Added and integrated a configuration model

CHANGELOG.md

@@ -6,8 +6,7 @@
 
 #### 🐛 Bug Fix
 
-- Remove list of required status checks [#159](https://github.com/con/nwb2bids/pull/159) ([@candleindark](https://github.com/candleindark))
-- Provide list of required status checks to `auto` [#158](https://github.com/con/nwb2bids/pull/158) ([@candleindark](https://github.com/candleindark) [@CodyCBakerPhD](https://github.com/CodyCBakerPhD))
+- Testing auto release (again) [#156](https://github.com/con/nwb2bids/pull/156) ([@CodyCBakerPhD](https://github.com/CodyCBakerPhD))
 - Testing auto release [#152](https://github.com/con/nwb2bids/pull/152) ([@CodyCBakerPhD](https://github.com/CodyCBakerPhD))
 - Resolved protected branch problem in execution of the "Release with Auto" GH workflow [#151](https://github.com/con/nwb2bids/pull/151) ([@candleindark](https://github.com/candleindark))
 - Add ability to read from raw dandiset metadata when invalid [#107](https://github.com/con/nwb2bids/pull/107) ([@CodyCBakerPhD](https://github.com/CodyCBakerPhD))
@@ -19,6 +18,7 @@
 
 #### 🏠 Internal
 
+- Automatic release [#155](https://github.com/con/nwb2bids/pull/155) ([@github-actions[bot]](https://github.com/github-actions[bot]) [@CodyCBakerPhD](https://github.com/CodyCBakerPhD))
 - Use two GitHub tokens in Release with Auto workflow [#154](https://github.com/con/nwb2bids/pull/154) ([@candleindark](https://github.com/candleindark) [@CodyCBakerPhD](https://github.com/CodyCBakerPhD))
 - Improved and consolidated release and deploy workflow [#138](https://github.com/con/nwb2bids/pull/138) ([@candleindark](https://github.com/candleindark))
 - Provided fix for Setup Release Labels workflow [#137](https://github.com/con/nwb2bids/pull/137) ([@candleindark](https://github.com/candleindark))
@@ -49,15 +49,14 @@
 - Blacklisted `h5py` version dependency for macOS platform [#136](https://github.com/con/nwb2bids/pull/136) ([@CodyCBakerPhD](https://github.com/CodyCBakerPhD))
 - [pre-commit.ci] pre-commit autoupdate [#122](https://github.com/con/nwb2bids/pull/122) ([@pre-commit-ci[bot]](https://github.com/pre-commit-ci[bot]))
 
-#### Authors: 4
+#### Authors: 5
 
+- [@github-actions[bot]](https://github.com/github-actions[bot])
 - [@pre-commit-ci[bot]](https://github.com/pre-commit-ci[bot])
 - Austin Macdonald ([@asmacdo](https://github.com/asmacdo))
 - Cody Baker ([@CodyCBakerPhD](https://github.com/CodyCBakerPhD))
 - Isaac To ([@candleindark](https://github.com/candleindark))
 
----
-
 
 # v0.5.1
 

src/nwb2bids/__init__.py

@@ -8,17 +8,19 @@
 from ._core._convert_nwb_dataset import convert_nwb_dataset
 from ._converters._dataset_converter import DatasetConverter
 from ._converters._session_converter import SessionConverter
+from ._converters._run_config import RunConfig
 from ._inspection._inspection_result import InspectionResult, Severity, Category, DataStandard
 
 __all__ = [
     # Public methods and classes
     "convert_nwb_dataset",
-    "Category",
+    "RunConfig",
     "DatasetConverter",
     "SessionConverter",
-    "Severity",
     "DataStandard",
     "InspectionResult",
+    "Category",
+    "Severity",
     # Public submodules
     "bids_models",
     "testing",

src/nwb2bids/_command_line_interface/_main.py

@@ -3,6 +3,7 @@
 
 import rich_click
 
+from .._converters._run_config import RunConfig
 from .._core._convert_nwb_dataset import convert_nwb_dataset
 from .._tools._pluralize import _pluralize
 
@@ -36,6 +37,17 @@ def _nwb2bids_cli():
     type=rich_click.Choice(["copy", "move", "symlink", "auto"], case_sensitive=False),
     default="auto",
 )
+@rich_click.option(
+    "--cache-directory",
+    "cache_directory",
+    help=(
+        "The directory where run specific files (e.g., notifications, sanitization reports) will be stored. "
+        "Defaults to `~/.nwb2bids`."
+    ),
+    required=False,
+    type=rich_click.Path(exists=True, dir_okay=False, readable=True),
+    default=None,
+)
 @rich_click.option(
     "--additional-metadata-file-path",
     "additional_metadata_file_path",
@@ -48,11 +60,25 @@ def _nwb2bids_cli():
     default=None,
 )
 @rich_click.option("--silent", "-s", is_flag=True, help="Suppress all console output.", default=False)
+@rich_click.option(
+    "--run-id",
+    help=(
+        "On each unique run of nwb2bids, a run ID is generated. "
+        "Set this option to override this to any identifying string. "
+        "This ID is used in the naming of the notification and sanitization reports saved to your cache directory. "
+        'The default ID uses runtime timestamp information of the form "date-%Y%m%d_time-%H%M%S."'
+    ),
+    required=False,
+    type=str,
+    default=None,
+)
 def _run_convert_nwb_dataset(
     nwb_paths: tuple[str, ...],
     bids_directory: str | None = None,
-    file_mode: typing.Literal["copy", "move", "symlink", "auto"] = "auto",
     additional_metadata_file_path: str | None = None,
+    file_mode: typing.Literal["copy", "move", "symlink", "auto"] = "auto",
+    cache_directory: str | None = None,
+    run_id: str | None = None,
     silent: bool = False,
 ) -> None:
     """
@@ -66,17 +92,32 @@ def _run_convert_nwb_dataset(
         raise ValueError(message)
     handled_nwb_paths = [pathlib.Path(nwb_path) for nwb_path in nwb_paths]
 
