more verbosity docs

Author: flying-sheep

docs/release-notes/1.10.0.md

@@ -47,7 +47,7 @@ Some highlights:
 
 * Updated {func}`~scanpy.read_visium` such that it can read spaceranger 2.0 files {smaller}`L Lehner`
 * Fix {func}`~scanpy.pp.normalize_total` for dask {pr}`2466` {smaller}`P Angerer`
-* Fix setting `sc.settings.verbosity` in some cases {pr}`2605` {smaller}`P Angerer`
+* Fix setting :attr:`scanpy.settings.verbosity` in some cases {pr}`2605` {smaller}`P Angerer`
 * Fix all remaining pandas warnings {pr}`2789` {smaller}`P Angerer`
 * Fix some annoying plotting warnings around violin plots {pr}`2844` {smaller}`P Angerer`
 * Scanpy now has a test job which tests against the minumum versions of the dependencies. In the process of implementing this, many bugs associated with using older versions of `pandas`, `anndata`, `numpy`, and `matplotlib` were fixed. {pr}`2816` {smaller}`I Virshup`

src/scanpy/_settings.py

@@ -109,13 +109,12 @@ def override(
         """Temporarily override verbosity.
 
         >>> import scanpy as sc
-        >>> sc.settings.verbosity
-        <Verbosity.hint: 3>
+        >>> sc.settings.verbosity = sc.Verbosity.info
         >>> with sc.settings.verbosity.override(settings.verbosity.debug):
         ...     sc.settings.verbosity
         <Verbosity.debug: 4>
         >>> sc.settings.verbosity
-        <Verbosity.hint: 3>
+        <Verbosity.info: 2>
         """
         settings.verbosity = verbosity
         yield self

src/scanpy/external/tl/_phate.py

@@ -111,8 +111,8 @@ def phate(  # noqa: PLR0913
     random_state
         Random seed. Defaults to the global `numpy` random number generator
     verbose
-        If `True` or an `int`/`Verbosity` ≥ 2/`hint`, print status messages.
-        If `None`, `sc.settings.verbosity` is used.
+        If `True` or an :class:`int`/:class:`~scanpy.Verbosity` ≥ 2/:attr:`~scanpy.Verbosity.hint`, print status messages.
+        If `None`, :attr:`scanpy.settings.verbosity` is used.
     copy
         Return a copy instead of writing to `adata`.
     kwargs