Merge pull request #4979 from neutrinoceros/dep/drop_cp39

DEP: drop support for Python 3.9

.git-blame-ignore-revs

@@ -50,3 +50,6 @@ ec8bb45ea1603f3862041fa9e8ec274afd9bbbfd
 
 # migration: black -> ruff-format
 3214662dc7d53f7ac56b3589c5a27ef075f83ab4
+
+# auto upgrade syntax from Python 3.9 to 3.10
+e86625e780b77a42aedad711e5a9a945ce650974

.github/workflows/build-test.yaml

@@ -22,43 +22,51 @@ jobs:
       # run all tests even if e.g. image tests fail early
       fail-fast: false
       matrix:
-        os: [
-          macos-latest,
-          windows-latest,
-          ubuntu-latest,
-        ]
+        os:
+          - ubuntu-latest
+          - macos-latest
         python-version: ['3.12']
         dependencies: [full]
         tests-type: [unit]
         test-runner: [pytest]
+        venv-loc: [bin]
         include:
+          - os: windows-latest
+            python-version: '3.12'
+            dependencies: full
+            tests-type: unit
+            test-runner: pytest
+            venv-loc: Scripts
           - os: ubuntu-20.04
-            python-version: '3.9.2'
+            python-version: '3.10.3'
             dependencies: minimal
             tests-type: unit
             test-runner: pytest
+            venv-loc: bin
           - os: ubuntu-latest
             # this job is necessary for non-answer, 'yield' based tests
-            # because pytest doesn't support such tests, and nose is not
-            # compatible with Python 3.10
-            python-version: '3.9'
+            # because pytest doesn't support such tests
+            python-version: '3.10'
             dependencies: full
             tests-type: unit
             test-runner: nose
+            venv-loc: bin
           - os: ubuntu-latest
             # answer tests use 'yield', so they require nose
             # they are also attached to a specific, occasionally updated, Python version
             # but it does *not* have to match the current minimal supported version
-            python-version: '3.9'
+            python-version: '3.10'
             dependencies: full
             tests-type: answer
             test-runner: nose
+            venv-loc: bin
           - os: ubuntu-latest
             # minimal tests with latest Python and no optional dependencies
             python-version: '3.x'
             dependencies: ''
             tests-type: unit
             test-runner: pytest
+            venv-loc: bin
 
     runs-on: ${{ matrix.os }}
 
@@ -84,15 +92,34 @@ jobs:
       shell: bash
       env:
         dependencies: ${{ matrix.dependencies }}
-      run: source ./tests/ci_install.sh
+      run: |
+        python -m venv .venv
+        source .venv/${{matrix.venv-loc}}/activate
+        source ./tests/ci_install.sh
+
+    - name: Install and patch nosetest
+      if: matrix.test-runner == 'nose'
+      run: |
+        source .venv/${{matrix.venv-loc}}/activate
+        python -m pip install -r nose_requirements.txt
+        find .venv/lib/python${{matrix.python-version}}/site-packages/nose -name '*.py' \
+          -exec sed -i -e s/collections.Callable/collections.abc.Callable/g '{}' ';'
+
+    - name: Show final env
+      run: |
+        source .venv/${{matrix.venv-loc}}/activate
+        python -m pip list
 
-    - run: python -m pip list
     - name: Run Unit Tests (pytest)
       if: matrix.test-runner == 'pytest'
-      run: pytest --color=yes
+      run: |
+        source .venv/${{matrix.venv-loc}}/activate
+        pytest --color=yes
     - name: Run Tests (nose)
       if: matrix.test-runner == 'nose'
-      run: cat nose_ignores.txt | xargs python -m nose -c nose_unit.cfg --traverse-namespace
+      run: |
+        source .venv/${{matrix.venv-loc}}/activate
+        cat nose_ignores.txt | xargs python -m nose -c nose_unit.cfg --traverse-namespace
 
   image-tests:
     name: Image tests

.github/workflows/type-checking.yaml

@@ -33,7 +33,7 @@ jobs:
         # run with oldest supported python version
         # so that we always get compatible versions of
         # core dependencies at type-check time
-        python-version: '3.9'
+        python-version: '3.10'
 
     - name: Build
       run: |

.github/workflows/wheels.yaml

@@ -52,7 +52,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
+          python-version: '3.10'
 
       - name: Build sdist
         run: pipx run build --sdist

.pre-commit-config.yaml

@@ -43,8 +43,6 @@ repos:
     args: [
       --fix,
       --show-fixes,
-      # the following line can be removed after support for Python 3.9 is dropped
-      --extend-select=B905, # zip-without-explicit-strict
     ]
 
 -   repo: https://github.com/pre-commit/pygrep-hooks

MANIFEST.in

@@ -73,4 +73,5 @@ recursive-include yt/frontends/amrvac *.par
 recursive-exclude requirements *.txt
 exclude minimal_requirements.txt
 exclude .codecov.yml .coveragerc .git-blame-ignore-revs .gitmodules .hgchurn .mailmap
-exclude .pre-commit-config.yaml clean.sh nose_answer.cfg nose_unit.cfg nose_ignores.txt
+exclude .pre-commit-config.yaml clean.sh
+exclude nose_answer.cfg nose_unit.cfg nose_ignores.txt nose_requirements.txt

doc/source/developing/testing.rst

@@ -162,6 +162,12 @@ Answer Testing
     an `older version of this documentation <https://yt-project.org/docs/4.0.0/developing/testing.html#answer-testing>`_
     decribes how the ``nose`` tests work.
 
