junifer 0.0.5__py3-none-any.whl → 0.0.5.dev11__py3-none-any.whl

junifer/__init__.py

@@ -20,20 +20,3 @@ from . import (
     onthefly,
 )
 from ._version import __version__
-
-
-__all__ = [
-    "api",
-    "configs",
-    "data",
-    "datagrabber",
-    "datareader",
-    "markers",
-    "pipeline",
-    "preprocess",
-    "stats",
-    "storage",
-    "utils",
-    "external",
-    "onthefly",
-]

junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.5'
-__version_tuple__ = version_tuple = (0, 0, 5)
+__version__ = version = '0.0.5.dev11'
+__version_tuple__ = version_tuple = (0, 0, 5, 'dev11')

junifer/api/__init__.py

@@ -1,4 +1,4 @@
-"""Public API and CLI components."""
+"""Provide imports for api sub-package."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Synchon Mandal <s.mandal@fz-juelich.de>
@@ -7,6 +7,3 @@
 from . import decorators
 from .cli import cli
 from .functions import collect, queue, run
-
-
-__all__ = ["decorators", "cli", "collect", "queue", "run"]

junifer/api/cli.py

@@ -8,7 +8,7 @@ import pathlib
 import subprocess
 import sys
 from pathlib import Path
-from typing import Dict, List, Optional, Tuple, Union
+from typing import Dict, List, Tuple, Union
 
 import click
 import pandas as pd
@@ -20,7 +20,6 @@ from ..utils.logging import (
     warn_with_log,
 )
 from .functions import collect as api_collect
-from .functions import list_elements as api_list_elements
 from .functions import queue as api_queue
 from .functions import reset as api_reset
 from .functions import run as api_run
@@ -452,69 +451,6 @@ def reset(
     api_reset(config)
 
 
-@cli.command()
-@click.argument(
-    "filepath",
-    type=click.Path(
-        exists=True, readable=True, dir_okay=False, path_type=pathlib.Path
-    ),
-)
-@click.option("--element", type=str, multiple=True)
-@click.option(
-    "-o",
-    "--output-file",
-    type=click.Path(dir_okay=False, writable=True, path_type=pathlib.Path),
-)
-@click.option(
-    "-v",
-    "--verbose",
-    type=click.UNPROCESSED,
-    callback=_validate_verbose,
-    default="info",
-)
-def list_elements(
-    filepath: click.Path,
-    element: Tuple[str],
-    output_file: Optional[click.Path],
-    verbose: Union[str, int],
-) -> None:
-    """Element listing command for CLI.
-
-    \f
-
-    Parameters
-    ----------
-    filepath : click.Path
-        The filepath to the configuration file.
-    element : tuple of str
-        The element to operate on.
-    output_file : click.Path or None
-        The path to write the output to. If not None, writing to
-        stdout is not performed.
-    verbose : click.Choice
-        The verbosity level: warning, info or debug (default "info").
-
-    """
-    configure_logging(level=verbose)
-    # Parse YAML
-    config = parse_yaml(filepath)  # type: ignore
-    # Fetch datagrabber
-    datagrabber = config["datagrabber"]
-    # Parse elements
-    elements = _parse_elements(element, config)
-    # Perform operation
-    listed_elements = api_list_elements(
-        datagrabber=datagrabber,
-        elements=elements,
-    )
-    # Check if output file is provided
-    if output_file is not None:
-        output_file.touch()
-        output_file.write_text(listed_elements)
-    else:
-        click.secho(listed_elements, fg="blue")
-
-
 @cli.group()
 def setup() -> None:  # pragma: no cover
     """Configure commands for Junifer."""
@@ -588,29 +524,3 @@ def ants_docker() -> None:  # pragma: no cover
     export PATH="$PATH:{ants_wrappers_path}"
     """
     click.secho(msg, fg="blue")
-
-
-@setup.command("freesurfer-docker")
-def freesurfer_docker() -> None:  # pragma: no cover
-    """Configure FreeSurfer-Docker wrappers."""
-    import junifer
-
-    pkg_path = Path(junifer.__path__[0])  # type: ignore
-    fs_wrappers_path = pkg_path / "api" / "res" / "freesurfer"
-    msg = f"""
-    Installation instructions for FreeSurfer-Docker wrappers:
-
-    1. Install Docker: https://docs.docker.com/get-docker/
-
-    2. Get the FreeSurfer-Docker image by running this on the command line:
-
-        docker pull freesurfer/freesurfer
-
-    3. Get license from: https://surfer.nmr.mgh.harvard.edu/registration.html .
-       You can skip this step if you already have one.
-
-    4. Add this line to the ~/.bashrc or ~/.zshrc file:
-
-    export PATH="$PATH:{fs_wrappers_path}"
-    """
-    click.secho(msg, fg="blue")

junifer/api/decorators.py

@@ -10,15 +10,6 @@ from typing import Type
 from ..pipeline.registry import register
 
