junifer 0.0.5__py3-none-any.whl → 0.0.5.dev24__py3-none-any.whl

junifer/storage/tests/test_hdf5.py

@@ -25,12 +25,7 @@ from junifer.storage.utils import (
 def test_get_valid_inputs() -> None:
     """Test valid inputs."""
     storage = HDF5FeatureStorage(uri="/tmp")
-    assert storage.get_valid_inputs() == [
-        "matrix",
-        "vector",
-        "timeseries",
-        "scalar_table",
-    ]
+    assert storage.get_valid_inputs() == ["matrix", "vector", "timeseries"]
 
 
 def test_single_output(tmp_path: Path) -> None:
@@ -813,7 +808,7 @@ def test_store_timeseries(tmp_path: Path) -> None:
     data = np.array([[10], [20], [30], [40], [50]])
     col_names = ["signal"]
 
-    # Store timeseries
+    # Store vector
     storage.store_timeseries(
         meta_md5=meta_md5,
         element=element_to_store,
@@ -827,53 +822,6 @@ def test_store_timeseries(tmp_path: Path) -> None:
     assert_array_equal(read_df.values, data)
 
 
-def test_store_scalar_table(tmp_path: Path) -> None:
-    """Test scalar table store.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
-    uri = tmp_path / "test_store_scalar_table.hdf5"
-    storage = HDF5FeatureStorage(uri=uri)
-    # Metadata to store
-    element = {"subject": "test"}
-    meta = {
-        "element": element,
-        "dependencies": ["numpy"],
-        "marker": {"name": "brainprint"},
-        "type": "FreeSurfer",
-    }
-    # Process the metadata
-    meta_md5, meta_to_store, element_to_store = process_meta(meta)
-    # Store metadata
-    storage.store_metadata(
-        meta_md5=meta_md5, element=element_to_store, meta=meta_to_store
-    )
-
-    # Data to store
-    data = np.array([[10, 20], [30, 40], [50, 60]])
-    col_names = ["roi1", "roi2"]
-    row_names = ["ev1", "ev2", "ev3"]
-
-    # Store timeseries
-    storage.store_scalar_table(
-        meta_md5=meta_md5,
-        element=element_to_store,
-        data=data,
-        col_names=col_names,
-        row_names=row_names,
-        row_header_col_name="eigenvalue",
-    )
-
-    # Read into dataframe
-    read_df = storage.read_df(feature_md5=meta_md5)
-    # Check if data are equal
-    assert_array_equal(read_df.values, data)
-
-
 def _create_data_to_store(n_elements: int, kind: str) -> Tuple[str, Dict]:
     """Create data to store.
 
@@ -906,19 +854,13 @@ def _create_data_to_store(n_elements: int, kind: str) -> Tuple[str, Dict]:
             "col_names": [f"col-{i}" for i in range(10)],
             "matrix_kind": "full",
         }
-    elif kind in "timeseries":
+    elif kind == "timeseries":
         data_to_store = {
             "data": np.arange(20).reshape(2, 10),
             "col_names": [f"col-{i}" for i in range(10)],
         }
-    elif kind in "scalar_table":
-        data_to_store = {
-            "data": np.arange(50).reshape(5, 10),
-            "row_names": [f"row-{i}" for i in range(5)],
-            "col_names": [f"col-{i}" for i in range(10)],
-            "row_header_col_name": "row",
-        }
-
+    else:
+        raise ValueError(f"Unknown kind {kind}.")
     for i in range(n_elements):
         element = {"subject": f"sub-{i // 2}", "session": f"ses-{i % 2}"}
         meta = {
@@ -961,7 +903,6 @@ def _create_data_to_store(n_elements: int, kind: str) -> Tuple[str, Dict]:
         (10, 3, "matrix"),
         (10, 5, "matrix"),
         (10, 5, "timeseries"),
-        (10, 5, "scalar_table"),
     ],
 )
 def test_multi_output_store_and_collect(
@@ -989,20 +930,21 @@ def test_multi_output_store_and_collect(
     meta_md5, all_data = _create_data_to_store(n_elements, kind)
 
     for t_data in all_data:
-        # Store metadata
+        # Store metadata for tables
         storage.store_metadata(
             meta_md5=meta_md5,
             element=t_data["element"],
             meta=t_data["meta"],
         )
-        # Store data
         if kind == "vector":
+            # Store tables
             storage.store_vector(
                 meta_md5=meta_md5,
                 element=t_data["element"],
                 **t_data["data"],
             )
         elif kind == "matrix":
+            # Store tables
             storage.store_matrix(
                 meta_md5=meta_md5,
                 element=t_data["element"],
@@ -1014,17 +956,11 @@ def test_multi_output_store_and_collect(
                 element=t_data["element"],
                 **t_data["data"],
             )
-        elif kind == "scalar_table":
-            storage.store_scalar_table(
-                meta_md5=meta_md5,
-                element=t_data["element"],
-                **t_data["data"],
-            )
     # Check that base URI does not exist yet
     assert not uri.exists()
 
     for t_data in all_data:
-        # Convert element to prefix
+        # Convert element to preifx
         prefix = element_to_prefix(t_data["element"])
         # URIs for data storage
         elem_uri = uri.parent / f"{prefix}{uri.name}"
@@ -1041,7 +977,7 @@ def test_multi_output_store_and_collect(
     # Check that base URI exists now
     assert uri.exists()
 
-    # Read unified metadata
+    # # Read unified metadata
     read_unified_meta = storage.list_features()
     assert meta_md5 in read_unified_meta
 
@@ -1053,10 +989,6 @@ def test_multi_output_store_and_collect(
         data_size = np.sum([x["data"]["data"].shape[0] for x in all_data])
         assert len(all_df) == data_size
         idx_names = [x for x in all_df.index.names if x != "timepoint"]
-    elif kind == "scalar_table":
-        data_size = np.sum([x["data"]["data"].shape[0] for x in all_data])
-        assert len(all_df) == data_size
-        idx_names = [x for x in all_df.index.names if x != "row"]
     else:
         assert len(all_df) == len(all_data)
         idx_names = all_df.index.names
@@ -1081,10 +1013,6 @@ def test_multi_output_store_and_collect(
             assert_array_equal(t_series.values, t_data["data"]["data"])
             series_names = t_series.columns.values.tolist()
             assert series_names == t_data["data"]["col_names"]
-        elif kind == "scalar_table":
-            assert_array_equal(t_series.values, t_data["data"]["data"])
-            series_names = t_series.columns.values.tolist()
-            assert series_names == t_data["data"]["col_names"]
 
 
 def test_collect_error_single_output() -> None:

junifer/storage/utils.py

@@ -14,15 +14,6 @@ import numpy as np
 from ..utils.logging import logger, raise_error
 
 
-__all__ = [
-    "get_dependency_version",
-    "process_meta",
-    "element_to_prefix",
-    "store_matrix_checks",
-    "matrix_to_vector",
-]
-
-
 def get_dependency_version(dependency: str) -> str:
     """Get dependency version.
 

junifer/testing/__init__.py

@@ -1,4 +1,4 @@
-"""Testing components."""
+"""Provide imports for testing sub-package."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Synchon Mandal <s.mandal@fz-juelich.de>
@@ -6,6 +6,3 @@
 
 from . import datagrabbers
 from .utils import get_testing_data
-
-
-__all__ = ["datagrabbers", "get_testing_data"]

junifer/testing/datagrabbers.py

@@ -1,4 +1,4 @@
-"""Testing DataGrabbers."""
+"""Provide testing DataGrabbers."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Synchon Mandal <s.mandal@fz-juelich.de>
@@ -14,13 +14,6 @@ from nilearn import datasets, image
 from ..datagrabber.base import BaseDataGrabber
 
 
-__all__ = [
-    "OasisVBMTestingDataGrabber",
-    "SPMAuditoryTestingDataGrabber",
-    "PartlyCloudyTestingDataGrabber",
-]
-
-
 class OasisVBMTestingDataGrabber(BaseDataGrabber):
     """DataGrabber for Oasis VBM testing data.
 
@@ -188,7 +181,7 @@ class PartlyCloudyTestingDataGrabber(BaseDataGrabber):
         """Initialize the class."""
         datadir = tempfile.mkdtemp()
         # Define types
-        types = ["BOLD"]
+        types = ["BOLD", "BOLD_confounds"]
         self.reduce_confounds = reduce_confounds
         self.age_group = age_group
         super().__init__(types=types, datadir=datadir)
@@ -249,10 +242,10 @@ class PartlyCloudyTestingDataGrabber(BaseDataGrabber):
         out["BOLD"] = {
             "path": Path(self._dataset["func"][i_sub]),
             "space": "MNI152NLin2009cAsym",
-            "confounds": {
-                "path": Path(self._dataset["confounds"][i_sub]),
-                "format": "fmriprep",
-            },
+        }
+        out["BOLD_confounds"] = {
+            "path": Path(self._dataset["confounds"][i_sub]),
+            "format": "fmriprep",
         }
 
         return out

junifer/testing/tests/test_partlycloudytesting_datagrabber.py

@@ -28,13 +28,13 @@ def test_PartlyCloudyTestingDataGrabber() -> None:
         assert out["BOLD"]["path"].exists()
         assert out["BOLD"]["path"].is_file()
 
