[MAINT] Update from v1.3.2 release

.github/workflows/release.yml

@@ -18,9 +18,9 @@ jobs:
   package:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - name: Set up Python
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version: '3.10'
       - name: Install dependencies

.github/workflows/unit_tests.yml

@@ -38,10 +38,10 @@ jobs:
       OPENBLAS_NUM_THREADS: "1"
       PYTHONUNBUFFERED: "1"
     steps:
-      - uses: actions/setup-python@v6
+      - uses: actions/setup-python@v7
         with:
           python-version: ${{ matrix.python-version }}
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - uses: pyvista/setup-headless-display-action@main
         with:
           qt: true
@@ -81,7 +81,7 @@ jobs:
       MKL_NUM_THREADS: '1'
       PYTHONUNBUFFERED: '1'
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - uses: pyvista/setup-headless-display-action@main
         with:
           qt: true
@@ -115,28 +115,25 @@ jobs:
       OPENBLAS_NUM_THREADS: "1"
       PYTHONUNBUFFERED: "1"
     steps:
-      - uses: actions/setup-python@v6
+      - uses: actions/setup-python@v7
         with:
           python-version: "3.10"
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - uses: pyvista/setup-headless-display-action@main
         with:
           qt: true
           pyvista: false
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip setuptools wheel
-          pip install --upgrade --upgrade-strategy eager .[test]
+          pip install -e . --no-deps
+          pip install -r tools/requirements_old.txt
       - name: Display versions and environment information
         run: |
           echo $TZ
           date
-          python --version
           which python
-      - run: |
-          pip install -e . --no-deps
-          pip install -r tools/requirements_old.txt
-      - run: python -c "import pybispectra; import mne; print(f'PyBispectra {pybispectra.__version__}\n'); mne.sys_info()"
+          python -c "import pybispectra; import mne; print(f'PyBispectra {pybispectra.__version__}\n'); mne.sys_info()"
       - name: Download testing data
         run: python -c "from pybispectra.utils import DATASETS, get_example_data_paths; (get_example_data_paths(data) for data in DATASETS.keys())"
       - name: Run pytest

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # ruff PyBispectra
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.8
+    rev: v0.16.0
     hooks:
       - id: ruff
         name: ruff lint pybispectra
@@ -10,7 +10,7 @@ repos:
 
   # ruff examples
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.8
+    rev: v0.16.0
     hooks:
       - id: ruff
         name: ruff lint examples
@@ -19,7 +19,7 @@ repos:
 
   # codespell
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.4.2
+    rev: v2.4.3
     hooks:
       - id: codespell
         additional_dependencies:

changelog.md

@@ -8,6 +8,13 @@ No changes.
 
 ## [Version 1.3](https://pybispectra.readthedocs.io/1.3/)
 
+### Version 1.3.2
+
+##### Dependencies
+- Dropped max supported Python version being pinned.
+
+<br>
+
 ### Version 1.3.1
 
 ##### Dependencies

docs/source/_static/css/custom.css

@@ -6,6 +6,29 @@ ul {
     text-align: left
 }
 
+/* widen main content area */
+.bd-page-width {
+    max-width: 100rem;
+}
+
+/* make versionadded smaller and inline with param name */
+/* don't do for deprecated / versionchanged; they have extra info (too long to fit) */
+div.versionadded>p {
+    margin-top: 0;
+    margin-bottom: 0;
+}
+
+div.versionadded {
+    margin: 0;
+    margin-left: 0.5rem;
+    display: inline-block;
+}
+
+/* when FF supports :has(), change to →  dd > p:has(+div.versionadded) */
+dd>p {
+    display: inline;
+}
+
 @media (max-width: 1199.98px) {
     .bd-header .navbar-header-items__start {
         flex-shrink: 1;

docs/source/_static/versions.json

@@ -6,7 +6,7 @@
     },
     {
         "name": "1.3 (stable)",
-        "version": "1.3.1",
+        "version": "1.3.2",
         "url": "https://pybispectra.readthedocs.io/1.3/"
     },
     {

docs/source/conf.py

@@ -16,7 +16,7 @@
 project = "PyBispectra"
 copyright = "2023-2026, Thomas S. Binns"
 author = "Thomas S. Binns"
-release = "1.3.1"
+release = "1.3.2"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

docs/source/installation.rst

@@ -7,6 +7,10 @@ for version ≥ 1.2.2.
 