 
-__all__ = [
-    "register_datagrabber",
-    "register_datareader",
-    "register_preprocessor",
-    "register_marker",
-    "register_storage",
-]
-
-
 def register_datagrabber(klass: Type) -> Type:
     """Register DataGrabber.
 

junifer/api/functions.py

@@ -5,7 +5,6 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-import os
 import shutil
 import typing
 from pathlib import Path
@@ -23,9 +22,6 @@ from .queue_context import GnuParallelLocalAdapter, HTCondorAdapter
 from .utils import yaml
 
 
-__all__ = ["run", "collect", "queue", "reset", "list_elements"]
-
-
 def _get_datagrabber(datagrabber_config: Dict) -> BaseDataGrabber:
     """Get DataGrabber.
 
@@ -95,7 +91,7 @@ def run(
     datagrabber : dict
         DataGrabber to use. Must have a key ``kind`` with the kind of
         DataGrabber to use. All other keys are passed to the DataGrabber
-        constructor.
+        init function.
     markers : list of dict
         List of markers to extract. Each marker is a dict with at least two
         keys: ``name`` and ``kind``. The ``name`` key is used to name the
@@ -105,11 +101,11 @@ def run(
     storage : dict
         Storage to use. Must have a key ``kind`` with the kind of
         storage to use. All other keys are passed to the storage
-        constructor.
+        init function.
     preprocessors : list of dict, optional
         List of preprocessors to use. Each preprocessor is a dict with at
         least a key ``kind`` specifying the preprocessor to use. All other keys
-        are passed to the preprocessor constructor (default None).
+        are passed to the preprocessor init function (default None).
     elements : str or tuple or list of str or tuple, optional
         Element(s) to process. Will be used to index the DataGrabber
         (default None).
@@ -191,7 +187,7 @@ def collect(storage: Dict) -> None:
     storage : dict
         Storage to use. Must have a key ``kind`` with the kind of
         storage to use. All other keys are passed to the storage
-        constructor.
+        init function.
 
     """
     storage_params = storage.copy()
@@ -343,12 +339,12 @@ def reset(config: Dict) -> None:
     storage = config["storage"]
     storage_uri = Path(storage["uri"])
     logger.info(f"Deleting {storage_uri.resolve()!s}")
-    # Delete storage
+    # Delete storage; will be str
     if storage_uri.exists():
-        # Delete files in the job storage directory
-        for file in storage_uri.parent.iterdir():
+        # Delete files in the directory
+        for file in storage_uri.iterdir():
             file.unlink(missing_ok=True)
-        # Remove job storage directory
+        # Remove directory
         storage_uri.parent.rmdir()
 
     # Fetch job name (if present)
@@ -363,47 +359,5 @@ def reset(config: Dict) -> None:
         if job_dir.exists():
             # Remove files and directories
             shutil.rmtree(job_dir)
-            # Remove parent directory (if empty)
-            if not next(os.scandir(job_dir.parent), None):
-                job_dir.parent.rmdir()
-
-
-def list_elements(
-    datagrabber: Dict,
-    elements: Union[str, List[Union[str, Tuple]], Tuple, None] = None,
-) -> str:
-    """List elements of the datagrabber filtered using `elements`.
-
-    Parameters
-    ----------
-    datagrabber : dict
-        DataGrabber to index. Must have a key ``kind`` with the kind of
-        DataGrabber to use. All other keys are passed to the DataGrabber
-        constructor.
-    elements : str or tuple or list of str or tuple, optional
-        Element(s) to filter using. Will be used to index the DataGrabber
-        (default None).
-
-    """
-    # Get datagrabber to use
-    datagrabber_object = _get_datagrabber(datagrabber)
-
-    # Fetch elements
-    raw_elements_to_list = []
-    with datagrabber_object:
-        if elements is not None:
-            for element in datagrabber_object.filter(elements):
-                raw_elements_to_list.append(element)
-        else:
-            for element in datagrabber_object:
-                raw_elements_to_list.append(element)
-
-    elements_to_list = []
-    for element in raw_elements_to_list:
-        # Stringify elements if tuple for operation
-        str_element = (
-            ",".join(element) if isinstance(element, tuple) else element
-        )
-        elements_to_list.append(str_element)
-
-    return "\n".join(elements_to_list)
+            # Remove directory
+            job_dir.parent.rmdir()

junifer/api/parser.py

@@ -14,9 +14,6 @@ from ..utils.logging import logger, raise_error
 from .utils import yaml
 
