Partseg

🐛 Bug Fixes

- Fix rendering of alternative representation if there are more components in the alternative representation than in ROI ([1240](https://github.com/4DNucleome/PartSeg/pull/1240))
- Enable czifile workaround for 2019.7.2.1 ([1246](https://github.com/4DNucleome/PartSeg/pull/1246))

🧪 Testing

- [Automatic] Constraints upgrades: `ipython`, `magicgui`, `numpy`, `partsegcore-compiled-backend`, `pydantic` ([1231](https://github.com/4DNucleome/PartSeg/pull/1231))
- [Automatic] Constraints upgrades: `imagecodecs` ([1233](https://github.com/4DNucleome/PartSeg/pull/1233))
- [Automatic] Constraints upgrades: `oiffile`, `pygments`, `scipy`, `superqt` ([1234](https://github.com/4DNucleome/PartSeg/pull/1234))
- [Automatic] Constraints upgrades: `imageio`, `napari`, `numpy`, `partsegcore-compiled-backend`, `pydantic`, `pygments`, `scipy`, `sentry-sdk`, `simpleitk`, `tifffile`, `xlsxwriter` ([1236](https://github.com/4DNucleome/PartSeg/pull/1236))
- [Automatic] Constraints upgrades: `ipython`, `xlsxwriter` ([1239](https://github.com/4DNucleome/PartSeg/pull/1239))
- [Automatic] Constraints upgrades: `numpy`, `partsegcore-compiled-backend`, `psygnal`, `qtpy`, `scipy`, `sentry-sdk` ([1241](https://github.com/4DNucleome/PartSeg/pull/1241))
- [Automatic] Constraints upgrades: `czifile`, `h5py`, `ipython`, `qtawesome`, `sentry-sdk`, `tifffile`, `traceback-with-variables` ([1247](https://github.com/4DNucleome/PartSeg/pull/1247))

⚙️ Miscellaneous Tasks

- [pre-commit.ci] pre-commit autoupdate ([1232](https://github.com/4DNucleome/PartSeg/pull/1232))
- [pre-commit.ci] pre-commit autoupdate ([1235](https://github.com/4DNucleome/PartSeg/pull/1235))
- [pre-commit.ci] pre-commit autoupdate ([1237](https://github.com/4DNucleome/PartSeg/pull/1237))
- Drop python 3.9 tests for napari repository ([1244](https://github.com/4DNucleome/PartSeg/pull/1244))
- Block ipykernel 7.0.0a1 ([1248](https://github.com/4DNucleome/PartSeg/pull/1248))
- [pre-commit.ci] pre-commit autoupdate ([1242](https://github.com/4DNucleome/PartSeg/pull/1242))
- Switch to `get_qapp` from `get_app` to handle napari deprecation ([1249](https://github.com/4DNucleome/PartSeg/pull/1249))

🚀 Features

- Allow set units that will be used for load/save data using PartSeg as napari plugin ([1228](https://github.com/4DNucleome/PartSeg/pull/1228))
- Show filename when importing with PartSeg in napari ([1226](https://github.com/4DNucleome/PartSeg/pull/1226))

🐛 Bug Fixes

- Fix error when image changed during segmentation ([1218](https://github.com/4DNucleome/PartSeg/pull/1218))
- Fix pre release tests ([1219](https://github.com/4DNucleome/PartSeg/pull/1219))
- Drop imagej LUTs of size `24*x` ([1227](https://github.com/4DNucleome/PartSeg/pull/1227))

