test: [Automatic] Constraints upgrades: numpy, pydantic (#1188)

This PR is automatically created and updated by PartSeg GitHub action cron to keep bundle dependencies modules up to date. The updated packages are: * build * fsspec * kiwisolver * numpy * platformdirs * pydantic * pydantic-core * pyside2 * setuptools * shiboken2  ## Summary by CodeRabbit - **New Features** - Updated various Python package dependencies to their latest versions, potentially introducing new features, bug fixes, and performance improvements. - **Bug Fixes** - Incremented versions of dependencies like `numpy`, `pydantic`, and `setuptools`, which may include important bug fixes. - **Chores** - Routine maintenance updates to ensure compatibility and leverage improvements in the libraries used across multiple Python version requirements. - **Documentation** - Added `pyqt6` as a new dependency in the documentation build process.  --------- Co-authored-by: Czaki <[email protected]>
4DNucleome · Sep 9, 2024 · 0b0b0f9 · 0b0b0f9
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diff --git a/.github/workflows/upgrade-dependencies.yml b/.github/workflows/upgrade-dependencies.yml
@@ -39,7 +39,7 @@ jobs:
             uv pip compile --python-version ${pyv} --upgrade --output-file requirements/constraints_py${pyv}.txt pyproject.toml requirements/version_denylist.txt "${flags[@]}"
             uv pip compile --python-version ${pyv} --upgrade --output-file requirements/constraints_py${pyv}_pydantic_1.txt pyproject.toml requirements/version_denylist.txt "${flags[@]}" --constraint requirements/pydantic_1.txt
           done
-          uv pip compile --python-version 3.11 --upgrade --output-file requirements/constraints_py3.11_docs.txt pyproject.toml requirements/version_denylist.txt --extra docs --extra pyqt6
+          uv pip compile --python-version 3.11 --upgrade --output-file requirements/constraints_py3.11_docs.txt pyproject.toml --extra docs --extra pyqt6
       # END PYTHON DEPENDENCIES
 
       - name: Check updated packages

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -32,3 +32,4 @@ python:
       path: .
       extra_requirements:
         - docs
+        - pyqt6
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -77,7 +77,7 @@ stages:
           - {task: UsePythonVersion@0, inputs: {versionSpec: '3.11', architecture: x64}}
           - template: .azure-pipelines/pip_cache.yaml
             parameters:
-              key: doc | requirements/constraints_py3.9.txt | "$(PY)"
+              key: doc | requirements/constraints_py3.11_docs.txt | "$(PY)"
               path: $(pip_cache_dir)
           - bash: |
               python -m pip install tox

diff --git a/requirements/constraints_py3.10.txt b/requirements/constraints_py3.10.txt
@@ -22,7 +22,7 @@ attrs==24.2.0
     #   referencing
 babel==2.16.0
     # via sphinx
-build==1.2.1
+build==1.2.2
     # via npe2
 cachey==0.2.1
     # via napari
@@ -73,7 +73,7 @@ fonticon-fontawesome6==6.4.0
     # via partseg (pyproject.toml)
 freetype-py==2.5.1
     # via vispy
-fsspec==2024.6.1
+fsspec==2024.9.0
     # via dask
 h5py==3.11.0
     # via partseg (pyproject.toml)
@@ -129,7 +129,7 @@ jupyter-core==5.7.2
     #   ipykernel
     #   jupyter-client
     #   qtconsole
-kiwisolver==1.4.5
+kiwisolver==1.4.7
     # via vispy
 lazy-loader==0.4
     # via
@@ -183,7 +183,7 @@ npe2==0.7.7
     # via
     #   -r requirements/version_denylist.txt
     #   napari
-numpy==2.1.0
+numpy==2.1.1
     # via
     #   partseg (pyproject.toml)
     #   czifile
@@ -245,7 +245,7 @@ pillow==10.4.0
     #   scikit-image
 pint==0.24.3
     # via napari
-platformdirs==4.2.2
+platformdirs==4.3.2
     # via
     #   jupyter-core
     #   pooch
@@ -274,7 +274,7 @@ pure-eval==0.2.3
     # via stack-data
 pyconify==0.1.6
     # via superqt
-pydantic==2.8.2
+pydantic==2.9.0
     # via
     #   partseg (pyproject.toml)
     #   app-model
@@ -283,7 +283,7 @@ pydantic==2.8.2
     #   pydantic-compat
 pydantic-compat==0.1.2
     # via app-model
-pydantic-core==2.20.1
+pydantic-core==2.23.2
     # via pydantic
 pygments==2.18.0
     # via
@@ -396,7 +396,7 @@ sentry-sdk==2.13.0
     # via
     #   -r requirements/version_denylist.txt
     #   partseg (pyproject.toml)
-setuptools==74.0.0
+setuptools==74.1.2
     # via
     #   pyinstaller
     #   pyinstaller-hooks-contrib
@@ -497,7 +497,9 @@ typing-extensions==4.12.2
     #   superqt
     #   typer
 tzdata==2024.1
-    # via pandas
+    # via
+    #   pandas
+    #   pydantic
 urllib3==2.2.2
     # via
     #   requests

