Double backticks rather than single ones for code in docs

CONTRIBUTING.rst

@@ -8,7 +8,7 @@ little bit helps, and credit will always be given.
 Bug reports
 ===========
 
-When `reporting a bug <https://github.com/scikit-hep/decaylanguage/issues>`_ please include:
+When ``reporting a bug <https://github.com/scikit-hep/decaylanguage/issues>``_ please include:
 
     * Your operating system name and version.
     * Any details about your local setup that might be helpful in troubleshooting.
@@ -37,7 +37,7 @@ Development
 
 To set up ``decaylanguage`` for local development:
 
-1. Fork `decaylanguage <https://github.com/scikit-hep/decaylanguage>`_
+1. Fork ``decaylanguage <https://github.com/scikit-hep/decaylanguage>``_
    (look for the "Fork" button).
 
 2. Clone your fork locally::
@@ -50,7 +50,7 @@ To set up ``decaylanguage`` for local development:
 
    Now you can make your changes locally.
 
-4. When you're done making changes, run all the checks, doc builder and spell checker with `nox <https://nox.thea.codes/en/stable/>`_ one command::
+4. When you're done making changes, run all the checks, doc builder and spell checker with ``nox <https://nox.thea.codes/en/stable/>``_ one command::
 
     nox
 

src/decaylanguage/dec/dec.py

@@ -169,7 +169,7 @@ def parse(self, include_ccdecays: bool = True) -> None:
         Parse the given .dec decay file(s) according to the default Lark parser
         and specified options.
 
-        Use the method `load_additional_decay_models` before `parse` to load decay models
+        Use the method ``load_additional_decay_models`` before ``parse`` to load decay models
         that might not yet be available in DecayLanguage.
 
         Parameters
@@ -274,7 +274,7 @@ def load_grammar(
         **options: Any,
     ) -> None:
         """
-        DEPRECATED, please use "`load_additional_decay_models`" instead.
+        DEPRECATED, please use "``load_additional_decay_models``" instead.
 
         Load a Lark grammar definition file, either the default one,
         or a user-specified one, optionally setting Lark parsing options.
@@ -296,7 +296,7 @@ def load_grammar(
 
         warnings.warn(
             "This method is deprecated, please add unknown decay models by passing them to "
-            "`load_additional_decay_models` instead before parsing the decayfile.",
+            "``load_additional_decay_models`` instead before parsing the decayfile.",
             DeprecationWarning,
             stacklevel=2,
         )
@@ -309,7 +309,7 @@ def load_grammar(
     def load_additional_decay_models(self, *models: str) -> None:
         """
         Add one or more EvtGen decay models in addition to the ones already provided via
-        `decaylanguage.dec.enums.known_decay_models`.
+        ``decaylanguage.dec.enums.known_decay_models``.
 
         Parameters
         ----------
@@ -373,7 +373,7 @@ def _generate_edit_terminals_callback(self) -> Callable[[TerminalDef], None]:
         def edit_model_name_terminals(t: TerminalDef) -> None:
             """
             Edits the terminals of the grammar to replace the model name placeholder with the actual names of the models,
-            see `Model_NAME_PLACEHOLDER` in the default grammar file `decaylanguage/data/decfile.lark`.
+            see ``Model_NAME_PLACEHOLDER`` in the default grammar file ``decaylanguage/data/decfile.lark``.
             The decay models are sorted by length and escaped to match the default Lark behavior.
             """
 
@@ -1151,7 +1151,7 @@ def _replacement(self, t: Token) -> Token:
         if t.value not in self.define_defs:
             raise ValueError(
                 f"Decay model or ModelAlias {t.value} is not defined. Please load the decay model with "
-                "`load_additional_decay_models` or define a ModelAlias in the decayfile."
+                "``load_additional_decay_models`` or define a ModelAlias in the decayfile."
             )
         return self.define_defs[t.value]
 
@@ -1289,8 +1289,8 @@ def find_charge_conjugate_match(
     Find the charge-conjugate particle name making use of user information
     from "ChargeConj" statements in a decay file.
 
-    The name `ChargeConj(pname)` is returned if all matching "routes" fail,
-    see `charge_conjugate_name(...)` function.
+    The name ``ChargeConj(pname)`` is returned if all matching "routes" fail,
+    see ``charge_conjugate_name(...)`` function.
     """
     # Check the list of particle-antiparticle matches provided ;-)
     if dict_cc_names:

src/decaylanguage/decay/decay.py

@@ -43,7 +43,7 @@ class DaughtersDict(CounterStr):
     Note
     ----
     This class assumes EvtGen particle names, though this assumption is only relevant
-    for the `charge_conjugate` method.
+    for the ``charge_conjugate`` method.
     Otherwise, all other class methods smoothly deal with
     any kind of particle names (basically an iterable of strings).
 
