Merge branch 'master' into guiomar-patch-1

.circleci/config.yml

@@ -2,7 +2,7 @@ version: 2.1
 jobs:
   build_docs:
     docker:
-      - image: cimg/python:3.8
+      - image: cimg/python:3.12-node
     steps:
       # checkout code to default ~/project
       - checkout
@@ -21,14 +21,15 @@ jobs:
       - persist_to_workspace:
           # the mkdocs build outputs are in ~/project/site
           root: ~/project
-          paths: site
+          paths:
+            - site
       - store_artifacts:
           path: ~/project/site/
           destination: dev_docs
 
   check_links:
     docker:
-      - image: cimg/python:3.8
+      - image: cimg/python:3.12
     steps:
       # checkout code to default ~/project
       - checkout
@@ -131,7 +132,8 @@ jobs:
       - persist_to_workspace:
           # raw generated changelog in ~/changelog_build/CHANGES.md
           root: ~/.
-          paths: changelog_build
+          paths:
+            - changelog_build
 
   # Lint and fix the auto generated changes.md file
   lint_generated_changelog:
@@ -164,7 +166,8 @@ jobs:
       - persist_to_workspace:
           # linted and fixed changelog in ~/changelog_build/CHANGES.md
           root: ~/.
-          paths: changelog_build
+          paths:
+            - changelog_build
 
   # Push built changelog to repo
   commit_generated_changelog:
@@ -178,7 +181,7 @@ jobs:
       - attach_workspace:
           # fixed+linted changelog in ~/changelog_build/CHANGES.md
           at: ~/.
-      - deploy:
+      - run:
           name: Changelog deployment
           # $CHANGE_TOKEN is generated via the GitHub web UI, and then securely stored within CircleCI web UI
           command: |
@@ -197,7 +200,6 @@ jobs:
             fi
 
 workflows:
-  version: 2
   search_build:
     jobs:
       - build_docs

.github/workflows/schemacode_ci.yml

@@ -44,7 +44,7 @@ jobs:
         run: python -m build tools/schemacode
       - name: "Check distribution metadata"
         run: twine check tools/schemacode/dist/*
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: dist
           path: tools/schemacode/dist/
@@ -76,7 +76,7 @@ jobs:
         run: python -c "import sys; print(sys.version)"
 
       - name: "Fetch packages"
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: dist
           path: dist/
@@ -91,7 +91,7 @@ jobs:
               --cov-append --cov-report=xml --cov=bidsschematools --doctest-modules
 
       - name: Upload artifacts
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: unit_${{ matrix.os }}_${{ matrix.python-version }}
           path: coverage.xml
@@ -108,7 +108,7 @@ jobs:
         python-version: ["3.11"]
     steps:
       - name: "Fetch packages"
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: dist
           path: dist/
@@ -146,7 +146,7 @@ jobs:
         run: python -m pytest --pyargs bidsschematools -m "validate_schema" --cov-append --cov-report=xml --cov=bidsschematools
 
       - name: Upload artifacts
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: schema_validation
           path: coverage.xml
@@ -161,10 +161,10 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Download artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
 
       - name: Upload to CodeCov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}  # not required but might help API rate limits
           fail_ci_if_error: true

.pre-commit-config.yaml

@@ -13,7 +13,7 @@ repos:
       - id: check-added-large-files
       - id: check-case-conflict
   - repo: https://github.com/psf/black
-    rev: 23.11.0
+    rev: 24.1.1
     hooks:
       - id: black
         files: ^tools/(?!schemacode)
@@ -23,7 +23,7 @@ repos:
         files: tools/schemacode
         args: ["--config", "tools/schemacode/pyproject.toml", "--verbose"]
   - repo: https://github.com/pyCQA/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
         files: ^tools/(?!schemacode)
@@ -33,12 +33,12 @@ repos:
         files: tools/schemacode
         args: ["--settings-file", "tools/schemacode/pyproject.toml"]
   - repo: https://github.com/pyCQA/flake8
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
       - id: flake8
         args: [--config=tools/schemacode/setup.cfg]
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v4.0.0-alpha.3
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
         entry: env PRETTIER_LEGACY_CLI=1 prettier # temporary fix for https://github.com/prettier/prettier/issues/15742
@@ -49,7 +49,7 @@ repos:
       - id: codespell
         args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.7.1
+    rev: v1.8.0
     hooks:
       - id: mypy
         # Sync with project.optional-dependencies.typing

Release_Protocol.md

@@ -267,7 +267,16 @@ Similarly update the version in CITATION.cff with a `dev` suffix.
 1. In a previous step you have secured a PDF version of the BIDS specification and the corresponding `CITATION.cff` file.
 1. Follow the steps described here: https://github.com/bids-standard/bids-specification-pdf-releases#release-instructions
 
-### 11. Sharing news of the release
+### 11. Update the BIDS website data
+
+Update the following files in the BIDS website repository (https://github.com/bids-standard/bids-website) if applicable:
+
+- `tools/timeline.csv`
+- `_data/beps.yml`
+- `_data/beps_completed.yml`
+- `_data/beps_other.yml`
+
+### 12. Sharing news of the release
 
 Please share news of the release on the [identified platforms](https://docs.google.com/spreadsheets/d/16SAGK3zG93WM2EWuoZDcRIC7ygPc5b7PDNGpFyC3obA/edit#gid=0).
 Please use our previous release posts as a guide.

src/appendices/schema.md

@@ -9,7 +9,7 @@ to the BIDS standard.
 
