Releases: 4DNucleome/PartSeg
Releases ยท 4DNucleome/PartSeg
0.16.2
0.16.2 - 2025-05-12
๐งช Testing
- [Automatic] Constraints upgrades:
numpy
,partsegcore-compiled-backend
,tifffile
(#1253) - [Automatic] Constraints upgrades:
imagecodecs
,ipython
,pydantic
,sentry-sdk
,superqt
,tifffile
(#1255) - [Automatic] Constraints upgrades:
ipython
,napari
,numpy
,packaging
,pydantic
,sentry-sdk
,simpleitk
,sympy
,xlsxwriter
(#1266) - [Automatic] Constraints upgrades:
oiffile
,psygnal
,scipy
,sentry-sdk
,tifffile
(#1267)
โ๏ธ Miscellaneous Tasks
- [pre-commit.ci] pre-commit autoupdate (#1251)
- Prepare for napari 0.6.0 deprecations (#1256)
- [pre-commit.ci] pre-commit autoupdate (#1254)
- [pre-commit.ci] pre-commit autoupdate (#1259)
- Update workflow to use Ubuntu 22.04 instead of 20.04 (#1261)
- [pre-commit.ci] pre-commit autoupdate (#1260)
- Try to fix Upgrade dependencies workflow part 2 (#1265)
- [pre-commit.ci] pre-commit autoupdate (#1268)
๐ก๏ธ Security
0.16.1
0.16.1 - 2025-03-10
๐ Bug Fixes
- Fix rendering of alternative representation if there are more components in the alternative representation than in ROI (#1240)
- Enable czifile workaround for 2019.7.2.1 (#1246)
๐งช Testing
- [Automatic] Constraints upgrades:
ipython
,magicgui
,numpy
,partsegcore-compiled-backend
,pydantic
(#1231) - [Automatic] Constraints upgrades:
imagecodecs
(#1233) - [Automatic] Constraints upgrades:
oiffile
,pygments
,scipy
,superqt
(#1234) - [Automatic] Constraints upgrades:
imageio
,napari
,numpy
,partsegcore-compiled-backend
,pydantic
,pygments
,scipy
,sentry-sdk
,simpleitk
,tifffile
,xlsxwriter
(#1236) - [Automatic] Constraints upgrades:
ipython
,xlsxwriter
(#1239) - [Automatic] Constraints upgrades:
numpy
,partsegcore-compiled-backend
,psygnal
,qtpy
,scipy
,sentry-sdk
(#1241) - [Automatic] Constraints upgrades:
czifile
,h5py
,ipython
,qtawesome
,sentry-sdk
,tifffile
,traceback-with-variables
(#1247)
โ๏ธ Miscellaneous Tasks
- [pre-commit.ci] pre-commit autoupdate (#1232)
- [pre-commit.ci] pre-commit autoupdate (#1235)
- [pre-commit.ci] pre-commit autoupdate (#1237)
- Drop python 3.9 tests for napari repository (#1244)
- Block ipykernel 7.0.0a1 (#1248)
- [pre-commit.ci] pre-commit autoupdate (#1242)
- Switch to
get_qapp
fromget_app
to handle napari deprecation (#1249)
0.16.0
0.16.0 - 2024-12-21
๐ Features
- Allow set units that will be used for load/save data using PartSeg as napari plugin (#1228)
- Show filename when importing with PartSeg in napari (#1226)
๐ Bug Fixes
- Fix error when image changed during segmentation (#1218)
- Fix pre release tests (#1219)
- Drop imagej LUTs of size
24*x
(#1227)
๐งช Testing
- [Automatic] Constraints upgrades:
h5py
,imageio
,ipython
,napari
,numpy
,sentry-sdk
(#1201) - [Automatic] Constraints upgrades:
sentry-sdk
(#1214) - [Automatic] Constraints upgrades:
ipython
,traceback-with-variables
(#1221) - [Automatic] Constraints upgrades:
numpy
,packaging
,pydantic
,qtconsole
,qtpy
,sentry-sdk
,traceback-with-variables
(#1223) - [Automatic] Constraints upgrades:
imageio
,ipython
,pydantic
(#1225) - [Automatic] Constraints upgrades:
napari
,numpy
,pydantic
,sentry-sdk
,six
,superqt
,tifffile
(#1229)
โ๏ธ Miscellaneous Tasks
- Stop using mambaforge in tests (#1203)
- [pre-commit.ci] pre-commit autoupdate (#1202)
- [pre-commit.ci] pre-commit autoupdate (#1204)
- Remove defining default version of language in pre-commit configuration (#1208)
- [pre-commit.ci] pre-commit autoupdate (#1209)
- Drop python 3.8 (#1206)
- Use
PublishPipelineArtifact
in place ofPublishBuildArtifacts
to reduce CI fragility (#1213) - Update CI configuration to use more modern OS and python versions (#1207)
- Fix
upgrade-dependencies.yaml
docs constraints (#1215) - [pre-commit.ci] pre-commit autoupdate (#1216)
- Add changelog 0.16.0a1
- [pre-commit.ci] pre-commit autoupdate (#1222)
- [pre-commit.ci] pre-commit autoupdate (#1230)
0.16.0a1
0.16.0 - 2024-10-22
This release drop support for python 3.8 and napari below 0.4.19.