🧪 Testing

- [Automatic] Constraints upgrades: `h5py`, `imageio`, `ipython`, `napari`, `numpy`, `sentry-sdk` ([1201](https://github.com/4DNucleome/PartSeg/pull/1201))
- [Automatic] Constraints upgrades: `sentry-sdk` ([1214](https://github.com/4DNucleome/PartSeg/pull/1214))
- [Automatic] Constraints upgrades: `ipython`, `traceback-with-variables` ([1221](https://github.com/4DNucleome/PartSeg/pull/1221))
- [Automatic] Constraints upgrades: `numpy`, `packaging`, `pydantic`, `qtconsole`, `qtpy`, `sentry-sdk`, `traceback-with-variables` ([1223](https://github.com/4DNucleome/PartSeg/pull/1223))
- [Automatic] Constraints upgrades: `imageio`, `ipython`, `pydantic` ([1225](https://github.com/4DNucleome/PartSeg/pull/1225))
- [Automatic] Constraints upgrades: `napari`, `numpy`, `pydantic`, `sentry-sdk`, `six`, `superqt`, `tifffile` ([1229](https://github.com/4DNucleome/PartSeg/pull/1229))

⚙️ Miscellaneous Tasks

- Stop using mambaforge in tests ([1203](https://github.com/4DNucleome/PartSeg/pull/1203))
- [pre-commit.ci] pre-commit autoupdate ([1202](https://github.com/4DNucleome/PartSeg/pull/1202))
- [pre-commit.ci] pre-commit autoupdate ([1204](https://github.com/4DNucleome/PartSeg/pull/1204))
- Remove defining default version of language in pre-commit configuration ([1208](https://github.com/4DNucleome/PartSeg/pull/1208))
- [pre-commit.ci] pre-commit autoupdate ([1209](https://github.com/4DNucleome/PartSeg/pull/1209))
- Drop python 3.8 ([1206](https://github.com/4DNucleome/PartSeg/pull/1206))
- Use `PublishPipelineArtifact` in place of `PublishBuildArtifacts` to reduce CI fragility ([1213](https://github.com/4DNucleome/PartSeg/pull/1213))
- Update CI configuration to use more modern OS and python versions ([1207](https://github.com/4DNucleome/PartSeg/pull/1207))
- Fix `upgrade-dependencies.yaml`docs constraints ([1215](https://github.com/4DNucleome/PartSeg/pull/1215))
- [pre-commit.ci] pre-commit autoupdate ([1216](https://github.com/4DNucleome/PartSeg/pull/1216))
- Add changelog 0.16.0a1
- [pre-commit.ci] pre-commit autoupdate ([1222](https://github.com/4DNucleome/PartSeg/pull/1222))
- [pre-commit.ci] pre-commit autoupdate ([1230](https://github.com/4DNucleome/PartSeg/pull/1230))

🚀 Features

- Add preview of image metadata ([1154](https://github.com/4DNucleome/PartSeg/pull/1154))
- Add option to combine channels using sum and max ([1159](https://github.com/4DNucleome/PartSeg/pull/1159))
- Add metadata viewer as napari widget ([1195](https://github.com/4DNucleome/PartSeg/pull/1195))
- Read channel colors from `*.czi` metadata ([1198](https://github.com/4DNucleome/PartSeg/pull/1198))
- Use image color when add layer to napari ([1200](https://github.com/4DNucleome/PartSeg/pull/1200))

🐛 Bug Fixes

- Fix selection of custom label colors for napari 0.5.0 ([1138](https://github.com/4DNucleome/PartSeg/pull/1138))
- Add pint call to enforce initialization of unit registry ([1146](https://github.com/4DNucleome/PartSeg/pull/1146))
- Workaround for lack of zsd support in czifile ([1142](https://github.com/4DNucleome/PartSeg/pull/1142))
- Fix preparing data for `mahotas.haralick` to avoid overflow problem ([1150](https://github.com/4DNucleome/PartSeg/pull/1150))
- Fix `use_convex` type from `int` to `bool` for segmentation algorithms ([1152](https://github.com/4DNucleome/PartSeg/pull/1152))
- Prevent propagation of decreasing contrast limits set by user ([1166](https://github.com/4DNucleome/PartSeg/pull/1166))
- Prevent error on searching component if there is no component ([1167](https://github.com/4DNucleome/PartSeg/pull/1167))
- Fix checking if channel requested by MeasurementProfile exists ([1165](https://github.com/4DNucleome/PartSeg/pull/1165))
- Fix trying to access to just deleted measurement profile from edit window. ([1168](https://github.com/4DNucleome/PartSeg/pull/1168))
- Fix bug in code for checking for survey file ([1174](https://github.com/4DNucleome/PartSeg/pull/1174))
- Fix plugin discovery in bundle to register them in napari viewer ([1175](https://github.com/4DNucleome/PartSeg/pull/1175))
- Fix problem with setting range of auto-generated widget ([1187](https://github.com/4DNucleome/PartSeg/pull/1187))
- Fix reading channel names from single channel czi files ([1194](https://github.com/4DNucleome/PartSeg/pull/1194))