 
-__all__ = ["parse_yaml"]
-
-
 def parse_yaml(filepath: Union[str, Path]) -> Dict:
     """Parse YAML.
 

junifer/api/queue_context/__init__.py

@@ -1,4 +1,4 @@
-"""Context adapters for queueing."""
+"""Provide imports for queue context sub-package."""
 
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
@@ -6,6 +6,3 @@
 from .queue_context_adapter import QueueContextAdapter
 from .htcondor_adapter import HTCondorAdapter
 from .gnu_parallel_local_adapter import GnuParallelLocalAdapter
-
-
-__all__ = ["QueueContextAdapter", "HTCondorAdapter", "GnuParallelLocalAdapter"]

junifer/api/res/afni/run_afni_docker.sh

@@ -31,7 +31,7 @@ if [ -d "${var}" ]; then
 done
 
 echo "Docker args: ${docker_args[*]}" >&2
-echo "Corrected args for AFNI: ${corrected_args[*]}" >&2
+echo "Corrected args for afni: ${corrected_args[*]}" >&2
 
 cwd=$(pwd)
 cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} afni/afni_make_build ${corrected_args[*]}"

junifer/api/res/ants/run_ants_docker.sh

@@ -31,7 +31,7 @@ if [ -d "${var}" ]; then
 done
 
 echo "Docker args: ${docker_args[*]}" >&2
-echo "Corrected args for ANTs: ${corrected_args[*]}" >&2
+echo "Corrected args for fsl: ${corrected_args[*]}" >&2
 
 cwd=$(pwd)
 cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} antsx/ants ${corrected_args[*]}"

junifer/api/res/fsl/run_fsl_docker.sh

@@ -31,7 +31,7 @@ if [ -d "${var}" ]; then
 done
 
 echo "Docker args: ${docker_args[*]}" >&2
-echo "Corrected args for FSL: ${corrected_args[*]}" >&2
+echo "Corrected args for fsl: ${corrected_args[*]}" >&2
 
 cwd=$(pwd)
 cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} brainlife/fsl ${corrected_args[*]}"

junifer/api/tests/test_api_utils.py

@@ -4,7 +4,6 @@
 # License: AGPL
 
 import platform as pl
-import sys
 
 import pytest
 
@@ -46,11 +45,11 @@ def test_get_dependency_information_short() -> None:
         "httpx",
         "tqdm",
         "templateflow",
-        "lapy",
         "looseversion",
     ]
 
-    if sys.version_info < (3, 11):
+    python_minor_version = int(pl.python_version_tuple()[1])
+    if python_minor_version < 10:
         dependency_list.append("importlib_metadata")
 
     assert frozenset(dependency_information.keys()) == frozenset(
@@ -75,7 +74,6 @@ def test_get_dependency_information_long() -> None:
         "httpx",
         "tqdm",
         "templateflow",
-        "lapy",
     ]
     for key in dependency_list:
         assert key in dependency_information_keys

junifer/api/tests/test_cli.py

@@ -14,7 +14,6 @@ from ruamel.yaml import YAML
 from junifer.api.cli import (
     _parse_elements_file,
     collect,
-    list_elements,
     queue,
     reset,
     run,
@@ -298,88 +297,6 @@ def test_reset(
         assert reset_result.exit_code == 0
 