๐ Bug Fixes
๐งช Testing
- [Automatic] Constraints upgrades:
h5py
,imageio
,ipython
,napari
,numpy
,sentry-sdk
(#1201) - [Automatic] Constraints upgrades:
sentry-sdk
(#1214)
โ๏ธ Miscellaneous Tasks
- Stop using mambaforge in tests (#1203)
- [pre-commit.ci] pre-commit autoupdate (#1202)
- [pre-commit.ci] pre-commit autoupdate (#1204)
- Remove defining default version of language in pre-commit configuration (#1208)
- [pre-commit.ci] pre-commit autoupdate (#1209)
- Drop python 3.8 (#1206)
- Use
PublishPipelineArtifact
in place ofPublishBuildArtifacts
to reduce CI fragility (#1213) - Update CI configuration to use more modern OS and python versions (#1207)
- Fix
upgrade-dependencies.yaml
docs constraints (#1215) - [pre-commit.ci] pre-commit autoupdate (#1216)
0.15.4
0.15.4 - 2024-09-27
๐ Features
- Add preview of image metadata (#1154)
- Add option to combine channels using sum and max (#1159)
- Add metadata viewer as napari widget (#1195)
- Read channel colors from
*.czi
metadata (#1198) - Use image color when add layer to napari (#1200)
๐ Bug Fixes
- Fix selection of custom label colors for napari 0.5.0 (#1138)
- Add pint call to enforce initialization of unit registry (#1146)
- Workaround for lack of zsd support in czifile (#1142)
- Fix preparing data for
mahotas.haralick
to avoid overflow problem (#1150) - Fix
use_convex
type fromint
tobool
for segmentation algorithms (#1152) - Prevent propagation of decreasing contrast limits set by user (#1166)
- Prevent error on searching component if there is no component (#1167)
- Fix checking if channel requested by MeasurementProfile exists (#1165)
- Fix trying to access to just deleted measurement profile from edit window. (#1168)
- Fix bug in code for checking for survey file (#1174)
- Fix plugin discovery in bundle to register them in napari viewer (#1175)
- Fix problem with setting range of auto-generated widget (#1187)
- Fix reading channel names from single channel czi files (#1194)
๐ Refactor
- Make warnings error in tests (#1192)
- Merge all channel-specific attributes of the Image class (#1191)
๐ Documentation
- Change homepage URL (#1139)
- Add link for download macOS arm bundle (#1140)
- Add changelog for 0.15.4 release
- Update changelog (#1176)
๐งช Testing
- [Automatic] Constraints upgrades:
napari
,sentry-sdk
,sympy
(#1128) - [Automatic] Constraints upgrades:
mahotas
,numpy
,sentry-sdk
,sympy
(#1145) - [Automatic] Constraints upgrades:
numpy
,tifffile
(#1163) - [Automatic] Constraints upgrades:
napari
,sentry-sdk
,tifffile
(#1169) - [Automatic] Constraints upgrades:
magicgui
,sentry-sdk
(#1172) - [Automatic] Constraints upgrades:
sympy
,tifffile
(#1177) - [Automatic] Constraints upgrades:
imageio
,napari
,numpy
(#1180) - Constraints upgrades:
sentry-sdk
and fix tests (#1182) napari==0.5.3
related fixes, Constraints upgrades:imageio
,ipython
,numpy
,qtconsole
,scipy
,simpleitk
,tifffile
(#1183)- [Automatic] Constraints upgrades:
numpy
,pydantic
(#1188) - [Automatic] Constraints upgrades:
imagecodecs
,pandas
,pydantic
,sentry-sdk
,sympy
,tifffile
(#1190)
โ๏ธ Miscellaneous Tasks
- Speedup tests by use
tox-uv
(#1141) - Get additional dict from PR branch for checking PR title (#1144)
- Relax numpy constraint (#1143)
- Allow to skip spellchecking PR title (#1147)
- [pre-commit.ci] pre-commit autoupdate (#1149)
- Create only archive with version in name on azures pipeline (#1151)
- Fix tests for napari from repository (#1148)
- Use python 3.11 to determine updated packages in PR description (#1160)
- [pre-commit.ci] pre-commit autoupdate (#1164)
- [pre-commit.ci] pre-commit autoupdate (#1170)
- Disable thumbnail generation in napari layer as it is fragile and not used (#1171)