diff --git a/requirements/constraints_py3.10_pydantic_1.txt b/requirements/constraints_py3.10_pydantic_1.txt
@@ -20,7 +20,7 @@ attrs==24.2.0
     #   referencing
 babel==2.16.0
     # via sphinx
-build==1.2.1
+build==1.2.2
     # via npe2
 cachey==0.2.1
     # via napari
@@ -71,7 +71,7 @@ fonticon-fontawesome6==6.4.0
     # via partseg (pyproject.toml)
 freetype-py==2.5.1
     # via vispy
-fsspec==2024.6.1
+fsspec==2024.9.0
     # via dask
 h5py==3.11.0
     # via partseg (pyproject.toml)
@@ -127,7 +127,7 @@ jupyter-core==5.7.2
     #   ipykernel
     #   jupyter-client
     #   qtconsole
-kiwisolver==1.4.5
+kiwisolver==1.4.7
     # via vispy
 lazy-loader==0.4
     # via
@@ -181,7 +181,7 @@ npe2==0.7.7
     # via
     #   -r requirements/version_denylist.txt
     #   napari
-numpy==2.1.0
+numpy==2.1.1
     # via
     #   partseg (pyproject.toml)
     #   czifile
@@ -243,7 +243,7 @@ pillow==10.4.0
     #   scikit-image
 pint==0.24.3
     # via napari
-platformdirs==4.2.2
+platformdirs==4.3.2
     # via
     #   jupyter-core
     #   pooch
@@ -393,7 +393,7 @@ sentry-sdk==2.13.0
     # via
     #   -r requirements/version_denylist.txt
     #   partseg (pyproject.toml)
-setuptools==74.0.0
+setuptools==74.1.2
     # via
     #   pyinstaller
     #   pyinstaller-hooks-contrib

diff --git a/requirements/constraints_py3.11.txt b/requirements/constraints_py3.11.txt
@@ -22,7 +22,7 @@ attrs==24.2.0
     #   referencing
 babel==2.16.0
     # via sphinx
-build==1.2.1
+build==1.2.2
     # via npe2
 cachey==0.2.1
     # via napari
@@ -69,7 +69,7 @@ fonticon-fontawesome6==6.4.0
     # via partseg (pyproject.toml)
 freetype-py==2.5.1
     # via vispy
-fsspec==2024.6.1
+fsspec==2024.9.0
     # via dask
 h5py==3.11.0
     # via partseg (pyproject.toml)
@@ -123,7 +123,7 @@ jupyter-core==5.7.2
     #   ipykernel
     #   jupyter-client
     #   qtconsole
-kiwisolver==1.4.5
+kiwisolver==1.4.7
     # via vispy
 lazy-loader==0.4
     # via
@@ -177,7 +177,7 @@ npe2==0.7.7
     # via
     #   -r requirements/version_denylist.txt
     #   napari
-numpy==2.1.0
+numpy==2.1.1
     # via
     #   partseg (pyproject.toml)
     #   czifile
@@ -239,7 +239,7 @@ pillow==10.4.0
     #   scikit-image
 pint==0.24.3
     # via napari
-platformdirs==4.2.2
+platformdirs==4.3.2
     # via
     #   jupyter-core
     #   pooch
@@ -268,7 +268,7 @@ pure-eval==0.2.3
     # via stack-data
 pyconify==0.1.6
     # via superqt
-pydantic==2.8.2
+pydantic==2.9.0
     # via
     #   partseg (pyproject.toml)
     #   app-model
@@ -277,7 +277,7 @@ pydantic==2.8.2
     #   pydantic-compat
 pydantic-compat==0.1.2
     # via app-model
-pydantic-core==2.20.1
+pydantic-core==2.23.2
     # via pydantic
 pygments==2.18.0
     # via
@@ -304,7 +304,7 @@ pyqt6-qt6==6.7.2
     # via pyqt6
 pyqt6-sip==13.8.0
     # via pyqt6
-pyside2==5.13.2
+pyside2==5.15.2.1
     # via
     #   -r requirements/version_denylist.txt
     #   partseg (pyproject.toml)
@@ -389,13 +389,13 @@ sentry-sdk==2.13.0
     # via
     #   -r requirements/version_denylist.txt
     #   partseg (pyproject.toml)
-setuptools==74.0.0
+setuptools==74.1.2
     # via
     #   pyinstaller
     #   pyinstaller-hooks-contrib
 shellingham==1.5.4
     # via typer
-shiboken2==5.13.2
+shiboken2==5.15.2.1
     # via pyside2
 shiboken6==6.4.2
     # via
@@ -483,7 +483,9 @@ typing-extensions==4.12.2
     #   superqt
     #   typer
 tzdata==2024.1
-    # via pandas
+    # via
+    #   pandas
+    #   pydantic
 urllib3==2.2.2
     # via
     #   requests

