Test on Python 3.13

Currently this is very slow because some binary wheels are missing for 3.13 (numcodecs being notable) and they need to be compiled before testing begins. Additionally, currently wsidicom requires numpy<2, partly because dicomweb-client isn't numpy 2.x compatible (yet). Since numpy < 2 doesn't have wheels for 3.13, this is part of the slowness. To avoid having CI timeout, this increases tox verbosity. A few optional packages don't have 3.13 support (scikit-learn, pillow-jxl-plugin, rawpy), so those are not included in install_requires options.
girder · Oct 9, 2024 · de2acd7 · de2acd7
1 parent 31527f8
commit de2acd7
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Showing 27 changed files with 88 additions and 31 deletions.
diff --git a/.circleci/config.yml b/.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:
@@ -163,7 +166,7 @@ jobs:
           version: "3.8"
           node: v14
       - tox:
-          env: test-py38
+          toxenv: test-py38
       - coverage
       - store_artifacts:
           path: build/test/artifacts
@@ -177,7 +180,7 @@ jobs:
           version: "3.9"
           node: v14
       - tox:
-          env: test-py39
+          toxenv: test-py39
       - coverage
       - store_artifacts:
           path: build/test/artifacts
@@ -191,7 +194,7 @@ jobs:
           version: "3.10"
           node: v14
       - tox:
-          env: test-py310
+          toxenv: test-py310
       - coverage
       - store_artifacts:
           path: build/test/artifacts
@@ -205,7 +208,7 @@ jobs:
           version: "3.11"
           node: v14
       - tox:
-          env: test-py311
+          toxenv: test-py311
       - coverage
       - store_artifacts:
           path: build/test/artifacts
@@ -219,7 +222,22 @@ 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
       - coverage
       - store_artifacts:
           path: build/test/artifacts
@@ -234,7 +252,7 @@ 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:
@@ -246,7 +264,7 @@ jobs:
     steps:
       - checkout
       - tox:
-          env: compare-py311
+          toxenv: compare-py311
       - store_artifacts:
           path: build/tox/compare.txt
       - store_artifacts:
@@ -257,7 +275,7 @@ jobs:
     steps:
       - checkout
       - tox:
-          env: type
+          toxenv: type
   wheels:
     executor: toxandnode
     steps:
@@ -373,6 +391,13 @@ workflows:
             branches:
               ignore:
                 - gh-pages
+      - py313:
+          filters:
+            tags:
+              only: /^v.*/
+            branches:
+              ignore:
+                - gh-pages
       - lint_and_docs:
           filters:
             tags:
@@ -416,6 +441,7 @@ workflows:
             - py310
             - py311
             - py312
+            - py313
             - lint_and_docs
             - type
             - wheels
@@ -431,6 +457,7 @@ workflows:
             - py310
             - py311
             - py312
+            - py313
             - lint_and_docs
             - type
             - wheels
@@ -456,6 +483,7 @@ workflows:
       - py310
       - py311
       - py312
+      - py313
       - lint_and_docs
       - type
       - compare

diff --git a/girder/setup.py b/girder/setup.py
@@ -50,6 +50,7 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
         'girder>=3.1.18',

diff --git a/girder_annotation/setup.py b/girder_annotation/setup.py
@@ -50,6 +50,7 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
         'jsonschema>=2.5.1',
@@ -62,7 +63,7 @@ def prerelease_local_scheme(version):
             'pandas ; python_version < "3.9"',
             'pandas>=2.2 ; python_version >= "3.9"',
             'python-calamine ; python_version >= "3.9"',
-            'umap-learn',
+            'umap-learn ; python_version < "3.13"',
         ],
         'tasks': [
             f'girder-large-image[tasks]{limit_version}',

diff --git a/setup.py b/setup.py
@@ -102,6 +102,7 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
         'cachetools',

diff --git a/slim.Dockerfile b/slim.Dockerfile
@@ -1,5 +1,5 @@
 # Build wheels
-FROM python:3.12.7-slim as build
+FROM python:3.12-slim as build
 
 # Need git for setuptools_scm
 RUN apt-get update \
@@ -19,7 +19,7 @@ RUN echo "pylibmc>=1.5.1\nmatplotlib\npyvips\nsimplejpeg\n" \
 
 
 # Geospatial Sources
-FROM python:3.12.7-slim as geo
+FROM python:3.12-slim as geo
 COPY --from=build /opt/build-context/wheels /opt/wheels
 LABEL maintainer="Kitware, Inc. <kitware@kitware.com>"
 LABEL repo="https://github.com/girder/large_image"
@@ -37,7 +37,7 @@ RUN pip install \
 