🚜 Refactor

- Make warnings error in tests ([1192](https://github.com/4DNucleome/PartSeg/pull/1192))
- Merge all channel-specific attributes of the Image class ([1191](https://github.com/4DNucleome/PartSeg/pull/1191))

📚 Documentation

- Change homepage URL ([1139](https://github.com/4DNucleome/PartSeg/pull/1139))
- Add link for download macOS arm bundle ([1140](https://github.com/4DNucleome/PartSeg/pull/1140))
- Add changelog for 0.15.4 release
- Update changelog ([1176](https://github.com/4DNucleome/PartSeg/pull/1176))

🧪 Testing

- [Automatic] Constraints upgrades: `napari`, `sentry-sdk`, `sympy` ([1128](https://github.com/4DNucleome/PartSeg/pull/1128))
- [Automatic] Constraints upgrades: `mahotas`, `numpy`, `sentry-sdk`, `sympy` ([1145](https://github.com/4DNucleome/PartSeg/pull/1145))
- [Automatic] Constraints upgrades: `numpy`, `tifffile` ([1163](https://github.com/4DNucleome/PartSeg/pull/1163))
- [Automatic] Constraints upgrades: `napari`, `sentry-sdk`, `tifffile` ([1169](https://github.com/4DNucleome/PartSeg/pull/1169))
- [Automatic] Constraints upgrades: `magicgui`, `sentry-sdk` ([1172](https://github.com/4DNucleome/PartSeg/pull/1172))
- [Automatic] Constraints upgrades: `sympy`, `tifffile` ([1177](https://github.com/4DNucleome/PartSeg/pull/1177))
- [Automatic] Constraints upgrades: `imageio`, `napari`, `numpy` ([1180](https://github.com/4DNucleome/PartSeg/pull/1180))
- Constraints upgrades: `sentry-sdk` and fix tests ([1182](https://github.com/4DNucleome/PartSeg/pull/1182))
- `napari==0.5.3` related fixes, Constraints upgrades: `imageio`, `ipython`, `numpy`, `qtconsole`, `scipy`, `simpleitk`, `tifffile` ([1183](https://github.com/4DNucleome/PartSeg/pull/1183))
- [Automatic] Constraints upgrades: `numpy`, `pydantic` ([1188](https://github.com/4DNucleome/PartSeg/pull/1188))
- [Automatic] Constraints upgrades: `imagecodecs`, `pandas`, `pydantic`, `sentry-sdk`, `sympy`, `tifffile` ([1190](https://github.com/4DNucleome/PartSeg/pull/1190))