diff --git a/requirements/constraints_py3.11_docs.txt b/requirements/constraints_py3.11_docs.txt
@@ -1,5 +1,5 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile --python-version 3.11 --output-file requirements/constraints_py3.11_docs.txt pyproject.toml requirements/version_denylist.txt --extra docs --extra pyqt6
+#    uv pip compile --python-version 3.11 --output-file requirements/constraints_py3.11_docs.txt pyproject.toml --extra docs --extra pyqt6
 alabaster==1.0.0
     # via sphinx
 annotated-types==0.7.0
@@ -22,7 +22,7 @@ autodoc-pydantic==2.2.0
     # via partseg (pyproject.toml)
 babel==2.16.0
     # via sphinx
-build==1.2.1
+build==1.2.2
     # via npe2
 cachey==0.2.1
     # via napari
@@ -69,7 +69,7 @@ fonticon-fontawesome6==6.4.0
     # via partseg (pyproject.toml)
 freetype-py==2.5.1
     # via vispy
-fsspec==2024.6.1
+fsspec==2024.9.0
     # via dask
 h5py==3.11.0
     # via partseg (pyproject.toml)
@@ -83,7 +83,6 @@ imagecodecs==2024.6.1
     # via partseg (pyproject.toml)
 imageio==2.35.1
     # via
-    #   -r requirements/version_denylist.txt
     #   partseg (pyproject.toml)
     #   napari
     #   napari-svg
@@ -121,7 +120,7 @@ jupyter-core==5.7.2
     #   ipykernel
     #   jupyter-client
     #   qtconsole
-kiwisolver==1.4.5
+kiwisolver==1.4.7
     # via vispy
 lazy-loader==0.4
     # via
@@ -166,10 +165,8 @@ networkx==3.3
 nme==0.1.8
     # via partseg (pyproject.toml)
 npe2==0.7.7
-    # via
-    #   -r requirements/version_denylist.txt
-    #   napari
-numpy==2.1.0
+    # via napari
+numpy==2.1.1
     # via
     #   partseg (pyproject.toml)
     #   czifile
@@ -228,7 +225,7 @@ pillow==10.4.0
     #   scikit-image
 pint==0.24.3
     # via napari
-platformdirs==4.2.2
+platformdirs==4.3.2
     # via
     #   jupyter-core
     #   pooch
@@ -253,7 +250,7 @@ pure-eval==0.2.3
     # via stack-data
 pyconify==0.1.6
     # via superqt
-pydantic==2.8.2
+pydantic==2.9.0
     # via
     #   partseg (pyproject.toml)
     #   app-model
@@ -264,7 +261,7 @@ pydantic==2.8.2
     #   pydantic-settings
 pydantic-compat==0.1.2
     # via app-model
-pydantic-core==2.20.1
+pydantic-core==2.23.2
     # via pydantic
 pydantic-settings==2.4.0
     # via autodoc-pydantic
@@ -289,16 +286,6 @@ pyqt6-qt6==6.7.2
     # via pyqt6
 pyqt6-sip==13.8.0
     # via pyqt6
-pyside2==5.13.2
-    # via -r requirements/version_denylist.txt
-pyside6==6.7.2
-    # via -r requirements/version_denylist.txt
-pyside6-addons==6.7.2
-    # via pyside6
-pyside6-essentials==6.7.2
-    # via
-    #   pyside6
-    #   pyside6-addons
 python-dateutil==2.9.0.post0
     # via
     #   jupyter-client
@@ -357,18 +344,9 @@ scipy==1.14.1
     #   napari
     #   scikit-image
 sentry-sdk==2.13.0
-    # via
-    #   -r requirements/version_denylist.txt
-    #   partseg (pyproject.toml)
+    # via partseg (pyproject.toml)
 shellingham==1.5.4
     # via typer
-shiboken2==5.13.2
-    # via pyside2
-shiboken6==6.7.2
-    # via
-    #   pyside6
-    #   pyside6-addons
-    #   pyside6-essentials
 simpleitk==2.4.0
     # via partseg (pyproject.toml)
 six==1.16.0
@@ -385,7 +363,7 @@ sphinx==8.0.2
     #   numpydoc
     #   sphinx-autodoc-typehints
     #   sphinx-qt-documentation
-sphinx-autodoc-typehints==2.3.0
+sphinx-autodoc-typehints==2.4.0
     # via partseg (pyproject.toml)
 sphinx-qt-documentation==0.4.1
     # via partseg (pyproject.toml)
@@ -459,7 +437,9 @@ typing-extensions==4.12.2
     #   superqt
     #   typer
 tzdata==2024.1
-    # via pandas
+    # via
+    #   pandas
+    #   pydantic
 urllib3==2.2.2
     # via
     #   requests
-Original file line number
+Diff line change
@@ Expand Up / @@ -32,3 +32,4 @@ python: @@
           path: .
           extra_requirements:
             - docs
+            - pyqt6