0.15.3

0.15.3 - 2024-07-08

🚀 Features

• Pydantic 2 compatibility (#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 compatibility (#1097)
• Fix napari 0.5.0 compatibility (#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)
• [Automatic] Constraints upgrades: pydantic (#1112)

⚙️ 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)
• Add workflow for releases from GHA (#1117)
• Add actionlint to CI to early prevent bug in github workflows (#1119)
• Fix release workflow, by update permissions
• Check if release notes are properly created (#1122)
• Proper use enum in checking new version (#1123)
• Refactor and simplify menu bar creation, add workaround for macOS numpy problem (#1124)
• Simplify release workflow (#1126)
• Fix make_release.yml to proper detect release, attempt 3 (#1127)

🛡️ 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](https://github.co...

0.15.3a5

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)

0.15.3a4

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)

v0.15.3a3

0.15.3 - 2024-07-03%0A%0A### 🚀 Features%0A%0A- Pydantic 2 compatybility (#1084)%0A%0A### 🐛 Bug Fixes%0A%0A- Fix rendering icons in colormap preview (#1040)%0A- Fix test for validation length of message for sentry-sdk 2.0 release (#1098)%0A- When fix reader check lowercase extension for validate compatybility (#1097)%0A- Fix napari 0.5.0 compatybility (#1116)%0A%0A### 🚜 Refactor%0A%0A- Fix Qt flags (#1041)%0A- Fix qt flags in roi mask code (#1042)%0A- Fix qt flags in roi analysis (#1043)%0A- Migrate from setup.cfg to pyproject.toml (#1070)%0A%0A### 📚 Documentation%0A%0A- Allow to use newer release of build docs dependencies (#1057)%0A%0A### 🧪 Testing%0A%0A- [Automatic] Constraints upgrades: imagecodecs, imageio, ipykernel, ipython, numpy, oiffile, pandas, psygnal, pyinstaller, qtconsole, qtpy, sentry-sdk, simpleitk, superqt, tifffile, xlsxwriter (#1020)%0A- [Automatic] Constraints upgrades: h5py, imageio, ipython, numpy, packaging, pydantic, pyinstaller, pyqt5, scipy, sentry-sdk, superqt, tifffile, xlsxwriter (#1027)%0A- [Automatic] Constraints upgrades: imageio, magicgui, xlsxwriter (#1030)%0A- [Automatic] Constraints upgrades: ipykernel, pandas, qtpy (#1032)%0A- [Automatic] Constraints upgrades: imageio, ipykernel, ipython, numpy, pandas, psygnal, pygments, pyinstaller, qtconsole, scipy, sentry-sdk, simpleitk (#1035)%0A- [Automatic] Constraints upgrades: imagecodecs, imageio, ipykernel, magicgui, pandas, pyinstaller, qtawesome, sentry-sdk, tifffile (#1048)%0A- [Automatic] Constraints upgrades: ipykernel, numpy, pandas, partsegcore-compiled-backend, pydantic, scipy, sentry-sdk (#1058)%0A- Improve test of PartSegImage (#1072)%0A- Improve test suite for PartSegCore (#1077)%0A- [Automatic] Constraints upgrades: imageio, ipykernel, local-migrator, napari, numpy, pandas, partsegcore-compiled-backend, pyinstaller, sentry-sdk, tifffile, vispy, xlsxwriter (#1063)%0A- [Automatic] Constraints upgrades: magicgui, packaging, psygnal, pyinstaller, sentry-sdk, superqt (#1086)%0A- [Automatic] Constraints upgrades: psygnal, pydantic, sentry-sdk, vispy (#1090)%0A- [Automatic] Constraints upgrades: h5py, ipykernel, mahotas, pandas, psygnal, pydantic, pyinstaller, qtawesome, scipy, sentry-sdk, superqt (#1092)%0A- [Automatic] Constraints upgrades: imageio, tifffile (#1100)%0A- [Automatic] Constraints upgrades: pydantic, sentry-sdk, superqt, tifffile (#1102)%0A- [Automatic] Constraints