Merge branch 'master' into zarr-sink-concurrency

girder · Jul 9, 2024 · ca6cb93 · ca6cb93
2 parents c2e1483 + b93b3d8
commit ca6cb93
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Showing 40 changed files with 317 additions and 201 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -1,3 +1,4 @@
+---
 version: 2.1
 executors:
   toxandnode:
@@ -26,7 +27,7 @@ commands:
           # 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: PYTEST_NUMPROCESSES=3 PYTEST_ADDOPTS="--reruns=3" 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
   switchpython:
     description: "Upgrade python"
     parameters:
@@ -82,7 +83,6 @@ commands:
             curl -k --retry 60 -f --retry-all-errors --retry-delay 1 -s -o /dev/null $KEYCLOAK_URL
             echo 'Updating keycloak token lifespan...'
             python -W ignore ./.circleci/dcm4chee/update_access_token_lifespan.py
-
             echo 'Creating keycloak access token...'
             # Now create the token
             export DICOMWEB_TEST_TOKEN=$(python -W ignore ./.circleci/dcm4chee/create_keycloak_token.py)
@@ -132,13 +132,12 @@ commands:
       - run:
           name: Install Codecov client
           command: |
-              curl -Os https://uploader.codecov.io/latest/linux/codecov
-              chmod +x codecov
+            curl -Os https://uploader.codecov.io/latest/linux/codecov
+            chmod +x codecov
       - run:
           name: Upload coverage
           command: |
-              ./codecov --disable search pycov gcov --file build/test/coverage/py_coverage.xml,build/test/coverage/cobertura-coverage.xml
-
+            ./codecov --disable search pycov gcov --file build/test/coverage/py_coverage.xml,build/test/coverage/cobertura-coverage.xml
 jobs:
   testdocker:
     machine:
@@ -151,8 +150,8 @@ jobs:
       - run:
           name: Publish the images to Docker Hub
           command: |
-              echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
-              docker push girder/tox-and-node:latest
+            echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+            docker push girder/tox-and-node:latest
   py38:
     machine:
       image: ubuntu-2204:current
@@ -308,7 +307,6 @@ jobs:
           command: |
             touch package.json
             gh-pages --dotfiles --message "Update documentation" --dist build/docs --no-history
-
 workflows:
   version: 2
   ci:

diff --git a/.circleci/dcm4chee/auth-docker-compose.yml b/.circleci/dcm4chee/auth-docker-compose.yml
@@ -1,11 +1,11 @@
+---
 volumes:
   db_data: {}
   arc_data: {}
   ldap_data: {}
   ldap_config: {}
   mysql: {}
   keycloak: {}
-
 services:
   ldap:
     image: dcm4che/slapd-dcm4chee:2.6.5-31.2

diff --git a/.circleci/dcm4chee/docker-compose.yml b/.circleci/dcm4chee/docker-compose.yml
@@ -1,11 +1,10 @@
+---
 version: "3"
-
 volumes:
   db_data: {}
   arc_data: {}
   ldap_data: {}
   ldap_config: {}
-
 services:
   ldap:
     image: dcm4che/slapd-dcm4chee:2.6.5-31.2

