Update argument handling for --derivatives

The initial implementation of bidsargs had --derivatives take the same
arguments as previously specified in the template app: action="+". This
made the argument alway look for one or more paths. This does not
reflect the pybids api, which additionally takes True and False

The fix adjusts this so that --derivatives defaults to False, if
provided by itself give True, and if provide with paths, gives a list of
Path().

snakebids/plugins/base.py

@@ -30,7 +30,7 @@ class AddArgumentArgs(TypedDict, Generic[_T], total=False):
         nargs: int | _NArgsStr | _SUPPRESS_T | None
         const: Any
         default: Any
-        type: Callable[[str], _T] | argparse.FileType
+        type: Callable[[Any], _T] | argparse.FileType
         choices: Iterable[_T] | None
         required: bool
         help: str | None
@@ -49,7 +49,7 @@ class AddArgumentArgs(TypedDict, total=False):
         nargs: int | _NArgsStr | _SUPPRESS_T | None
         const: Any
         default: Any
-        type: Callable[[str], Any] | argparse.FileType
+        type: Callable[[Any], Any] | argparse.FileType
         choices: Iterable[Any] | None
         required: bool
         help: str | None

snakebids/plugins/bidsargs.py

@@ -2,7 +2,7 @@
 
 import argparse
 from pathlib import Path
-from typing import Any, Iterable
+from typing import Any, Iterable, Sequence
 
 import attrs
 import more_itertools as itx
@@ -17,6 +17,27 @@ def _list_or_none(arg: str | Iterable[str] | None) -> list[str] | None:
     return arg if arg is None else list(itx.always_iterable(arg))
 
 
+class _Derivative(argparse.Action):
+    def __call__(
+        self,
+        parser: argparse.ArgumentParser,
+        namespace: argparse.Namespace,
+        values: str | Sequence[Any] | None,
+        option_string: str | None = None,
+    ):
+        # the below two conditions are to cover the typing. They are not actually
+        # encountered at this time in the code
+        if values is None:  # pragma: no cover
+            result = False
+        elif isinstance(values, str):  # pragma: no cover
+            result = [Path(values)]
+        elif not len(values):
+            result = True
+        else:
+            result = [Path(p) for p in values]
+        setattr(namespace, self.dest, result)
+
+
 @attrs.define
 class BidsArgs(PluginBase):
     """Add basic BIDSApp arguments.
@@ -182,7 +203,9 @@ def add_cli_arguments(
                 "--derivatives",
                 help="Path(s) to a derivatives dataset, for folder(s) that contains "
                 "multiple derivatives datasets",
-                nargs="+",
+                nargs="*",
                 dest="derivatives",
                 metavar="PATH",
+                action=_Derivative,
+                default=False,
             )

snakebids/tests/strategies.py

@@ -36,6 +36,8 @@
 alphanum = ascii_letters + digits
 valid_entities: tuple[str, ...] = tuple(BidsConfig.load("bids").entities.keys())
 
+path_characters = st.characters(blacklist_characters=["/", "\x00"], codec="UTF-8")
+
 
 def nothing() -> Any:
     return st.nothing()  # type: ignore
@@ -48,9 +50,10 @@ def paths(
     absolute: bool | None = None,
     resolve: bool = False,
 ) -> st.SearchStrategy[Path]:
-    valid_chars = st.characters(blacklist_characters=["/", "\x00"], codec="UTF-8")
     paths = st.lists(
-        st.text(valid_chars, min_size=1), min_size=min_segments, max_size=max_segments
+        st.text(path_characters, min_size=1),
+        min_size=min_segments,
+        max_size=max_segments,
     ).map(lambda x: Path(*x))
 
     relative_paths = paths.filter(lambda p: not p.is_absolute())

snakebids/tests/test_plugins/test_bidsargs.py

@@ -2,6 +2,7 @@
 
 import itertools as it
 from argparse import ArgumentParser
+from pathlib import Path
 from typing import Iterable
 
 import pytest
@@ -10,6 +11,7 @@
 
 from snakebids.exceptions import ConfigError
 from snakebids.plugins.bidsargs import BidsArgs
+from snakebids.tests import strategies as sb_st
 
 
 class _St:
@@ -65,3 +67,32 @@ def test_analysis_levels_can_be_defined_in_config(
         for arg in choices:
             nspc = parser.parse_args(["...", "...", arg])
             assert nspc.analysis_level == arg
+
+    @given(
+        derivatives=st.lists(
+            st.text(sb_st.path_characters).filter(lambda s: not s.startswith("-")),
+            min_size=1,
+        )
+    )
+    def test_derivatives_converted_to_paths(self, derivatives: list[str]):
+        parser = ArgumentParser()
+        bidsargs = BidsArgs()
+        bidsargs.add_cli_arguments(parser, {}, {})
+        nspc = parser.parse_args(
+            ["...", "...", "participant", "--derivatives", *derivatives]
+        )
+        assert nspc.derivatives == [Path(p) for p in derivatives]
+
+    def test_derivatives_true_if_no_paths_given(self):
+        parser = ArgumentParser()
+        bidsargs = BidsArgs()
+        bidsargs.add_cli_arguments(parser, {}, {})
+        nspc = parser.parse_args(["...", "...", "participant", "--derivatives"])
+        assert nspc.derivatives is True
+
+    def test_derivatives_false_by_default(self):
+        parser = ArgumentParser()
+        bidsargs = BidsArgs()
+        bidsargs.add_cli_arguments(parser, {}, {})
+        nspc = parser.parse_args(["...", "...", "participant"])
+        assert nspc.derivatives is False