to dark, remove blinking windows on startup. (#809)
  • ff4319a [pre-commit.ci] pre-commit autoupdate (#806)
  • 9d084f5 docs: Update README and project metadata (#805)
  • d7dca1f feat: Add PARTSEG_SENTRY_URL env variable support and basic documentation about error reporting (#802)
  • 431bef7 Absolutify all imports (#800)
  • d2ace1b fix: Print all exceptions instead of the latest one in exception dialog (#799)
  • 523884a Add information about alternative representation component to bottom text (#797)
  • 5e2ff77 [pre-commit.ci] pre-commit autoupdate (#793)
  • e019a00 Drop python 3.7 support (#792)
  • 79cd221 Bump pyinstaller bundle requirements (#791)

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