Sync README dependencies with pyproject.toml (#12890)

Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com>

Author: drammock

.pre-commit-config.yaml

@@ -63,6 +63,21 @@ repos:
       - id: toml-sort-fix
         files: pyproject.toml
 
+  # dependencies
+  - repo: local
+    hooks:
+      - id: dependency-sync
+        name: Sync dependency list between pyproject.toml and README.rst
+        language: python
+        entry: ./tools/hooks/sync_dependencies.py
+        files: pyproject.toml
+        additional_dependencies: ["mne"]
+
+
+# these should *not* be run on CIs:
+ci:
+  skip: [dependency-sync]  # needs MNE to work, which exceeds the free tier space alloc.
+
 # The following are too slow to run on local commits, so let's only run on CIs:
 #
 #   - repo: https://github.com/pre-commit/mirrors-mypy

README.rst

@@ -43,9 +43,6 @@ only, use pip_ in a terminal:
 
     $ pip install --upgrade mne
 
-The current MNE-Python release requires Python 3.9 or higher. MNE-Python 0.17
-was the last release to support Python 2.7.
-
 For more complete instructions, including our standalone installers and more
 advanced installation methods, please refer to the `installation guide`_.
 
@@ -73,42 +70,20 @@ Dependencies
 
 The minimum required dependencies to run MNE-Python are:
 
+.. ↓↓↓ BEGIN CORE DEPS LIST. DO NOT EDIT! HANDLED BY PRE-COMMIT HOOK ↓↓↓
+
 - `Python <https://www.python.org>`__ ≥ 3.9
-- `NumPy <https://numpy.org>`__ ≥ 1.24
-- `SciPy <https://scipy.org>`__ ≥ 1.10
+- `NumPy <https://numpy.org>`__ ≥ 1.23
+- `SciPy <https://scipy.org>`__ ≥ 1.9
 - `Matplotlib <https://matplotlib.org>`__ ≥ 3.6
 - `Pooch <https://www.fatiando.org/pooch/latest/>`__ ≥ 1.5
 - `tqdm <https://tqdm.github.io>`__
 - `Jinja2 <https://palletsprojects.com/p/jinja/>`__
 - `decorator <https://github.com/micheles/decorator>`__
-- `lazy_loader <https://pypi.org/project/lazy_loader/>`__
-
-For full functionality, some functions require:
-
-- `scikit-learn <https://scikit-learn.org/stable/>`__ ≥ 1.2
-- `Joblib <https://joblib.readthedocs.io/en/latest/index.html>`__ ≥ 1.2 (for parallelization)
-- `mne-qt-browser <https://github.com/mne-tools/mne-qt-browser>`__ ≥ 0.5 (for fast raw data visualization)
-- `Qt <https://www.qt.io>`__ ≥ 5.15 via one of the following bindings (for fast raw data visualization and interactive 3D visualization):
-
-  - `PySide6 <https://doc.qt.io/qtforpython-6/>`__ ≥ 6.0
-  - `PyQt6 <https://www.riverbankcomputing.com/software/pyqt/>`__ ≥ 6.0
-  - `PyQt5 <https://www.riverbankcomputing.com/software/pyqt/>`__ ≥ 5.15
-
-- `Numba <https://numba.pydata.org>`__ ≥ 0.56.4
-- `NiBabel <https://nipy.org/nibabel/>`__ ≥ 3.2.1
-- `OpenMEEG <https://openmeeg.github.io>`__ ≥ 2.5.6
-- `pandas <https://pandas.pydata.org>`__ ≥ 1.5.2
-- `Picard <https://pierreablin.github.io/picard/>`__ ≥ 0.3
-- `CuPy <https://cupy.dev>`__ ≥ 9.0.0 (for NVIDIA CUDA acceleration)
-- `DIPY <https://dipy.org>`__ ≥ 1.4.0
-- `imageio <https://imageio.readthedocs.io/en/stable/>`__ ≥ 2.8.0
-- `PyVista <https://pyvista.org>`__ ≥ 0.37 (for 3D visualization)
-- `PyVistaQt <https://qtdocs.pyvista.org>`__ ≥ 0.9 (for 3D visualization)
-- `mffpy <https://github.com/BEL-Public/mffpy>`__ ≥ 0.5.7
-- `h5py <https://www.h5py.org>`__
-- `h5io <https://github.com/h5io/h5io>`__
-- `pymatreader <https://pymatreader.readthedocs.io/en/latest/>`__
+- `lazy-loader <https://pypi.org/project/lazy_loader>`__ ≥ 0.3
+- `packaging <https://packaging.pypa.io/en/stable/>`__
 