-    notifications = convert_nwb_dataset(
-        nwb_paths=handled_nwb_paths,
-        bids_directory=bids_directory,
-        file_mode=file_mode,
-        additional_metadata_file_path=additional_metadata_file_path,
-    )
+    run_config_kwargs = {
+        "bids_directory": bids_directory,
+        "additional_metadata_file_path": additional_metadata_file_path,
+        "file_mode": file_mode,
+        "cache_directory": cache_directory,
+        "run_id": run_id,
+    }
+
+    # Filter out values that indicate absence of direct user input or signal to use default
+    non_missing_run_config_kwargs = {
+        key: value
+        for key, value in run_config_kwargs.items()
+        if (key != "file_mode" and value is not None) or (key == "file_mode" and value != "auto")
+    }
+    run_config = RunConfig(**non_missing_run_config_kwargs)
 
-    if notifications and not silent:
-        text = (
+    converter = convert_nwb_dataset(nwb_paths=handled_nwb_paths, run_config=run_config)
+
+    notifications = converter.messages
+    console_notification = ""
+    if notifications:
+        notification_text = (
             f'\n{(n:=len(notifications))} {_pluralize(n=n, word="suggestion")} for improvement '
             f'{_pluralize(n=n, word="was", plural="were")} found during conversion.'
         )
-        console_notification = rich_click.style(text=text, fg="yellow")
+        console_notification += rich_click.style(text=notification_text, fg="yellow")
+
+    if console_notification != "" and not silent:
         rich_click.echo(message=console_notification)

src/nwb2bids/_converters/_base_converter.py

@@ -1,97 +1,19 @@
 import abc
-import json
-import pathlib
-import tempfile
-import typing
 
 import pydantic
 
+from ._run_config import RunConfig
+
 
 class BaseConverter(pydantic.BaseModel, abc.ABC):
+    run_config: RunConfig = pydantic.Field(
+        description="The configuration for this conversion run.", default_factory=RunConfig
+    )
+
     @abc.abstractmethod
     def extract_metadata(self) -> None:
         """
         Extract essential metadata used by the BIDS standard from the source NWB files.
         """
         message = f"The `extract_metadata` method has not been implemented by the `{self.__class__.__name__}` class."
         raise NotImplementedError(message)
-
-    def _handle_bids_directory(self, bids_directory: str | pathlib.Path | None = None) -> pathlib.Path:
-        """
-        Handle the BIDS directory path.
-
-        If the directory does not exist, create it.
-        If it exists, validate that it is a valid BIDS dataset.
-        """
-        if bids_directory is None:
-            bids_directory = pathlib.Path.cwd()
-        bids_directory = pathlib.Path(bids_directory)
-
-        if bids_directory.exists():
-            self._validate_existing_directory_as_bids(bids_directory=bids_directory)
-        else:
-            bids_directory.mkdir(exist_ok=True)
-        self.extract_metadata()
-
-        return bids_directory
-
-    @staticmethod
-    def _validate_existing_directory_as_bids(bids_directory: pathlib.Path) -> None:
-        """
-        Validate that the existing directory is a valid BIDS dataset.
-
-        Parameters
-        ----------
-        bids_directory : pathlib.Path
-            The path to the directory to validate.
-        """
-        dataset_description_file_path = bids_directory / "dataset_description.json"
-
-        current_directory_contents = {
-            path.stem for path in bids_directory.iterdir() if not path.name.startswith(".")
-        } - {"README", "CHANGES", "derivatives", "dandiset"}
-        if len(current_directory_contents) == 0:
-            default_dataset_description = {"BIDSVersion": "1.10"}
-            with dataset_description_file_path.open(mode="w") as file_stream:
-                json.dump(obj=default_dataset_description, fp=file_stream, indent=4)
-            return
-
-        if not dataset_description_file_path.exists():
-            message = (
-                f"The directory ({bids_directory}) exists and is not empty, but is not a valid BIDS dataset: "
-                "missing 'dataset_description.json'."
-            )
-            raise ValueError(message)
-
-        with dataset_description_file_path.open(mode="r") as file_stream:
-            dataset_description = json.load(fp=file_stream)
-        if dataset_description.get("BIDSVersion", None) is None:
-            message = (
-                f"The directory ({bids_directory}) exists but is not a valid BIDS dataset: "
-                "missing 'BIDSVersion' in 'dataset_description.json'."
-            )
-            raise ValueError(message)
-
-    @staticmethod
-    def _handle_file_mode(
-        file_mode: typing.Literal["move", "copy", "symlink", "auto"] = "auto",
-    ) -> typing.Literal["move", "copy", "symlink"]:
-        if file_mode != "auto":
-            return file_mode
-
-        with tempfile.TemporaryDirectory(prefix="nwb2bids-") as temp_dir_str:
-            temp_dir_path = pathlib.Path(temp_dir_str)
-
-            # Create a test file
-            test_file_path = temp_dir_path / "test_file.txt"
-            test_file_path.touch()
-
-            try:
-                # Create a symlink to the test file
-                (temp_dir_path / "test_symlink.txt").symlink_to(target=test_file_path)
-            except (OSError, PermissionError, NotImplementedError):  # Windows can sometimes have trouble with symlinks
-                # TODO: log a INFO message here when logging is set up
-                return "copy"
-            else:
-                # If symlink creation was successful, return "symlink"
-                return "symlink"