New UI for creating and editing views

.circleci/config.yml

@@ -9,8 +9,11 @@ commands:
   tox:
     description: "Run tox"
     parameters:
-      env:
+      toxenv:
         type: string
+      environ:
+        type: string
+        default: ""
     steps:
       - run:
           name: Upgrade pip
@@ -25,9 +28,9 @@ commands:
           name: Run tests via tox
           # Piping through cat does less buffering of the output but can
           # consume the exit code
-          # command: PYTEST_ADDOPTS=--forked tox -e << parameters.env >> | cat; test ${PIPESTATUS[0]} -eq 0
-          # command: PYTEST_ADDOPTS="--reruns=3 --numprocesses=0" tox -e << parameters.env >> | cat; test ${PIPESTATUS[0]} -eq 0
-          command: COVERAGE_CORE=sysmon PYTEST_NUMPROCESSES=3 PYTEST_ADDOPTS="--reruns=3" tox -e << parameters.env >> | cat; test ${PIPESTATUS[0]} -eq 0
+          # 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: COVERAGE_CORE=sysmon PYTEST_NUMPROCESSES=3 PYTEST_ADDOPTS="--reruns=3" << parameters.environ >> tox -e << parameters.toxenv >> | cat; test ${PIPESTATUS[0]} -eq 0
   switchpython:
     description: "Upgrade python"
     parameters:
@@ -38,7 +41,8 @@ commands:
           name: Upgrade pyenv
           command: |
             sudo rm -rf /opt/circleci/.pyenv
-            curl -L https://github.com/pyenv/pyenv-installer/raw/master/bin/pyenv-installer | bash
+            sudo bash -c 'curl -L https://github.com/pyenv/pyenv-installer/raw/master/bin/pyenv-installer | PYENV_ROOT=/opt/circleci/.pyenv bash'
+            sudo chmod -R 777 /opt/circleci/.pyenv/
             pyenv install --list list
       - run:
           name: Use pyenv to install python
@@ -75,7 +79,7 @@ commands:
             docker-compose -f ./.circleci/dcm4chee/auth-docker-compose.yml up -d
             export DICOMWEB_TEST_URL=http://localhost:8008/dcm4chee-arc/aets/DCM4CHEE/rs
             echo "export DICOMWEB_TEST_URL=$DICOMWEB_TEST_URL" >> $BASH_ENV
-            pip install dicomweb_client 'python-keycloak<4.1'
+            pip install dicomweb_client tenacity 'python-keycloak<4.1'
 