+.. ↑↑↑ END CORE DEPS LIST. DO NOT EDIT! HANDLED BY PRE-COMMIT HOOK ↑↑↑
 
 Contributing
 ^^^^^^^^^^^^

pyproject.toml

@@ -51,7 +51,7 @@ scripts = {mne = "mne.commands.utils:main"}
 [project.optional-dependencies]
 # Leave this one here for backward-compat
 data = []
-dev = ["mne[test,doc]", "rcssmin"]
+dev = ["mne[doc,test]", "rcssmin"]
 # Dependencies for building the documentation
 doc = [
   "graphviz",

tools/hooks/sync_dependencies.py

@@ -0,0 +1,95 @@
+#!/usr/bin/env python
+
+# Authors: The MNE-Python contributors.
+# License: BSD-3-Clause
+# Copyright the MNE-Python contributors.
+
+import re
+from importlib.metadata import metadata
+from pathlib import Path
+
+from mne.utils import _pl, warn
+
+README_PATH = Path(__file__).parents[2] / "README.rst"
+BEGIN = ".. ↓↓↓ BEGIN CORE DEPS LIST. DO NOT EDIT! HANDLED BY PRE-COMMIT HOOK ↓↓↓"
+END = ".. ↑↑↑ END CORE DEPS LIST. DO NOT EDIT! HANDLED BY PRE-COMMIT HOOK ↑↑↑"
+
+CORE_DEPS_URLS = {
+    "Python": "https://www.python.org",
+    "NumPy": "https://numpy.org",
+    "SciPy": "https://scipy.org",
+    "Matplotlib": "https://matplotlib.org",
+    "Pooch": "https://www.fatiando.org/pooch/latest/",
+    "tqdm": "https://tqdm.github.io",
+    "Jinja2": "https://palletsprojects.com/p/jinja/",
+    "decorator": "https://github.com/micheles/decorator",
+    "lazy-loader": "https://pypi.org/project/lazy_loader",
+    "packaging": "https://packaging.pypa.io/en/stable/",
+}
+
+
+def _prettify_pin(pin):
+    if pin is None:
+        return ""
+    pins = pin.split(",")
+    replacements = {
+        "<=": " ≤ ",
+        ">=": " ≥ ",
+        "<": " < ",
+        ">": " > ",
+    }
+    for old, new in replacements.items():
+        pins = [p.replace(old, new) for p in pins]
+    pins = reversed(pins)
+    return ",".join(pins)
+
+
+# get the dependency info
+py_pin = metadata("mne").get("Requires-Python")
+all_deps = metadata("mne").get_all("Requires-Dist")
+core_deps = [f"python{py_pin}", *[dep for dep in all_deps if "extra ==" not in dep]]
+pattern = re.compile(r"(?P<name>[A-Za-z_\-\d]+)(?P<pin>[<>=]+.*)?")
+core_deps_pins = {
+    dep["name"]: _prettify_pin(dep["pin"]) for dep in map(pattern.match, core_deps)
+}
+# don't show upper pin on NumPy (not important for users, just devs)
+new_pin = core_deps_pins["numpy"].split(",")
+new_pin.remove(" < 3")
+core_deps_pins["numpy"] = new_pin[0]
+
+# make sure our URLs dict is minimal and complete
+missing_urls = set(core_deps_pins) - {dep.lower() for dep in CORE_DEPS_URLS}
+extra_urls = {dep.lower() for dep in CORE_DEPS_URLS} - set(core_deps_pins)
+update_msg = (
+    "please update `CORE_DEPS_URLS` mapping in `tools/hooks/sync_dependencies.py`."
+)
+if missing_urls:
+    _s = _pl(missing_urls)
+    raise RuntimeError(
+        f"Missing URL{_s} for package{_s} {', '.join(missing_urls)}; {update_msg}"
+    )
+if extra_urls:
+    _s = _pl(extra_urls)
+    warn(f"Superfluous URL{_s} for package{_s} {', '.join(extra_urls)}; {update_msg}")
+
+# construct the rST
+core_deps_bullets = [
+    f"- `{key} <{url}>`__{core_deps_pins[key.lower()]}"
+    for key, url in CORE_DEPS_URLS.items()
+]
+core_deps_rst = "\n" + "\n".join(core_deps_bullets) + "\n"
+
+# rewrite the README file
+lines = README_PATH.read_text("utf-8").splitlines()
+out_lines = list()
+skip = False
+for line in lines:
+    if line.strip() == BEGIN:
+        skip = True
+        out_lines.append(line)
+        out_lines.append(core_deps_rst)
+    if line.strip() == END:
+        skip = False
+    if not skip:
+        out_lines.append(line)
+README_PATH.write_text("\n".join(out_lines) + "\n", encoding="utf-8")