 
-@pytest.mark.parametrize(
-    "elements",
-    [
-        ("sub-01", "sub-02"),
-        ("sub-03", "sub-04"),
-    ],
-)
-def test_list_elements_stdout(
-    elements: Tuple[str, ...],
-) -> None:
-    """Test elements listing to stdout.
-
-    Parameters
-    ----------
-    elements : tuple of str
-        The parametrized elements for filtering.
-
-    """
-    # Get test config
-    infile = Path(__file__).parent / "data" / "partly_cloudy_agg_mean_tian.yml"
-    # List elements command arguments
-    list_elements_args = [
-        str(infile.absolute()),
-        "--verbose",
-        "debug",
-        "--element",
-        elements[0],
-        "--element",
-        elements[1],
-    ]
-    # Invoke list elements command
-    list_elements_result = runner.invoke(list_elements, list_elements_args)
-    # Check
-    assert list_elements_result.exit_code == 0
-    assert f"{elements[0]}\n{elements[1]}" in list_elements_result.stdout
-
-
-@pytest.mark.parametrize(
-    "elements",
-    [
-        ("sub-01", "sub-02"),
-        ("sub-03", "sub-04"),
-    ],
-)
-def test_list_elements_output_file(
-    tmp_path: Path,
-    elements: Tuple[str, ...],
-) -> None:
-    """Test elements listing to output file.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-    elements : tuple of str
-        The parametrized elements for filtering.
-
-    """
-    # Get test config
-    infile = Path(__file__).parent / "data" / "partly_cloudy_agg_mean_tian.yml"
-    # Output file
-    output_file = tmp_path / "elements.txt"
-    # List elements command arguments
-    list_elements_args = [
-        str(infile.absolute()),
-        "--verbose",
-        "debug",
-        "--element",
-        elements[0],
-        "--element",
-        elements[1],
-        "--output-file",
-        str(output_file.resolve()),
-    ]
-    # Invoke list elements command
-    list_elements_result = runner.invoke(list_elements, list_elements_args)
-    # Check
-    assert list_elements_result.exit_code == 0
-    with open(output_file) as f:
-        assert f"{elements[0]}\n{elements[1]}" == f.read()
-
-
 def test_wtf_short() -> None:
     """Test short version of wtf command."""
     # Invoke wtf command

junifer/api/tests/test_functions.py

@@ -7,13 +7,13 @@
 
 import logging
 from pathlib import Path
-from typing import Dict, List, Optional, Tuple, Union
+from typing import Dict, List, Tuple, Union
 
 import pytest
 from ruamel.yaml import YAML
 
 import junifer.testing.registry  # noqa: F401
-from junifer.api.functions import collect, list_elements, queue, reset, run
+from junifer.api.functions import collect, queue, reset, run
 from junifer.datagrabber.base import BaseDataGrabber
 from junifer.pipeline.registry import build
 
@@ -637,28 +637,3 @@ def test_reset_queue(
 
         assert not Path(storage["uri"]).exists()
         assert not (tmp_path / "junifer_jobs" / job_name).exists()
-
-
-@pytest.mark.parametrize(
-    "elements",
-    [
-        ["sub-01"],
-        None,
-    ],
-)
-def test_list_elements(
-    datagrabber: Dict[str, str],
-    elements: Optional[List[str]],
-) -> None:
-    """Test elements listing.
-
-    Parameters
-    ----------
-    datagrabber : dict
-        Testing datagrabber as dictionary.
-    elements : str of list of str
-        The parametrized elements for filtering.
-
-    """
-    listed_elements = list_elements(datagrabber, elements)
-    assert "sub-01" in listed_elements

junifer/configs/__init__.py

@@ -1,4 +1,4 @@
-"""Custom components for specific platforms."""
+"""Provide imports for configs sub-package."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 # License: AGPL

junifer/configs/juseless/__init__.py

@@ -1,9 +1,6 @@
-"""Custom components for FZJ INM-7's beloved juseless."""
+"""Provide imports for juseless sub-package."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 # License: AGPL
 
 from . import datagrabbers
-
-
-__all__ = ["datagrabbers"]

junifer/configs/juseless/datagrabbers/__init__.py

@@ -1,4 +1,4 @@
-"""Custom DataGrabbers for FZJ INM-7's beloved juseless."""
+"""Provide imports for datagrabbers sub-package."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
@@ -10,12 +10,3 @@ from .camcan_vbm import JuselessDataladCamCANVBM
 from .ixi_vbm import JuselessDataladIXIVBM
 from .ucla import JuselessUCLA
 from .ukb_vbm import JuselessDataladUKBVBM
-
-
-__all__ = [
-    "JuselessDataladAOMICID1000VBM",
-    "JuselessDataladCamCANVBM",
-    "JuselessDataladIXIVBM",
-    "JuselessUCLA",
-    "JuselessDataladUKBVBM",
-]

junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py

@@ -11,9 +11,6 @@ from ....api.decorators import register_datagrabber
 from ....datagrabber import PatternDataladDataGrabber
 
