junifer 0.0.4.dev470__tar.gz → 0.0.4.dev486__tar.gz

{junifer-0.0.4.dev470 → junifer-0.0.4.dev486}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev470
+Version: 0.0.4.dev486
 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>
@@ -28,6 +28,7 @@ License-File: LICENSE.md
 License-File: AUTHORS.rst
 Requires-Dist: click<8.2,>=8.1.3
 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
@@ -73,6 +74,7 @@ Requires-Dist: sphinxcontrib-mermaid<0.10,>=0.8.1; extra == "docs"
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/charliermarsh/ruff)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8176570.svg)](https://doi.org/10.5281/zenodo.8176570)
+[![FAIR checklist badge](https://fairsoftwarechecklist.net/badge.svg)](https://fairsoftwarechecklist.net/v0.2?f=31&a=32113&i=32322&r=133)
 
 ## About
 

{junifer-0.0.4.dev470 → junifer-0.0.4.dev486}/README.md

@@ -12,6 +12,7 @@
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/charliermarsh/ruff)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8176570.svg)](https://doi.org/10.5281/zenodo.8176570)
+[![FAIR checklist badge](https://fairsoftwarechecklist.net/badge.svg)](https://fairsoftwarechecklist.net/v0.2?f=31&a=32113&i=32322&r=133)
 
 ## About
 

junifer-0.0.4.dev486/docs/changes/newsfragments/287.enh

@@ -0,0 +1 @@
+Add ``mode`` as an aggregation function option in :func:`.get_aggfunc_by_name` by `Synchon Mandal`_

junifer-0.0.4.dev486/docs/changes/newsfragments/294.misc

@@ -0,0 +1 @@
+Update ``pyproject.toml`` and add FAIR shield in ``README.md`` by `Synchon Mandal`_

{junifer-0.0.4.dev470 → junifer-0.0.4.dev486}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.4.dev470'
-__version_tuple__ = version_tuple = (0, 0, 4, 'dev470')
+__version__ = version = '0.0.4.dev486'
+__version_tuple__ = version_tuple = (0, 0, 4, 'dev486')

{junifer-0.0.4.dev470 → junifer-0.0.4.dev486}/junifer/api/tests/test_api_utils.py

@@ -35,6 +35,7 @@ def test_get_dependency_information_short() -> None:
     assert list(dependency_information.keys()) == [
         "click",
         "numpy",
+        "scipy",
         "datalad",
         "pandas",
         "nibabel",
@@ -51,6 +52,7 @@ def test_get_dependency_information_long() -> None:
     for key in [
         "click",
         "numpy",
+        "scipy",
         "datalad",
         "pandas",
         "nibabel",

{junifer-0.0.4.dev470 → junifer-0.0.4.dev486}/junifer/stats.py

@@ -7,7 +7,7 @@
 from typing import Any, Callable, Dict, List, Optional
 
 import numpy as np
-from scipy.stats import trim_mean
+from scipy.stats import mode, trim_mean
 from scipy.stats.mstats import winsorize
 
 from .utils import logger, raise_error
@@ -24,10 +24,11 @@ def get_aggfunc_by_name(
         Name to identify the function. Currently supported names and
         corresponding functions are:
 
-        * ``winsorized_mean`` -> :func:`scipy.stats.mstats.winsorize`
         * ``mean`` -> :func:`numpy.mean`
-        * ``std`` -> :func:`numpy.std`
+        * ``winsorized_mean`` -> :func:`scipy.stats.mstats.winsorize`
         * ``trim_mean`` -> :func:`scipy.stats.trim_mean`
+        * ``mode`` -> :func:`scipy.stats.mode`
+        * ``std`` -> :func:`numpy.std`
         * ``count`` -> :func:`.count`
         * ``select`` -> :func:`.select`
 
@@ -40,6 +41,7 @@ def get_aggfunc_by_name(
     -------
     function
         Respective function with ``func_params`` parameter set.
+
     """
     from functools import partial  # local import to avoid sphinx error
 
@@ -51,6 +53,7 @@ def get_aggfunc_by_name(
         "trim_mean",
         "count",
         "select",
+        "mode",
     }
     if func_params is None:
         func_params = {}
@@ -93,6 +96,8 @@ def get_aggfunc_by_name(
         elif pick is not None and drop is not None:
             raise_error("Either pick or drop must be specified, not both.")
         func = partial(select, **func_params)
+    elif name == "mode":
+        func = partial(mode, **func_params)
     else:
         raise_error(
             f"Function {name} unknown. Please provide any of "
@@ -115,6 +120,7 @@ def count(data: np.ndarray, axis: int = 0) -> np.ndarray:
     -------
     numpy.ndarray
         Number of elements along the given axis.
+
     """
     ax_size = data.shape[axis]
     if axis < 0:
@@ -137,7 +143,7 @@ def winsorized_mean(
         The axis to calculate winsorized mean on (default None).
     **win_params : dict
         Dictionary containing the keyword arguments for the winsorize function.
-        E.g. ``{'limits': [0.1, 0.1]}``.
+        E.g., ``{'limits': [0.1, 0.1]}``.
 
