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3f28c77
Convert large_image plugin to Girder 5
zachmullen Jun 12, 2024
3849dd8
Convert large_image_annotation plugin to Girder 5
zachmullen Jun 20, 2024
f5f6dcf
Fix CI
zachmullen Jun 20, 2024
9b77e3c
Add vue components to plugin namespace
zachmullen Jun 27, 2024
3a4ef9c
Expose setFrameQuad in module namespace
zachmullen Jul 1, 2024
c1b5c84
Expose ElementCollection in public namespace
zachmullen Jul 2, 2024
b069a69
Extend prototype when extending viewers
zachmullen Jul 8, 2024
dcaa218
Load geojs library in front-end before plugin code
zachmullen Jul 9, 2024
54dab7e
Don't double-load geojs
zachmullen Jul 10, 2024
29bd5ea
Undo removal of d3
zachmullen Jul 11, 2024
a088901
Load geojs after plugin JS in large_image plugin
zachmullen Jul 11, 2024
045e80a
Upgrade d3 version to use modules
zachmullen Jul 11, 2024
5e87bc8
Manually cache-bust geojs JS bundle
zachmullen Jul 16, 2024
0316ea6
Remove remaining girder.logger references
zachmullen Jul 22, 2024
ae9f8e3
Add watch commands for front-end rebuilds
zachmullen Jul 24, 2024
e7f1de8
Use more robust front-end file copy mechanism
zachmullen Jul 25, 2024
2df66ee
Make in-place extension of large_image views in the annotation plugin…
zachmullen Jul 25, 2024
f7daa9c
Remove asynchronous job flags
zachmullen Jul 25, 2024
3bdc4c9
Port zarr dep changes to girder-5 branch
zachmullen Oct 4, 2024
cb7cf2a
Also add imagecodecs to zarr source reqs
zachmullen Oct 4, 2024
d6202e1
Clean up old code by requiring somewhat new packages
manthey Jul 18, 2024
8b848b5
Merge branch 'master' into update-with-master
naglepuff Oct 31, 2024
ee99616
Use girder 5 style logging
naglepuff Nov 1, 2024
2e3c9c3
Merge branch 'master' into update-with-master
naglepuff Nov 1, 2024
75a10a0
Merge branch 'master' into update-with-master
naglepuff Nov 6, 2024
d046aa5
Merge pull request #1712 from girder/update-with-master
naglepuff Nov 7, 2024
b199123
Update tox config for girder 5
naglepuff Nov 8, 2024
c84c993
Remove girder 3 style logging
naglepuff Nov 22, 2024
7f37dfe
Remove web client test from python test suite
naglepuff Nov 22, 2024
56f7a35
Import WorkerSettings properly
naglepuff Nov 22, 2024
f4e8f8b
Use test.Dockerfile image for large image tests
naglepuff Dec 9, 2024
22333fb
Pin zarr
naglepuff Dec 11, 2024
574cc87
Update eslint config
naglepuff Dec 11, 2024
3bff277
Format client directories
naglepuff Dec 11, 2024
04a3e13
Ignore G002 and G004 errors
naglepuff Dec 11, 2024
c1ba777
Format python
naglepuff Dec 11, 2024
6f77174
Add format-only commits to blame ignore revs
naglepuff Dec 12, 2024
5e85390
Use node 20 for tests
naglepuff Dec 12, 2024
197b853
Merge pull request #1728 from girder/girder-5-tox
naglepuff Dec 12, 2024
549de44
Build pre-release version from girder-5 branch
naglepuff Dec 16, 2024
f2b7a0e
Merge pull request #1745 from girder/girder-5-installable
naglepuff Dec 16, 2024
f787b31
Ignore type error for now
naglepuff Dec 20, 2024
0476e9f
Merge branch 'master' into girder-5
naglepuff Jan 17, 2025
3f20013
Add missing comma
naglepuff Jan 17, 2025
7da9dcd
Remove unused type: ignore
naglepuff Jan 17, 2025
3b4a78c
Disable dicom plugin tests
naglepuff Jan 20, 2025
e16cf14
Pin numpy to fix type tests
naglepuff Jan 20, 2025
434d736
Merge pull request #1779 from girder/girder-5-cleanup-tests
naglepuff Jan 20, 2025
9f98ec6
Merge branch 'master' into girder-5-unpin-numpy
naglepuff Jan 21, 2025
1b5e1a8
Unpin numpy
naglepuff Jan 21, 2025
2a74a9b
Merge pull request #1782 from girder/girder-5-unpin-numpy
naglepuff Jan 21, 2025