 
-__all__ = ["JuselessDataladAOMICID1000VBM"]
-
-
 @register_datagrabber
 class JuselessDataladAOMICID1000VBM(PatternDataladDataGrabber):
     """Concrete implementation for Juseless AOMIC ID1000 VBM data fetching.

junifer/configs/juseless/datagrabbers/camcan_vbm.py

@@ -12,9 +12,6 @@ from ....api.decorators import register_datagrabber
 from ....datagrabber import PatternDataladDataGrabber
 
 
-__all__ = ["JuselessDataladCamCANVBM"]
-
-
 @register_datagrabber
 class JuselessDataladCamCANVBM(PatternDataladDataGrabber):
     """Concrete implementation for Juseless CamCAN VBM data fetching.

junifer/configs/juseless/datagrabbers/ixi_vbm.py

@@ -13,9 +13,6 @@ from ....datagrabber import PatternDataladDataGrabber
 from ....utils import raise_error
 
 
-__all__ = ["JuselessDataladIXIVBM"]
-
-
 @register_datagrabber
 class JuselessDataladIXIVBM(PatternDataladDataGrabber):
     """Concrete implementation for Juseless IXI VBM data fetching.

junifer/configs/juseless/datagrabbers/tests/test_ucla.py

@@ -27,6 +27,7 @@ def test_JuselessUCLA() -> None:
 
         types = [
             "BOLD",
+            "BOLD_confounds",
             "T1w",
             "VBM_CSF",
             "VBM_GM",
@@ -42,11 +43,12 @@ def test_JuselessUCLA() -> None:
     "types",
     [
         "BOLD",
+        "BOLD_confounds",
         "T1w",
         "VBM_CSF",
         "VBM_GM",
         "VBM_WM",
-        ["BOLD", "VBM_CSF"],
+        ["BOLD", "BOLD_confounds"],
         ["T1w", "VBM_CSF"],
         ["VBM_GM", "VBM_WM"],
         ["BOLD", "T1w"],

junifer/configs/juseless/datagrabbers/ucla.py

@@ -12,9 +12,6 @@ from ....datagrabber import PatternDataGrabber
 from ....utils import raise_error
 
 
-__all__ = ["JuselessUCLA"]
-
-
 @register_datagrabber
 class JuselessUCLA(PatternDataGrabber):
     """Concrete implementation for Juseless UCLA data fetching.
@@ -26,8 +23,8 @@ class JuselessUCLA(PatternDataGrabber):
     datadir : str or Path, optional
         The directory where the dataset is stored.
         (default "/data/project/psychosis_thalamus/data/fmriprep").
-    types: {"BOLD", "T1w", "VBM_CSF", "VBM_GM", "VBM_WM"} or \
-           list of the options, optional
+    types: {"BOLD", "BOLD_confounds", "T1w", "VBM_CSF", "VBM_GM", \
+           "VBM_WM"} or a list of the options, optional
         UCLA data types. If None, all available data types are selected.
         (default None).
     tasks : {"rest", "bart", "bht", "pamenc", "pamret", \
@@ -79,13 +76,13 @@ class JuselessUCLA(PatternDataGrabber):
                     "MNI152NLin2009cAsym_preproc.nii.gz"
                 ),
                 "space": "MNI152NLin2009cAsym",
-                "confounds": {
-                    "pattern": (
-                        "{subject}/func/{subject}_"
-                        "task-{task}_bold_confounds.tsv"
-                    ),
-                    "space": "fmriprep",
-                },
+            },
+            "BOLD_confounds": {
+                "pattern": (
+                    "{subject}/func/{subject}_"
+                    "task-{task}_bold_confounds.tsv"
+                ),
+                "space": "fmriprep",
             },
             "T1w": {
                 "pattern": (

junifer/configs/juseless/datagrabbers/ukb_vbm.py

@@ -12,9 +12,6 @@ from ....api.decorators import register_datagrabber
 from ....datagrabber import PatternDataladDataGrabber
 
 
-__all__ = ["JuselessDataladUKBVBM"]
-
-
 @register_datagrabber
 class JuselessDataladUKBVBM(PatternDataladDataGrabber):
     """Concrete implementation for Juseless UKB VBM data fetching.