PartSeg - segmentation and reconstruction tool for 3D microscopy images

0.15.3 - 2024-07-03

🚀 Features

• Pydantic 2 compatybility (#1084)

🐛 Bug Fixes

• Fix rendering icons in colormap preview (#1040)
• Fix test for validation length of message for sentry-sdk 2.0 release (#1098)
• When fix reader check lowercase extension for validate compatybility (#1097)
• Fix napari 0.5.0 compatybility (#1116)

🚜 Refactor

• Fix Qt flags (#1041)
• Fix qt flags in roi mask code (#1042)
• Fix qt flags in roi analysis (#1043)
• Migrate from setup.cfg to pyproject.toml (#1070)

📚 Documentation

• Allow to use newer release of build docs dependencies (#1057)

🧪 Testing

• [Automatic] Constraints upgrades: imagecodecs, imageio, ipykernel, ipython, numpy, oiffile, pandas, psygnal, pyinstaller, qtconsole, qtpy, sentry-sdk, simpleitk, superqt, tifffile, xlsxwriter (#1020)
• [Automatic] Constraints upgrades: h5py, imageio, ipython, numpy, packaging, pydantic, pyinstaller, pyqt5, scipy, sentry-sdk, superqt, tifffile, xlsxwriter (#1027)
• [Automatic] Constraints upgrades: imageio, magicgui, xlsxwriter (#1030)
• [Automatic] Constraints upgrades: ipykernel, pandas, qtpy (#1032)
• [Automatic] Constraints upgrades: imageio, ipykernel, ipython, numpy, pandas, psygnal, pygments, pyinstaller, qtconsole, scipy, sentry-sdk, simpleitk (#1035)
• [Automatic] Constraints upgrades: imagecodecs, imageio, ipykernel, magicgui, pandas, pyinstaller, qtawesome, sentry-sdk, tifffile (#1048)
• [Automatic] Constraints upgrades: ipykernel, numpy, pandas, partsegcore-compiled-backend, pydantic, scipy, sentry-sdk (#1058)
• Improve test of PartSegImage (#1072)
• Improve test suite for PartSegCore (#1077)
• [Automatic] Constraints upgrades: imageio, ipykernel, local-migrator, napari, numpy, pandas, partsegcore-compiled-backend, pyinstaller, sentry-sdk, tifffile, vispy, xlsxwriter (#1063)
• [Automatic] Constraints upgrades: magicgui, packaging, psygnal, pyinstaller, sentry-sdk, superqt (#1086)
• [Automatic] Constraints upgrades: psygnal, pydantic, sentry-sdk, vispy (#1090)
• [Automatic] Constraints upgrades: h5py, ipykernel, mahotas, pandas, psygnal, pydantic, pyinstaller, qtawesome, scipy, sentry-sdk, superqt (#1092)
• [Automatic] Constraints upgrades: imageio, tifffile (#1100)
• [Automatic] Constraints upgrades: pydantic, sentry-sdk, superqt, tifffile (#1102)
• [Automatic] Constraints upgrades: psygnal, pygments, qtconsole, sentry-sdk, superqt, tifffile (#1105)
• [Automatic] Constraints upgrades: imagecodecs, magicgui, oiffile, openpyxl, packaging, pydantic, pyinstaller, requests, scipy, sentry-sdk, superqt, sympy, tifffile, vispy (#1107)

⚙️ Miscellaneous Tasks

• [pre-commit.ci] pre-commit autoupdate (#1019)
• Remove plugin page preview as it is no longer maintained (#1021)
• [pre-commit.ci] pre-commit autoupdate (#1022)
• [pre-commit.ci] pre-commit autoupdate (#1026)
• [pre-commit.ci] pre-commit autoupdate (#1031)
• [pre-commit.ci] pre-commit autoupdate (#1034)
• Use new semgrep configuration (#1039)
• Upload raw coverage information (#1044)
• [pre-commit.ci] pre-commit autoupdate (#1036)
• Run coverage upload in separate steep (#1053)
• Generate local report in Tests workflow and use proper script for fetch report (#1054)
• Move coverage back to main workflow (#1055)
• [pre-commit.ci] pre-commit autoupdate (#1056)
• [pre-commit.ci] pre-commit autoupdate (#1059)
• Update actions/upload-artifact and actions/download-artifact from 3 to 4 (#1062)
• [pre-commit.ci] pre-commit autoupdate (#1064)
• Group actions update (#1065)
• [pre-commit.ci] pre-commit autoupdate (#1068)
• Remove requirement of 2 builds upload to codecov.io (#1073)
• Re add tests to coverage report (#1074)
• Switch from setup.cfg to pyproject.toml in workflows (#1076)
• Fix compiling pyinstaller pre-deps (#1075)
• Add codespell to pre-commit and fix pointed bugs (#1078)
• Add new ruff rules and apply them (#1079)
• [pre-commit.ci] pre-commit autoupdate (#1080)
• [pre-commit.ci] pre-commit autoupdate (#1081)
• Fix upgrade depenecies workflow (#1083)
• Block using mpmath==1.4.0a0 and sentry-sdk 2.0.0a1/a2 in pre-test (#1085)
• [pre-commit.ci] pre-commit autoupdate (#1089)
• Fix jupyter failing test by using constraints (#1093)
• [pre-commit.ci] pre-commit autoupdate (#1091)
• [pre-commit.ci] pre-commit autoupdate (#1096)
• Add python 3.12 testing (#1087)
• Exclude pyside2 on python 3.11 and 3.12 from testing (#1099)
• [pre-commit.ci] pre-commit autoupdate (#1101)
• [pre-commit.ci] pre-commit autoupdate (#1103)
• Bump macos runners to macos-13 (both azure and GHA) (#1113)
• [pre-commit.ci] pre-commit autoupdate (#1108)
• Remove pyqt5 from constraints (#1118)

🛡️ Security

• (deps) Bump actions/checkout from 3 to 4 (#1029)
• (deps) Bump conda-incubator/setup-miniconda from 2 to 3 (#1038)
• (deps) Bump aganders3/headless-gui from 1 to 2 (#1047)
• (deps) Bump actions/checkout from 3 to 4 (#1045)
• (deps) Bump hynek/build-and-inspect-python-package from 1 to 2 (#1050)
• (deps) Bump actions/setup-python from 4 to 5 (#1046)
• (deps) Bump github/codeql-action from 2 to 3 (#1051)
• (deps) Bump peter-evans/create-pull-request from 5 to 6 (#1067)
• (deps) Bump codecov/codecov-action from 3 to 4 (#1066)

Build

• Fix not bundling Font Awesome 6 Free-Solid-900.otf file to executable (#1114)
• Update readme and release to point to GitHub releases (#1115)