Allow builtins and resolved paths as cli types

docs/bids_app/config.md

@@ -79,7 +79,28 @@ A mapping from the name of each ``analysis_level`` to the list of rules or files
 
 ### `parse_args`
 
-A dictionary of command-line parameters to make available as part of the BIDS app. Each item of the mapping is passed to [argparse's add_argument function](#argparse.ArgumentParser.add_argument). A number of default entries are present in a new snakebids project's config file that structure the BIDS app's CLI, but additional command-line arguments can be added as necessary.
+A dictionary of command-line parameters to make available as part of the BIDS app. Each item of the mapping is passed to [argparse's `add_argument` function](#argparse.ArgumentParser.add_argument). A number of default entries are present in a new snakebids project's config file that structure the BIDS app's CLI, but additional command-line arguments can be added as necessary.
+
+As in [`ArgumentParser.add_argument()`](#argparse.ArgumentParser.add_argument), `type` may be used to convert the argument to the specified type. It may be set to any type that can be serialized into yaml, for instance, `str`, `int`, `float`, and `boolean`.
+
+```yaml
+parse_args:
+  --a-string:
+    help: args are string by default
+  --a-path:
+    help: |
+      A path pointing to data needed for the pipeline. These are still converted
+      into strings, but are first resolved into absolute paths (see below)
+    type: Path
+  --another-path:
+    help: This type annotation does the same thing as above
+    type: pathlib.Path
+  --a-number:
+    help: A number important for the analysis
+    type: float
+```
+
+When CLI parameters are used to collect paths, `type` should be set to [`Path`](#pathlib.Path) (or [`pathlib.Path`](#pathlib.Path)). These arguments will still be serialized as strings (since yaml doesn't have a path type), but snakebids will automatically resolve all arguments into absolute paths. This is important to prevent issues with snakebids and relative paths.
 
 
 ### `debug`

pyproject.toml

@@ -39,7 +39,6 @@ snakemake = [
     { version = ">=5.28.0,<8", python = ">=3.8" },
     { version = ">=7.18.2,<8", python = ">=3.11" },
 ]
-PyYAML = ">=6"
 typing-extensions = ">=3.10.0"
 attrs = ">=21.2.0"
 boutiques = "^0.5.25"
@@ -70,6 +69,7 @@ copier = ">=8.2.0"
 jinja2-time = ">=0.2.0"
 # minimum 2.31.0 because of security vulnerability
 requests = ">=2.31.0"
+ruamel-yaml = ">=0.17.2"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.0.0"

snakebids/app.py

@@ -21,10 +21,10 @@
     parse_snakebids_args,
 )
 from snakebids.exceptions import ConfigError, RunError
+from snakebids.io.config import write_config
 from snakebids.types import OptionalFilter
 from snakebids.utils.output import (
     prepare_bidsapp_output,
-    write_config_file,
     write_output_mode,
 )
 from snakebids.utils.utils import DEPRECATION_FLAG, to_resolved_path
@@ -234,7 +234,7 @@ def run_snakemake(self) -> None:
             app = plugin(app) or app
 
         # Write the config file
-        write_config_file(
+        write_config(
             config_file=new_config_file,
             data=dict(
                 app.config,

snakebids/cli.py

@@ -11,7 +11,8 @@
 import snakemake
 from typing_extensions import override
 
-from snakebids.exceptions import MisspecifiedCliFilterError
+from snakebids.exceptions import ConfigError, MisspecifiedCliFilterError
+from snakebids.io.yaml import get_yaml_io
 from snakebids.types import InputsConfig, OptionalFilter
 from snakebids.utils.utils import to_resolved_path
 
@@ -204,6 +205,26 @@ def create_parser(include_snakemake: bool = False) -> argparse.ArgumentParser:
     return parser
 
 
+def _find_type(name: str, *, yamlsafe: bool = True) -> type[Any]:
+    import importlib
+
+    if name == "Path":
+        return Path
+    *module_name, obj_name = name.split(".") if "." in name else ("builtins", name)
+    try:
+        type_ = getattr(importlib.import_module(".".join(module_name)), obj_name)
+    except (ImportError, AttributeError) as err:
+        msg = f"{name} could not be resolved"
+        raise ConfigError(msg) from err
+    if not callable(type_):
+        msg = f"{name} cannot be used as a type"
+        raise ConfigError(msg)
+    if yamlsafe and type_ not in get_yaml_io().representer.yaml_representers:
+        msg = f"{name} cannot be serialized into yaml"
+        raise ConfigError(msg)
+    return type_
+
+
 def add_dynamic_args(
     parser: argparse.ArgumentParser,
     parse_args: Mapping[str, Any],
@@ -220,16 +241,12 @@ def add_dynamic_args(
         # a str to allow the edge case where it's already
         # been converted
         if "type" in arg:
-            try:
-                arg_dict = {**arg, "type": globals()[str(arg["type"])]}
-            except KeyError as err:
-                msg = f"{arg['type']} is not available as a type for {name}"
-                raise TypeError(msg) from err
+            arg_dict = {**arg, "type": _find_type(str(arg["type"]))}
         else:
             arg_dict = arg
         app_group.add_argument(
             *_make_underscore_dash_aliases(name),
-            **arg_dict,
+            **arg_dict,  # type: ignore
         )
 
     # general parser for