Address comments

docs/bids_app/config.md

@@ -26,10 +26,10 @@ The value of `filters` should be a dictionary where each key corresponds to a BI
   the bold component would match any paths under the `func/` datatype folder, with the suffix `bold` and the extension `.nii.gz`.
 
   ```
-  sub-xxx/.../func/ent1-xxx_ent2-xxx_..._bold.nii.gz
+  sub-xxx/.../func/sub-xxx_ses-xxx_..._bold.nii.gz
   ```
 
-* [`boolean`](#bool): constrains presence or absence of the entity without restricting its value. `False` requires that the entity be **absent**, while `True` requires that the  entity be **present**, regardless of value.
+* [`boolean`](#bool): constrains presence or absence of the entity without restricting its value. `False` requires that the entity be **absent**, while `True` requires the entity to be **present**, regardless of value.
   ```yaml
   pybids_inputs:
     derivs:
@@ -38,9 +38,12 @@ The value of `filters` should be a dictionary where each key corresponds to a BI
         desc: True
         acquisition: False
   ```
-  The above example maps all paths in the `func/` datatype folder that have a `_desc-` entity but do not have the `_acq-` entity.
+  The above example selects all paths in the `func/` datatype folder that have a `_desc-` entity but do not have the `_acq-` entity.
 
 * [`list`](#list): Specify multiple string or boolean filters. Any path matching any one of the filters will be selected. Using `False` as one of the filters allows the entity to optionally be absent in addition to matching one of the string filters. Using `True` along with text is redundant, as `True` will cause any value to be selected. Using `True` with `False` is equivalent to not providing the filter at all.
+
+  These filters:
+
   ```yaml
   pybids_inputs:
     derivs:
@@ -51,7 +54,19 @@ The value of `filters` should be a dictionary where each key corresponds to a BI
           - MP2RAGE
   ```
 
+  would select all of the following paths:
+
+  ```
+  sub-001/ses-1/anat/sub-001_ses-001_acq-MPRAGE_run-1_T1w.nii.gz
+  sub-001/ses-1/anat/sub-001_ses-001_acq-MP2RAGE_run-1_T1w.nii.gz
+  sub-001/ses-1/anat/sub-001_ses-001_run-1_T1w.nii.gz
+  ```
+
+
 * To use regex for filtering, use an additional subkey set either to [`match`](#re.match) or [`search`](#re.search), depending on which regex method you wish to use. This key may be set to any one of the above items (`str`, `bool`, or `list`). Only one such key may be used.
+
+  These filters:
+
   ```yaml
   pybids_inputs:
     derivs:
@@ -62,8 +77,16 @@ The value of `filters` should be a dictionary where each key corresponds to a BI
           match: MP2?RAGE
   ```
 
+  would select all of the following paths:
+
+  ```
+  sub-001/ses-1/anat/sub-001_ses-001_acq-MPRAGE_run-1_T1.nii.gz
+  sub-001/ses-1/anat/sub-001_ses-001_acq-MP2RAGE_run-1_t1w.nii.gz
+  sub-001/ses-1/anat/sub-001_ses-001_acq-MPRAGE_run-1_qT1w.nii.gz
+  ```
+
 ````{note}
-`match` and `search` are both filtering methods. In addition to these, `get` is also a valid filtering method and may be used as the subkey for a filter. However, this is equivalent to directly providing the desired filter without a subkey:
+`match` and `search` are both _filtering methods_. In addition to these, `get` is also a valid filtering method and may be used as the subkey for a filter. However, this is equivalent to directly providing the desired filter without a subkey:
 
 ```yaml
 pybids_inputs:

snakebids/core/_querying.py

@@ -37,20 +37,20 @@ def add_filter(
 
         Converts a list of values to include or exclude into Pybids compatible filters.
         Exclusion filters are appropriately formatted as regex. Raises an exception if
-        both include and exclude are stipulated
+        both include and exclude are stipulated.
 