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -13,3 +13,5 @@
 23ab7f011abaa71d0a4904a9da599174c38f64c3
 # PR 1257: Use ruff for linting
 dcda95e659a4eaa73cae85ab02f1b89059e63c32
+# PR 1563: Use yamlfix for linting
+f517ecb2b7d8c454d1374156452be42b87ca3fd1
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -1,15 +1,14 @@
+---
 name: Docker Package
 on:
   push:
     tags: "*"
     branches:
       - master
   pull_request:
-
 env:
   REGISTRY: ghcr.io
   IMAGE_NAME: ${{ github.repository }}
-
 jobs:
   build-and-publish-base:
     runs-on: ubuntu-latest
@@ -40,14 +39,16 @@ jobs:
           push: ${{ github.actor != 'dependabot[bot]' }}
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
-
   build-and-publish-targets:
     runs-on: ubuntu-latest
     if: github.event_name == 'push' || github.event_name == 'workflow_dispatch' || ( github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == github.repository )
     strategy:
       fail-fast: false
       matrix:
-        target: ["geo", "jupyter", "jupyter-geo"]
+        target:
+          - "geo"
+          - "jupyter"
+          - "jupyter-geo"
     steps:
       - uses: actions/checkout@v4
         with:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,95 +1,107 @@
+---
 # Initially run
 #   pre-commit install
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
-- repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
-  hooks:
-  - id: check-added-large-files
-  - id: check-ast
-  - id: check-builtin-literals
-  - id: check-case-conflict
-  - id: check-docstring-first
-  - id: check-executables-have-shebangs
-  - id: check-json
-  - id: check-merge-conflict
-  - id: check-shebang-scripts-are-executable
-  # - id: check-symlinks
-  # - id: check-toml
-  # - id: check-xml
-  - id: check-yaml
-  - id: debug-statements
-  - id: destroyed-symlinks
-  - id: detect-private-key
-  - id: double-quote-string-fixer
-  - id: end-of-file-fixer
-  - id: fix-byte-order-marker
-  - id: forbid-new-submodules
-  - id: mixed-line-ending
-  - id: no-commit-to-branch
-  - id: trailing-whitespace
-- repo: https://github.com/pre-commit/pygrep-hooks
-  rev: v1.10.0
-  hooks:
-  - id: python-no-eval
-  - id: python-no-log-warn
-  - id: rst-backticks
-  - id: rst-directive-colons
-  - id: rst-inline-touching-normal
-  - id: text-unicode-replacement-char
-- repo: https://github.com/Lucas-C/pre-commit-hooks-markup
-  rev: v1.0.1
-  hooks:
-  - id: rst-linter
-    files: README.rst
-    name: rst-linter of README.rst
-- repo: https://github.com/codespell-project/codespell
-  rev: v2.2.6
-  hooks:
-  - id: codespell
-    args:
-      - --ignore-words-list
-      - "hist,indext,pixelx,thex,subtile,slippy,fram"
-- repo: https://github.com/syntaqx/git-hooks
-  rev: v0.0.18
-  hooks:
-  - id: circleci-config-validate
-- repo: https://github.com/ThisIsManta/stylus-supremacy
-  rev: v2.17.5
-  hooks:
-    - id: stylus-supremacy
-      args:
-        - '--options'
-        - './girder/girder_large_image/web_client/package.json'
-- repo: https://github.com/asottile/pyupgrade
-  rev: v3.15.2
-  hooks:
-    - id: pyupgrade
-      args:
-        - --py38-plus
-        - --keep-percent-format
-- repo: https://github.com/astral-sh/ruff-pre-commit
-  # Ruff version.
-  rev: v0.3.5
-  hooks:
-    - id: ruff
-      args: [--fix, --exit-non-zero-on-fix]
-      types_or: [python, pyi, jupyter]
-- repo: https://github.com/pre-commit/mirrors-autopep8
-  rev: v2.0.4
-  hooks:
-    - id: autopep8
-- repo: https://github.com/PyCQA/flake8
-  rev: 7.0.0
-  hooks:
-    - id: flake8
-- repo: https://github.com/pycqa/isort
-  rev: 5.13.2
-  hooks:
-    - id: isort
-      name: isort (python)
-- repo: https://github.com/asottile/yesqa
-  rev: v1.5.0
-  hooks:
-    - id: yesqa
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-builtin-literals
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-executables-have-shebangs
+      - id: check-json
+      - id: check-merge-conflict
+      - id: check-shebang-scripts-are-executable
+      # - id: check-symlinks
+      # - id: check-toml
+      # - id: check-xml
+      - id: check-yaml
+      - id: debug-statements
+      - id: destroyed-symlinks
+      - id: detect-private-key
+      - id: double-quote-string-fixer
+      - id: end-of-file-fixer
+      - id: fix-byte-order-marker
+      - id: forbid-new-submodules
+      - id: mixed-line-ending
+      - id: no-commit-to-branch
+      - id: trailing-whitespace
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: python-no-eval
+      - id: python-no-log-warn
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+      - id: text-unicode-replacement-char
+  - repo: https://github.com/Lucas-C/pre-commit-hooks-markup
+    rev: v1.0.1
+    hooks:
+      - id: rst-linter
+        files: README.rst
+        name: rst-linter of README.rst
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        args:
+          - --ignore-words-list
+          - "hist,indext,pixelx,thex,subtile,slippy,fram"
+  - repo: https://github.com/syntaqx/git-hooks
+    rev: v0.0.18
+    hooks:
+      - id: circleci-config-validate
+  - repo: https://github.com/ThisIsManta/stylus-supremacy
+    rev: v2.17.5
+    hooks:
+      - id: stylus-supremacy
+        args:
+          - '--options'
+          - './girder/girder_large_image/web_client/package.json'
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.16.0
+    hooks:
+      - id: pyupgrade
+        args:
+          - --py38-plus
+          - --keep-percent-format
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.0
+    hooks:
+      - id: ruff
+        args:
+          - --fix
+          - --exit-non-zero-on-fix
+        types_or:
+          - python
+          - pyi
+          - jupyter
+  - repo: https://github.com/pre-commit/mirrors-autopep8
+    rev: v2.0.4
+    hooks:
+      - id: autopep8
+  - repo: https://github.com/PyCQA/flake8
+    rev: 7.1.0
+    hooks:
+      - id: flake8
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        name: isort (python)
+  - repo: https://github.com/asottile/yesqa
+    rev: v1.5.0
+    hooks:
+      - id: yesqa
+  - repo: https://github.com/lyz-code/yamlfix
+    rev: 1.16.0
+    hooks:
+      - id: yamlfix
+        args:
+          - -c
+          - pyproject.toml
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,15 +1,28 @@
 # Change Log
 
+## 1.29.2
+
+### Improvements
+- Show a loading spinner on the image display in geojs in girder ([#1559](../../pull/1559))
+- Better handle images that are composed of a folder and an item ([#1561](../../pull/1561))
+- Allow specifying which sources are checked with canReadList ([#1562](../../pull/1562))
+
+### Bug Fixes
+- Fix a compositing error in transformed multi source images ([#1560](../../pull/1560))
+
 ## 1.29.1
 
 ### Improvements
 - Improved zarr sink metadata handling ([#1508](../../pull/1508))
+- Speed up decoding jp2k tiff with an optional library ([#1555](../../pull/1555))
 
 ### Changes
 - Work with newer python-mapnik ([#1550](../../pull/1550))
+- Use the new official yaml mime-type of application/yaml ([#1558](../../pull/1558))
 
 ### Bug Fixes
 - Fix an issue emitting rectangles in geojson ([#1552](../../pull/1552))
+- Fix an issue writing zarr channel metadata ([#1557](../../pull/1557))
 
 ## 1.29.0
 

diff --git a/codecov.yml b/codecov.yml
@@ -1,3 +1,4 @@
+---
 comment: false
 coverage:
   status: