chore(backport): Update pre-commit hooks (#2424)

* Backport:
   - PR #2378
   - PR #2380
   - PR #2381
   - PR #2382
   - PR #2383
   - PR #2386
   - PR #2412
   - PR #2414

Author: matthewfeickert

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
     - id: check-added-large-files
     - id: check-case-conflict
@@ -22,29 +22,38 @@ repos:
     - id: name-tests-test
       args: ["--pytest-test-first"]
     - id: requirements-txt-fixer
+      exclude: tests/constraints.txt
     - id: trailing-whitespace
       # exclude generated files
       exclude: ^validation/|\.dtd$|\.xml$
 
+- repo: https://github.com/pre-commit/pygrep-hooks
+  rev: "v1.10.0"
+  hooks:
+    - id: rst-backticks
+    - id: rst-directive-colons
+    - id: rst-inline-touching-normal
+
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: "v0.0.292"
+  rev: "v0.1.9"
   hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]
 
 -   repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 23.9.1
+    rev: 23.12.1
     hooks:
     - id: black-jupyter
+      types_or: [python, pyi, jupyter]
 
 -   repo: https://github.com/adamchainz/blacken-docs
     rev: 1.16.0
     hooks:
     - id: blacken-docs
-      additional_dependencies: [black==23.7.0]
+      additional_dependencies: [black==23.12.1]
 
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.8.0
     # check the oldest and newest supported Pythons
     hooks:
       - &mypy
@@ -58,13 +67,6 @@ repos:
         name: mypy with Python 3.11
         args: ["--python-version=3.11"]
 
--   repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.0
-    hooks:
-    - id: nbqa-ruff
-      additional_dependencies: [ruff==0.0.292]
-      args: ["--extend-ignore=F821,F401,F841,F811"]
-
 -   repo: https://github.com/codespell-project/codespell
     rev: v2.2.6
     hooks:

docs/index.rst

@@ -1,7 +1,7 @@
 .. pyhf documentation master file, created by
    sphinx-quickstart on Fri Feb  9 11:58:49 2018.
    You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
+   contain the root ``toctree`` directive.
 
 .. toctree::
    :hidden:

pyproject.toml

@@ -222,14 +222,15 @@ filterwarnings = [
     'ignore:Call to deprecated create function:DeprecationWarning',  # protobuf via tensorflow
     'ignore:`np.bool8` is a deprecated alias for `np.bool_`:DeprecationWarning',  # numpy via tensorflow
     "ignore:module 'sre_constants' is deprecated:DeprecationWarning",  # tensorflow v2.12.0+ for Python 3.11+
+    "ignore:ml_dtypes.float8_e4m3b11 is deprecated.",  #FIXME: Can remove when jaxlib>=0.4.12
+    "ignore:Skipping device Apple Paravirtual device that does not support Metal 2.0:UserWarning",  # Can't fix given hardware/virtualized device
 ]
 
 [tool.mypy]
 files = "src"
 python_version = "3.11"
 warn_unused_configs = true
 strict = true
-show_error_codes = true
 enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
 warn_unreachable = true
 
@@ -276,25 +277,28 @@ module = [
 ignore_errors = true
 
 [tool.ruff]
+src = ["src"]
+line-length = 88
+
+[tool.ruff.lint]
 select = [
   "E", "F", "W", # flake8
   "UP",          # pyupgrade
   "RUF",         # Ruff-specific
   "TID",         # flake8-tidy-imports
 ]
-line-length = 88
 ignore = [
   "E402",
   "E501",
   "RUF001", # String contains ambiguous unicode character
   "RUF005", # unpack-instead-of-concatenating-to-collection-literal
 ]
-src = ["src"]
 typing-modules = ["pyhf.typing"]
 unfixable = [
   "F841", # Removes unused variables
 ]
 flake8-tidy-imports.ban-relative-imports = "all"
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "docs/lite/jupyterlite.py" = ["F401", "F704"]
+"**.ipynb" = ["F821", "F401", "F841", "F811", "E703"]