Apply Repo-Review rules (#3592)

## Changes proposed in this pull request

* PC170: Uses PyGrep hooks (only needed if rST present)
* PC191: Ruff show fixes if fixes enabled
* PC903: Specified pre-commit CI schedule
* ~~PP006: The dev dependency group should be defined~~ (it looks like
the tox/uv combination cannot support PEP 735 out-of-the-box)

## Documentation that should be reviewed
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Author: effigies

.pre-commit-config.yaml

@@ -11,9 +11,18 @@ repos:
       - id: check-json
       - id: check-toml
       - id: check-added-large-files
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: rst-backticks
+        exclude: ^CHANGES.rst
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.14.10
     hooks:
       - id: ruff-check
-        args: [ --fix ]
+        args: [ --fix, --show-fixes ]
       - id: ruff-format
+ci:
+  autoupdate_schedule: monthly

docs/index.rst

@@ -1,7 +1,7 @@
 .. fmriprep documentation master file, created by
    sphinx-quickstart on Mon May  9 09:04:25 2016.
    You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
+   contain the root ``toctree`` directive.
 
 .. include:: links.rst
 .. include:: ../README.rst

docs/spaces.rst

@@ -45,7 +45,7 @@ Therefore, *fMRIPrep* will run nonlinear registration processes against the temp
 T1w image corresponding to all the standard spaces supplied with the argument
 ``--output-spaces``.
 By default, *fMRIPrep* will resample the preprocessed data on those spaces (labeling the
-corresponding outputs with the `space-<template-identifier>` BIDS entity) but keeping
+corresponding outputs with the ``space-<template-identifier>`` BIDS entity) but keeping
 the original resolution of the BOLD data to produce smaller files, more consistent with
 the original data gridding.
 However, many users will be interested in utilizing a coarse gridding (typically 2mm isotropic)

docs/workflows.rst

@@ -445,8 +445,8 @@ No action is required by users, as this module is included in *fMRIPrep*.
 Details about the BIDS specification for field maps can be found at
 <https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#types-of-fieldmaps>
 
-**NOTE** SDCFlows prefers `B0FieldIdentifier`/`B0FieldSource` and will use that
-to the exclusion of `IntendedFor`, if it is present anywhere in the dataset.
+**NOTE** SDCFlows prefers ``B0FieldIdentifier``/``B0FieldSource`` and will use that
+to the exclusion of ``IntendedFor``, if it is present anywhere in the dataset.
 
 For more detailed documentation on
 :abbr:`SDC (susceptibility-derived distortion correction)`
@@ -597,7 +597,7 @@ HCP Grayordinates
     )
 
 If CIFTI output is enabled, the motion-corrected functional timeseries (in T1w space) is
-resampled onto the subject-native surface, optionally using the `HCP Pipelines_`'s
+resampled onto the subject-native surface, optionally using the `HCP Pipelines`_'s
 "goodvoxels" masking method to exclude voxels with local peaks of temporal variation.
 After dilating the surface-sampled time series to fill sampling holes, the result is
 resampled to the ``fsLR`` mesh (with the left and right hemisphere aligned).
@@ -627,7 +627,7 @@ Confounds estimation
     )
 
 Given a motion-corrected fMRI, a brain mask, ``mcflirt`` movement parameters and a
-segmentation, the `discover_wf` sub-workflow calculates potential
+segmentation, the ``discover_wf`` sub-workflow calculates potential
 confounds per volume.
 
 Calculated confounds include the mean global signal, mean tissue class signal,