⚙️ Miscellaneous Tasks

- Speedup tests by use `tox-uv` ([1141](https://github.com/4DNucleome/PartSeg/pull/1141))
- Get additional dict from PR branch for checking PR title ([1144](https://github.com/4DNucleome/PartSeg/pull/1144))
- Relax numpy constraint ([1143](https://github.com/4DNucleome/PartSeg/pull/1143))
- Allow to skip spellchecking PR title ([1147](https://github.com/4DNucleome/PartSeg/pull/1147))
- [pre-commit.ci] pre-commit autoupdate ([1149](https://github.com/4DNucleome/PartSeg/pull/1149))
- Create only archive with version in name on azures pipeline ([1151](https://github.com/4DNucleome/PartSeg/pull/1151))
- Fix tests for napari from repository ([1148](https://github.com/4DNucleome/PartSeg/pull/1148))
- Use python 3.11 to determine updated packages in PR description ([1160](https://github.com/4DNucleome/PartSeg/pull/1160))
- [pre-commit.ci] pre-commit autoupdate ([1164](https://github.com/4DNucleome/PartSeg/pull/1164))
- [pre-commit.ci] pre-commit autoupdate ([1170](https://github.com/4DNucleome/PartSeg/pull/1170))
- Disable thumbnail generation in napari layer as it is fragile and not used ([1171](https://github.com/4DNucleome/PartSeg/pull/1171))
- [pre-commit.ci] pre-commit autoupdate ([1173](https://github.com/4DNucleome/PartSeg/pull/1173))
- [pre-commit.ci] pre-commit autoupdate ([1178](https://github.com/4DNucleome/PartSeg/pull/1178))
- Fix call of logger to properly pass arguments to messages ([1179](https://github.com/4DNucleome/PartSeg/pull/1179))
- Fix coverage files upload by enable hidden files upload ([1186](https://github.com/4DNucleome/PartSeg/pull/1186))
- [pre-commit.ci] pre-commit autoupdate ([1184](https://github.com/4DNucleome/PartSeg/pull/1184))
- Use PyQt6 in pre-tests ([1196](https://github.com/4DNucleome/PartSeg/pull/1196))
- Add missed code from 1191 ([1197](https://github.com/4DNucleome/PartSeg/pull/1197))
- [pre-commit.ci] pre-commit autoupdate ([1189](https://github.com/4DNucleome/PartSeg/pull/1189))
- Auto add "skip check PR title" label in update dependencies PR ([1199](https://github.com/4DNucleome/PartSeg/pull/1199))

Build

- Remove PyOpenGL-accelerate from dependencies because of numpy incompatibility ([1155](https://github.com/4DNucleome/PartSeg/pull/1155))
- Update install constraints on numpy and qt packages ([1157](https://github.com/4DNucleome/PartSeg/pull/1157))
- Enforce napari 0.5.0 for Qt6 bindings ([1161](https://github.com/4DNucleome/PartSeg/pull/1161))
- Require napari>=0.5.0 only for python 3.9+ ([1162](https://github.com/4DNucleome/PartSeg/pull/1162))

🚀 Features

- Pydantic 2 compatibility ([1084](https://github.com/4DNucleome/PartSeg/pull/1084))

🐛 Bug Fixes

- Fix rendering icons in colormap preview ([1040](https://github.com/4DNucleome/PartSeg/pull/1040))
- Fix test for validation length of message for sentry-sdk 2.0 release ([1098](https://github.com/4DNucleome/PartSeg/pull/1098))
- When fix reader check lowercase extension for validate compatibility ([1097](https://github.com/4DNucleome/PartSeg/pull/1097))
- Fix napari 0.5.0 compatibility ([1116](https://github.com/4DNucleome/PartSeg/pull/1116))

🚜 Refactor

- Fix Qt flags ([1041](https://github.com/4DNucleome/PartSeg/pull/1041))
- Fix qt flags in roi mask code ([1042](https://github.com/4DNucleome/PartSeg/pull/1042))
- Fix qt flags in roi analysis ([1043](https://github.com/4DNucleome/PartSeg/pull/1043))
- Migrate from setup.cfg to `pyproject.toml` ([1070](https://github.com/4DNucleome/PartSeg/pull/1070))

📚 Documentation

- Allow to use newer release of build docs dependencies ([1057](https://github.com/4DNucleome/PartSeg/pull/1057))

