Merge branch 'main' into docstrings

Author: singlesp

.circleci/config.yml

@@ -7,7 +7,7 @@ jobs:
     parameters:
       python_version:
         type: string
-        default: "3.8"
+        default: "3.12"
     machine:
       image: ubuntu-2404:2024.08.1
     working_directory: /home/circleci/src/CuBIDS
@@ -105,10 +105,11 @@ workflows:
           matrix:
             parameters:
               python_version:
-                - "3.8"
                 - "3.9"
                 - "3.10"
                 - "3.11"
+                - "3.12"
+                - "3.13"
           filters:
             tags:
               only: /.*/

.readthedocs.yml

@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.8"
+    python: "3.12"
 
 sphinx:
   configuration: docs/conf.py

CONTRIBUTING.rst

@@ -103,7 +103,7 @@ Before you submit a pull request, check that it meets these guidelines:
 2.  If the pull request adds functionality, the docs should be updated. Put
     your new functionality into a function with a docstring, and add the
     feature to the list in README.rst.
-3.  The pull request should work for Python 3.5, 3.6, 3.7 and 3.8, and for PyPy.
+3.  The pull request should work for Python 3.9, 3.10, 3.11, 3.12 and 3.13, and for PyPI.
     Check https://circleci.com/gh/PennLINC/CuBIDS
     and make sure that the tests pass for all supported Python versions.
 

cubids/cli.py

@@ -74,7 +74,7 @@ def _parse_validate():
         default=None,
     )
     parser.add_argument(
-        "--ignore_nifti_headers",
+        "--ignore-nifti-headers",
         action="store_true",
         default=False,
         help="Disregard NIfTI header content during validation",

cubids/config.py

@@ -1,10 +1,8 @@
 """Functions for configuring CuBIDS."""
 
 from pathlib import Path
-
+import importlib.resources
 import yaml
-from pkg_resources import resource_filename as pkgrf
-
 
 def load_config(config_file):
     """
@@ -21,7 +19,7 @@ def load_config(config_file):
         The configuration loaded from the YAML file.
     """
     if config_file is None:
-        config_file = Path(pkgrf("cubids", "data/config.yml"))
+        config_file = Path(importlib.resources.files("cubids") / "data/config.yml")
 
     with config_file.open() as f:
         config = yaml.safe_load(f)

cubids/tests/utils.py

@@ -9,9 +9,9 @@
 import nibabel as nb
 import numpy as np
 import pandas as pd
-from pkg_resources import resource_filename as pkgrf
+import importlib.resources
 
-TEST_DATA = pkgrf("cubids", "tests/data")
+TEST_DATA = importlib.resources.files("cubids") / "tests/data"
 
 
 def get_data(tmp_path):
@@ -117,18 +117,6 @@ def _add_deletion(summary_tsv):
     return df.loc[3, "KeyParamGroup"]
 
 
-# def _edit_tsv(summary_tsv):
-#     df = pd.read_table(summary_tsv)
-#     df['RenameEntitySet'] = df['RenameEntitySet'].apply(str)
-#     df['EntitySet'] = df['EntitySet'].apply(str)
-#     for row in range(len(df)):
-#         if df.loc[row, 'EntitySet'] == \
-#             "acquisition-v4_datatype-fmap_fmap-magnitude1_suffix-magnitude1":
-#             df.at[row, 'RenameEntitySet'] = \
-#                 "acquisition-v5_datatype-fmap_fmap-magnitude1_suffix-magnitude1"
-#     df.to_csv(summary_tsv)
-
-
 def _add_ext_files(img_path):
     """
     Add and save extension files in the same directory as the image file.

cubids/workflows.py

@@ -231,7 +231,7 @@ def validate(
             linked_output_prefix_t,
         ]
         if ignore_nifti_headers:
-            cmd.append("--ignore_nifti_headers")
+            cmd.append("--ignore-nifti-headers")
 
     elif container_type == "singularity":
         cmd = [
@@ -250,7 +250,7 @@ def validate(
             linked_output_prefix_t,
         ]
         if ignore_nifti_headers:
-            cmd.append("--ignore_nifti_headers")
+            cmd.append("--ignore-nifti-headers")
 
         if sequential:
             cmd.append("--sequential")

docs/api.rst

@@ -1,5 +1,3 @@
-.. include:: links.rst
-
 ===
 API
 ===

docs/example.rst

@@ -1,5 +1,3 @@
-.. include:: links.rst
-
 ===================
 Example Walkthrough
 ===================