junifer 0.0.3.dev188__py3-none-any.whl → 0.0.4__py3-none-any.whl

junifer/_version.py

@@ -1,4 +1,16 @@
 # file generated by setuptools_scm
 # don't change, don't track in version control
-__version__ = version = '0.0.3.dev188'
-__version_tuple__ = version_tuple = (0, 0, 3, 'dev188')
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple, Union
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '0.0.4'
+__version_tuple__ = version_tuple = (0, 0, 4)

junifer/api/cli.py

@@ -8,9 +8,10 @@ import pathlib
 import subprocess
 import sys
 from pathlib import Path
-from typing import Dict, List, Union
+from typing import Dict, List, Tuple, Union
 
 import click
+import pandas as pd
 
 from ..utils.logging import (
     configure_logging,
@@ -20,6 +21,7 @@ from ..utils.logging import (
 )
 from .functions import collect as api_collect
 from .functions import queue as api_queue
+from .functions import reset as api_reset
 from .functions import run as api_run
 from .parser import parse_yaml
 from .utils import (
@@ -32,27 +34,45 @@ from .utils import (
 )
 
 
-def _parse_elements(element: str, config: Dict) -> Union[List, None]:
+def _parse_elements(element: Tuple[str], config: Dict) -> Union[List, None]:
     """Parse elements from cli.
 
     Parameters
     ----------
-    element : str
-        The element to operate on.
+    element : tuple of str
+        The element(s) to operate on.
     config : dict
         The configuration to operate using.
 
     Returns
     -------
-    list
-        The element(s) as list.
+    list or None
+        The element(s) as list or None.
+
+    Raises
+    ------
+    ValueError
+        If no element is found either in the command-line options or
+        the configuration file.
+
+    Warns
+    -----
+    RuntimeWarning
+        If elements are specified both via the command-line options and
+        the configuration file.
 
     """
     logger.debug(f"Parsing elements: {element}")
+    # Early return None to continue with all elements
     if len(element) == 0:
         return None
-    # TODO: If len == 1, check if its a file, then parse elements from file
-    elements = [tuple(x.split(",")) if "," in x else x for x in element]
+    # Check if the element is a file for single element;
+    # if yes, then parse elements from it
+    if len(element) == 1 and Path(element[0]).resolve().is_file():
+        elements = _parse_elements_file(Path(element[0]).resolve())
+    else:
+        # Process multi-keyed elements
+        elements = [tuple(x.split(",")) if "," in x else x for x in element]
     logger.debug(f"Parsed elements: {elements}")
     if elements is not None and "elements" in config:
         warn_with_log(
@@ -61,19 +81,48 @@ def _parse_elements(element: str, config: Dict) -> Union[List, None]:
             "over the configuration file. That is, the elements specified "
             "in the command line will be used. The elements specified in "
             "the configuration file will be ignored. To remove this warning, "
-            'please remove the "elements" item from the configuration file.'
+            "please remove the `elements` item from the configuration file."
         )
     elif elements is None:
+        # Check in config
         elements = config.get("elements", None)
         if elements is None:
             raise_error(
-                "The 'elements' key is set in the configuration, but its value"
-                " is 'None'. It is likely that there is an empty 'elements' "
+                "The `elements` key is set in the configuration, but its value"
+                " is `None`. It is likely that there is an empty `elements` "
                 "section in the yaml configuration file."
             )
     return elements
 
 
+def _parse_elements_file(filepath: Path) -> List[Tuple[str, ...]]:
+    """Parse elements from file.
+
+    Parameters
+    ----------
+    filepath : pathlib.Path
+        The path to the element file.
+
+    Returns
+    -------
+    list of tuple of str
+        The element(s) as list.
+
+    """
+    # Read CSV into dataframe
+    csv_df = pd.read_csv(
+        filepath,
+        header=None,  # no header  # type: ignore
+        index_col=False,  # no index column
+        dtype=str,
+        skipinitialspace=True,  # no leading space after delimiter
+    )
+    # Remove trailing whitespace in cell entries
+    csv_df_trimmed = csv_df.apply(lambda x: x.str.strip())
+    # Convert to list of tuple of str
+    return list(map(tuple, csv_df_trimmed.to_numpy()))
+
+
 def _validate_verbose(
     ctx: click.Context, param: str, value: str
 ) -> Union[str, int]:
@@ -92,6 +141,7 @@ def _validate_verbose(
     -------
     str or int
         The validated value.
+
     """
     if isinstance(value, int):
         return value
@@ -133,7 +183,9 @@ def cli() -> None:  # pragma: no cover
     callback=_validate_verbose,
     default="info",
 )
-def run(filepath: click.Path, element: str, verbose: Union[str, int]) -> None:
+def run(
+    filepath: click.Path, element: Tuple[str], verbose: Union[str, int]
+) -> None:
     """Run command for CLI.
 