-        _Postfilter is modified in-place
+        PostFilter is modified in-place.
 
         Parameters
         ----------
         key
             Name of entity to be filtered
         inclusions
             Values to include, values not found in this list will be excluded, by
-            default None
+            default ``None``
         exclusions
             Values to exclude, only values not found in this list will be included, by
-            default None
+            default ``None``
 
         Raises
         ------
@@ -143,9 +143,9 @@ def prefilters(self) -> FilterMap:
 
     @ft.cached_property
     def get(self) -> CompiledFilter:
-        """The combination pre- and post- filters for indexing pybids via ``.get()``.
+        """The combination of pre- and post- filters for indexing pybids via ``.get()``.
 
-        Includes pre-filters not annotated for regex match or search and all inclusion
+        Includes pre-filters not annotated for regex querying and all inclusion
         post-filters. Empty post-filters are replaced with Query.ANY. This allows valid
         paths to be found and processed later. Post-filters are not applied when an
         equivalent prefilter is present
@@ -171,7 +171,7 @@ def get(self) -> CompiledFilter:
     def search(self) -> CompiledFilter:
         """Pre-filters for indexing pybids via ``.get(regex_search=True)``.
 
-        As with :func:`_UnifiedFilter.get`, but only prefilters labelled for regex
+        As with :prop:`UnifiedFilter.get`, but only prefilters labelled for regex
         matching using ``search:`` or ``match:``.
 
         Raises
@@ -251,10 +251,10 @@ def get_matching_files(
             "dataset."
         )
         raise PybidsError(msg) from err
-    else:
-        if search is not None:
-            return [p for p in get if p in search]
-        return get
+
+    if search is not None:
+        return [p for p in get if p in search]
+    return get
 
 
 @attrs.define
@@ -279,8 +279,8 @@ class _TooFewKeysError(FilterSpecError):
     @override
     def get_config_error(self, component_name: str) -> ConfigError:
         msg = (
-            f"Filter '{self.entity}' for component '{component_name}'  was specified a "
-            f"dict but was not given any keys. {self.requirement} Got: {self.value}"
+            f"Filter '{self.entity}' for component '{component_name}' was specified as "
+            f"a dict but was not given any keys. {self.requirement} Got: {self.value}"
         )
         return ConfigError(msg)
 
@@ -352,6 +352,8 @@ def _compile_filt(filt: Iterable[str | bool]):
         result[key] = _compile_filt(itx.always_iterable(f))
 
         if filt_type == "match":
+            # pybids only does search, so surround string filters with position anchors
+            # to simulate match
             result[key] = [
                 f"^(?:{filt})$" if isinstance(filt, str) else filt
                 for filt in result[key]

snakebids/core/input_generation.py

@@ -526,10 +526,10 @@ def _get_component(
 
     Parameters
     ----------
-    bids_layout : BIDSLayout
+    bids_layout
         Layout from pybids for accessing the BIDS dataset to grab paths
 
-    pybids_inputs : dict
+    component
         Dictionary indexed by modality name, specifying the filters and
         wildcards for each pybids input.
 
@@ -539,11 +539,6 @@ def _get_component(
     postfilters
         Filters to component after delineation
 
-    Yields
-    ------
-    BidsComponent
-        One BidsComponent is yielded for each modality described by ``pybids_inputs``.
-
     Raises
     ------
     ConfigError
@@ -554,12 +549,6 @@ def _get_component(
     filters = UnifiedFilter(component, postfilters or {})
 
     if "custom_path" in component:
-        # a custom path was specified for this input, skip pybids:
-        # get input_wildcards by parsing path for {} entries (using a set
-        # to get unique only)
-        # get zip_lists by using glob_wildcards (but need to modify
-        # to deal with multiple wildcards
-
         path = component["custom_path"]
         zip_lists = _parse_custom_path(path, filters=filters)
         return BidsComponent(name=input_name, path=path, zip_lists=zip_lists)