Raise minimum requirements

.github/workflows/build_wheels.yml

@@ -28,7 +28,7 @@ jobs:
       #   uses: docker/setup-qemu-action@v3
       #   with:
       #     platforms: all
-      - uses: pypa/[email protected].0
+      - uses: pypa/[email protected].1
         env:
           # Building and testing manylinux2014_aarch64 too is slow.
           # See https://github.com/phasorpy/phasorpy/pull/135

.github/workflows/coverage.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.13"]
+        python-version: ["3.11", "3.13"]
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}

.github/workflows/run-tests.yml

@@ -24,7 +24,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-20.04"]
-        python-version: ["3.10", "3.12"]
+        python-version: ["3.12", "3.13"]
         # 3.11 tested with cibuildwheel
     steps:
       - uses: actions/checkout@v4
@@ -56,7 +56,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["windows-2019", "macos-13"]
-        python-version: ["3.10"]
+        python-version: ["3.11"]
         # 3.12 tested with cibuildwheel
     steps:
       - uses: actions/checkout@v4
@@ -87,7 +87,7 @@ jobs:
         os: ["ubuntu-22.04", "windows-2019", "macos-13"]
     steps:
       - uses: actions/checkout@v4
-      - uses: pypa/[email protected].0
+      - uses: pypa/[email protected].1
         env:
           # CIBW_ENVIRONMENT: "PIP_PRE=1"
           CIBW_BUILD_VERBOSITY: 3
@@ -115,7 +115,7 @@ jobs:
   #        uses: docker/setup-qemu-action@v3
   #        with:
   #          platforms: all
-  #      - uses: pypa/[email protected].0
+  #      - uses: pypa/[email protected].1
   #        env:
   #          CIBW_ARCHS_LINUX: aarch64
   #          CIBW_BUILD_VERBOSITY: 2

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
       - id: check-case-conflict
@@ -32,7 +32,7 @@ repos:
       - id: python-use-type-annotations
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
       - id: codespell
 
@@ -43,7 +43,7 @@ repos:
         args: []
 
   - repo: https://github.com/rbubley/mirrors-prettier
-    rev: v3.3.3
+    rev: v3.5.3
     hooks:
       - id: prettier
         args: [--end-of-line=auto]
@@ -55,42 +55,42 @@ repos:
       - id: autoflake
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.17.0
+    rev: v3.19.1
     hooks:
       - id: pyupgrade
-        args: [--py310-plus, --keep-runtime-typing]
+        args: [--py311-plus, --keep-runtime-typing]
 
   - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
+    rev: 6.0.1
     hooks:
       - id: isort
 
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.8.0
+    rev: 25.1.0
     hooks:
       - id: black
 
   - repo: https://github.com/keewis/blackdoc
     rev: v0.3.9
     hooks:
       - id: blackdoc
-        additional_dependencies: ["black==24.8.0"]
+        additional_dependencies: ["black==25.1.0"]
       - id: blackdoc-autoupdate-black
 
 # - repo: https://github.com/PyCQA/flake8
-#   rev: 7.1.1
+#   rev: 7.1.2
 #   hooks:
 #   - id: flake8
 #     additional_dependencies: [flake8-typing-imports, flake8-docstrings]
 
 # - repo: https://github.com/astral-sh/ruff-pre-commit
-#   rev: v0.6.4
+#   rev: v0.11.1
 #   hooks:
 #   - id: ruff
 #     args: [--show-fixes]
 
 # - repo: https://github.com/pre-commit/mirrors-mypy
-#   rev: v1.11.1
+#   rev: v1.15.0
 #   hooks:
 #   - id: mypy
 #     files: src

pyproject.toml

@@ -14,36 +14,36 @@ dynamic = ["version"]
 dependencies = [
     # sync with requirements_min.txt
     # https://scientific-python.org/specs/spec-0000/
-    "numpy>=1.24.0",
-    "matplotlib>=3.7.0",
+    "numpy>=1.25.0",
+    "matplotlib>=3.8.0",
     "scipy>=1.11.0",
     "click",
     "pooch",
     "tqdm",
-    # "scikit-image>=0.20.0",
-    # "scikit-learn>=1.2.2",
-    # "pandas>=2.0.0",
+    "scikit-learn>=1.3.0",
+    # "scikit-image>=0.21.0",
+    # "pandas>=2.1.0",
     "xarray>=2023.4.0",
     "tifffile>=2024.8.30",
 ]
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Intended Audience :: Developers",
     "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: MIT License",
     "Programming Language :: Python",
     "Topic :: Software Development :: Libraries :: Python Modules",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.10",
+
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
 ]
 authors = [{ name = "PhasorPy Contributors" }]
-license = { text = "MIT" }
+license = "MIT"
+license-files = ["LICENSE.txt"]
 
 [project.urls]
 Homepage = "https://www.phasorpy.org"
@@ -84,7 +84,6 @@ all = [
 [tool.setuptools]
 package-dir = { "" = "src" }
 packages = ["phasorpy"]
-license-files = ["LICENSE.txt"]
 zip-safe = false
 
 [tool.setuptools.dynamic]
@@ -124,7 +123,7 @@ disable = [
 
 [tool.black]
 line-length = 79
-target-version = ["py310"]
+target-version = ["py311"]
 skip-string-normalization = true
 