upgrades: psygnal, pygments, qtconsole, sentry-sdk, superqt, tifffile (#1105)%0A- [Automatic] Constraints upgrades: imagecodecs, magicgui, oiffile, openpyxl, packaging, pydantic, pyinstaller, requests, scipy, sentry-sdk, superqt, sympy, tifffile, vispy (#1107)%0A%0A### ⚙️ Miscellaneous Tasks%0A%0A- [pre-commit.ci] pre-commit autoupdate (#1019)%0A- Remove plugin page preview as it is no longer maintained (#1021)%0A- [pre-commit.ci] pre-commit autoupdate (#1022)%0A- [pre-commit.ci] pre-commit autoupdate (#1026)%0A- [pre-commit.ci] pre-commit autoupdate (#1031)%0A- [pre-commit.ci] pre-commit autoupdate (#1034)%0A- Use new semgrep configuration (#1039)%0A- Upload raw coverage information (#1044)%0A- [pre-commit.ci] pre-commit autoupdate (#1036)%0A- Run coverage upload in separate steep (#1053)%0A- Generate local report in Tests workflow and use proper script for fetch report (#1054)%0A- Move coverage back to main workflow (#1055)%0A- [pre-commit.ci] pre-commit autoupdate (#1056)%0A- [pre-commit.ci] pre-commit autoupdate (#1059)%0A- Update actions/upload-artifact and actions/download-artifact from 3 to 4 (#1062)%0A- [pre-commit.ci] pre-commit autoupdate (#1064)%0A- Group actions update (#1065)%0A- [pre-commit.ci] pre-commit autoupdate (#1068)%0A- Remove requirement of 2 builds upload to codecov.io (#1073)%0A- Re add tests to coverage report (#1074)%0A- Switch from setup.cfg to pyproject.toml in workflows (#1076)%0A- Fix compiling pyinstaller pre-deps (#1075)%0A- Add codespell to pre-commit and fix pointed bugs (#1078)%0A- Add new ruff rules and apply them (#1079)%0A- [pre-commit.ci] pre-commit autoupdate (#1080)%0A- [pre-commit.ci] pre-commit autoupdate (#1081)%0A- Fix upgrade depenecies workflow (#1083)%0A- Block using mpmath==1.4.0a0 and sentry-sdk 2.0.0a1/a2 in pre-test (#1085)%0A- [pre-commit.ci] pre-commit autoupdate (#1089)%0A- Fix jupyter failing test by using constraints (#1093)%0A- [pre-commit.ci] pre-commit autoupdate (#1091)%0A- [pre-commit.ci] pre-commit autoupdate (#1096)%0A- Add python 3.12 testing (#1087)%0A- Exclude pyside2 on python 3.11 and 3.12 from testing (#1099)%0A- [pre-commit.ci] pre-commit autoupdate (#1101)%0A- [pre-commit.ci] pre-commit autoupdate (#1103)%0A- Bump macos runners to macos-13 (both azure and GHA) (#1113)%0A- [pre-commit.ci] pre-commit autoupdate (#1108)%0A- Remove pyqt5 from constraints (#1118)%0A%0A### 🛡️ Security%0A%0A- (deps) Bump actions/checkout from 3 to 4 (#1029)%0A- (deps) Bump conda-incubator/setup-miniconda from 2 to 3 (#1038)%0A- (deps) Bump aganders3/headless-gui from 1 to 2 (#1047)%0A- (deps) Bump actions/checkout from 3 to 4 (#1045)%0A- (deps) Bump hynek/build-and-inspect-python-package from 1 to 2 (#1050)%0A- (deps) Bump actions/setup-python from 4 to 5 (#1046)%0A- (deps) Bump github/codeql-action from 2 to 3 (#1051)%0A- (deps) Bump peter-evans/create-pull-request from 5 to 6 (#1067)%0A- (deps) Bump codecov/codecov-action from 3 to 4 (#1066)%0A%0A### Build%0A%0A- Fix not bundling Font Awesome 6 Free-Solid-900.otf file to executable (#1114)%0A- Update readme and release to point to GitHub releases (#1115)

v0.15.3a2

ci: fix release workflow, by update permissions

v0.15.2

0.15.2 - 2023-08-28

Bug Fixes

• Fix range threshold selection of algorithms (#1009)
• When run batch check if file extension is supported by loader (#1016)
• Do not allow to select and render corrupted batch plans (#1015)

Testing

• [Automatic] Constraints upgrades: imagecodecs, ipykernel, magicgui, psygnal, scipy, superqt, tifffile (#1011)
• [Automatic] Constraints upgrades: imageio, pyinstaller, tifffile (#1018)

Ci

• Use faster version of black (#1010)
• [pre-commit.ci] pre-commit autoupdate (#1013)

Changes:

• f98e32a add release notes
• 0180435 test: [Automatic] Constraints upgrades: imageio, pyinstaller, tifffile (#1018)
• 84b09d0 test: [Automatic] Constraints upgrades: imagecodecs, ipykernel, magicgui, psygnal, scipy, superqt, tifffile (#1011)
• df3663c fix: Do not allow to select and render corrupted batch plans (#1015)
• ae9a4d0 fix: When run batch check if file extension is supported by loader (#1016)
• c06d745 ci: [pre-commit.ci] pre-commit autoupdate (#1013)
• 45c385b ci: Use faster version of black (#1010)
• 82d705d fix: Fix range threshold selection of algorithms (#1009)

This list of changes was auto generated.

v0.15.1

0.15.1 - 2023-08-09

Bug Fixes

• Fix possible problem of double registration napari plugin in PartSeg bundle (#974)
• Bump OS versions for part of testing workflows. (#977)
• Bump os version for main tests workflow. (#979)
• Ensure that the module PartSegCore.channel_class is present in bundle (#980)
• Lower npe2 schema version to work with older napari version (#981)
• Generate test report per platfom (#978)
• Importing plugins in bundle keeping proper module names (#983)
• Fix napari repo workflow (#985)
• Fix bug in read tiff files with double Q in axes but one related to dummy dimmension (#992)
• Fix bug that lead to corupted state when saving calculation plan to excel file (#995)
• Enable python 3.11 test on CI, fix minor errors (#869)

Features

• Allow to save multiple napari image layers to single tiff file (#1000)
• Add option to export batch project with data (#996)

Testing

• [Automatic] Constraints upgrades: imageio, ipython, psygnal, scipy, sentry-sdk (#975)
• [Automatic] Constraints upgrades: h5py, imagecodecs, imageio, ipykernel, napari, numpy, pandas, pydantic, pyinstaller, scipy, sentry-sdk, tifffile, vispy (#986)
• [Automatic] Constraints upgrades: imagecodecs, sentry-sdk, tifffile (#997)
• [Automatic] Constraints upgrades: ipykernel, pydantic (#1002)
• [Automatic] Constraints upgrades: numpy, pygments, sentry-sdk, superqt (#1007)

Ci

• [pre-commit.ci] pre-commit autoupdate (#973)
• [pre-commit.ci] pre-commit autoupdate (#982)
• [pre-commit.ci] pre-commit autoupdate (#987)
• [pre-commit.ci] pre-commit autoupdate (#988)
• [pre-commit.ci] pre-commit autoupdate (#991)
• [pre-commit.ci] pre-commit autoupdate (#998)
• [pre-commit.ci] pre-commit autoupdate (#1004)
• Change markdown linter from pre-commit to mdformat (#1006)

Changes:

• 3594793 add release notes
• d9efd0b ci: [pre-commit.ci] pre-commit autoupdate (#1008)
• 3104c5c feat: Add option to export batch project with data (#996)
• 112c4fe test: [Automatic] Constraints upgrades: numpy, pygments, sentry-sdk, superqt (#1007)
• 10244c5 ci: Change markdown linter from pre-commit to mdformat (#1006)
• 9016e95 ci: [pre-commit.ci] pre-commit autoupdate (#1004)
• d77717b fix: Enable python 3.11 test on CI, fix minor errors (#869)
• 4fc34bf test: [Automatic] Constraints upgrades: ipykernel, pydantic (#1002)
• b38933b feat: allow to save multiple napari image layers to single tiff file (#1000)
• 1fb01af ci: [pre-commit.ci] pre-commit autoupdate (#998)

