Merge tag '0.19.0'

Version 0.19.0 (March 05, 2025)

New feature release in the 0.19.x series.

This release adds plus signs to labels and suffixes, anticipating the
release of BIDS 1.10.1 or 1.11.0 (whichever is next).
Until the BIDS specification is updated and the ``bidsschematools``
package containing the updated schema is published, files with ``+`` will
not validate, but can still be indexed with ``BIDSLayout(..., validate=False)``.

Several small fixes resolving issues with BIDS Stats Models are included,
and complex JSON metadata (lists and objects) will now play more nicely with
contexts where they need to be hashed.

* FIX: Catch StopIteration on directory walk (#1124)
* FIX: Ensure dotfiles are always filtered (#1123)
* FIX: Copy entities dict before modifying run variable type (#1120)
* FIX: Allow numpy arrays to treat PaddedInt like int (#1119)
* FIX: Make lists and dicts hashable (#1112)
* ENH: Allow plus signs in labels (#1117)
* MNT: Remove formulaic upper bound (#1121)
* MNT: Use tox-uv to ease lower bound checking, test on Python 3.13 (#1109)

Author: effigies

.zenodo.json

@@ -218,6 +218,11 @@
       "name": "Rokem, Ariel",
       "orcid": "0000-0003-0679-1985"
     },
+    {
+      "affiliation": "University of Montréal, Montréal, Canada",
+      "name": "Pinsard, Basile",
+      "orcid": "0000-0002-4391-3075"
+    },
     {
       "affiliation": "Ottawa Hospital Research Institute",
       "name": "Boulay, Chadwick",
@@ -237,11 +242,6 @@
       "affiliation": "CEA, Inria",
       "name": "Thual, Alexis"
     },
-    {
-      "affiliation": "University of Montréal, Montréal, Canada",
-      "name": "Pinsard, Basile",
-      "orcid": "0000-0002-4391-3075"
-    },
     {
       "affiliation": "Berkeley Institute for Data Science; University of California at Berkeley",
       "name": "Holdgraf, Chris",

CHANGELOG.rst

@@ -1,6 +1,30 @@
 Changelog
 =========
 
+Version 0.19.0 (March 05, 2025)
+-------------------------------
+
+New feature release in the 0.19.x series.
+
+This release adds plus signs to labels and suffixes, anticipating the
+release of BIDS 1.10.1 or 1.11.0 (whichever is next).
+Until the BIDS specification is updated and the ``bidsschematools``
+package containing the updated schema is published, files with ``+`` will
+not validate, but can still be indexed with ``BIDSLayout(..., validate=False)``.
+
+Several small fixes resolving issues with BIDS Stats Models are included,
+and complex JSON metadata (lists and objects) will now play more nicely with
+contexts where they need to be hashed.
+
+* FIX: Catch StopIteration on directory walk (#1124)
+* FIX: Ensure dotfiles are always filtered (#1123)
+* FIX: Copy entities dict before modifying run variable type (#1120)
+* FIX: Allow numpy arrays to treat PaddedInt like int (#1119)
+* FIX: Make lists and dicts hashable (#1112)
+* ENH: Allow plus signs in labels (#1117)
+* MNT: Remove formulaic upper bound (#1121)
+* MNT: Use tox-uv to ease lower bound checking, test on Python 3.13 (#1109)
+
 Version 0.18.1 (December 05, 2024)
 ----------------------------------
 

doc/examples/pybids_tutorial.md

@@ -63,7 +63,7 @@ The utility of the `BIDSLayout` would be pretty limited if all we could do was r
 layout.get(subject='01', extension='nii.gz', suffix='bold', return_type='filename')
 ```
 
-If you're wondering what entities you can pass in as filtering arguments, the answer is contained in the `.json` configuration files [housed here](https://github.com/bids-standard/pybids/tree/master/bids/layout/config). To save you the trouble, here are a few of the most common entities:
+If you're wondering what entities you can pass in as filtering arguments, the answer is contained in the `.json` configuration files [housed here](https://github.com/bids-standard/pybids/tree/master/src/bids/layout/config). To save you the trouble, here are a few of the most common entities:
 
 * `suffix`: The part of a BIDS filename just before the extension (e.g., `'bold'`, `'events'`, `'physio'`, etc.).
 * `subject`: The subject label

pyproject.toml

@@ -23,17 +23,17 @@ classifiers = [
   "Topic :: Scientific/Engineering",
 ]
 dependencies = [
-  "numpy >=1.22",  # SPEC 0 + 1yr (3yr)
-  "scipy >=1.8",   # SPEC 0 + 1yr (3yr)
+  "numpy >=1.23",  # SPEC 0 + 1yr (3yr)
+  "scipy >=1.9",   # SPEC 0 + 1yr (3yr)
   "nibabel >=4.0",  # SPEC 0 + 1yr (3yr)
-  "pandas >=1.4.0",  # SPEC 0 + 1yr (3yr)
-  "formulaic >=0.2.4",
-  "sqlalchemy >=1.3.16",
+  "pandas >=1.5",  # SPEC 0 + 1yr (3yr)
+  "formulaic >=0.3",
+  "sqlalchemy >=1.4.31",
   "bids-validator>=1.14.7",  # Keep up-to-date to ensure support for recent modalities
-  "num2words >=0.5.5",
+  "num2words >=0.5.10",
   "click >=8.0",
   "universal_pathlib >=0.2.2",
-  "frozendict >=2",
+  "frozendict >=2.3",
 ]
 dynamic = ["version"]
 
@@ -106,4 +106,4 @@ source = [
 ]
 
 [tool.coverage.report]
-include = ["src/", "tests/"]
+include = ["src/*", "tests/*"]