- [pre-commit.ci] pre-commit autoupdate (#1173)
- [pre-commit.ci] pre-commit autoupdate (#1178)
- Fix call of logger to properly pass arguments to messages (#1179)
- Fix coverage files upload by enable hidden files upload (#1186)
- [pre-commit.ci] pre-commit autoupdate (#1184)
- Use PyQt6 in pre-tests (#1196)
- Add missed code from #1191 (#1197)
- [pre-commit.ci] pre-commit autoupdate (#1189)
- Auto add "skip check PR title" label in update dependencies PR (#1199)
Build
0.15.4b7
0.15.4 - 2024-08-13
๐ Features
๐ Bug Fixes
- Fix selection of custom label colors for napari 0.5.0 (#1138)
- Add pint call to enforce initialization of unit registry (#1146)
- Workaround for lack of zsd support in czifile (#1142)
- Fix preparing data for
mahotas.haralick
to avoid overflow problem (#1150) - Fix
use_convex
type fromint
tobool
for segmentation algorithms (#1152) - Prevent propagation of decreasing contrast limits set by user (#1166)
- Prevent error on searching component if there is no component (#1167)
- Fix checking if channel requested by MeasurementProfile exists (#1165)
- Fix trying to access to just deleted measurement profile from edit window. (#1168)
- Fix bug in code for checking for survey file (#1174)
- Fix plugin discovery in bundle to register them in napari viewer (#1175)
- Fix call of logging
๐ Documentation
- Change homepage URL (#1139)
- Add link for download macOS arm bundle (#1140)
- Add changelog for 0.15.4 release
- Update changelog (#1176)
๐งช Testing
- [Automatic] Constraints upgrades:
napari
,sentry-sdk
,sympy
(#1128) - [Automatic] Constraints upgrades:
mahotas
,numpy
,sentry-sdk
,sympy
(#1145) - [Automatic] Constraints upgrades:
numpy
,tifffile
(#1163) - [Automatic] Constraints upgrades:
napari
,sentry-sdk
,tifffile
(#1169) - [Automatic] Constraints upgrades:
magicgui
,sentry-sdk
(#1172) - [Automatic] Constraints upgrades:
sympy
,tifffile
(#1177)
โ๏ธ Miscellaneous Tasks
- Speedup tests by use
tox-uv
(#1141) - Get additional dict from PR branch for checking PR title (#1144)
- Relax numpy constraint (#1143)
- Allow to skip spellchecking PR title (#1147)
- [pre-commit.ci] pre-commit autoupdate (#1149)
- Create only archive with version in name on azures pipeline (#1151)
- Fix tests for napari from repository (#1148)
- Use python 3.11 to determine updated packages in PR description (#1160)
- [pre-commit.ci] pre-commit autoupdate (#1164)
- [pre-commit.ci] pre-commit autoupdate (#1170)
- Disable thumbnail generation in napari layer as it is fragile and not used (#1171)
- [pre-commit.ci] pre-commit autoupdate (#1173)
- [pre-commit.ci] pre-commit autoupdate (#1178)
Build
0.15.4b6
0.15.4 - 2024-08-13
๐ Features
๐ Bug Fixes
- Fix selection of custom label colors for napari 0.5.0 (#1138)
- Add pint call to enforce initialization of unit registry (#1146)
- Workaround for lack of zsd support in czifile (#1142)
- Fix preparing data for
mahotas.haralick
to avoid overflow problem (#1150) - Fix
use_convex
type fromint
tobool
for segmentation algorithms (#1152) - Prevent propagation of decreasing contrast limits set by user (#1166)
- Prevent error on searching component if there is no component (#1167)
- Fix checking if channel requested by MeasurementProfile exists (#1165)
- Fix trying to access to just deleted measurement profile from edit window. (#1168)
- Fix bug in code for checking for survey file (#1174)
- Fix plugin discovery in bundle to register them in napari viewer (#1175)
- Fix call of logging
๐ Documentation
- Change homepage URL (#1139)
- Add link for download macOS arm bundle (#1140)
- Add changelog for 0.15.4 release
- Update changelog (#1176)
๐งช Testing
- [Automatic] Constraints upgrades:
napari
,sentry-sdk