     Returns
     -------
@@ -149,6 +155,7 @@ def winsorized_mean(
     --------
     scipy.stats.mstats.winsorize :
         The winsorize function used in this function.
+
     """
     win_dat = winsorize(data, axis=axis, **win_params)
     win_mean = win_dat.mean(axis=axis)
@@ -180,6 +187,13 @@ def select(
     numpy.ndarray
         Subset of the inputted data with the select settings
         applied as specified in ``select_params``.
+
+    Raises
+    ------
+    ValueError
+        If both ``pick`` and ``drop`` are None or
+        if both ``pick`` and ``drop`` are not None.
+
     """
 
     if pick is None and drop is None:

{junifer-0.0.4.dev470 → junifer-0.0.4.dev486}/junifer/tests/test_stats.py

@@ -21,6 +21,8 @@ from junifer.stats import count, get_aggfunc_by_name, select, winsorized_mean
         ("count", None),
         ("trim_mean", None),
         ("trim_mean", {"proportiontocut": 0.1}),
+        ("mode", None),
+        ("mode", {"keepdims": True}),
     ],
 )
 def test_get_aggfunc_by_name(name: str, params: Optional[Dict]) -> None:

{junifer-0.0.4.dev470 → junifer-0.0.4.dev486}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev470
+Version: 0.0.4.dev486
 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>
@@ -28,6 +28,7 @@ License-File: LICENSE.md
 License-File: AUTHORS.rst
 Requires-Dist: click<8.2,>=8.1.3
 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
@@ -73,6 +74,7 @@ Requires-Dist: sphinxcontrib-mermaid<0.10,>=0.8.1; extra == "docs"
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/charliermarsh/ruff)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8176570.svg)](https://doi.org/10.5281/zenodo.8176570)
+[![FAIR checklist badge](https://fairsoftwarechecklist.net/badge.svg)](https://fairsoftwarechecklist.net/v0.2?f=31&a=32113&i=32322&r=133)
 
 ## About
 

{junifer-0.0.4.dev470 → junifer-0.0.4.dev486}/junifer.egg-info/SOURCES.txt

@@ -95,8 +95,10 @@ docs/changes/newsfragments/281.misc
 docs/changes/newsfragments/282.bugfix
 docs/changes/newsfragments/283.bugfix
 docs/changes/newsfragments/286.bugfix
+docs/changes/newsfragments/287.enh
 docs/changes/newsfragments/288.misc
 docs/changes/newsfragments/291.doc
+docs/changes/newsfragments/294.misc
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/extension.rst

{junifer-0.0.4.dev470 → junifer-0.0.4.dev486}/junifer.egg-info/requires.txt

@@ -1,5 +1,6 @@
 click<8.2,>=8.1.3
 numpy<1.27,>=1.24
+scipy<=1.11.4,>=1.9.0
 datalad<0.20,>=0.15.4
 pandas<2.2,>=1.4.0
 nibabel<5.11,>=3.2.0

{junifer-0.0.4.dev470 → junifer-0.0.4.dev486}/pyproject.toml

@@ -1,9 +1,5 @@
 [build-system]
-requires = [
-  "setuptools >= 61.0.0",
-  "wheel",
-  "setuptools_scm[toml] >= 6.2"
-]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -41,13 +37,14 @@ classifiers = [
 dependencies = [
     "click>=8.1.3,<8.2",
     "numpy>=1.24,<1.27",
+    "scipy>=1.9.0,<=1.11.4",
     "datalad>=0.15.4,<0.20",
     "pandas>=1.4.0,<2.2",
     "nibabel>=3.2.0,<5.11",
     "nilearn>=0.9.0,<=0.11.0",
-    "sqlalchemy>=1.4.27,<= 2.1.0",
+    "sqlalchemy>=1.4.27,<=2.1.0",
     "ruamel.yaml>=0.17,<0.18",
-    "importlib_metadata; python_version < '3.10'",
+    "importlib_metadata; python_version<'3.10'",
     "h5py>=3.8.0,<3.10",
 ]
 dynamic = ["version"]
@@ -153,7 +150,7 @@ extend-exclude = [
     "examples",
     "tools",
 ]
-extend-ignore = [
+ignore = [
     # Use of `functools.lru_cache` or `functools.cache` on methods can lead to
     # memory leaks. The cache may retain instance references, preventing garbage
     # collection.
@@ -181,12 +178,15 @@ known-first-party = ["junifer"]
 known-third-party =[
     "click",
     "numpy",
+    "scipy",
     "datalad",
     "pandas",
     "nibabel",
     "nilearn",
     "sqlalchemy",
     "yaml",
+    "bct",
+    "neurokit2",
     "pytest",
 ]