 The BIDS schema is available in two machine readable formats:
 
--   as a set of [YAML](https://en.wikipedia.org/wiki/YAML) files in the [BIDS specification repository](https://github.com/bids-standard/bids-specification/src/schema)
+-   as a set of [YAML](https://en.wikipedia.org/wiki/YAML) files in the [BIDS specification repository](https://github.com/bids-standard/bids-specification/tree/master/src/schema)
 -   as a [single dereferenced json file](https://bids-specification.readthedocs.io/en/stable/schema.json)
 
 A didactic walkthrough of the schema can be found in the [BEP Guide](https://bids-extensions.readthedocs.io/en/latest/schema/),

src/schema/rules/files/raw/fmap.yaml

@@ -38,6 +38,7 @@ pepolar:
     ceagent: optional
     direction: required
     run: optional
+    part: optional
     chunk: optional
 
 TB1DAM:

tools/examplecode/__init__.py

@@ -1,4 +1,5 @@
 """A Python package to render BIDS example with tree like output."""
+
 from examplecode.example import DirectoryTree
 
 __all__ = [

tools/mkdocs_macros_bids/macros.py

@@ -1,4 +1,5 @@
 """Functions used by the macros mkdocs plugin."""
+
 import os
 import sys
 

tools/mkdocs_macros_bids/main.py

@@ -4,6 +4,7 @@
 Functions decorated in "define_env()" are callable throughout the
 specification and are run/rendered with the mkdocs plugin "macros".
 """
+
 import os
 import sys
 

tools/pull_files.py

@@ -7,6 +7,7 @@
 https://github.com/alan-turing-institute/the-turing-way/blob/af98c94/tests/pull_files.py
 
 """
+
 import argparse
 
 import requests

tools/schemacode/bidsschematools/data/__init__.py

@@ -2,6 +2,7 @@
 
 .. autofunction:: load_resource
 """
+
 import atexit
 import os
 from contextlib import ExitStack

tools/schemacode/bidsschematools/data/tests/test_rules.py

@@ -1,4 +1,5 @@
 """Simple validation tests on schema rules."""
+
 import warnings
 from collections.abc import Mapping
 

tools/schemacode/bidsschematools/expressions.py

@@ -1,5 +1,6 @@
 """Parsing utilities for BIDS Schema expression language
 """
+
 from functools import partial
 
 from pyparsing import (

tools/schemacode/bidsschematools/render/__init__.py

@@ -1,4 +1,5 @@
 """Functions for rendering elements of the schema in the specification text."""
+
 from bidsschematools.render.tables import (
     make_columns_table,
     make_entity_table,

tools/schemacode/bidsschematools/render/tables.py

@@ -1,4 +1,5 @@
 """Functions for rendering portions of the schema as text."""
+
 from __future__ import annotations
 
 import logging

tools/schemacode/bidsschematools/render/text.py

@@ -1,4 +1,5 @@
 """Functions for rendering portions of the schema as text."""
+
 import logging
 import os
 

tools/schemacode/bidsschematools/render/utils.py

@@ -1,4 +1,5 @@
 """Utility functions for specification rendering tools."""
+
 import math
 import posixpath
 

tools/schemacode/bidsschematools/rules.py

@@ -3,6 +3,7 @@
 This module is currently limited to constructing filename rules from
 ``schema.rules.files``.
 """
+
 import re
 import typing as ty
 from collections.abc import Mapping

tools/schemacode/bidsschematools/schema.py

@@ -1,4 +1,5 @@
 """Schema loading- and processing-related functions."""
+
 import logging
 import os
 import re

tools/schemacode/bidsschematools/tests/data/__init__.py

@@ -2,6 +2,7 @@
 
 .. autofunction:: load_test_data
 """
+
 from ...data import Loader
 
 __all__ = ("load_test_data",)

tools/schemacode/bidsschematools/tests/test_render_tables.py

@@ -1,4 +1,5 @@
 """Tests for the bidsschematools package."""
+
 from bidsschematools.render import tables
 
 

tools/schemacode/bidsschematools/tests/test_render_text.py

@@ -1,4 +1,5 @@
 """Tests for the bidsschematools package."""
+
 import os
 
 import pytest

tools/schemacode/bidsschematools/tests/test_schema.py

@@ -1,4 +1,5 @@
 """Tests for the bidsschematools package."""
+
 import os
 from collections.abc import Mapping
 

tools/schemacode/bidsschematools/types/namespace.py

@@ -4,6 +4,7 @@
 YAML files available as a single dictionary and allow attribute (``.``)
 lookups.
 """
+
 import json
 import typing as ty
 from collections.abc import ItemsView, KeysView, Mapping, MutableMapping, ValuesView

tools/schemacode/bidsschematools/utils.py

@@ -1,4 +1,5 @@
 """Utility functions for the bids-specification schema."""
+
 import logging
 
 from . import data