+.. note::
+    Given that nose never had support for Python 3.10 (which as of yt 4.4 is our
+    oldest supported version), it is necessary to patch it to get tests running.
+    This is the command we run on CI to this end
+    ``find .venv/lib/python3.10/site-packages/nose -name '*.py' -exec sed -i -e s/collections.Callable/collections.abc.Callable/g '{}' ';'``
+
 What Do Answer Tests Do
 ^^^^^^^^^^^^^^^^^^^^^^^
 

doc/source/installing.rst

@@ -32,7 +32,9 @@ Here's a summary for most recent releases
 +------------+------------+----------------+-----------------+
 | yt release | Python 2.7 | Python3 min    | Python3 max     |
 +============+============+================+=================+
-| 4.3.x      | no         | 3.9            | 3.12 (expected) |
+| 4.4.x      | no         | 3.10.3         | 3.13 (expected) |
++------------+------------+----------------|-----------------|
+| 4.3.x      | no         | 3.9.2          | 3.12            |
 +------------+------------+----------------+-----------------+
 | 4.2.x      | no         | 3.8            | 3.11            |
 +------------+------------+----------------+-----------------+

minimal_requirements.txt

@@ -1,5 +1,5 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile pyproject.toml --python=3.9 --python-platform=x86_64-unknown-linux-gnu --resolution=lowest-direct --no-build
+#    uv pip compile pyproject.toml --python=3.10 --python-platform=x86_64-unknown-linux-gnu --resolution=lowest-direct --no-build
 cmyt==1.1.2
     # via yt (pyproject.toml)
 colorspacious==1.1.2
@@ -22,7 +22,7 @@ more-itertools==8.4.0
     #   cmyt
 mpmath==1.3.0
     # via sympy
-numpy==1.19.3
+numpy==1.21.3
     # via
     #   yt (pyproject.toml)
     #   cmyt
@@ -35,7 +35,7 @@ packaging==20.9
     #   yt (pyproject.toml)
     #   matplotlib
     #   setuptools-scm
-pillow==8.0.0
+pillow==8.3.2
     # via
     #   yt (pyproject.toml)
     #   matplotlib
@@ -62,8 +62,6 @@ tomli-w==0.4.0
 tqdm==3.4.0
     # via yt (pyproject.toml)
 typing-extensions==4.4.0
-    # via
-    #   yt (pyproject.toml)
-    #   setuptools-scm
+    # via yt (pyproject.toml)
 unyt==2.9.2
     # via yt (pyproject.toml)

nose_requirements.txt

@@ -0,0 +1,3 @@
+nose~=1.3.7
+nose-exclude
+nose-timer~=1.0.0

pyproject.toml

@@ -27,7 +27,6 @@ classifiers = [
     "Programming Language :: C",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
@@ -39,19 +38,19 @@ classifiers = [
 keywords = [
     "astronomy astrophysics visualization amr adaptivemeshrefinement",
 ]
-requires-python = ">=3.9.2"
+requires-python = ">=3.10.3"
 
 # keep in sync with minimal_requirements.txt
 dependencies = [
     "cmyt>=1.1.2",
     "ewah-bool-utils>=1.2.0",
     "matplotlib>=3.5",
     "more-itertools>=8.4",
-    "numpy>=1.19.3, <3", # keep minimal requirement in sync with NPY_TARGET_VERSION
+    "numpy>=1.21.3, <3", # keep minimal requirement in sync with NPY_TARGET_VERSION
     # https://github.com/numpy/numpy/issues/27037
     "numpy!=2.0.1 ; platform_machine=='arm64' and platform_system=='Darwin'",
     "packaging>=20.9",
-    "pillow>=8.0.0",
+    "pillow>=8.3.2",
     "tomli-w>=0.4.0",
     "tqdm>=3.4.0",
     "unyt>=2.9.2",
@@ -200,9 +199,6 @@ test = [
     "pytest>=6.1",
     "pytest-mpl>=0.16.1",
     "sympy!=1.10,!=1.9", # see https://github.com/sympy/sympy/issues/22241
-    "nose~=1.3.7; python_version < '3.10'",
-    "nose-exclude; python_version < '3.10'",
-    "nose-timer~=1.0.0; python_version < '3.10'",
     "imageio!=2.35.0", # see https://github.com/yt-project/yt/issues/4966
 ]
 
@@ -456,7 +452,7 @@ ignore = [
 
 
 [tool.mypy]
-python_version = 3.9
+python_version = '3.10'
 show_error_codes = true
 ignore_missing_imports = true
 warn_unused_configs = true
@@ -466,7 +462,7 @@ show_error_context = true
 exclude = "(test_*|lodgeit)"
 
 [tool.cibuildwheel]
-build = "cp39-* cp310-* cp311-* cp312-* cp313-*"
+build = "cp310-* cp311-* cp312-* cp313-*"
 build-verbosity = 1
 test-skip = "*-musllinux*"
 test-extras = "test"

setupext.py

@@ -397,7 +397,7 @@ def get_python_include_dirs():
 NUMPY_MACROS = [
     ("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION"),
     # keep in sync with runtime requirements (pyproject.toml)
-    ("NPY_TARGET_VERSION", "NPY_1_19_API_VERSION"),
+    ("NPY_TARGET_VERSION", "NPY_1_21_API_VERSION"),
 ]
 
 

tests/ci_install.sh

@@ -5,11 +5,6 @@ cp tests/matplotlibrc .
 