🧪 Testing

- [Automatic] Constraints upgrades: `imagecodecs`, `imageio`, `ipykernel`, `ipython`, `numpy`, `oiffile`, `pandas`, `psygnal`, `pyinstaller`, `qtconsole`, `qtpy`, `sentry-sdk`, `simpleitk`, `superqt`, `tifffile`, `xlsxwriter` ([1020](https://github.com/4DNucleome/PartSeg/pull/1020))
- [Automatic] Constraints upgrades: `h5py`, `imageio`, `ipython`, `numpy`, `packaging`, `pydantic`, `pyinstaller`, `pyqt5`, `scipy`, `sentry-sdk`, `superqt`, `tifffile`, `xlsxwriter` ([1027](https://github.com/4DNucleome/PartSeg/pull/1027))
- [Automatic] Constraints upgrades: `imageio`, `magicgui`, `xlsxwriter` ([1030](https://github.com/4DNucleome/PartSeg/pull/1030))
- [Automatic] Constraints upgrades: `ipykernel`, `pandas`, `qtpy` ([1032](https://github.com/4DNucleome/PartSeg/pull/1032))
- [Automatic] Constraints upgrades: `imageio`, `ipykernel`, `ipython`, `numpy`, `pandas`, `psygnal`, `pygments`, `pyinstaller`, `qtconsole`, `scipy`, `sentry-sdk`, `simpleitk` ([1035](https://github.com/4DNucleome/PartSeg/pull/1035))
- [Automatic] Constraints upgrades: `imagecodecs`, `imageio`, `ipykernel`, `magicgui`, `pandas`, `pyinstaller`, `qtawesome`, `sentry-sdk`, `tifffile` ([1048](https://github.com/4DNucleome/PartSeg/pull/1048))
- [Automatic] Constraints upgrades: `ipykernel`, `numpy`, `pandas`, `partsegcore-compiled-backend`, `pydantic`, `scipy`, `sentry-sdk` ([1058](https://github.com/4DNucleome/PartSeg/pull/1058))
- Improve test of PartSegImage ([1072](https://github.com/4DNucleome/PartSeg/pull/1072))
- Improve test suite for `PartSegCore` ([1077](https://github.com/4DNucleome/PartSeg/pull/1077))
- [Automatic] Constraints upgrades: `imageio`, `ipykernel`, `local-migrator`, `napari`, `numpy`, `pandas`, `partsegcore-compiled-backend`, `pyinstaller`, `sentry-sdk`, `tifffile`, `vispy`, `xlsxwriter` ([1063](https://github.com/4DNucleome/PartSeg/pull/1063))
- [Automatic] Constraints upgrades: `magicgui`, `packaging`, `psygnal`, `pyinstaller`, `sentry-sdk`, `superqt` ([1086](https://github.com/4DNucleome/PartSeg/pull/1086))
- [Automatic] Constraints upgrades: `psygnal`, `pydantic`, `sentry-sdk`, `vispy` ([1090](https://github.com/4DNucleome/PartSeg/pull/1090))
- [Automatic] Constraints upgrades: `h5py`, `ipykernel`, `mahotas`, `pandas`, `psygnal`, `pydantic`, `pyinstaller`, `qtawesome`, `scipy`, `sentry-sdk`, `superqt` ([1092](https://github.com/4DNucleome/PartSeg/pull/1092))
- [Automatic] Constraints upgrades: `imageio`, `tifffile` ([1100](https://github.com/4DNucleome/PartSeg/pull/1100))
- [Automatic] Constraints upgrades: `pydantic`, `sentry-sdk`, `superqt`, `tifffile` ([1102](https://github.com/4DNucleome/PartSeg/pull/1102))
- [Automatic] Constraints upgrades: `psygnal`, `pygments`, `qtconsole`, `sentry-sdk`, `superqt`, `tifffile` ([1105](https://github.com/4DNucleome/PartSeg/pull/1105))
- [Automatic] Constraints upgrades: `imagecodecs`, `magicgui`, `oiffile`, `openpyxl`, `packaging`, `pydantic`, `pyinstaller`, `requests`, `scipy`, `sentry-sdk`, `superqt`, `sympy`, `tifffile`, `vispy` ([1107](https://github.com/4DNucleome/PartSeg/pull/1107))
- [Automatic] Constraints upgrades: `pydantic` ([1112](https://github.com/4DNucleome/PartSeg/pull/1112))