,sympy
(#1128) - [Automatic] Constraints upgrades:
mahotas
,numpy
,sentry-sdk
,sympy
(#1145) - [Automatic] Constraints upgrades:
numpy
,tifffile
(#1163) - [Automatic] Constraints upgrades:
napari
,sentry-sdk
,tifffile
(#1169) - [Automatic] Constraints upgrades:
magicgui
,sentry-sdk
(#1172) - [Automatic] Constraints upgrades:
sympy
,tifffile
(#1177)
โ๏ธ Miscellaneous Tasks
- Speedup tests by use
tox-uv
(#1141) - Get additional dict from PR branch for checking PR title (#1144)
- Relax numpy constraint (#1143)
- Allow to skip spellchecking PR title (#1147)
- [pre-commit.ci] pre-commit autoupdate (#1149)
- Create only archive with version in name on azures pipeline (#1151)
- Fix tests for napari from repository (#1148)
- Use python 3.11 to determine updated packages in PR description (#1160)
- [pre-commit.ci] pre-commit autoupdate (#1164)
- [pre-co 10000 mmit.ci] pre-commit autoupdate (#1170)
- Disable thumbnail generation in napari layer as it is fragile and not used (#1171)
- [pre-commit.ci] pre-commit autoupdate (#1173)
- [pre-commit.ci] pre-commit autoupdate (#1178)
Build
0.15.4b5
0.15.4 - 2024-08-13
๐ Features
๐ Bug Fixes
- Fix selection of custom label colors for napari 0.5.0 (#1138)
- Add pint call to enforce initialization of unit registry (#1146)
- Workaround for lack of zsd support in czifile (#1142)
- Fix preparing data for
mahotas.haralick
to avoid overflow problem (#1150) - Fix
use_convex
type fromint
tobool
for segmentation algorithms (#1152) - Prevent propagation of decreasing contrast limits set by user (#1166)
- Prevent error on searching component if there is no component (#1167)
- Fix checking if channel requested by MeasurementProfile exists (#1165)
- Fix trying to access to just deleted measurement profile from edit window. (#1168)
- Fix bug in code for checking for survey file (#1174)
- Fix plugin discovery in bundle to register them in napari viewer (#1175)
- Fix call of logging
๐ Documentation
- Change homepage URL (#1139)
- Add link for download macOS arm bundle (#1140)
- Add changelog for 0.15.4 release
- Update changelog (#1176)
๐งช Testing
- [Automatic] Constraints upgrades:
napari
,sentry-sdk
,sympy
(#1128) - [Automatic] Constraints upgrades:
mahotas
,numpy
,sentry-sdk
,sympy
(#1145) - [Automatic] Constraints upgrades:
numpy
,tifffile
(#1163) - [Automatic] Constraints upgrades:
napari
,sentry-sdk
,tifffile
(#1169) - [Automatic] Constraints upgrades:
magicgui
,sentry-sdk
(#1172) - [Automatic] Constraints upgrades:
sympy
,tifffile
(#1177)
โ๏ธ Miscellaneous Tasks
- Speedup tests by use
tox-uv
(#1141) - Get additional dict from PR branch for checking PR title (#1144)
- Relax numpy constraint (#1143)
- Allow to skip spellchecking PR title (#1147)
- [pre-commit.ci] pre-commit autoupdate (#1149)
- Create only archive with version in name on azures pipeline (#1151)
- Fix tests for napari from repository (#1148)
- Use python 3.11 to determine updated packages in PR description (#1160)
- [pre-commit.ci] pre-commit autoupdate (#1164)
- [pre-commit.ci] pre-commit autoupdate (#1170)
- Disable thumbnail generation in napari layer as it is fragile and not used (#1171)
- [pre-commit.ci] pre-commit autoupdate (#1173)
- [pre-commit.ci] pre-commit autoupdate (#1178)
Build
0.15.4b4
0.15.4 - 2024-08-13
๐ Features
๐ Bug Fixes
- Fix selection of custom label colors for napari 0.5.0 (#1138)
- Add pint call to enforce initialization of unit registry (#1146)
- Workaround for lack of zsd support in czifile (#1142)
- Fix preparing data for
mahotas.haralick
to avoid overflow problem (#1150) - Fix
use_convex
type fromint
tobool
for segmentation algorithms (#1152) - Prevent propagation of decreasing contrast limits set by user (#1166)