 [tool.isort]
@@ -144,7 +143,7 @@ strict = true
 warn_unreachable = true
 
 [[tool.mypy.overrides]]
-module = ["phasorpy._phasorpy", "pooch.*", "scipy.*", "mkl_fft.*"]
+module = ["phasorpy._phasorpy", "pooch.*", "scipy.*", "mkl_fft.*", "sklearn.*"]
 ignore_missing_imports = true
 
 [tool.coverage.run]
@@ -188,6 +187,6 @@ norecursedirs = [
 ]
 
 [tool.cibuildwheel]
-skip = "pp* cp37* cp38* cp39* *musllinux* *i686 *ppc64le *s390x cp39*win*arm64 cp310*win*arm64"
-test-requires = ["lfdfiles", "sdtfile", "ptufile", "liffile", "pawflim", "pytest", "pytest-cov", "pytest-runner", "pytest-doctestplus", "coverage"]
+skip = "pp* cp37* cp38* cp39* cp310* *musllinux* *i686 *ppc64le *s390x cp39*win*arm64"
+test-requires = ["scikit-learn", "lfdfiles", "sdtfile", "ptufile", "liffile", "pawflim", "pytest", "pytest-cov", "pytest-runner", "pytest-doctestplus", "coverage"]
 test-command = "pytest {project}/tests"

requirements_dev.txt

@@ -40,7 +40,6 @@ pytest-runner
 pytest-doctestplus
 #
 # tools requirements
-tomli; python_version < "3.11"
 black
 blackdoc
 flake8
@@ -55,11 +54,11 @@ pre-commit-hooks
 #
 # optional requirements
 # scikit-image
-# scikit-learn
 # pandas
 # zarr
 # fsspec
 # bioio
+scikit-learn
 lfdfiles
 sdtfile
 ptufile

requirements_min.txt

@@ -1,15 +1,15 @@
 # Minimum version requirements for the PhasorPy library
 #
-numpy==1.24.4; python_version == "3.10"
-matplotlib==3.7.5; python_version == "3.10"
-pandas==2.0.3; python_version == "3.10"
-scipy==1.11.4; python_version == "3.10"
-scikit-image==0.20.0; python_version == "3.10"
-# scikit-learn==1.2.2; python_version == "3.10"
-xarray==2023.4.0; python_version == "3.10"
-tifffile==2024.8.30; python_version == "3.10"
-lfdfiles==2024.5.24; python_version == "3.10"
-sdtfile==2024.5.24; python_version == "3.10"
-ptufile==2024.9.14; python_version == "3.10"
-liffile==2025.2.10; python_version == "3.10"
-pawflim==1.0.4; python_version == "3.10"
+numpy==1.25.2; python_version == "3.11"
+matplotlib==3.8.4; python_version == "3.11"
+pandas==2.1.4; python_version == "3.11"
+scipy==1.11.4; python_version == "3.11"
+scikit-image==0.21.0; python_version == "3.11"
+scikit-learn==1.3.2; python_version == "3.11"
+xarray==2023.4.0; python_version == "3.11"
+tifffile==2024.8.30; python_version == "3.11"
+lfdfiles==2024.5.24; python_version == "3.11"
+sdtfile==2024.5.24; python_version == "3.11"
+ptufile==2024.9.14; python_version == "3.11"
+liffile==2025.2.10; python_version == "3.11"
+pawflim==1.0.4; python_version == "3.11"

tools/build_manylinux2014.cmd

@@ -3,7 +3,7 @@
 setlocal
 set PATH=C:\Windows;C:\Windows\System32;C:\Program Files\Docker\Docker\resources\bin
 set CIBW_ARCHS_LINUX=auto
-set CIBW_SKIP=pp* cp37* cp38* cp39* *musllinux*
+set CIBW_SKIP=pp* cp37* cp38* cp39* cp310* *musllinux*
 :: set CIBW_TEST_SKIP=*
 set CIBW_TEST_COMMAND=python -m pytest {project}/tests
 set CIBW_BUILD_VERBOSITY=3

tools/build_manylinux2014.sh

@@ -1,7 +1,7 @@
 # Build PhasorPy manylinux2014 wheels on Linux or macOS using Docker
 
 export CIBW_ARCHS_LINUX=auto
-export CIBW_SKIP="pp* cp37* cp38* cp39* *musllinux*"
+export CIBW_SKIP="pp* cp37* cp38* cp39* cp310* *musllinux*"
 # export CIBW_TEST_SKIP="*"
 export CIBW_TEST_COMMAND="pytest {project}/tests"
 export CIBW_BUILD_VERBOSITY=3

tutorials/phasorpy_introduction.py

@@ -16,12 +16,15 @@
 # Install Python
 # --------------
 #
-# An installation of Python version 3.10 or higher is required to use the
+# An installation of Python version 3.11 or higher is required to use the
 # PhasorPy library.
 # Python is an easy to learn, powerful programming language.
 # Python installers can be obtained from, for example,
 # `Python.org <https://www.python.org/downloads/>`_ or
 # `Anaconda.com <https://www.anaconda.com/>`_.
+# Alternatively, Python can be used via
+# `Google Colab <https://colab.research.google.com/>`_,
+# a free, cloud-based service.
 # Refer to the `Python Tutorial <https://docs.python.org/3/tutorial/>`_
 # for an introduction to Python.
 #