⚙️ Miscellaneous Tasks

- [pre-commit.ci] pre-commit autoupdate ([1019](https://github.com/4DNucleome/PartSeg/pull/1019))
- Remove plugin page preview as it is no longer maintained ([1021](https://github.com/4DNucleome/PartSeg/pull/1021))
- [pre-commit.ci] pre-commit autoupdate ([1022](https://github.com/4DNucleome/PartSeg/pull/1022))
- [pre-commit.ci] pre-commit autoupdate ([1026](https://github.com/4DNucleome/PartSeg/pull/1026))
- [pre-commit.ci] pre-commit autoupdate ([1031](https://github.com/4DNucleome/PartSeg/pull/1031))
- [pre-commit.ci] pre-commit autoupdate ([1034](https://github.com/4DNucleome/PartSeg/pull/1034))
- Use new semgrep configuration ([1039](https://github.com/4DNucleome/PartSeg/pull/1039))
- Upload raw coverage information ([1044](https://github.com/4DNucleome/PartSeg/pull/1044))
- [pre-commit.ci] pre-commit autoupdate ([1036](https://github.com/4DNucleome/PartSeg/pull/1036))
- Run coverage upload in separate steep ([1053](https://github.com/4DNucleome/PartSeg/pull/1053))
- Generate local report in `Tests` workflow and use proper script for fetch report ([1054](https://github.com/4DNucleome/PartSeg/pull/1054))
- Move coverage back to main workflow ([1055](https://github.com/4DNucleome/PartSeg/pull/1055))
- [pre-commit.ci] pre-commit autoupdate ([1056](https://github.com/4DNucleome/PartSeg/pull/1056))
- [pre-commit.ci] pre-commit autoupdate ([1059](https://github.com/4DNucleome/PartSeg/pull/1059))
- Update `actions/upload-artifact` and `actions/download-artifact` from 3 to 4 ([1062](https://github.com/4DNucleome/PartSeg/pull/1062))
- [pre-commit.ci] pre-commit autoupdate ([1064](https://github.com/4DNucleome/PartSeg/pull/1064))
- Group actions update ([1065](https://github.com/4DNucleome/PartSeg/pull/1065))
- [pre-commit.ci] pre-commit autoupdate ([1068](https://github.com/4DNucleome/PartSeg/pull/1068))
- Remove requirement of 2 builds upload to codecov.io ([1073](https://github.com/4DNucleome/PartSeg/pull/1073))
- Re add tests to coverage report ([1074](https://github.com/4DNucleome/PartSeg/pull/1074))
- Switch from setup.cfg to pyproject.toml in workflows ([1076](https://github.com/4DNucleome/PartSeg/pull/1076))
- Fix compiling pyinstaller pre-deps ([1075](https://github.com/4DNucleome/PartSeg/pull/1075))
- Add codespell to pre-commit and fix pointed bugs ([1078](https://github.com/4DNucleome/PartSeg/pull/1078))
- Add new ruff rules and apply them ([1079](https://github.com/4DNucleome/PartSeg/pull/1079))
- [pre-commit.ci] pre-commit autoupdate ([1080](https://github.com/4DNucleome/PartSeg/pull/1080))
- [pre-commit.ci] pre-commit autoupdate ([1081](https://github.com/4DNucleome/PartSeg/pull/1081))
- Fix upgrade depenecies workflow ([1083](https://github.com/4DNucleome/PartSeg/pull/1083))
- Block using `mpmath==1.4.0a0` and `sentry-sdk` 2.0.0a1/a2 in pre-test ([1085](https://github.com/4DNucleome/PartSeg/pull/1085))
- [pre-commit.ci] pre-commit autoupdate ([1089](https://github.com/4DNucleome/PartSeg/pull/1089))
- Fix jupyter failing test by using constraints ([1093](https://github.com/4DNucleome/PartSeg/pull/1093))
- [pre-commit.ci] pre-commit autoupdate ([1091](https://github.com/4DNucleome/PartSeg/pull/1091))
- [pre-commit.ci] pre-commit autoupdate ([1096](https://github.com/4DNucleome/PartSeg/pull/1096))
- Add python 3.12 testing ([1087](https://github.com/4DNucleome/PartSeg/pull/1087))
- Exclude pyside2 on python 3.11 and 3.12 from testing ([1099](https://github.com/4DNucleome/PartSeg/pull/1099))
- [pre-commit.ci] pre-commit autoupdate ([1101](https://github.com/4DNucleome/PartSeg/pull/1101))
- [pre-commit.ci] pre-commit autoupdate ([1103](https://github.com/4DNucleome/PartSeg/pull/1103))
- Bump macos runners to macos-13 (both azure and GHA) ([1113](https://github.com/4DNucleome/PartSeg/pull/1113))
- [pre-commit.ci] pre-commit autoupdate ([1108](https://github.com/4DNucleome/PartSeg/pull/1108))
- Remove pyqt5 from constraints ([1118](https://github.com/4DNucleome/PartSeg/pull/1118))
- Add workflow for releases from GHA ([1117](https://github.com/4DNucleome/PartSeg/pull/1117))
- Add actionlint to CI to early prevent bug in github workflows ([1119](https://github.com/4DNucleome/PartSeg/pull/1119))
- Fix release workflow, by update permissions
- Check if release notes are properly created ([1122](https://github.com/4DNucleome/PartSeg/pull/1122))
- Proper use enum in checking new version ([1123](https://github.com/4DNucleome/PartSeg/pull/1123))
- Refactor and simplify menu bar creation, add workaround for macOS numpy problem ([1124](https://github.com/4DNucleome/PartSeg/pull/1124))
- Simplify release workflow ([1126](https://github.com/4DNucleome/PartSeg/pull/1126))
- Fix `make_release.yml` to proper detect release, attempt 3 ([1127](https://github.com/4DNucleome/PartSeg/pull/1127))

🛡️ Security

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

Build

- Fix not bundling `Font Awesome 6 Free-Solid-900.otf` file to executable ([1114](https://github.com/4DNucleome/PartSeg/pull/1114))
- Update readme and release to point to GitHub releases ([1115](https://github.com/4DNucleome/PartSeg/pull/1115))
- Do not create archive twice when create bundle ([1120](https://github.com/4DNucleome/PartSeg/pull/1120))
- Enable macOS-arm bundle builds ([1121](https://github.com/4DNucleome/PartSeg/pull/1121))

🐛 Bug Fixes

- Fix range threshold selection of algorithms ([1009](https://github.com/4DNucleome/PartSeg/pull/1009))
- When run batch check if file extension is supported by loader ([1016](https://github.com/4DNucleome/PartSeg/pull/1016))
- Do not allow to select and render corrupted batch plans ([1015](https://github.com/4DNucleome/PartSeg/pull/1015))

🧪 Testing

- [Automatic] Constraints upgrades: `imagecodecs`, `ipykernel`, `magicgui`, `psygnal`, `scipy`, `superqt`, `tifffile` ([1011](https://github.com/4DNucleome/PartSeg/pull/1011))
- [Automatic] Constraints upgrades: `imageio`, `pyinstaller`, `tifffile` ([1018](https://github.com/4DNucleome/PartSeg/pull/1018))

⚙️ Miscellaneous Tasks

- Use faster version of black ([1010](https://github.com/4DNucleome/PartSeg/pull/1010))
- [pre-commit.ci] pre-commit autoupdate ([1013](https://github.com/4DNucleome/PartSeg/pull/1013))

🚀 Features

- Allow to save multiple napari image layers to single tiff file ([1000](https://github.com/4DNucleome/PartSeg/pull/1000))
- Add option to export batch project with data ([996](https://github.com/4DNucleome/PartSeg/pull/996))

🐛 Bug Fixes

- Fix possible problem of double registration napari plugin in PartSeg bundle ([974](https://github.com/4DNucleome/PartSeg/pull/974))
- Bump OS versions for part of testing workflows. ([977](https://github.com/4DNucleome/PartSeg/pull/977))
- Bump os version for main tests workflow. ([979](https://github.com/4DNucleome/PartSeg/pull/979))
- Ensure that the module `PartSegCore.channel_class` is present in bundle ([980](https://github.com/4DNucleome/PartSeg/pull/980))
- Lower npe2 schema version to work with older napari version ([981](https://github.com/4DNucleome/PartSeg/pull/981))
- Generate test report per platform ([978](https://github.com/4DNucleome/PartSeg/pull/978))
- Importing plugins in bundle keeping proper module names ([983](https://github.com/4DNucleome/PartSeg/pull/983))
- Fix napari repo workflow ([985](https://github.com/4DNucleome/PartSeg/pull/985))
- Fix bug in read tiff files with double `Q` in axes but one related to dummy dimension ([992](https://github.com/4DNucleome/PartSeg/pull/992))
- Fix bug that lead to corrupted state when saving calculation plan to excel file ([995](https://github.com/4DNucleome/PartSeg/pull/995))
- Enable python 3.11 test on CI, fix minor errors ([869](https://github.com/4DNucleome/PartSeg/pull/869))

🧪 Testing

- [Automatic] Constraints upgrades: `imageio`, `ipython`, `psygnal`, `scipy`, `sentry-sdk` ([975](https://github.com/4DNucleome/PartSeg/pull/975))
- [Automatic] Constraints upgrades: `h5py`, `imagecodecs`, `imageio`, `ipykernel`, `napari`, `numpy`, `pandas`, `pydantic`, `pyinstaller`, `scipy`, `sentry-sdk`, `tifffile`, `vispy` ([986](https://github.com/4DNucleome/PartSeg/pull/986))
- [Automatic] Constraints upgrades: `imagecodecs`, `sentry-sdk`, `tifffile` ([997](https://github.com/4DNucleome/PartSeg/pull/997))
- [Automatic] Constraints upgrades: `ipykernel`, `pydantic` ([1002](https://github.com/4DNucleome/PartSeg/pull/1002))
- [Automatic] Constraints upgrades: `numpy`, `pygments`, `sentry-sdk`, `superqt` ([1007](https://github.com/4DNucleome/PartSeg/pull/1007))

⚙️ Miscellaneous Tasks

- [pre-commit.ci] pre-commit autoupdate ([973](https://github.com/4DNucleome/PartSeg/pull/973))
- [pre-commit.ci] pre-commit autoupdate ([982](https://github.com/4DNucleome/PartSeg/pull/982))
- [pre-commit.ci] pre-commit autoupdate ([987](https://github.com/4DNucleome/PartSeg/pull/987))
- [pre-commit.ci] pre-commit autoupdate ([988](https://github.com/4DNucleome/PartSeg/pull/988))
- [pre-commit.ci] pre-commit autoupdate ([991](https://github.com/4DNucleome/PartSeg/pull/991))
- [pre-commit.ci] pre-commit autoupdate ([998](https://github.com/4DNucleome/PartSeg/pull/998))
- [pre-commit.ci] pre-commit autoupdate ([1004](https://github.com/4DNucleome/PartSeg/pull/1004))
- Change markdown linter from pre-commit to mdformat ([1006](https://github.com/4DNucleome/PartSeg/pull/1006))
- [pre-commit.ci] pre-commit autoupdate ([1008](https://github.com/4DNucleome/PartSeg/pull/1008))