Merge branch 'master' into pre-commit-ci-update-config

Author: smoia

.gitattributes

@@ -1,4 +1,4 @@
-phys2bids/_version.py export-subst
+nigsp/_version.py export-subst
 
 *.py eol=lf
 *.rst eol=lf

.pre-commit-config.yaml

@@ -13,17 +13,6 @@ repos:
           - id: check-case-conflict
           - id: check-merge-conflict
 
-    - repo: https://github.com/pycqa/isort
-      rev: 6.1.0
-      hooks:
-          - id: isort
-
-    - repo: https://github.com/pycqa/pydocstyle
-      rev: 6.3.0
-      hooks:
-          - id: pydocstyle
-
-
     - repo: https://github.com/pre-commit/pygrep-hooks
       rev: v1.10.0
       hooks:
@@ -38,7 +27,7 @@ repos:
 
 
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.13.3
+      rev: v0.14.2
       hooks:
           - id: ruff
             name: ruff linter

.zenodo.json

@@ -7,6 +7,22 @@
             "orcid":"0000-0002-2553-3327",
             "affiliation":"Medical Imaging Processing Lab, Center for Neuroprosthetics, École Polytechnique Fédérale de Lausanne",
             "name":"Stefano Moia"
+        },
+        {
+            "affiliation":"Medical Imaging Processing Lab, Center for Neuroprosthetics, École Polytechnique Fédérale de Lausanne",
+            "name": "Nawal Kinani"
+        },
+        {
+            "affiliation":"Medical Imaging Processing Lab, Center for Neuroprosthetics, École Polytechnique Fédérale de Lausanne",
+            "name": "Mathieu Scheltienne"
+        },
+        {
+            "affiliation":"Medical Imaging Processing Lab, Center for Neuroprosthetics, École Polytechnique Fédérale de Lausanne",
+            "name": "Maria Giulia Preti"
+        },
+        {
+            "affiliation":"Medical Imaging Processing Lab, Center for Neuroprosthetics, École Polytechnique Fédérale de Lausanne",
+            "name": "Dimitri Van De Ville"
         }
     ],
     "access_right":"open"

nigsp/conftest.py

@@ -3,8 +3,8 @@
 import os
 import ssl
 from typing import TYPE_CHECKING
-from urllib.request import urlretrieve
 
+import requests
 from pytest import fixture
 
 if TYPE_CHECKING:
@@ -62,7 +62,11 @@ def fetch_file(osf_id, path, filename):
     url = f"https://osf.io/{osf_id}/download"
     full_path = os.path.join(path, filename)
     if not os.path.isfile(full_path):
-        urlretrieve(url, full_path)
+        req = requests.get(url, allow_redirects=True)
+        req.raise_for_status()
+        with open(full_path, "wb") as f:
+            f.write(req.content)
+            f.close()
     return full_path
 
 

nigsp/io.py

@@ -250,7 +250,7 @@ def load_txt(fname, shape=None):
     mtx : numpy.ndarray
         Data matrix.
 
-    See also
+    See Also
     --------
     check_mtx_dim
     """
@@ -297,7 +297,7 @@ def load_mat(fname, shape=None):
     -----
     Requires module ``pymatreader`` to work.
 
-    See also
+    See Also
     --------
     check_mtx_dim
 
@@ -361,7 +361,7 @@ def load_xls(fname, shape=""):
     shape : None | ``'square'`` | ``'rectangle'``
         Shape of matrix, if empty, skip check.
 
-    See also
+    See Also
     --------
     check_mtx_dim
 

nigsp/operations/timeseries.py

@@ -297,8 +297,7 @@ def _trapezoid_compat(*args, **kwargs):
 
 def median_cutoff_frequency_idx(energy):
     """
-    Find the frequency that splits the energy of a timeseries in two roughly equal
-    parts.
+    Estimate frequency splitting the energy of timeseries in two roughly equal parts.
 
     Parameters
     ----------

nigsp/workflow.py

@@ -84,7 +84,7 @@ def nigsp(
     lgr_degree="info",
 ):
     """
-    Main workflow for nigsp, following the methods described in [1]_.
+    Run main workflow for nigsp, following the methods described in [1]_.
 
     Parameters
     ----------

pyproject.toml

@@ -18,17 +18,6 @@ omit = [
   '**/tests/**',
 ]
 
-[tool.isort]
-extend_skip_glob = [
-  'docs/*',
-  'setup.py',
-  'tutorials/*',
-]
-line_length = 88
-multi_line_output = 3
-profile = 'black'
-py_version = 37
-
 [tool.ruff]
 extend-exclude = ['docs', 'versioneer.py', 'setup.py']
 line-length = 88
@@ -40,7 +29,10 @@ line-ending = 'lf'
 
 [tool.ruff.lint]
 ignore = []
-select = ['A', 'B', 'E', 'F', 'UP', 'W']
+select = ['A', 'B', 'E', 'D', 'F', 'I', 'UP', 'W']
+
+[tool.ruff.lint.pydocstyle]
+convention = 'numpy'
 
 [tool.ruff.lint.per-file-ignores]
 '*' = [
@@ -50,3 +42,9 @@ select = ['A', 'B', 'E', 'F', 'UP', 'W']
 '*.pyi' = ['E501']
 '__init__.py' = ['F401']
 '_version.py' = ['UP031']
+'nigsp/tests/*' = ['D']
+'nigsp/__init__.py' = ['F401', 'D']
+'nigsp/*/__init__.py' = ['F401', 'D']
+'nigsp/_version.py' = ['UP031', 'D']
+'nigsp/conftest.py' = ['D']
+'nigsp/due.py' = ['D']

setup.cfg

@@ -9,12 +9,12 @@ classifiers =
     Development Status :: 4 - Beta
     Intended Audience :: Science/Research
     License :: OSI Approved :: Apache Software License
-    Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
 license = Apache-2.0
 description = A python library (and toolbox!) to run Graph Signal Processing on multimodal MRI data.
 long_description = file:README.md
@@ -63,10 +63,8 @@ doc =
     sphinx-gallery
     sphinx-issues
 style =
-    isort
-    pydocstyle
     codespell>=2.2.4
-    ruff>=0.4.1
+    ruff>=0.14.2
 test =
     %(all)s
     %(style)s
@@ -84,12 +82,6 @@ dev =
 console_scripts =
     nigsp=nigsp.workflow:_main
 
-[pydocstyle]
-convention = numpy
-match =
-    nigsp/*.py
-match_dir = nigsp/[^tests]*
-
 [codespell]
 skip = versioneer.py,.git,build,./docs/_build
 ignore-words-list = nd,commun