-        assert "confounds" in out["BOLD"]
-        assert out["BOLD"]["confounds"]["path"].exists()
-        assert out["BOLD"]["confounds"]["path"].is_file()
-        assert "format" in out["BOLD"]["confounds"]
-        assert "fmriprep" == out["BOLD"]["confounds"]["format"]
+        assert "BOLD_confounds" in out
+        assert out["BOLD_confounds"]["path"].exists()
+        assert out["BOLD_confounds"]["path"].is_file()
+        assert "format" in out["BOLD_confounds"]
+        assert "fmriprep" == out["BOLD_confounds"]["format"]
 
     with PartlyCloudyTestingDataGrabber(reduce_confounds=False) as dg:
         out = dg["sub-01"]
-        assert "format" in out["BOLD"]["confounds"]
-        assert "fmriprep" == out["BOLD"]["confounds"]["format"]
+        assert "format" in out["BOLD_confounds"]
+        assert "fmriprep" == out["BOLD_confounds"]["format"]

junifer/testing/utils.py

@@ -6,9 +6,6 @@
 from pathlib import Path
 
 
-__all__ = ["get_testing_data"]
-
-
 def get_testing_data(fname: str) -> Path:
     """Get the path to a testing data file.
 

junifer/utils/__init__.py

@@ -1,4 +1,4 @@
-"""General utilities and helpers."""
+"""Provide imports for utils sub-package."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Synchon Mandal <s.mandal@fz-juelich.de>
@@ -6,15 +6,4 @@
 
 from .fs import make_executable
 from .logging import configure_logging, logger, raise_error, warn_with_log
-from .helpers import run_ext_cmd, deep_update
-
-
-__all__ = [
-    "make_executable",
-    "configure_logging",
-    "logger",
-    "raise_error",
-    "warn_with_log",
-    "run_ext_cmd",
-    "deep_update",
-]
+from .helpers import run_ext_cmd

junifer/utils/fs.py

@@ -8,9 +8,6 @@ import stat
 from pathlib import Path
 
 
-__all__ = ["make_executable"]
-
-
 def make_executable(path: Path) -> None:
     """Make ``path`` executable.
 

junifer/utils/helpers.py

@@ -3,16 +3,12 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-import collections.abc
 import subprocess
-from typing import Dict, List
+from typing import List
 
 from .logging import logger, raise_error
 
 
-__all__ = ["run_ext_cmd", "deep_update"]
-
-
 def run_ext_cmd(name: str, cmd: List[str]) -> None:
     """Run external command via subprocess.
 
@@ -55,30 +51,3 @@ def run_ext_cmd(name: str, cmd: List[str]) -> None:
             ),
             klass=RuntimeError,
         )
-
-
-def deep_update(d: Dict, u: Dict) -> Dict:
-    """Deep update `d` with `u`.
-
-    From: "https://stackoverflow.com/questions/3232943/update-value-of-a-nested
-    -dictionary-of-varying-depth"
-
-    Parameters
-    ----------
-    d : dict
-        The dictionary to deep-update.
-    u : dict
-        The dictionary to deep-update `d` with.
-
-    Returns
-    -------
-    dict
-        The updated dictionary.
-
-    """
-    for k, v in u.items():
-        if isinstance(v, collections.abc.Mapping):
-            d[k] = deep_update(d.get(k, {}), v)
-        else:
-            d[k] = v
-    return d

junifer/utils/logging.py

@@ -4,16 +4,13 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-import sys
-
-
-if sys.version_info < (3, 12):
+try:
     from distutils.version import LooseVersion
-else:  # pragma: no cover
+except ImportError:  # pragma: no cover
     from looseversion import LooseVersion
 
 import logging
-import warnings
+import sys
 from pathlib import Path
 from subprocess import PIPE, Popen, TimeoutExpired
 from typing import Dict, NoReturn, Optional, Type, Union
@@ -22,16 +19,6 @@ from warnings import warn
 import datalad
 
 
-__all__ = [
-    "WrapStdOut",
-    "get_versions",
-    "log_versions",
-    "configure_logging",
-    "raise_error",
-    "warn_with_log",
-]
-
-
 logger = logging.getLogger("JUNIFER")
 
 # Set up datalad logger level to warning by default
@@ -45,23 +32,6 @@ _logging_types = {
 }
 
 
-# Copied over from stdlib and tweaked to our use-case.
-def _showwarning(message, category, filename, lineno, file=None, line=None):
-    s = warnings.formatwarning(message, category, filename, lineno, line)
-    logger.warning(str(s))
-
-
-# Overwrite warnings display to integrate with logging
-
-
-def capture_warnings():
-    """Capture warnings and log them."""
-    warnings.showwarning = _showwarning
-
-
-capture_warnings()
-
-
 class WrapStdOut(logging.StreamHandler):
     """Dynamically wrap to sys.stdout.
 
@@ -343,4 +313,5 @@ def warn_with_log(
         The warning subclass (default RuntimeWarning).
 