 
 # All Sources
-FROM python:3.12.7-slim as all
+FROM python:3.12-slim as all
 COPY --from=build /opt/build-context/wheels /opt/wheels
 LABEL maintainer="Kitware, Inc. <kitware@kitware.com>"
 LABEL repo="https://github.com/girder/large_image"
@@ -52,7 +52,7 @@ RUN pip install \
 
 
 # All Sources and Girder Packages
-FROM python:3.12.7-slim as girder
+FROM python:3.12-slim as girder
 COPY --from=build /opt/build-context/wheels /opt/wheels
 LABEL maintainer="Kitware, Inc. <kitware@kitware.com>"
 LABEL repo="https://github.com/girder/large_image"

diff --git a/sources/bioformats/setup.py b/sources/bioformats/setup.py
@@ -50,6 +50,7 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
         f'large-image{limit_version}',

diff --git a/sources/deepzoom/setup.py b/sources/deepzoom/setup.py
@@ -50,6 +50,7 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
         f'large-image{limit_version}',

diff --git a/sources/dicom/setup.py b/sources/dicom/setup.py
@@ -69,6 +69,7 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
         f'large-image{limit_version}',

diff --git a/sources/dummy/setup.py b/sources/dummy/setup.py
@@ -50,6 +50,7 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
         f'large-image{limit_version}',

diff --git a/sources/gdal/setup.py b/sources/gdal/setup.py
@@ -50,6 +50,7 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
         f'large-image{limit_version}',

diff --git a/sources/mapnik/setup.py b/sources/mapnik/setup.py
@@ -50,6 +50,7 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
         f'large-image{limit_version}',

diff --git a/sources/multi/setup.py b/sources/multi/setup.py
@@ -50,6 +50,7 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
         'jsonschema',

diff --git a/sources/nd2/setup.py b/sources/nd2/setup.py
@@ -50,6 +50,7 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
         f'large-image{limit_version}',

diff --git a/sources/ometiff/setup.py b/sources/ometiff/setup.py
@@ -50,6 +50,7 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
         f'large-image{limit_version}',

diff --git a/sources/openjpeg/setup.py b/sources/openjpeg/setup.py
@@ -50,6 +50,7 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
         f'large-image{limit_version}',

diff --git a/sources/openslide/setup.py b/sources/openslide/setup.py
@@ -50,6 +50,7 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
         f'large-image{limit_version}',

diff --git a/sources/pil/setup.py b/sources/pil/setup.py
@@ -50,15 +50,16 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
         f'large-image{limit_version}',
     ],
     extras_require={
         'all': [
-            'rawpy',
+            'rawpy ; python_version < "3.13"',
             'pillow-heif',
-            'pillow-jxl-plugin',
+            'pillow-jxl-plugin ; python_version < "3.13"',
             'pillow-jpls',
         ],
         'girder': f'girder-large-image{limit_version}',

diff --git a/sources/rasterio/setup.py b/sources/rasterio/setup.py
@@ -53,6 +53,7 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
         f'large-image{limit_version}',

diff --git a/sources/test/setup.py b/sources/test/setup.py
@@ -50,6 +50,7 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
         f'large-image{limit_version}',

diff --git a/sources/tiff/setup.py b/sources/tiff/setup.py
@@ -50,6 +50,7 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
         f'large-image{limit_version}',

diff --git a/sources/tifffile/setup.py b/sources/tifffile/setup.py
@@ -50,6 +50,7 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
         f'large-image{limit_version}',

diff --git a/sources/vips/setup.py b/sources/vips/setup.py
@@ -50,6 +50,7 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
         f'large-image{limit_version}',

diff --git a/sources/zarr/setup.py b/sources/zarr/setup.py
@@ -50,6 +50,7 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
         f'large-image{limit_version}',

diff --git a/test.Dockerfile b/test.Dockerfile
@@ -13,7 +13,7 @@ ENV DEBIAN_FRONTEND=noninteractive \
     LANG=en_US.UTF-8 \
     PYENV_ROOT="/.pyenv" \
     PATH="/.pyenv/bin:/.pyenv/shims:$PATH" \
-    PYTHON_VERSIONS="3.11 3.8 3.9 3.10 3.12"
+    PYTHON_VERSIONS="3.11 3.8 3.9 3.10 3.12 3.13"
 
 # Consumers of this package aren't expecting an existing ubuntu user (there
 # wasn't one in the ubuntu:22.04 base)