 PyBispectra requires Python ≥ 3.10.
 
+
+Package installation
+--------------------
+
 To install PyBispectra, activate the desired environment or project in which you want
 the package, then install it using `pip <https://pip.pypa.io/en/stable/>`_:
 
@@ -34,21 +38,37 @@ or `pixi <https://pixi.prefix.dev/latest/>`_:
 
 |
 
+.. dropdown:: Compatibility for newly released Python versions
+    :icon: alert
+    :color: info
+
+    If you encounter issues installing PyBispectra in environments with newly released Python versions, this may be due to a lack of compatible ``numba`` releases, one of PyBispectra's core dependencies.
+
+    ``numba`` is not always immediately compatible with new Python versions, and there may be a delay of several weeks before a compatible version is released.
+
+    You can find the supported Python versions for ``numba`` in this `table <https://numba.readthedocs.io/en/stable/user/installing.html#numba-support-info>`_.
+
+    If a compatible ``numba`` release is available for your environment's Python version and you are still encountering installation issues, please report this on the `PyBispectra issue page <https://github.com/braindatalab/PyBispectra/issues>`_.
+
 .. dropdown:: Compatibility with Python ≥ 3.14 on macOS Intel systems
+    :icon: alert
+    :color: info
 
-    Support for macOS Intel systems is limited to Python < 3.14 due to wheel availability limitations for `llvmlite`, which can lead to installation issues using ``pip`` and ``uv``.
+    Due to wheel availability limitations for ``llvmlite`` on macOS Intel systems with Python ≥ 3.14, installation issues can arise when using ``pip`` and ``uv``. 
 
-    If you have a macOS Intel system and need to use Python ≥ 3.14, consider using ``conda`` or ``pixi`` for installation.
+    If you have a macOS Intel system and need to use Python ≥ 3.14, consider using ``conda`` or ``pixi`` for an easier installation.
 
-|
+
+Creating an environment or project for installation
+---------------------------------------------------
 
 If you need to create an environment or project in which to install PyBispectra, you can
 do so using `venv <https://docs.python.org/3/library/venv.html>`_,
 `uv <https://docs.astral.sh/uv/>`_, `pixi <https://pixi.prefix.dev/latest/>`_, or
 `conda <https://docs.conda.io/en/latest/>`_.
 
 With ``venv``
--------------
+~~~~~~~~~~~~~
 
 In a shell with Python available, navigate to your project location and create the
 environment:
@@ -66,7 +86,7 @@ then install the package:
     pip install pybispectra
 
 With ``uv``
------------
+~~~~~~~~~~~
 
 In a shell with ``uv`` available, navigate to your project location and create the
 environment:
@@ -84,7 +104,7 @@ then install the package:
     uv pip install pybispectra
 
 With ``pixi``
--------------
+~~~~~~~~~~~~~
 
 In a shell with ``pixi`` available, run the following commands:
 
@@ -95,7 +115,7 @@ In a shell with ``pixi`` available, run the following commands:
     pixi add pybispectra
 
 With ``conda``
---------------
+~~~~~~~~~~~~~~
 
 In a shell with ``conda`` available, run the following commands:
 

environment.yml

@@ -2,7 +2,7 @@ name: pybispectra
 channels:
   - conda-forge
 dependencies:
-  - python>=3.10,<3.15
+  - python>=3.10
   - joblib>=1.2
   - matplotlib>=3.6
   - mne-base>=1.7

examples/plot_compute_time_resolved.py

@@ -18,7 +18,7 @@
 from matplotlib import pyplot as plt
 from numpy.random import RandomState
 
-from pybispectra import WaveShape, get_example_data_paths, compute_tfr
+from pybispectra import WaveShape, compute_tfr, get_example_data_paths
 
 ########################################################################################
 # Background

pyproject.toml

@@ -16,7 +16,7 @@ dynamic = [
 ] # check tools/hatch_build.py for details
 name = "pybispectra"
 readme = "README.md"
-version = "1.3.1"
+version = "1.3.2"
 
 [project.optional-dependencies]
 dev = ["pybispectra[doc]", "pybispectra[lint]", "pybispectra[test]"]
@@ -126,7 +126,11 @@ ignore_roles = [
 report_level = "WARNING"
 
 [tool.ruff]
-extend-exclude = ["docs", "examples/compute_*.py"]
+extend-exclude = [
+  "docs",
+  "examples/compute_*.py",
+  "src/pybispectra/utils/_docs.py",
+]
 line-length = 88
 
 [tool.ruff.lint.per-file-ignores]

src/pybispectra/__init__.py

@@ -1,6 +1,6 @@
 """Initialisation of the PyBispectra package."""
 
-__version__ = "1.3.1"
+__version__ = "1.3.2"
 
 from .cfc import AAC, PAC, PPC
 from .general import Bispectrum, Threenorm

src/pybispectra/cfc/aac.py

@@ -7,9 +7,9 @@
 from pybispectra.utils._defaults import _precision
 from pybispectra.utils._process import _ProcessFreqBase
 from pybispectra.utils._utils import (
+    _compute_in_parallel,
     _compute_pearsonr_2d,
     _fast_find_first,
-    _compute_in_parallel,
 )
 
 
@@ -61,7 +61,7 @@ class AAC(_ProcessFreqBase):
 
     verbose : bool
         Whether or not to report the progress of the processing.
-    """  # noqa: E501
+    """
 
     _data_precision: type = _precision.real  # Real-valued TFR power
 
@@ -72,9 +72,9 @@ class AAC(_ProcessFreqBase):
     def compute(
         self,
         indices: tuple[tuple[int]] | None = None,
-        f1s: tuple[int | float] | None = None,
-        f2s: tuple[int | float] | None = None,
-        times: tuple[int | float] | None = None,
+        f1s: tuple[float] | None = None,
+        f2s: tuple[float] | None = None,
+        times: tuple[float] | None = None,
         n_jobs: int = 1,
     ) -> None:
         r"""Compute AAC, averaged over epochs.

src/pybispectra/cfc/pac.py

@@ -80,9 +80,9 @@ class PAC(_ProcessBispectrum):
     def compute(
         self,
         indices: tuple[tuple[int]] | None = None,
-        f1s: tuple[int | float] | None = None,
-        f2s: tuple[int | float] | None = None,
-        times: tuple[int | float] | None = None,
+        f1s: tuple[float] | None = None,
+        f2s: tuple[float] | None = None,
+        times: tuple[float] | None = None,
         antisym: bool | tuple[bool] = False,
         norm: bool | tuple[bool] = False,
         n_jobs: int = 1,
@@ -181,7 +181,7 @@ def compute(
         References
         ----------
         .. footbibliography::
-        """  # noqa: E501
+        """
         self._reset_attrs()
 
         self._sort_metrics(antisym, norm)

src/pybispectra/cfc/ppc.py

@@ -6,7 +6,7 @@
 from pybispectra.utils import ResultsCFC
 from pybispectra.utils._defaults import _precision
 from pybispectra.utils._process import _ProcessFreqBase
-from pybispectra.utils._utils import _fast_find_first, _compute_in_parallel
+from pybispectra.utils._utils import _compute_in_parallel, _fast_find_first
 
 
 class PPC(_ProcessFreqBase):
@@ -73,9 +73,9 @@ class PPC(_ProcessFreqBase):
     def compute(
         self,
         indices: tuple[tuple[int]] | None = None,
-        f1s: tuple[int | float] | None = None,
-        f2s: tuple[int | float] | None = None,
-        times: tuple[int | float] | None = None,
+        f1s: tuple[float] | None = None,
+        f2s: tuple[float] | None = None,
+        times: tuple[float] | None = None,
         n_jobs: int = 1,
     ) -> None:
         r"""Compute PPC, averaged over epochs.