See More

• b03118c test: [Automatic] Constraints upgrades: imagecodecs, sentry-sdk, tifffile (#997)
• 6945822 fix: Fix bug that lead to corupted state when saving calculation plan to excel file (#995)
• 152a026 fix: Fix bug in read tiff files with double Q in axes but one related to dummy dimmension (#992)
• 3b08337 ci: [pre-commit.ci] pre-commit autoupdate (#991)
• dd3ca25 test: [Automatic] Constraints upgrades: h5py, imagecodecs, imageio, ipykernel, napari, numpy, pandas, pydantic, pyinstaller, scipy, sentry-sdk, tifffile, vispy (#986)
• aacc428 ci: [pre-commit.ci] pre-commit autoupdate (#988)
• 072f558 ci: [pre-commit.ci] pre-commit autoupdate (#987)
• da4c370 fix: Fix napari repo workflow (#985) [ #984 ]
• c7325d4 fix: importing plugins in bundle keeping proper module names (#983)
• 43e9bc2 fix: Generate test report per platfom (#978)
• 26b4c44 ci: [pre-commit.ci] pre-commit autoupdate (#982)
• 0de056e fix: Lower npe2 schema version to work with older napari version (#981)
• 18aa3ac fix: Ensure that the module PartSegCore.channel_class is present in bundle (#980)
• d8bdb93 fix: Bump os version for main tests workflow. (#979) [ #977 ]
• 889a728 fix: Bump OS versions for part of testing workflows. (#977) [ #976 ]
• d3a26d6 test: [Automatic] Constraints upgrades: imageio, ipython, psygnal, scipy, sentry-sdk (#975)
• 91c3c1d fix: Fix possible problem of double registration napari plugin in PartSeg bundle (#974)
• 0dff2f0 ci: [pre-commit.ci] pre-commit autoupdate (#973)

This list of changes was auto generated.

v0.15.0

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...

v0.14.6

0.14.6 - 2022-11-13

Bug Fixes

• Fix bug when loading already created project causing hide of ROI layer (#787)

Features

• Improve error message if segmentation do not fit in ROI Mask (#788)

Changes:

• 994088d fix: Fix bug when loading already created project causing hide of ROI layer (#787)
• 426b918 Improve error message if segmentation do not fit in ROI Mask (#788)

This list of changes was auto generated.

v0.14.5

0.14.5 - 2022-11-09

Bug Fixes

• Fix scalebar color (#774)
• Fix bug when saving segmentation parameters in mask analysis (#781)
• Fix multiple errors related to loading a new file in interactive mode (#784)

Features

• Add an option for ensuring type in EventedDict and use it to validate profiles structures (#776)
• Add an option to create an issue from the error report dialog (#782)
• Add option for the multiline field in algorithm parameters (#766)

Refactor

• Optimize CLI actions (#772)
• Clean warnings about threshold methods (#783)

Build

• Bump chanzuckerberg/napari-hub-preview-action from 0.1.5 to 0.1.6 (#775)

Changes:

• 7510307 Update changelog (#786)
• 37813e5 fix: Fix multiple error related to loading new file in interactive mode (#784)
• 3906d27 refactor: Clean warnings about threshold methods (#783)
• 4b836c1 feat: Add option for multiline field in algorithm parameters (#766)
• d783ed9 feat: Add option to create issue from error report dialog (#782)
• fa1a6d1 fix: Fix bug when saving segmentation prameters in mask analysis (#781)
• 42b1d71 add roi and mask aliases (#780)
• 9fca75a [pre-commit.ci] pre-commit autoupdate (#778)
• 1e0c7f4 feat: Add option for ensure type in EventedDict and use it to validate profiles structures (#776)
• 691e800 build(deps): bump chanzuckerberg/napari-hub-preview-action from 0.1.5 to 0.1.6 (#775)

See More

• 6ed8e46 fix: Fix scalebar color (#774)
• 37b4578 refactor: optimize CLI actions (#772)
• 944ade4 [pre-commit.ci] pre-commit autoupdate (#773)

This list of changes was auto generated.