     """
+    logger.warning(msg)
     warn(msg, category=category, stacklevel=2)

junifer/utils/tests/test_logging.py

@@ -145,16 +145,8 @@ def test_log_file(tmp_path: Path) -> None:
         assert any("Warn3 message" in line for line in lines)
         assert any("Error3 message" in line for line in lines)
 
-    # This should raise a warning (test that it was raised)
     with pytest.warns(RuntimeWarning, match=r"Warn raised"):
         warn_with_log("Warn raised")
-
-    # This should log the warning (workaround for pytest messing with logging)
-    from junifer.utils.logging import capture_warnings
-
-    capture_warnings()
-
-    warn_with_log("Warn raised 2")
     with pytest.raises(ValueError, match=r"Error raised"):
         raise_error("Error raised")
     with open(tmp_path / "test4.log") as f:

{junifer-0.0.5.dist-info → junifer-0.0.5.dev24.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5
+Version: 0.0.5.dev24
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
@@ -29,20 +29,19 @@ Description-Content-Type: text/markdown
 License-File: LICENSE.md
 License-File: AUTHORS.rst
 Requires-Dist: click <8.2,>=8.1.3
-Requires-Dist: numpy <2.0.0,>=1.24.0
-Requires-Dist: scipy <=1.14.0,>=1.10.0
-Requires-Dist: datalad <1.2.0,>=1.0.0
-Requires-Dist: pandas <2.3.0,>=2.0.0
-Requires-Dist: nibabel <5.3.0,>=5.2.0
-Requires-Dist: nilearn <=0.10.4,>=0.10.3
-Requires-Dist: sqlalchemy <=2.1.0,>=2.0.25
+Requires-Dist: numpy <1.27,>=1.24
+Requires-Dist: scipy <=1.11.4,>=1.9.0
+Requires-Dist: datalad <0.20,>=0.15.4
+Requires-Dist: pandas <2.2,>=1.4.0
+Requires-Dist: nibabel <5.11,>=3.2.0
+Requires-Dist: nilearn <=0.10.2,>=0.9.0
+Requires-Dist: sqlalchemy <=2.1.0,>=1.4.27
 Requires-Dist: ruamel.yaml <0.18,>=0.17
 Requires-Dist: h5py >=3.10
 Requires-Dist: httpx[http2] ==0.26.0
 Requires-Dist: tqdm ==4.66.1
 Requires-Dist: templateflow >=23.0.0
-Requires-Dist: lapy <2.0.0,>=1.0.0
-Requires-Dist: importlib-metadata ; python_version < "3.9"
+Requires-Dist: importlib-metadata ; python_version < "3.10"
 Requires-Dist: looseversion ==1.3.0 ; python_version >= "3.12"
 Provides-Extra: all
 Requires-Dist: bctpy ==0.6.0 ; extra == 'all'
@@ -53,14 +52,14 @@ Provides-Extra: dev
 Requires-Dist: tox ; extra == 'dev'
 Requires-Dist: pre-commit ; extra == 'dev'
 Provides-Extra: docs
-Requires-Dist: seaborn <0.14.0,>=0.13.0 ; extra == 'docs'
-Requires-Dist: sphinx <7.4.0,>=7.3.0 ; extra == 'docs'
-Requires-Dist: sphinx-gallery <0.17.0,>=0.15.0 ; extra == 'docs'
-Requires-Dist: furo <2024.6.0,>=2024.4.27 ; extra == 'docs'
-Requires-Dist: numpydoc <1.8.0,>=1.6.0 ; extra == 'docs'
-Requires-Dist: julearn ==0.3.3 ; extra == 'docs'
+Requires-Dist: seaborn <0.13,>=0.11.2 ; extra == 'docs'
+Requires-Dist: sphinx <7.3,>=5.3.0 ; extra == 'docs'
+Requires-Dist: sphinx-gallery <0.15.0,>=0.11.0 ; extra == 'docs'
+Requires-Dist: furo <2023.10.0,>=2022.9.29 ; extra == 'docs'
+Requires-Dist: numpydoc <1.6,>=1.5.0 ; extra == 'docs'
+Requires-Dist: julearn <0.4,>=0.3.0 ; extra == 'docs'
 Requires-Dist: sphinx-copybutton <0.5.3,>=0.5.1 ; extra == 'docs'
-Requires-Dist: towncrier <23.12.0,>=23.10.0 ; extra == 'docs'
+Requires-Dist: towncrier <23.7,>=22.12.0 ; extra == 'docs'
 Requires-Dist: sphinxcontrib-mermaid <0.10,>=0.8.1 ; extra == 'docs'
 Provides-Extra: neurokit2
 Requires-Dist: neurokit2 >=0.1.7 ; extra == 'neurokit2'