Fix tox config for Girder 5

.circleci/config.yml

@@ -4,7 +4,7 @@ executors:
   toxandnode:
     working_directory: ~/project
     docker:
-      - image: girder/girder_test:py38-node16
+      - image: girder/tox-and-node
 commands:
   tox:
     description: "Run tox"
@@ -125,6 +125,12 @@ 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
       - save_cache:
           name: Save nvm cache
           key: v1-nvm-cache-<< parameters.node >>
@@ -169,7 +175,7 @@ jobs:
       - checkout
       - allservices:
           version: "3.8"
-          node: v14
+          node: v16
       - tox:
           toxenv: test-py38
       - coverage
@@ -183,7 +189,7 @@ jobs:
       - checkout
       - allservices:
           version: "3.9"
-          node: v14
+          node: v16
       - tox:
           toxenv: test-py39
       - coverage
@@ -197,7 +203,7 @@ jobs:
       - checkout
       - allservices:
           version: "3.10"
-          node: v14
+          node: v16
       - tox:
           toxenv: test-py310
       - coverage
@@ -211,7 +217,7 @@ jobs:
       - checkout
       - allservices:
           version: "3.11"
-          node: v14
+          node: v16
       - tox:
           toxenv: test-py311
       - coverage
@@ -225,7 +231,7 @@ jobs:
       - checkout
       - allservices:
           version: "3.12"
-          node: v14
+          node: v16
       - tox:
           toxenv: test-py312
       - coverage
@@ -239,7 +245,7 @@ jobs:
       - checkout
       - allservices:
           version: "3.13"
-          node: v14
+          node: v16
       - tox:
           toxenv: test-py313
           environ: TOX_VERBOSE=4 TOX_PREFER_BINARY=1

girder/girder_large_image/__init__.py

@@ -243,7 +243,7 @@ def checkForLargeImageFiles(event):  # noqa
             except Exception:
                 pass
     # We couldn't automatically set this as a large image
-    girder.logger.info(
+    logger.info(
         'Saved file %s cannot be automatically used as a largeImage' % str(file['_id']))
 
 

girder/test_girder/conftest.py

@@ -11,7 +11,7 @@ def unavailableWorker(db):
     """
     Make sure that Girder Worker can't be reached and times out quickly.
     """
-    from girder_worker.girder_plugin.constants import PluginSettings as WorkerSettings
+    from girder_plugin_worker.constants import PluginSettings as WorkerSettings
 
     from girder.models.setting import Setting
 
@@ -47,7 +47,7 @@ def girderWorker(db, girderWorkerProcess):
     Run an instance of Girder worker, connected to rabbitmq.  The rabbitmq
     service must be running.
     """
-    from girder_worker.girder_plugin.constants import PluginSettings as WorkerSettings
+    from girder_plugin_worker.constants import PluginSettings as WorkerSettings
 
     from girder.models.setting import Setting
 

girder/test_girder/test_large_image.py

@@ -16,7 +16,7 @@
     from girder_jobs.models.job import Job
     from girder_large_image import constants
     from girder_large_image.models.image_item import ImageItem
-    from girder_worker.girder_plugin.status import CustomJobStatus
+    from girder_plugin_worker.status import CustomJobStatus
 
     from girder import events
     from girder.exceptions import ValidationException

requirements-dev.txt

@@ -1,6 +1,4 @@
 # Top level dependencies
-girder>=3.1.18
-girder-jobs>=3.0.3
 -e sources/bioformats
 -e sources/deepzoom
 -e sources/dicom

requirements-girder5.txt

@@ -0,0 +1,6 @@
+# Dependencies needed from Girder 5 during prerelease
+--pre
+girder
+girder-jobs
+girder-worker
+girder-plugin-worker

tox.ini

@@ -31,19 +31,22 @@ deps =
   pytest
   pytest-cov
   pytest-custom-exit-code
-  pytest-girder
+  pytest-girder==5.0.0a4
   pytest-rerunfailures
   pytest-xdist
 allowlist_externals =
   rm
-  npx
+  npm
+  cd
+  sh
+commands_pre =
+  sh -c "cd girder/girder_large_image/web_client && npm run build"
 # Run most tests in parallel and conflicting tests sequentially
 commands =
   rm -rf build/test/coverage/web_temp
-  girder build --dev {env:GIRDER_BUILD_OPTIONS}
+  # girder build --dev {env:GIRDER_BUILD_OPTIONS}
   pytest --numprocesses 0 -m 'singular' --cov-config tox.ini --suppress-no-test-exit-code {posargs}
   pytest --numprocesses {env:PYTEST_NUMPROCESSES:logical} -m 'not singular and not notebook' --cov-config tox.ini --cov-append --suppress-no-test-exit-code {posargs}
-  - npx nyc report --temp-dir build/test/coverage/web_temp --report-dir build/test/coverage --reporter cobertura --reporter text-summary
 # Reduce npm chatter
 setenv =
   NPM_CONFIG_FUND=false
@@ -66,39 +69,44 @@ package=editable
 passenv = {[testenv:test]passenv}
 extras = {[testenv:test]extras}
 deps =
+  -rrequirements-girder5.txt
   -rrequirements-dev.txt
   coverage
   mock
   pooch
   pytest
   pytest-cov
   pytest-custom-exit-code
-  pytest-girder
+  pytest-girder==5.0.0a4
   pytest-rerunfailures
   pytest-xdist
+  numcodecs
+  imagecodecs
 allowlist_externals = {[testenv:test]allowlist_externals}
+commands_pre = {[testenv:test]commands_pre}
 commands = {[testenv:test]commands}
 setenv = {[testenv:test]setenv}
 
 [testenv:monkeytype-py{38,39,310,311,312,313}]
 passenv = {[testenv:test]passenv}
 deps =
+  -rrequirements-girder5.txt
   -rrequirements-dev.txt
   coverage
   mock
   pooch
   pytest
   pytest-cov
   pytest-custom-exit-code
-  pytest-girder
+  pytest-girder==5.0.0a5.dev117
   pytest-monkeytype
   pytest-rerunfailures
   pytest-xdist
 allowlist_externals = {[testenv:test]allowlist_externals}
 commands =
   rm -rf build/test/coverage/web_temp
   -rm ./monkeytype.sqlite3
-  girder build --dev
+  # girder build --dev
   pytest --numprocesses 0 -m 'not notebook' --no-cov --suppress-no-test-exit-code --monkeytype-output=./monkeytype.sqlite3 {posargs}
   - npx nyc report --temp-dir build/test/coverage/web_temp --report-dir build/test/coverage --reporter cobertura --reporter text-summary
 # After running tox, you can do

utilities/tasks/large_image_tasks/tasks.py

@@ -202,7 +202,6 @@ def cache_histograms_job(job):
     from girder_jobs.models.job import Job
     from girder_large_image.models.image_item import ImageItem
 
-    from girder import logger
 
     kwargs = job['kwargs']
     item = ImageItem().load(kwargs.pop('itemId'), force=True)