- Prevent error on searching component if there is no component (#1167)
- Fix checking if channel requested by MeasurementProfile exists (#1165)
- Fix trying to access to just deleted measurement profile from edit window. (#1168)
- Fix bug in code for checking for survey file (#1174)
- Fix plugin discovery in bundle to register them in napari viewer (#1175)
- Fix call of logging
๐ Documentation
- Change homepage URL (#1139)
- Add link for download macOS arm bundle (#1140)
- Add changelog for 0.15.4 release
- Update changelog (#1176)
๐งช Testing
- [Automatic] Constraints upgrades:
napari
,sentry-sdk
,sympy
(#1128) - [Automatic] Constraints upgrades:
mahotas
,numpy
,sentry-sdk
,sympy
(#1145) - [Automatic] Constraints upgrades:
numpy
,tifffile
(#1163) - [Automatic] Constraints upgrades:
napari
,sentry-sdk
,tifffile
(#1169) - [Automatic] Constraints upgrades:
magicgui
,sentry-sdk
(#1172) - [Automatic] Constraints upgrades:
sympy
,tifffile
(#1177)
โ๏ธ Miscellaneous Tasks
- Speedup tests by use
tox-uv
(#1141) - Get additional dict from PR branch for checking PR title (#1144)
- Relax numpy constraint (#1143)
- Allow to skip spellchecking PR title (#1147)
- [pre-commit.ci] pre-commit autoupdate (#1149)
- Create only archive with version in name on azures pipeline (#1151)
- Fix tests for napari from repository (#1148)
- Use python 3.11 to determine updated packages in PR description (#1160)
- [pre-commit.ci] pre-commit autoupdate (#1164)
- [pre-commit.ci] pre-commit autoupdate (#1170)
- Disable thumbnail generation in napari layer as it is fragile and not used (#1171)
- [pre-commit.ci] pre-commit autoupdate (#1173)
- [pre-commit.ci] pre-commit autoupdate (#1178)
Build
0.15.4b3
0.15.4b - 2024-08-09
๐ Features
๐ Bug Fixes
- Fix selection of custom label colors for napari 0.5.0 (#1138)
- Add pint call to enforce initialization of unit registry (#1146)
- Workaround for lack of zsd support in czifile (#1142)
- Fix preparing data for
mahotas.haralick
to avoid overflow problem (#1150) - Fix
use_convex
type fromint
tobool
for segmentation algorithms (#1152) - Prevent propagation of decreasing contrast limits set by user (#1166)
- Prevent error on searching component if there is no component (#1167)
- Fix checking if channel requested by MeasurementProfile exists (#1165)
- Fix trying to access to just deleted measurement profile from edit window. (#1168)
- Fix bug in code for checking for survey file (#1174)
- Fix plugin discovery in bundle to register them in napari viewer (#1175)
๐ Documentation
- Change homepage URL (#1139)
- Add link for download macOS arm bundle (#1140)
- Add changelog for 0.15.4 release
๐งช Testing
- [Automatic] Constraints upgrades:
napari
,sentry-sdk
,sympy
(#1128) - [Automatic] Constraints upgrades:
mahotas
,numpy
,sentry-sdk
,sympy
(#1145) - [Automatic] Constraints upgrades:
numpy
,tifffile
(#1163) - [Automatic] Constraints upgrades:
napari
,sentry-sdk
,tifffile
(#1169) - [Automatic] Constraints upgrades:
magicgui
,sentry-sdk
(#1172)
โ๏ธ Miscellaneous Tasks
- Speedup tests by use
tox-uv
(#1141) - Get additional dict from PR branch for checking PR title (#1144)
- Relax numpy constraint (#1143)
- Allow to skip spellchecking PR title (#1147)
- [pre-commit.ci] pre-commit autoupdate (#1149)
- Create only archive with version in name on azures pipeline (#1151)
- Fix tests for napari from repository (#1148)
- Use python 3.11 to determine updated packages in PR description (#1160)
- [pre-commit.ci] pre-commit autoupdate (#1164)
- [pre-commit.ci] pre-commit autoupdate (#1170)
- Disable thumbnail generation in napari layer as it is fragile and not used (#1171)
- [pre-commit.ci] pre-commit autoupdate (#1173)