@@ -64,7 +64,7 @@ def __init__(
         Note
         ----
         This class assumes EvtGen particle names, though this assumption is only relevant
-        for the `charge_conjugate` method (refer to its documentation).
+        for the ``charge_conjugate`` method (refer to its documentation).
         Otherwise, all other class methods smoothly deal with
         any kind of particle names (basically an iterable of strings).
 
@@ -188,7 +188,7 @@ class DecayMode:
     Note
     ----
     This class assumes EvtGen particle names, though this assumption is only
-    relevant for the `charge_conjugate` method.
+    relevant for the ``charge_conjugate`` method.
     Otherwise, all other class methods smoothly deal
     with any kind of particle names (basically an iterable of strings).
     """
@@ -224,7 +224,7 @@ def __init__(
         Note
         ----
         This class assumes EvtGen particle names, though this assumption is only
-        relevant for the `charge_conjugate` method.
+        relevant for the ``charge_conjugate`` method.
         Otherwise, all other class methods smoothly deal
         with any kind of particle names (basically an iterable of strings).
 
@@ -277,7 +277,7 @@ def from_dict(
         Note
         ----
         This class assumes EvtGen particle names, though this assumption is only
-        relevant for the `charge_conjugate` method.
+        relevant for the ``charge_conjugate`` method.
         Otherwise, all other class methods smoothly deal
         with any kind of particle names (basically an iterable of strings).
 
@@ -386,7 +386,7 @@ def describe(self) -> str:
     def to_dict(self) -> dict[str, int | float | str | list[str]]:
         """
         Return the decay mode as a dictionary in the format understood
-        by the `DecayChainViewer` class.
+        by the ``DecayChainViewer`` class.
 
         Examples
         --------
@@ -470,17 +470,17 @@ def _build_decay_modes(
     decay_modes: dict[str, DecayMode], dc_dict: DecayChainDict
 ) -> None:
     """
-    Internal recursive function that identifies and creates all `DecayMode` instances
-    effectively contained in the dict representation of a `DecayChain`,
-    which is for example the format returned by `DecFileParser.build_decay_chains(...)`,
+    Internal recursive function that identifies and creates all ``DecayMode`` instances
+    effectively contained in the dict representation of a ``DecayChain``,
+    which is for example the format returned by ``DecFileParser.build_decay_chains(...)``,
 
-    Given the input dict representation of a `DecayChain`
-    it returns a dict of mother particles and their final states as `DecayMode` instances.
+    Given the input dict representation of a ``DecayChain``
+    it returns a dict of mother particles and their final states as ``DecayMode`` instances.
 
     Parameters
     ----------
     decay_modes: dict
-        A dict to be populated with the decay modes `DecayMode`
+        A dict to be populated with the decay modes ``DecayMode``
         built from the input decay chain dictionary.
     dc_dict: dict
         The input decay chain dictionary.
@@ -740,7 +740,7 @@ class DecayChain:
     can only define a single decay mode.
     2) This class does not assume any kind of particle names (EvtGen, PDG).
     It is nevertheless advised to default use EvtGen names for consistency
-    with the defaults used in the related classes `DecayMode` and `DaughtersDict`,
+    with the defaults used in the related classes ``DecayMode`` and ``DaughtersDict``,
     unless there is a good motivation not to.
     """
 
@@ -777,7 +777,7 @@ def from_dict(cls, decay_chain_dict: DecayChainDict) -> Self:
         """
         Constructor from a decay chain represented as a dictionary.
         The format is the same as that returned by
-        `DecFileParser.build_decay_chains(...)`.
+        ``DecFileParser.build_decay_chains(...)``.
         """
         try:
             assert len(decay_chain_dict.keys()) == 1
@@ -792,7 +792,7 @@ def from_dict(cls, decay_chain_dict: DecayChainDict) -> Self:
 
     def top_level_decay(self) -> DecayMode:
         """
-        Return the top-level decay as a `DecayMode` instance.
+        Return the top-level decay as a ``DecayMode`` instance.
         """
         return self.decays[self.mother]
 
@@ -928,7 +928,7 @@ def _print(
     def to_dict(self) -> DecayChainDict:
         """
         Return the decay chain as a dictionary representation.
-        The format is the same as `DecFileParser.build_decay_chains(...)`.
+        The format is the same as ``DecFileParser.build_decay_chains(...)``.
 
         Examples
         --------
@@ -980,7 +980,7 @@ def flatten(
 
         Note
         ----
-        After flattening the only `DecayMode` metadata kept is that of the top-level decay,
+        After flattening the only ``DecayMode`` metadata kept is that of the top-level decay,
         i.e. that of the mother particle (nothing else would make sense).
 