a22b0f0
Build large_image and annotation plugins on release
naglepuff Jan 17, 2025
8d46d01
Use tox-and-node image for release check job
naglepuff Jan 17, 2025
ce785ef
Check node versions in check_release
naglepuff Jan 17, 2025
fee1ebc
Use correct node version
naglepuff Jan 17, 2025
ec069cb
Use nvm in check_release environment
naglepuff Jan 17, 2025
0e0c946
Specify toxandnode executor
naglepuff Jan 22, 2025
6eaeb9c
Make sure to source bashrc for nvm scripts to work
naglepuff Jan 22, 2025
127d733
Include built client code in distribution
naglepuff Jan 22, 2025
8346aa2
Use environment with nvm/node for release
naglepuff Jan 22, 2025
0327550
Combine the wheels and check release jobs
manthey Jan 23, 2025
d9391e7
Merge pull request #1777 from girder/girder-5-build-client-on-release
naglepuff Jan 23, 2025
0abce78
Fix building docker images
manthey Jan 23, 2025
8b214e1
Merge pull request #1786 from girder/single-twine
manthey Jan 23, 2025
b1e576d
Merge branch 'master' into girder-5-update-20253101
naglepuff Jan 31, 2025
7ceab78
Use the `girder` constant to get `restRequest`
naglepuff Jan 31, 2025
8383cdf
Adjust import paths to fit new structure
naglepuff Jan 31, 2025
9587bed
Merge pull request #1799 from girder/girder-5-update-20253101
naglepuff Jan 31, 2025
a71bc89
Initial girder 5 conversion
naglepuff Jan 31, 2025
8558b7e
Build client code for dicom plugin on release
naglepuff Jan 31, 2025
806a38c
Use `export default` over `module.exports`
naglepuff Feb 4, 2025
78c5115
Ignore lint errors for now
naglepuff Feb 5, 2025
bdbb469
Add missing arg for registerPluginStaticContent
naglepuff Feb 6, 2025
04ae9fe
Re-enable dicom tests
naglepuff Feb 6, 2025
ceb9c97
Register dicomweb plugin namespace
naglepuff Feb 7, 2025
716197e
Fix JS bug in metadata editor widget
zachmullen Feb 10, 2025
8bc55cc
Merge pull request #1817 from girder/fix-metadata-editor-widget
zachmullen Feb 10, 2025
91842f3
Fix metadata widget bug in addMetadataByKey
zachmullen Feb 11, 2025
4a05f17
Merge pull request #1820 from girder/fix-metadata-editor-widget
zachmullen Feb 11, 2025
552a856
WIP run dicom tests
naglepuff Feb 11, 2025
c995116
Import widgets
naglepuff Feb 11, 2025
deb79d8
Merge pull request #1822 from girder/girder5-fix-widget-imports
naglepuff Feb 12, 2025
b0b838e
Require girder 5
naglepuff Feb 14, 2025
f2b3d6a
Fix watch script
naglepuff Feb 14, 2025
13b6e11
Export views
naglepuff Feb 14, 2025
ca2e20f
Fix imports
naglepuff Feb 14, 2025
3f7384c
Remove old girder 3 style client tests
naglepuff Feb 14, 2025
f5c51e8
Fix path for DICOMweb assetstore plugin
naglepuff Feb 14, 2025
2a2b559
Remove dependency on phantomjs
naglepuff Feb 14, 2025
5f98f17
Merge pull request #1800 from girder/convert-dicomweb-plugin-to-girder5
naglepuff Feb 19, 2025
879e083
Guard the assetstoreImportViewMap update
manthey Mar 5, 2025
a2d26ec
Merge pull request #1845 from girder/guard-asseststore-map
manthey Mar 5, 2025
1fe1c80
Merge branch 'master' into merge-master-250310
manthey Mar 10, 2025
cc1271a
Merge pull request #1848 from girder/merge-master-250310
manthey Mar 10, 2025
9aefadc
Run playwright tests in CI
manthey Mar 10, 2025
6b1c8f9
Merge pull request #1849 from girder/playwright-ci
zachmullen Mar 11, 2025
973b481
Re-enable tox tests
zachmullen Mar 11, 2025
3e09eb1
Merge pull request #1850 from girder/run-pytest-tests
zachmullen Mar 11, 2025
72cac68
Merge branch 'master' into girder-5
manthey Mar 13, 2025
5205d81
Merge branch 'master' into girder-5
manthey Apr 2, 2025
4c898ba
Use environment variables for worker tests in girder 5.
