Create documentation compatibility for old apps

Include add_dynamic_args as deprecated placeholder. Some apps were using
it to prepare a documentation cli. Include it with a deprecation warning
for a more graceful change. It's otherwise a no-op, it's funcationality
subsumed by SnakeBidsApp and the underlying bidsapp

Expose .parser and .config on SnakeBidsApp

Lazily construct app in SnakeBidsApp: Improves compatibility for some
tests

snakebids/app.py

@@ -20,16 +20,17 @@
 from pathlib import Path
 from typing import Any, Callable
 
-import attr
+import attrs
 import boutiques.creator as bc  # type: ignore
 
 from snakebids import bidsapp
 from snakebids import plugins as sb_plugins
+from snakebids.bidsapp.run import _Runner
 
 logger = logging.Logger(__name__)
 
 
-@attr.define(slots=False)
+@attrs.define
 class SnakeBidsApp:
     """Snakebids app with config and arguments.
 
@@ -69,23 +70,36 @@ class SnakeBidsApp:
     """
 
     snakemake_dir: Path
-    plugins: list[Callable[[SnakeBidsApp], None | SnakeBidsApp]] = attr.Factory(list)
+    plugins: list[Callable[[SnakeBidsApp], None | SnakeBidsApp]] = attrs.Factory(list)
     skip_parse_args: bool = False
-    parser: Any = None
+    _parser: Any = attrs.field(default=None, alias="parser")
     configfile_path: Path | None = None
     snakefile_path: Path | None = None
-    config: Any = None
+    _config: Any = attrs.field(default=None, alias="config")
     version: str | None = None
     args: Any = None
 
+    _app_holder: _Runner | None = attrs.field(default=None, init=False)
+
+    @property
+    def _app(self):
+        if self._app_holder is None:
+            self._check_deprecations()
+
+            self._app_holder = bidsapp.app(
+                [sb_plugins.SnakemakeBidsApp(**self._get_args()), *self.plugins],
+                description="Snakebids helps build BIDS Apps with Snakemake",
+            )
+        return self._app_holder
+
     def _check_deprecations(self):
-        if self.parser is not None:
+        if self._parser is not None:
             msg = (
                 "`SnakeBidsApp.parser` is deprecated and no longer has any effect. To "
                 "modify the parser, use the new `bidsapp` module."
             )
             warnings.warn(msg, stacklevel=3)
-        if self.config is not None:
+        if self._config is not None:
             msg = (
                 "`SnakeBidsApp.config` is deprecated and no longer has any effect. To "
                 "modify the config, use the new `bidsapp` module."
@@ -105,6 +119,16 @@ def _check_deprecations(self):
             )
             warnings.warn(msg, stacklevel=3)
 
+    @property
+    def config(self):
+        """Get config dict (before arguments are parsed)."""
+        return self._app.build_parser().config
+
+    @property
+    def parser(self):
+        """Get parser."""
+        return self._app.build_parser().parser
+
     def _get_args(self):
         args: dict[str, Any] = {}
         args["snakemake_dir"] = self.snakemake_dir
@@ -116,26 +140,11 @@ def _get_args(self):
 
     def run_snakemake(self) -> None:
         """Run snakemake with the given config, after applying plugins."""
-        self._check_deprecations()
-
-        bidsapp.app(
-            [sb_plugins.SnakemakeBidsApp(**self._get_args()), *self.plugins],
-            description="Snakebids helps build BIDS Apps with Snakemake",
-        ).run()
+        self._app.run()
 
     def create_descriptor(self, out_file: PathLike[str] | str) -> None:
         """Generate a boutiques descriptor for this Snakebids app."""
-        self._check_deprecations()
-
-        parser = (
-            bidsapp.app(
-                [sb_plugins.SnakemakeBidsApp(**self._get_args()), *self.plugins],
-                description="Snakebids helps build BIDS Apps with Snakemake",
-            )
-            .build_parser()
-            .parser
-        )
         new_descriptor = bc.CreateDescriptor(  # type: ignore
-            parser, execname="run.py"
+            self.parser, execname="run.py"
         )
         new_descriptor.save(out_file)  # type: ignore

snakebids/cli.py

@@ -0,0 +1,26 @@
+from __future__ import annotations
+
+import argparse
+import warnings
+from typing import Any, Mapping
+
+from snakebids.types import InputsConfig
+
+
+def add_dynamic_args(
+    parser: argparse.ArgumentParser,
+    parse_args: Mapping[str, Any],
+    pybids_inputs: InputsConfig,
+) -> None:
+    """Do nothing.
+
+    Originally added --filter-<comp> and --wildcards-<comp> argumets to the CLI. Kept
+    as a placeholder for apps that relied on it for generating documentation. This
+    functionality is now native to `SnakeBidsApp`.
+    """
+    warnings.warn(
+        "add_dynamic_args() is deprecated and no longer has any effect. Its function "
+        "is now provided natively by `SnakeBidsApp`. It will be removed in an upcoming "
+        "release",
+        stacklevel=2,
+    )

snakebids/tests/test_app.py

@@ -3,11 +3,15 @@
 import argparse
 import json
 from pathlib import Path
+from typing import Any
 
 import pytest
+from hypothesis import given
 from pytest_mock import MockerFixture
 
 from snakebids.app import SnakeBidsApp
+from snakebids.cli import add_dynamic_args
+from snakebids.tests import strategies as sb_st
 
 
 class TestDeprecations:
@@ -70,6 +74,40 @@ def test_plugins_carried_forward(mocker: MockerFixture):
     assert len(plugins) == 3  # type: ignore  # noqa: PLR2004
 
 
+def test_parser_can_be_directly_accessed(tmpdir: Path):
+    config_path = Path(tmpdir) / "config.json"
+    config_path.write_text("{}")
+    app = SnakeBidsApp(
+        Path(),
+        configfile_path=config_path,
+        snakefile_path=Path("Snakefile"),
+    )
+    assert app.parser is app._app.parser
+
+
+def test_config_can_be_directly_accessed(tmpdir: Path):
+    config_path = Path(tmpdir) / "config.json"
+    config_path.write_text("{}")
+    app = SnakeBidsApp(
+        Path(),
+        configfile_path=config_path,
+        snakefile_path=Path("Snakefile"),
+    )
+    assert app.config is app._app.config
+
+
+@given(
+    parser=sb_st.everything(),
+    parse_args=sb_st.everything(),
+    pybids_inputs=sb_st.everything(),
+)
+def test_add_dynamic_args_raises_warning(
+    parser: Any, parse_args: Any, pybids_inputs: Any
+):
+    with pytest.warns(UserWarning, match="is deprecated and no longer has any effect"):
+        add_dynamic_args(parser, parse_args, pybids_inputs)
+
+
 class TestGenBoutiques:
     def test_boutiques_descriptor(self, tmp_path: Path):
         configpth = tmp_path / "config.json"