     \f
@@ -142,20 +194,30 @@ def run(filepath: click.Path, element: str, verbose: Union[str, int]) -> None:
     ----------
     filepath : click.Path
         The filepath to the configuration file.
-    element : str
-        The element to operate using.
+    element : tuple of str
+        The element to operate on.
     verbose : click.Choice
         The verbosity level: warning, info or debug (default "info").
 
     """
     configure_logging(level=verbose)
-    # TODO: add validation
+    # TODO(synchon): add validation
+    # Parse YAML
     config = parse_yaml(filepath)  # type: ignore
+    # Retrieve working directory
     workdir = config["workdir"]
+    # Fetch datagrabber
     datagrabber = config["datagrabber"]
+    # Fetch markers
     markers = config["markers"]
+    # Fetch storage
     storage = config["storage"]
-    preprocessor = config.get("preprocess")
+    # Fetch preprocessors
+    preprocessors = config.get("preprocess")
+    # Convert to list if single preprocessor
+    if preprocessors is not None and not isinstance(preprocessors, list):
+        preprocessors = [preprocessors]
+    # Parse elements
     elements = _parse_elements(element, config)
     # Perform operation
     api_run(
@@ -163,7 +225,7 @@ def run(filepath: click.Path, element: str, verbose: Union[str, int]) -> None:
         datagrabber=datagrabber,
         markers=markers,
         storage=storage,
-        preprocessor=preprocessor,
+        preprocessors=preprocessors,
         elements=elements,
     )
 
@@ -352,6 +414,43 @@ def selftest(subpkg: str) -> None:
         click.secho("Failure.", fg="red")
 
 
+@cli.command()
+@click.argument(
+    "filepath",
+    type=click.Path(
+        exists=True, readable=True, dir_okay=False, path_type=pathlib.Path
+    ),
+)
+@click.option(
+    "-v",
+    "--verbose",
+    type=click.UNPROCESSED,
+    callback=_validate_verbose,
+    default="info",
+)
+def reset(
+    filepath: click.Path,
+    verbose: Union[str, int],
+) -> None:
+    """Reset command for CLI.
+
+    \f
+
+    Parameters
+    ----------
+    filepath : click.Path
+        The filepath to the configuration file.
+    verbose : click.Choice
+        The verbosity level: warning, info or debug (default "info").
+
+    """
+    configure_logging(level=verbose)
+    # Parse YAML
+    config = parse_yaml(filepath)
+    # Perform operation
+    api_reset(config)
+
+
 @cli.group()
 def setup() -> None:  # pragma: no cover
     """Configure commands for Junifer."""
@@ -379,3 +478,49 @@ def afni_docker() -> None:  # pragma: no cover
     export PATH="$PATH:{afni_wrappers_path}"
     """
     click.secho(msg, fg="blue")
+
+
+@setup.command("fsl-docker")
+def fsl_docker() -> None:  # pragma: no cover
+    """Configure FSL-Docker wrappers."""
+    import junifer
+
+    pkg_path = Path(junifer.__path__[0])  # type: ignore
+    fsl_wrappers_path = pkg_path / "api" / "res" / "fsl"
+    msg = f"""
+    Installation instructions for FSL-Docker wrappers:
+
+    1. Install Docker: https://docs.docker.com/get-docker/
+
+    2. Get the FSL-Docker image by running this on the command line:
+
+        docker pull brainlife/fsl
+
+    3. Add this line to the ~/.bashrc or ~/.zshrc file:
+
+    export PATH="$PATH:{fsl_wrappers_path}"
+    """
+    click.secho(msg, fg="blue")
+
+
+@setup.command("ants-docker")
+def ants_docker() -> None:  # pragma: no cover
+    """Configure ANTs-Docker wrappers."""
+    import junifer
+
+    pkg_path = Path(junifer.__path__[0])  # type: ignore
+    ants_wrappers_path = pkg_path / "api" / "res" / "ants"
+    msg = f"""
+    Installation instructions for ANTs-Docker wrappers:
+
+    1. Install Docker: https://docs.docker.com/get-docker/
+
+    2. Get the ANTs-Docker image by running this on the command line:
+
+        docker pull antsx/ants
+
+    3. Add this line to the ~/.bashrc or ~/.zshrc file:
+
+    export PATH="$PATH:{ants_wrappers_path}"
+    """
+    click.secho(msg, fg="blue")