Merge pull request #1712 from girder/update-with-master

Bring recent changes to `large_image` into the `girder5` branch
girder · Nov 7, 2024 · d046aa5 · d046aa5
2 parents d6202e1 + 75a10a0
commit d046aa5
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -1,3 +1,4 @@
+---
 version: 2.1
 executors:
   toxandnode:
@@ -8,8 +9,11 @@ commands:
   tox:
     description: "Run tox"
     parameters:
-      env:
+      toxenv:
         type: string
+      environ:
+        type: string
+        default: ""
     steps:
       - run:
           name: Upgrade virtualenv and tox
@@ -21,9 +25,9 @@ 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: 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 ${PIPESTATUS[0]} -eq 0
   switchpython:
     description: "Upgrade python"
     parameters:
@@ -34,7 +38,8 @@ commands:
           name: Upgrade pyenv
           command: |
             sudo rm -rf /opt/circleci/.pyenv
-            curl -L https://github.com/pyenv/pyenv-installer/raw/master/bin/pyenv-installer | bash
+            sudo bash -c 'curl -L https://github.com/pyenv/pyenv-installer/raw/master/bin/pyenv-installer | PYENV_ROOT=/opt/circleci/.pyenv bash'
+            sudo chmod -R 777 /opt/circleci/.pyenv/
             pyenv install --list list
       - run:
           name: Use pyenv to install python
@@ -71,15 +76,14 @@ commands:
             docker-compose -f ./.circleci/dcm4chee/auth-docker-compose.yml up -d
             export DICOMWEB_TEST_URL=http://localhost:8008/dcm4chee-arc/aets/DCM4CHEE/rs
             echo "export DICOMWEB_TEST_URL=$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...'
             KEYCLOAK_URL=https://localhost:8843
             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)
@@ -111,13 +115,21 @@ 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" >> $BASH_ENV
+      - save_cache:
+          name: Save nvm cache
+          key: v1-nvm-cache-<< parameters.node >>
+          paths:
+            - /opt/circleci/.nvm/.cache
       - run:
           name: Check node versions
           command: |
@@ -129,13 +141,12 @@ commands:
       - run:
           name: Install Codecov client
           command: |
-              curl -Os https://uploader.codecov.io/latest/linux/codecov
-              chmod +x codecov
+            curl -Os https://uploader.codecov.io/latest/linux/codecov
+            chmod +x codecov
       - run:
           name: Upload coverage
           command: |
-              ./codecov --disable search pycov gcov --file build/test/coverage/py_coverage.xml,build/test/coverage/cobertura-coverage.xml
-
+            ./codecov --disable search pycov gcov --file build/test/coverage/py_coverage.xml,build/test/coverage/cobertura-coverage.xml
 jobs:
   testdocker:
     machine:
@@ -144,12 +155,12 @@ jobs:
       - checkout
       - run:
           name: Build the test docker
-          command: docker build --force-rm -t girder/tox-and-node -f test.Dockerfile .
+          command: docker build --progress=plain --force-rm -t girder/tox-and-node -f test.Dockerfile .
       - run:
           name: Publish the images to Docker Hub
           command: |
-              echo "$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
@@ -160,7 +171,7 @@ jobs:
           version: "3.8"
           node: v14
       - tox:
-          env: test-py38
+          toxenv: test-py38
       - coverage
       - store_artifacts:
           path: build/test/artifacts
@@ -174,7 +185,7 @@ jobs:
           version: "3.9"
           node: v14
       - tox:
-          env: test-py39
+          toxenv: test-py39
       - coverage
       - store_artifacts:
           path: build/test/artifacts
@@ -188,7 +199,7 @@ jobs:
           version: "3.10"
           node: v14
       - tox:
-          env: test-py310
+          toxenv: test-py310
       - coverage
       - store_artifacts:
           path: build/test/artifacts
@@ -202,7 +213,7 @@ jobs:
           version: "3.11"
           node: v14
       - tox:
-          env: test-py311
+          toxenv: test-py311
       - coverage
       - store_artifacts:
           path: build/test/artifacts
@@ -216,7 +227,22 @@ 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
@@ -227,8 +253,11 @@ jobs:
       - run:
           name: Install dependencies
           command: apt-get update -yq && apt-get install -yq pandoc && pandoc --version
+      - run:
+          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:
@@ -240,7 +269,7 @@ jobs:
     steps:
       - checkout
       - tox:
-          env: compare-py311
+          toxenv: compare-py311
       - store_artifacts:
           path: build/tox/compare.txt
       - store_artifacts:
@@ -251,7 +280,7 @@ jobs:
     steps:
       - checkout
       - tox:
-          env: type
+          toxenv: type
   wheels:
     executor: toxandnode
     steps:
@@ -264,6 +293,22 @@ jobs:
           command: python ./.circleci/make_index.py ~/wheels
       - store_artifacts:
           path: ~/wheels
+  check_release:
+    docker:
+      - image: cimg/python:3.10
+    steps:
+      - checkout
+      - run:
+          name: Setup virtual environment
+          command: |
+            if [ ! -d env ]; then python -m virtualenv env || python -m venv env; fi
+            echo ". $CIRCLE_WORKING_DIRECTORY/env/bin/activate" >> $BASH_ENV
+      - run:
+          name: Install python packages
+          command: pip install setuptools_scm twine
+      - run:
+          name: Check release to PyPi
+          command: ./.circleci/release_pypi.sh check
   release:
     docker:
       - image: cimg/python:3.10
@@ -279,7 +324,7 @@ jobs:
           command: pip install setuptools_scm twine
       - run:
           name: Release to PyPi
-          command: ./.circleci/release_pypi.sh
+          command: ./.circleci/release_pypi.sh upload
   docs-deploy:
     working_directory: ~/project
     docker:
@@ -305,7 +350,6 @@ jobs:
           command: |
             touch package.json
             gh-pages --dotfiles --message "Update documentation" --dist build/docs --no-history
-
 workflows:
   version: 2
   ci:
@@ -352,6 +396,13 @@ workflows:
             branches:
               ignore:
                 - gh-pages
+      - py313:
+          filters:
+            tags:
+              only: /^v.*/
+            branches:
+              ignore:
+                - gh-pages
       - lint_and_docs:
           filters:
             tags:
@@ -380,13 +431,22 @@ workflows:
             branches:
               ignore:
                 - gh-pages
+      - check_release:
+          filters:
+            tags:
+              only: /^v.*/
+            branches:
+              ignore:
+                - gh-pages
       - release:
           requires:
+            - check_release
             - py38
             - py39
             - py310
             - py311
             - py312
+            - py313
             - lint_and_docs
             - type
             - wheels
@@ -402,6 +462,7 @@ workflows:
             - py310
             - py311
             - py312
+            - py313
             - lint_and_docs
             - type
             - wheels
@@ -427,6 +488,7 @@ workflows:
       - py310
       - py311
       - py312
+      - py313
       - lint_and_docs
       - type
       - compare

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/.circleci/dcm4chee/upload_example_data.py b/.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)