manthey Apr 2, 2025
1a7555e
Merge pull request #1865 from girder/worker-settings
manthey Apr 2, 2025
4cebb4c
Merge branch 'master' into girder-5
manthey Apr 8, 2025
6802c30
Merge branch 'master' into girder-5
manthey Apr 8, 2025
faafb92
Better handle long rest requests
manthey Apr 9, 2025
5bb9baa
Merge pull request #1871 from girder/long-requests
manthey Apr 10, 2025
39bca88
Merge branch 'master' into girder-5
manthey Apr 14, 2025
2f70973
Use a local task to ingest annotations
manthey Apr 14, 2025
f128fc6
Merge pull request #1876 from girder/ingest-annotations
manthey Apr 14, 2025
115c962
Make a change to make process_annotations easier for HUI to call
manthey Apr 14, 2025
8e20a39
Properly expose task to celery
manthey Apr 14, 2025
255e3d8
Merge pull request #1877 from girder/process-annotations
manthey Apr 14, 2025
a6db886
Generalize itemFromEvent
manthey Apr 15, 2025
97445d4
Merge branch 'master' into generalize-item-from-event
manthey Apr 15, 2025
b437894
Merge pull request #1880 from girder/generalize-item-from-event
manthey Apr 15, 2025
46e0db4
Improve task name
manthey Apr 16, 2025
fefc0b9
Don't schedule a needless annotation handling task
manthey Apr 17, 2025
1a76049
Merge branch 'master' into girder-5
manthey May 5, 2025
b847db0
Remove explicit cache busting as girder now handles it
manthey May 12, 2025
dc21aea
Merge pull request #1901 from girder/remove-geojs-cache-busting
manthey May 12, 2025
5d65cc1
Merge branch 'master' into girder-5
manthey May 14, 2025
9ac8f24
Merge branch 'master' into girder-5
manthey May 19, 2025
cf886a6
Fix girder-5 patch elements endpoint
manthey May 19, 2025
9c8c128
Merge branch 'master' into girder-5
manthey Jun 3, 2025
0d4084e
Merge branch 'master' into girder-5
manthey Jun 5, 2025
15ff090
Conform to new notifications API from Girder core
zachmullen Jun 9, 2025
815f702
Merge branch 'master' into girder-5
manthey Jun 13, 2025
60d4c67
Merge branch 'more-documentdb-workarounds' into girder-5
manthey Jun 24, 2025
2d0ca1b
Merge branch 'master' into girder-5
manthey Jul 29, 2025
6666866
Merge branch 'girder-5' into updated-notifications-api
manthey Jul 29, 2025
41e24cb
Update girder version needs for girder-5 branch
manthey Jul 30, 2025
b777111
Merge pull request #1961 from girder/girder-version
manthey Jul 31, 2025
d36b808
Merge pull request #1938 from girder/updated-notifications-api
zachmullen Jul 31, 2025
54ff3e3
Hook events in girder_worker
manthey Aug 5, 2025
de9bbde
Merge pull request #1962 from girder/gw_plugin
manthey Aug 5, 2025
13d7210
Refactor how girder objects are tracked for annotations
manthey Aug 6, 2025
f1b61ff
Merge pull request #1963 from girder/refactor-annotation-reprocess
manthey Aug 6, 2025
427908a
Update girder-5 version
manthey Aug 8, 2025
916fd1f
Merge pull request #1964 from girder/update-girder-5
manthey Aug 8, 2025
96022ec
Merge branch 'master' into girder-5
naglepuff Aug 27, 2025
d1d5c3d
Remove event stream polling fallback
manthey Sep 3, 2025
79d34ba
Merge pull request #1974 from girder/remove-eventstream-fallback
manthey Sep 4, 2025
01c1054
Merge branch 'master' into girder-5
manthey Sep 4, 2025
e5997f8
Satisfy client linter
manthey Sep 4, 2025
47f28e2
Merge branch 'master' into girder-5
manthey Sep 17, 2025
faab1e3
Merge branch 'master' into girder-5
manthey Sep 25, 2025
0e3ac5b
Merge branch 'master' into girder-5
manthey Oct 1, 2025
b507a9a
Merge branch 'master' into girder-5
manthey Oct 2, 2025
4f7429f
Merge branch 'master' into girder-5
manthey Oct 6, 2025
fba6d84
Merge branch 'master' into girder-5
manthey Oct 10, 2025
4bb871b
Merge branch 'master' into girder-5
manthey Oct 15, 2025
83f4b93
Merge branch 'master' into girder-5
manthey Oct 16, 2025
bbc9d02
Merge branch 'master' into girder-5
manthey Nov 12, 2025
7df4095
Merge branch 'master' into girder-5
manthey Nov 17, 2025
e80efd7
Merge branch 'master' into girder-5
manthey Dec 2, 2025
fdf7bd2
Merge branch 'master' into girder-5
manthey Dec 3, 2025
04b1a82
Fix node version in python 3.14 test
manthey Dec 4, 2025
fbfc5f3
Update package-lock
manthey Dec 4, 2025
14aee15
Merge pull request #2024 from girder/girder-5-update-package-lock
manthey Dec 5, 2025
62fa262
Merge branch 'master' into girder-5
manthey Jan 8, 2026
11a0c4c
Merge branch 'master' into girder-5
manthey Jan 9, 2026
5a8ba54
Merge branch 'master' into girder-5
manthey Jan 12, 2026
3af0f14
Merge branch 'master' into girder-5
manthey Jan 21, 2026
517cfe7
Merge branch 'master' into girder-5
manthey Jan 30, 2026
d0be72a
Merge branch 'master' into girder-5
manthey Mar 19, 2026
18790a1
Merge branch 'master' into girder-5
manthey Mar 24, 2026
0c076eb
Merge branch 'master' into girder-5
manthey Mar 31, 2026
148807b
Merge branch 'master' into girder-5
manthey Apr 21, 2026
29dc7ed
Merge branch 'master' into girder-5
manthey Apr 21, 2026
f8f4c52
Expose channel colors so other plugins can use them.
manthey Apr 22, 2026
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135 changes: 96 additions & 39 deletions .circleci/config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -15,23 +15,24 @@ commands:
type: string
default: ""
steps:
- run:
name: Upgrade pip
command: pip install -U pip
- run:
name: Upgrade virtualenv and tox
command: pip install -U virtualenv tox
# - run:
# name: Preinstall phantomjs to work around an npm permission issue
# command: npm install -g phantomjs-prebuilt --unsafe-perm
- run:
name: Run tests via tox
environment:
GIRDER_CLIENT_TESTING_MONGO_URI: mongodb://localhost:27017
COVERAGE_CORE: sysmon
PYTEST_NUMPROCESSES: 3
LARGE_IMAGE_CACHE_TILESOURCE_MAXIMUM: 3
PYTEST_ADDOPTS: "--reruns=3"
HEADLESS: "true"
_JAVA_OPTIONS: "-Xmx2g"
# Piping through cat does less buffering of the output but can
# consume the exit code
# command: PYTEST_ADDOPTS=--forked tox -e << parameters.toxenv >> | cat; test ${PIPESTATUS[0]} -eq 0
# command: PYTEST_ADDOPTS="--reruns=3 --numprocesses=0" tox -e << parameters.toxenv >> | cat; test ${PIPESTATUS[0]} -eq 0
command: _JAVA_OPTIONS="-Xmx2g" LARGE_IMAGE_CACHE_TILESOURCE_MAXIMUM=3 COVERAGE_CORE=sysmon PYTEST_NUMPROCESSES=2 PYTEST_ADDOPTS="--reruns=3" << parameters.environ >> tox -e << parameters.toxenv
>> | cat; test ${PIPESTATUS[0]} -eq 0
command: << parameters.environ >> tox -e << parameters.toxenv >> | cat; test ${PIPESTATUS[0]} -eq 0
switchpython:
description: "Upgrade python"
parameters:
Expand Down Expand Up @@ -61,6 +62,7 @@ commands:
type: string
node:
type: string
default: v20
steps:
- switchpython:
version: << parameters.version >>
Expand Down Expand Up @@ -129,11 +131,36 @@ commands:
nvm alias default << parameters.node >>
NODE_DIR=$(dirname $(which node))
echo "export PATH=$NODE_DIR:\$PATH" >> $BASH_ENV
- run:
name: Install and build large_image plugin
command: |
npm ci
npm run build
working_directory: girder/girder_large_image/web_client
- run:
name: Install and build large_image_annotation plugin
command: |
npm ci
npm run build
working_directory: girder_annotation/girder_large_image_annotation/web_client
- run:
name: Install and build large_image_source_dicom plugin
command: |
npm ci
npm run build
working_directory: sources/dicom/large_image_source_dicom/web_client
- save_cache:
name: Save nvm cache
key: v1-nvm-cache-<< parameters.node >>
paths:
- /opt/circleci/.nvm/.cache
- run:
name: Install playwright with dependencies
environment:
DEBIAN_FRONTEND: noninteractive
command: |
npx playwright install --with-deps
working_directory: girder/girder_large_image/web_client
- run:
name: Check node versions
command: |
Expand Down Expand Up @@ -188,7 +215,6 @@ jobs:
- checkout
- allservices:
version: "3.10"
node: v14
- tox:
toxenv: test-py310
- coverage
Expand All @@ -202,7 +228,6 @@ jobs:
- checkout
- allservices:
version: "3.11"
node: v14
- tox:
toxenv: test-py311
- coverage
Expand All @@ -216,7 +241,6 @@ jobs:
- checkout
- allservices:
version: "3.12"
node: v14
- tox:
toxenv: test-py312
- coverage
Expand All @@ -230,7 +254,6 @@ jobs:
- checkout
- allservices:
version: "3.13"
node: v14
- tox:
toxenv: test-py313
# environ: TOX_VERBOSE=4 TOX_PREFER_BINARY=1
Expand All @@ -245,7 +268,6 @@ jobs:
- checkout
- allservices:
version: "3.14"
node: v14
- tox:
toxenv: test-py314
# environ: TOX_VERBOSE=4 TOX_PREFER_BINARY=1
Expand Down Expand Up @@ -290,21 +312,12 @@ jobs:
- checkout
- tox:
toxenv: type
wheels:
executor: toxandnode
steps:
- checkout
- run:
name: Build wheels
command: ./.circleci/make_wheels.sh
- run:
name: Make index file
command: python ./.circleci/make_index.py ~/wheels
- store_artifacts:
path: ~/wheels
check_release:
docker:
- image: cimg/python:3.10
executor: toxandnode
parameters:
node:
type: string
default: v20
steps:
- checkout
- run:
Expand All @@ -315,12 +328,42 @@ jobs:
- run:
name: Install python packages
command: pip install setuptools_scm twine
- run:
name: Use nvm
# see https://discuss.circleci.com/t/nvm-does-not-change-node-version-on-machine/28973/14
command: |
echo 'export NVM_DIR="/opt/circleci/.nvm"' >> $BASH_ENV
echo '[ -s "$NVM_DIR/nvm.sh" ] && \. "$NVM_DIR/nvm.sh"' >> $BASH_ENV
- restore_cache:
name: Restore nvm cache
key: v1-nvm-cache-<< parameters.node >>
- run:
name: Switch node versions
command: |
. ~/.bashrc
nvm install << parameters.node >>
nvm alias default << parameters.node >>
NODE_DIR=$(dirname $(which node))
echo "export PATH=$NODE_DIR:\$PATH" >> $BASH_ENV
- run:
name: Check node versions
command: |
node --version
npm --version
- run:
name: Check release to PyPi
command: ./.circleci/release_pypi.sh check
- run:
name: Make index file
command: python ./.circleci/make_index.py ~/wheels
- store_artifacts:
path: ~/wheels
release:
docker:
- image: cimg/python:3.10
executor: toxandnode
parameters:
node:
type: string
default: v20
steps:
- checkout
- run:
Expand All @@ -331,6 +374,28 @@ jobs:
- run:
name: Install python packages
command: pip install setuptools_scm twine
- run:
name: Use nvm
# see https://discuss.circleci.com/t/nvm-does-not-change-node-version-on-machine/28973/14
command: |
echo 'export NVM_DIR="/opt/circleci/.nvm"' >> $BASH_ENV
echo '[ -s "$NVM_DIR/nvm.sh" ] && \. "$NVM_DIR/nvm.sh"' >> $BASH_ENV
- restore_cache:
name: Restore nvm cache
key: v1-nvm-cache-<< parameters.node >>
- run:
name: Switch node versions
command: |
. ~/.bashrc
nvm install << parameters.node >>
nvm alias default << parameters.node >>
NODE_DIR=$(dirname $(which node))
echo "export PATH=$NODE_DIR:\$PATH" >> $BASH_ENV
- run:
name: Check node versions
command: |
node --version
npm --version
- run:
name: Release to PyPi
command: ./.circleci/release_pypi.sh upload
Expand Down Expand Up @@ -435,13 +500,6 @@ workflows:
branches:
ignore:
- gh-pages
- wheels:
filters:
tags:
only: /^v.*/
branches:
ignore:
- gh-pages
- check_release:
filters:
tags:
Expand All @@ -459,7 +517,6 @@ workflows:
- py314
- lint_and_docs
- type
- wheels
filters:
tags:
only: /^v.*/
Expand All @@ -476,7 +533,7 @@ workflows:
- py314
- lint_and_docs
- type
- wheels
- check_release
filters:
tags:
only: /^v.*/
Expand All @@ -502,4 +559,4 @@ workflows:
- lint_and_docs
- type
- compare
- wheels
- check_release
59 changes: 0 additions & 59 deletions .circleci/make_wheels.sh

This file was deleted.

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