         Examples

src/decaylanguage/decay/viewer.py

@@ -6,7 +6,7 @@
 """
 Submodule with classes and utilities to visualize decay chains.
 Decay chains are typically provided by the parser of .dec decay files,
-see the `DecFileParser` class.
+see the ``DecFileParser`` class.
 """
 
 from __future__ import annotations
@@ -42,7 +42,7 @@ class DecayChainViewer:
     >>> dcv    # doctest: +SKIP
 
     When not in notebooks the graph can easily be visualized with the
-    `graphviz.Digraph.render` or `graphviz.Digraph.view` functions, e.g.:
+    ``graphviz.Digraph.render`` or ``graphviz.Digraph.view`` functions, e.g.:
     >>> dcv.graph.render(filename="test", format="pdf", view=True, cleanup=True)    # doctest: +SKIP
     """
 
@@ -59,10 +59,10 @@ def __init__(
         Parameters
         ----------
         decaychain: dict
-            Input decay chain in dict format, typically created from `decaylanguage.DecFileParser.build_decay_chains`
-            after parsing a .dec decay file, or from building a decay chain representation with `decaylanguage.DecayChain.to_dict`.
+            Input decay chain in dict format, typically created from ``decaylanguage.DecFileParser.build_decay_chains``
+            after parsing a .dec decay file, or from building a decay chain representation with ``decaylanguage.DecayChain.to_dict``.
         attrs: optional
-            User input `graphviz.Digraph` class attributes.
+            User input ``graphviz.Digraph`` class attributes.
 
         See also
         --------
@@ -91,7 +91,7 @@ def safe_html_name(name: str) -> str:
             Note
             ----
             The match is done using a conversion map rather than via
-            `Particle.from_evtgen_name(name).html_name` for 2 reasons:
+            ``Particle.from_evtgen_name(name).html_name`` for 2 reasons:
             - Some decay-file-specific "particle" names (e.g. cs_0)
               are not in the PDG table.
             - No need to load all particle information if all that's needed
@@ -183,23 +183,23 @@ def has_subdecay(ds: list[Any]) -> bool:
     @property
     def graph(self) -> graphviz.Digraph:
         """
-        Get the actual `graphviz.Digraph` object.
+        Get the actual ``graphviz.Digraph`` object.
         The user now has full control ...
         """
         return self._graph
 
     def to_string(self) -> str:
         """
         Return a string representation of the built graph in the DOT language.
-        The function is a trivial shortcut for ``graphviz.Digraph.source`.
+        The function is a trivial shortcut for ``graphviz.Digraph.source``.
         """
         return self.graph.source  # type: ignore[no-any-return]
 
     def _instantiate_graph(
         self, **attrs: dict[str, bool | int | float | str]
     ) -> graphviz.Digraph:
         """
-        Return a ``graphviz.Digraph` class instance using the default attributes
+        Return a ``graphviz.Digraph`` class instance using the default attributes
         specified in this class:
         - Default graph attributes are overridden by input by the user.
         - Class and node and edge defaults.
@@ -226,7 +226,7 @@ def _instantiate_graph(
 
     def _get_default_arguments(self) -> dict[str, bool | int | float | str]:
         """
-        `graphviz.Digraph` default arguments.
+        ``graphviz.Digraph`` default arguments.
         """
         return {
             "name": "DecayChainGraph",

src/decaylanguage/utils/particleutils.py

@@ -50,7 +50,7 @@ def charge_conjugate_name(name: str, pdg_name: bool = False) -> str:
     -------
     out: str
         Either the EvtGen or PDG charge-conjugate particle name
-        depending on the value of parameter `pdg_name`.
+        depending on the value of parameter ``pdg_name``.
     """
     if pdg_name:
         try:
@@ -121,7 +121,7 @@ def particle_list_from_string_name(name: str) -> list[Particle]:
 
 def _from_group_dict_list(mat: dict[str, Any]) -> list[Particle]:
     """
-    Internal helper class for the functions `from_string` and `from_string_list`
+    Internal helper class for the functions ``from_string`` and ``from_string_list``
     for fuzzy finding of particle names used by AmpGen.
     """
     kw: dict[str, Any] = {

src/decaylanguage/utils/utilities.py

@@ -64,7 +64,7 @@ def filter_lines(
 class DescriptorFormat:
     """
     Class to help with setting the decay descriptor format. The format is stored as a
-    class-level variable: `DescriptorFormat.config`.
+    class-level variable: ``DescriptorFormat.config``.
 
     Examples
     --------
@@ -140,7 +140,7 @@ def set_config(decay_pattern: str, sub_decay_pattern: str) -> None:
     def format_descriptor(mother: str, daughters: str, top: bool = True) -> str:
         """
         Apply the format to one "layer" of the decay. Does not handle nested
-        decays itself. It is assumed that the `daughters` string already contains
+        decays itself. It is assumed that the ``daughters`` string already contains
         any sub-decays.
 
         Parameters