 # Step 1: pre-install required packages
 if [[ ${dependencies} == "full" || ${dependencies} == "cartopy" ]]; then
-    # upgrading pip to guarantee installing extra dependencies with [full] is supported
-    # this is only necessary for some versions of Python 3.8 and 3.9
-    # see https://github.com/yt-project/yt/issues/4270
-    python -m pip install 'pip>=21.2'
-
     case ${RUNNER_OS} in
     linux|Linux)
         sudo apt-get -qqy update

yt/_maintenance/backports.py

@@ -63,18 +63,3 @@ def _generate_next_value_(name, start, count, last_values):  # noqa B902
             Return the lower-cased version of the member name.
             """
             return name.lower()
-
-
-builtin_zip = zip
-if sys.version_info >= (3, 10):
-    zip = builtin_zip
-else:
-    # this function is deprecated in more_itertools
-    # because it is superseded by the standard library
-    from more_itertools import zip_equal
-
-    def zip(*args, strict=False):
-        if strict:
-            return zip_equal(*args)
-        else:
-            return builtin_zip(*args)

yt/_maintenance/deprecation.py

@@ -1,15 +1,14 @@
 import warnings
 from functools import wraps
 from types import FunctionType
-from typing import Optional
 
 
 def issue_deprecation_warning(
     msg: str,
     *,
     stacklevel: int,
     since: str,
-    removal: Optional[str] = None,
+    removal: str | None = None,
 ):
     """
     Parameters

yt/_maintenance/numpy2_compat.py

@@ -1,12 +1,9 @@
 # avoid deprecation warnings in numpy >= 2.0
 
-from importlib.metadata import version
+import numpy as np
 
-from packaging.version import Version
-
-NUMPY_VERSION = Version(version("numpy"))
-
-if NUMPY_VERSION >= Version("2.0.0dev0"):
-    from numpy import trapezoid as trapezoid  # type: ignore [attr-defined]
+if hasattr(np, "trapezoid"):
+    # np.trapz is deprecated in numpy 2.0 in favor of np.trapezoid
+    trapezoid = np.trapezoid
 else:
-    from numpy import trapz as trapezoid  # type: ignore [attr-defined] # noqa: F401
+    trapezoid = np.trapz  # type: ignore [attr-defined] # noqa: NPY201

yt/_typing.py

@@ -1,34 +1,34 @@
-from typing import Any, Optional, Union
+from typing import Any, Optional, TypeAlias
 
 import numpy as np
 import unyt as un
 
-FieldDescT = tuple[str, tuple[str, list[str], Optional[str]]]
+FieldDescT = tuple[str, tuple[str, list[str], str | None]]
 KnownFieldsT = tuple[FieldDescT, ...]
 
 ParticleType = str
 FieldType = str
 FieldName = str
 FieldKey = tuple[FieldType, FieldName]
 ImplicitFieldKey = FieldName
-AnyFieldKey = Union[FieldKey, ImplicitFieldKey]
-DomainDimensions = Union[tuple[int, ...], list[int], np.ndarray]
+AnyFieldKey = FieldKey | ImplicitFieldKey
+DomainDimensions = tuple[int, ...] | list[int] | np.ndarray
 
 ParticleCoordinateTuple = tuple[
     str,  # particle type
     tuple[np.ndarray, np.ndarray, np.ndarray],  # xyz
-    Union[float, np.ndarray],  # hsml
+    float | np.ndarray,  # hsml
 ]
 
 # Geometry specific types
 AxisName = str
 AxisOrder = tuple[AxisName, AxisName, AxisName]
 
 # types that can be converted to un.Unit
-Unit = Union[un.Unit, str]
+Unit: TypeAlias = un.Unit | str
 
 # types that can be converted to un.unyt_quantity
-Quantity = Union[un.unyt_quantity, tuple[float, Unit]]
+Quantity = un.unyt_quantity | tuple[float, Unit]
 
 # np.ndarray[...] syntax is runtime-valid from numpy 1.22, we quote it until our minimal
 # runtime requirement is bumped to, or beyond this version

yt/data_objects/analyzer_objects.py

@@ -1,11 +1,7 @@
 import inspect
-import sys
 
 from yt.utilities.object_registries import analysis_task_registry
 
-if sys.version_info < (3, 10):
-    from yt._maintenance.backports import zip
-
 
 class AnalysisTask:
     def __init_subclass__(cls, *args, **kwargs):