DigitalSlideArchive/HistomicsTK issues and pull requests

#1149 - Update to newer machine images on CI

Pull Request - State: closed - Opened by manthey about 2 months ago

#1148 - Bump pypa/cibuildwheel from 2.21.3 to 2.22.0

Pull Request - State: closed - Opened by dependabot[bot] about 2 months ago
Labels: dependencies, github_actions

#1147 - Clean up a variety of warnings and deprecations.

Pull Request - State: closed - Opened by manthey 2 months ago

#1146 - Drop Python 3.8

Pull Request - State: closed - Opened by manthey 2 months ago

#1145 - Fix working with latest dask

Issue - State: open - Opened by manthey 2 months ago - 2 comments

#1144 - Pin dask so CI passes

Pull Request - State: closed - Opened by manthey 2 months ago

#1143 - Update boundary detection in FSD feature extraction

Pull Request - State: open - Opened by FattanePourakpour 3 months ago - 5 comments

#1142 - Update README

Pull Request - State: closed - Opened by manthey 3 months ago

#1141 - Remove install of bokeh from dockerfile

Pull Request - State: closed - Opened by manthey 3 months ago

#1140 - Fix an issue with numpy 2.

Pull Request - State: closed - Opened by manthey 3 months ago

#1139 - Logical error in function compute_fsd_features

Issue - State: closed - Opened by name-used 3 months ago - 7 comments

#1138 - Test that CLIs emit no warnings

Pull Request - State: closed - Opened by manthey 3 months ago

#1137 - Bump pypa/cibuildwheel from 2.21.2 to 2.21.3

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago
Labels: dependencies, github_actions

#1136 - Bump python from 3.12-slim to 3.13-slim

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago - 1 comment
Labels: dependencies, docker

#1135 - Fix sphinx builds

Pull Request - State: closed - Opened by manthey 4 months ago

#1134 - Bump pypa/cibuildwheel from 2.21.1 to 2.21.2

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago - 3 comments
Labels: dependencies, github_actions

#1133 - Bump pypa/cibuildwheel from 2.21.0 to 2.21.1

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies, github_actions

#1132 - Make color deconvolution annotation optional

Pull Request - State: closed - Opened by manthey 4 months ago

#1131 - Remove 'vectorized' from the shapely dependency.

Pull Request - State: closed - Opened by manthey 4 months ago

#1130 - Remove 'vectorized' from the shapely dependency.

Pull Request - State: closed - Opened by manthey 4 months ago

#1129 - Bump pypa/cibuildwheel from 2.20.0 to 2.21.0

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies, github_actions

#1128 - Error occurred while using Docker for build

Issue - State: open - Opened by XmySz 5 months ago - 3 comments

#1127 - New error when trying to pip install HistomicsTK - rasterio failing

Issue - State: closed - Opened by pearcetm 5 months ago - 5 comments

#1126 - Remove some pre python 3.8 fallback code

Pull Request - State: closed - Opened by manthey 5 months ago

#1125 - Use rdfind to make the docker image slightly smaller

Pull Request - State: closed - Opened by manthey 5 months ago

#1124 - Speed up listing xml for clis

Pull Request - State: closed - Opened by manthey 5 months ago

#1123 - Bump pypa/cibuildwheel from 2.19.2 to 2.20.0

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies, github_actions

#1122 - Harden haralick computation.

Pull Request - State: closed - Opened by manthey 6 months ago

#1121 - Optionally add properties to polygon elements

Pull Request - State: closed - Opened by manthey 6 months ago

#1120 - Bump pypa/cibuildwheel from 2.19.1 to 2.19.2

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies, github_actions

#1119 - Fix the name of a centroid feature

Pull Request - State: closed - Opened by manthey 7 months ago

#1118 - histomicstk.features.compute_nuclei_features output column name 'Identifier.Centroid' is wrong

Issue - State: closed - Opened by Bejsernia 7 months ago - 1 comment

#1117 - Update ruff command in tox

Pull Request - State: closed - Opened by manthey 7 months ago

#1116 - calculation error while computing haralick features for a set of images

Issue - State: closed - Opened by me-nobody 7 months ago - 1 comment

#1115 - Bump pypa/cibuildwheel from 2.18.1 to 2.19.1

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies, github_actions

#1114 - histomics wheels can't be found at https://girder.github.io/large_image_wheels any more

Issue - State: closed - Opened by iRyoka 7 months ago - 2 comments

#1113 - Bump pypa/cibuildwheel from 2.18.0 to 2.18.1

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies, github_actions

#1112 - fix: redundant writes to dataframe #1105 (#1106)

Pull Request - State: closed - Opened by manthey 8 months ago

#1111 - Bump pypa/cibuildwheel from 2.17.0 to 2.18.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies, github_actions

#1110 - Update tests to handle variations in upstream libraries

Pull Request - State: closed - Opened by manthey 10 months ago

#1109 - Add the large_image_converter to requirements

Pull Request - State: closed - Opened by manthey 10 months ago

#1108 - Update precommit versions and remove some needless items from setup.py

Pull Request - State: closed - Opened by manthey 10 months ago

#1107 - 946 compute haralick features works incorrectly when im intensity is a float with 0 1 values

Pull Request - State: closed - Opened by cooperlab 10 months ago

#1106 - fix: redundant writes to dataframe #1105

Pull Request - State: closed - Opened by X-TRON404 10 months ago - 1 comment

#1105 - Remove redundant access to DataFrame

Issue - State: closed - Opened by X-TRON404 10 months ago
Labels: enhancement

#1104 - Bump pypa/cibuildwheel from 2.16.5 to 2.17.0

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago
Labels: dependencies, github_actions

#1103 - Fix some typos

Pull Request - State: closed - Opened by manthey 11 months ago

#1102 - Add a console entry point.

