Merge branch 'main' into switch-pkg_resources-to-importlib.resources

singlesp · web-flow · commit 93aaa42cd1b0 · 2025-01-15T14:32:39.000-05:00
diff --git a/.circleci/config.yml b/.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: /.*/
diff --git a/.readthedocs.yml b/.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
diff --git a/CONTRIBUTING.rst b/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.
 
diff --git a/cubids/cli.py b/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",
diff --git a/cubids/workflows.py b/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")
diff --git a/docs/api.rst b/docs/api.rst
@@ -1,5 +1,3 @@
-.. include:: links.rst
-
 ===
 API
 ===
diff --git a/docs/example.rst b/docs/example.rst
@@ -1,5 +1,3 @@
-.. include:: links.rst
-
 ===================
 Example Walkthrough
 ===================
diff --git a/docs/examples.rst b/docs/examples.rst
diff --git a/docs/glossary.rst b/docs/glossary.rst
@@ -1,4 +1,4 @@
-.. include:: links.rst
+.. _BIDS filename key-value pairs: https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#file-name-key-value-pairs
 
 Glossary
 ========
diff --git a/docs/index.rst b/docs/index.rst
@@ -13,7 +13,6 @@ Contents
    usage
    cli
    example
-   examples
    ../CONTRIBUTING
    ../AUTHORS
    ../HISTORY
diff --git a/docs/links.rst b/docs/links.rst
diff --git a/pyproject.toml b/pyproject.toml
@@ -13,13 +13,14 @@ classifiers = [
     "Natural Language :: English",
     "Topic :: Scientific/Engineering :: Image Recognition",
     "License :: OSI Approved :: MIT License",
-    "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 = {file = "LICENSE"}
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 dependencies = [
     "datalad>=0.13.5,!=0.17.3,!=0.17.0,!=0.16.1",
     "numpy<=2.2.1",

Original file line number	Diff line number	Diff line change
`@@ -74,7 +74,7 @@ def _parse_validate():`
`74`	`74`	`default=None,`
`75`	`75`	`)`
`76`	`76`	`parser.add_argument(`
`77`		`- "--ignore_nifti_headers",`
	`77`	`+ "--ignore-nifti-headers",`
`78`	`78`	`action="store_true",`
`79`	`79`	`default=False,`
`80`	`80`	`help="Disregard NIfTI header content during validation",`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,3 @@`
`1`		`-.. include:: links.rst`
`2`		`-`
`3`	`1`	`===`
`4`	`2`	`API`
`5`	`3`	`===`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,3 @@`
`1`		`-.. include:: links.rst`
`2`		`-`
`3`	`1`	`===================`
`4`	`2`	`Example Walkthrough`
`5`	`3`	`===================`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-.. include:: links.rst`
	`1`	`+.. _BIDS filename key-value pairs: https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#file-name-key-value-pairs`
`2`	`2`
`3`	`3`	`Glossary`
`4`	`4`	`========`