             # Wait up to 60 seconds for keycloak to be ready
             echo 'Waiting for keycloak to start...'
@@ -114,13 +118,21 @@ commands:
           command: |
             echo 'export NVM_DIR="/opt/circleci/.nvm"' >> $BASH_ENV
             echo '[ -s "$NVM_DIR/nvm.sh" ] && \. "$NVM_DIR/nvm.sh"' >> $BASH_ENV
+      - restore_cache:
+          name: Restore nvm cache
+          key: v1-nvm-cache-<< parameters.node >>
       - run:
           name: Switch node versions
           command: |
             nvm install << parameters.node >>
             nvm alias default << parameters.node >>
             NODE_DIR=$(dirname $(which node))
             echo "export PATH=$NODE_DIR:\$PATH" >> $BASH_ENV
+      - save_cache:
+          name: Save nvm cache
+          key: v1-nvm-cache-<< parameters.node >>
+          paths:
+            - /opt/circleci/.nvm/.cache
       - run:
           name: Check node versions
           command: |
@@ -162,7 +174,7 @@ jobs:
           version: "3.8"
           node: v14
       - tox:
-          env: test-py38
+          toxenv: test-py38
       - coverage
       - store_artifacts:
           path: build/test/artifacts
@@ -176,7 +188,7 @@ jobs:
           version: "3.9"
           node: v14
       - tox:
-          env: test-py39
+          toxenv: test-py39
       - coverage
       - store_artifacts:
           path: build/test/artifacts
@@ -190,7 +202,7 @@ jobs:
           version: "3.10"
           node: v14
       - tox:
-          env: test-py310
+          toxenv: test-py310
       - coverage
       - store_artifacts:
           path: build/test/artifacts
@@ -204,7 +216,7 @@ jobs:
           version: "3.11"
           node: v14
       - tox:
-          env: test-py311
+          toxenv: test-py311
       - coverage
       - store_artifacts:
           path: build/test/artifacts
@@ -218,7 +230,22 @@ jobs:
           version: "3.12"
           node: v14
       - tox:
-          env: test-py312
+          toxenv: test-py312
+      - coverage
+      - store_artifacts:
+          path: build/test/artifacts
+  py313:
+    machine:
+      image: ubuntu-2204:current
+    resource_class: large
+    steps:
+      - checkout
+      - allservices:
+          version: "3.13"
+          node: v14
+      - tox:
+          toxenv: test-py313
+          environ: TOX_VERBOSE=4 TOX_PREFER_BINARY=1
       - coverage
       - store_artifacts:
           path: build/test/artifacts
@@ -233,7 +260,7 @@ jobs:
           name: Permissions for link checker
           command: find /root -type d -exec chmod 755 {} \+
       - tox:
-          env: docs,lint,lintclient,notebook
+          toxenv: docs,lint,lintclient,notebook
       - store_artifacts:
           path: build/docs
       - persist_to_workspace:
@@ -245,7 +272,7 @@ jobs:
     steps:
       - checkout
       - tox:
-          env: compare-py311
+          toxenv: compare-py311
       - store_artifacts:
           path: build/tox/compare.txt
       - store_artifacts:
@@ -256,7 +283,7 @@ jobs:
     steps:
       - checkout
       - tox:
-          env: type
+          toxenv: type
   wheels:
     executor: toxandnode
     steps:
@@ -372,6 +399,13 @@ workflows:
             branches:
               ignore:
                 - gh-pages
+      - py313:
+          filters:
+            tags:
+              only: /^v.*/
+            branches:
+              ignore:
+                - gh-pages
       - lint_and_docs:
           filters:
             tags:
@@ -415,6 +449,7 @@ workflows:
             - py310
             - py311
             - py312
+            - py313
             - lint_and_docs
             - type
             - wheels
@@ -430,6 +465,7 @@ workflows:
             - py310
             - py311
             - py312
+            - py313
             - lint_and_docs
             - type
             - wheels
@@ -455,6 +491,7 @@ workflows:
       - py310
       - py311
       - py312
+      - py313
       - lint_and_docs
       - type
       - compare

.circleci/dcm4chee/docker-compose.yml

@@ -7,7 +7,7 @@ volumes:
   ldap_config: {}
 services:
   ldap:
-    image: dcm4che/slapd-dcm4chee:2.6.6-33.0
+    image: dcm4che/slapd-dcm4chee:2.6.5-31.2
     logging:
       driver: json-file
       options:
@@ -20,7 +20,7 @@ services:
       - ldap_data:/var/lib/openldap/openldap-data
       - ldap_config:/etc/openldap/slapd.d
   db:
-    image: dcm4che/postgres-dcm4chee:16.4-33
+    image: dcm4che/postgres-dcm4chee:15.4-31
     logging:
       driver: json-file
       options:
@@ -34,7 +34,7 @@ services:
     volumes:
       - db_data:/var/lib/postgresql/data
   arc:
-    image: dcm4che/dcm4chee-arc-psql:5.33.0
+    image: dcm4che/dcm4chee-arc-psql:5.31.2
     logging:
       driver: json-file
       options:

.circleci/dcm4chee/upload_example_data.py

@@ -6,6 +6,7 @@
 from dicomweb_client import DICOMwebClient
 from pydicom import dcmread
 from requests import Session
+from tenacity import Retrying, stop_after_attempt, wait_exponential
 
 
 def upload_example_data(server_url, token=None):
@@ -22,8 +23,11 @@ def upload_example_data(server_url, token=None):
 
     datasets = []
     for url in download_urls:
-        resp = urllib.request.urlopen(url)
-        data = resp.read()
+        for attempt in Retrying(stop=stop_after_attempt(5),
+                                wait=wait_exponential(multiplier=1, min=0.5, max=5)):
+            with attempt:
+                resp = urllib.request.urlopen(url)
+                data = resp.read()
         dataset = dcmread(BytesIO(data))
         datasets.append(dataset)
 

.pre-commit-config.yaml

@@ -5,7 +5,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
       - id: check-ast
@@ -58,21 +58,22 @@ repos:
     hooks:
       - id: circleci-config-validate
   - repo: https://github.com/ThisIsManta/stylus-supremacy
-    rev: v2.17.5
+    rev: v4.0.0
     hooks:
       - id: stylus-supremacy
+        language_version: "22.10.0"
         args:
           - '--options'
           - './girder/girder_large_image/web_client/package.json'
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.17.0
+    rev: v3.18.0
     hooks:
       - id: pyupgrade
         args:
           - --py38-plus
           - --keep-percent-format
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.1
+    rev: v0.7.0
     hooks:
       - id: ruff
         args:

CHANGELOG.md

@@ -1,15 +1,84 @@
 # Change Log
 
-## 1.29.12
+## 1.30.3
+
+### Improvements
+
+- Format dates in item lists ([#1707](../../pull/1707))
+- Guard dtype types ([#1711](../../pull/1711), [#1714](../../pull/1714), [#1716](../../pull/1716))
+- Better handle IndicaLabs tiff files ([#1717](../../pull/1717))
+- Better detect files with geotransform data that aren't geospatial ([#1718](../../pull/1718))
+- Better scale float-valued tiles ([#1725](../../pull/1725))
+
+### Changes
+
+- Openslide now requires the binary wheel on appropriate platforms ([#1709](../../pull/1709), [#1710](../../pull/1710))
+
+### Bug Fixes
+
+- Fix an issue searching for annotation metadata on items that a user doesn't have permissions to view ([#1723](../../pull/1723))
+- Fix a typo in a column header ([#1727](../../pull/1727))
+
+## 1.30.2
+
+### Features
+
+- Support setting axis actual values in the zarr sink.  Display these in the frame selector ([#1625](../../pull/1625))
+
+### Improvements
+
+- Speed up recursive item lists ([#1694](../../pull/1694))
+- Better handle images with signed pixel data ([#1695](../../pull/1695))
+- Reduce loading geojs when switching views in Girder ([#1699](../../pull/1699))
+
+### Bug Fixes
+
+- Don't compute channel window in zarr sinks ([#1705](../../pull/1705))
+
+## 1.30.1
+
+### Improvements
+
+- Support generalized application buttons ([#1692](../../pull/1692))
+
+### Bug Fixes
+
+- Don't use a default for yaml config files except .large_image_config.yaml ([#1685](../../pull/1685))
+- Some checks for repeated values in the item lists were wrong ([#1686](../../pull/1686))
+- Better support creating zarr sinks from multiple processes ([#1687](../../pull/1687))
+
+## 1.30.0
+
+### Features
+
+- Add support for Python 3.13 ([#1675](../../pull/1675))
 
 ### Improvements
 
 - Better handle images without enough tile layers ([#1648](../../pull/1648))
 - Add users option to config files; have a default config file ([#1649](../../pull/1649))
+- Remove no longer used code; adjust item list slightly ([#1651](../../pull/1651), [#1668](../../pull/1668))
+- Reduce updates when showing item lists; add a waiting spinner ([#1653](../../pull/1653))
+- Update item lists check for large images when toggling recurse ([#1654](../../pull/1654))
+- Support named item lists ([#1665](../../pull/1665))
+- Add options to group within item lists ([#1666](../../pull/1666))
+- Make the filter field in item lists wider ([#1669](../../pull/1669), [#1671](../../pull/1671))
+- Add a navigate option to item lists ([#1659](../../pull/1659))
+
+### Changes
+
+- Handle a rasterio deprecation ([#1655](../../pull/1655))
+- Handle a variation in a bioformats exception ([#1656](../../pull/1656))
+- Increase logging slow histograms ([#1658](../../pull/1658))
+- Use paginated item lists ([#1664](../../pull/1664))
+- When in-line editing yaml and other files, the tab key now uses spaces ([#1667](../../pull/1667))
+- Changed the parsing of the open parameter in the algorithm progression example ([#1677](../../pull/1677))
 
 ### Bug Fixes
 
 - Fix styling images with empty tile layers ([#1650](../../pull/1650))
+- Add a guard around sorting item lists ([#1663](../../pull/1663))
+- Fix some issues with possible numpy 2.x overflows ([#1672](../../pull/1672))
 
 ## 1.29.11
 

docs/conf.py

@@ -13,8 +13,6 @@
 import os
 import sys
 
-import sphinx_rtd_theme
-
 docs_dir = os.path.dirname(__file__)
 sys.path.insert(0, os.path.abspath(os.path.join(docs_dir, '..', '..')))
 
@@ -62,7 +60,6 @@
 # a list of builtin themes.
 #
 html_theme = 'sphinx_rtd_theme'
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 pygments_style = 'sphinx'