Pull Request - State: closed - Opened by manthey 11 months ago

#1098 - Bump pypa/cibuildwheel from 2.16.4 to 2.16.5

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago
Labels: dependencies, github_actions

#1097 - Don't serialize some options to json

Pull Request - State: closed - Opened by manthey 12 months ago

#1096 - Update for lint rule D413

Pull Request - State: closed - Opened by manthey 12 months ago

#1095 - Bump pypa/cibuildwheel from 2.16.2 to 2.16.4

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago
Labels: dependencies, github_actions

#1094 - Make some of the tests more consistent

Pull Request - State: closed - Opened by manthey 12 months ago

#1093 - Update artifact actions

Pull Request - State: closed - Opened by manthey 12 months ago

#1092 - Update artifact actions

Pull Request - State: closed - Opened by manthey 12 months ago

#1091 - Bump actions/upload-artifact from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 2 comments
Labels: dependencies, github_actions

#1090 - Bump actions/download-artifact from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 2 comments
Labels: dependencies, github_actions

#1089 - Revert artifact workflow version changes.

Pull Request - State: closed - Opened by manthey about 1 year ago

#1088 - Bump actions/upload-artifact from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies, github_actions

#1087 - Bump actions/download-artifact from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies, github_actions

#1086 - Bump actions/setup-python from 4 to 5

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies, github_actions

#1085 - Update .git-blame-ignore-revs

Pull Request - State: closed - Opened by manthey about 1 year ago

#1084 - Improve linting and consistency

Pull Request - State: closed - Opened by manthey about 1 year ago - 1 comment

#1083 - Compact Nuclei Notation

Pull Request - State: closed - Opened by subinkitware about 1 year ago

#1082 - NucleiClassification annotation name

Issue - State: closed - Opened by manthey about 1 year ago - 2 comments

#1081 - Script for database migration

Issue - State: open - Opened by kwsp about 1 year ago - 3 comments

#1080 - Unable to Convert annotations to Object Detections using HistomicsTK

Issue - State: closed - Opened by digs1998 about 1 year ago - 9 comments

#1079 - Guard empty list

Pull Request - State: closed - Opened by manthey about 1 year ago

#1078 - Fix a format string.

Pull Request - State: closed - Opened by manthey about 1 year ago

#1077 - Bump actions/checkout from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies, github_actions

#1076 - Bump python from 3.11-slim to 3.12-slim

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies, docker

#1075 - Update tests for Python 3.12

Pull Request - State: closed - Opened by manthey about 1 year ago

#1074 - Update some tests to handle minor version changes

Pull Request - State: closed - Opened by manthey over 1 year ago

#1073 - Test more of the CLI code.

Pull Request - State: closed - Opened by manthey over 1 year ago

#1072 - Use the common exta_requires on non-linux platforms

Pull Request - State: closed - Opened by manthey over 1 year ago

#1071 - How to render text annotation on frontend?

Issue - State: open - Opened by abhisheklomsh over 1 year ago - 2 comments

#1070 - synced nuclei features and nuclei detection.

Pull Request - State: closed - Opened by subinkitware over 1 year ago

#1069 - Sync number of nuclei and features

Pull Request - State: closed - Opened by subinkitware over 1 year ago - 1 comment
Labels: Working on it

#1068 - Only release with github actions.

Pull Request - State: closed - Opened by manthey over 1 year ago

#1067 - Explicitly ask for macosx_arm64

Pull Request - State: closed - Opened by manthey over 1 year ago

#1066 - Tell setuptools-scm not to use local versions

Pull Request - State: closed - Opened by manthey over 1 year ago

#1065 - Fix version on github actions.

Pull Request - State: closed - Opened by manthey over 1 year ago

#1064 - Fix collect artifacts for release

Pull Request - State: closed - Opened by manthey over 1 year ago

#1063 - Publish wheels with github actions

Pull Request - State: closed - Opened by manthey over 1 year ago

#1062 - Don't use a futures pool to compute polygons.

Pull Request - State: closed - Opened by manthey over 1 year ago - 2 comments

#1061 - Fix artifact download.

Pull Request - State: closed - Opened by manthey over 1 year ago

#1060 - Use github actions to build wheels.

Pull Request - State: closed - Opened by manthey over 1 year ago - 1 comment

#1059 - supress rank warning

Pull Request - State: closed - Opened by subinkitware over 1 year ago
Labels: Review required

#1058 - find_stain_index comparison bug

Pull Request - State: closed - Opened by cooperlab over 1 year ago

#1057 - find_stain_index bug

Issue - State: closed - Opened by cooperlab over 1 year ago

#1056 - How to get started with fetching region of interest drawn by user and replacing it with resultant region returned by python after processing

Issue - State: closed - Opened by abhisheklomsh over 1 year ago - 2 comments

GitHub / DigitalSlideArchive/HistomicsTK issues and pull requests