Merge branch 'master' into fix/acquisitionduration

Author: effigies

.circleci/config.yml

@@ -2,22 +2,14 @@ version: 2.1
 jobs:
   build_docs:
     docker:
-      - image: cimg/python:3.12-node
+      - image: cimg/python:3.12
     steps:
       # checkout code to default ~/project
       - checkout
-      - run:
-          name: install dependencies
-          command: |
-            python -m venv env
-            source env/bin/activate
-            python -m pip install --upgrade pip
-            pip install -r requirements.txt
       - run:
           name: generate docs
           command: |
-            source env/bin/activate
-            mkdocs build --clean --strict --verbose
+            uv run mkdocs build --clean --strict --verbose
       - persist_to_workspace:
           # the mkdocs build outputs are in ~/project/site
           root: ~/project
@@ -31,26 +23,16 @@ jobs:
     docker:
       - image: cimg/python:3.12
     steps:
-      # checkout code to default ~/project
       - checkout
       - attach_workspace:
-          # mkdocs build outputs will be in ~/project/site
           at: ~/project
-      - run:
-          name: install linkchecker
-          command: |
-            python -m venv env
-            source env/bin/activate
-            python -m pip install --upgrade pip
-            python -m pip install linkchecker
       - run:
           name: check links
           command: |
-            source env/bin/activate
             git status
             if (! git log -1 --pretty=oneline | grep REL:) ; then
               chmod a+rX -R ~
-              linkchecker -t 1 ~/project/site/
+              uvx linkchecker -t 1 ~/project/site/
               # check external separately by pointing to all *html so no
               # failures for local file:/// -- yoh found no better way,
               linkchecker -t 1 --check-extern \
@@ -75,20 +57,17 @@ jobs:
       # checkout code to default ~/project
       - checkout
       - run:
-          name: install dependencies
+          name: install uv
           command: |
-            apt-get update && apt install -y python3-pip python3-venv pandoc
-            python3 -m venv .venv
-            source .venv/bin/activate
-            python3 -m pip install --upgrade pip
-            python3 -m pip install -r  ~/project/requirements.txt
-            python3 -m pip install ~/project/tools/schemacode/[render]
+            curl -LsSf https://astral.sh/uv/install.sh | XDG_BIN_HOME=/usr/local/bin sh
       - run:
-          name: install font that works with unicode emojis
-          command: apt-get update && apt-get install -y fonts-symbola
+          name: install dependencies
+          command: |
+            apt-get update && apt install -y fonts-symbola pandoc
       - run:
           name: generate pdf version docs
           command: |
+            uv sync
             source .venv/bin/activate
             cd ~/project/pdf_build_src
             bash build_pdf.sh

.github/dependabot.yml

@@ -1,10 +1,21 @@
 # Documentation
 # https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
 version: 2
+enable-beta-ecosystems: true
 updates:
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
-      interval: "weekly"
+      interval: "monthly"
+    labels:
+      - "exclude-from-changelog"
+    groups:
+      actions-infrastructure:
+        patterns:
+         - "actions/*"
+  - package-ecosystem: "uv"
+    directory: "/"
+    schedule:
+      interval: "monthly"
     labels:
       - "exclude-from-changelog"

.gitignore

@@ -45,9 +45,6 @@ share/python-wheels/
 *.egg
 MANIFEST
 
-# Poetry requirements / packaging
-/pyproject.toml
-
 # PyInstaller
 #  Usually these files are written by a python script from a template
 #  before PyInstaller builds the exe, so as to inject date/other infos into it.

CONTRIBUTING.md

@@ -196,7 +196,18 @@ cd bids-specification
 
 Enter all commands below from the command line prompt located at the root of the local version of the specification.
 
-### 3. Install MkDocs, the Material theme and the required extensions
+### 3. Prepare your virtual environment
+
+The simplest way to prepare a Python environment for building the specification is
+with [uv](https://docs.astral.sh/uv/).
+
+```bash
+uv sync
+```
+
+(If you use `uv run` in the next section, this will be run implicitly.)
+
+<details><summary>Expand for detailed instructions that do not use `uv`.</summary>
 
 In the following links, you can find more information about
 
@@ -252,13 +263,17 @@ This installs the `bidsschemacode` package in "editable" mode,
 so that any changes you make to the code will be reflected when you use it,
 such as when you build the documentation locally.
 
+</details>
+
 ### 4. Ready to build!
 
-Using the terminal (command line) please enter `mkdocs serve`.
+Using the terminal (command line) please enter `uv run mkdocs serve`.
 This will allow you to see a local version of the specification.
 The local address will be `http://127.0.0.1:8000`.
 You may enter that into your browser and this will bring up the specification!
 
+(If you are not using `uv`, activate your environment and then run `mkdocs serve`.)
+
 ## Fixing Markdown style errors
 
 We use a linter called [Remarkjs](https://github.com/remarkjs/remark-lint) to

pyproject.toml

@@ -0,0 +1,25 @@
+[project]
+name = "bids-specification"
+requires-python = ">=3.11"
+dependencies = [
+  "bidsschematools[render]",
+  "mkdocs>=1.1.0",
+  "mkdocs-material>=5.4",
+  "pymdown-extensions>=7.0.0",
+  "mkdocs-branchcustomization-plugin~=0.1.3",
+  "mkdocs-macros-plugin",
+  "mkdocs-redirects",
+  "numpy",
+]
+dynamic = ["version"]
+
+[tool.uv.sources]
+bidsschematools = { path = "tools/schemacode", editable = true }
+
+[dependency-groups]
+doc = [
+  "sphinx>=7.2.2",
+  "furo",
+  "myst_parser",
+  "bidsschematools[expressions]",
+]

readthedocs.yml

@@ -5,26 +5,22 @@ build:
   tools:
     python: latest
   jobs:
-    # The *_create_environment and post_install steps replace RTD's virtual environment
+    # The *create_environment steps replace RTD's virtual environment
     # steps with uv, a much faster alternative to virtualenv+pip.
-    pre_create_environment:
+    create_environment:
       # Install jq and uv
       - asdf plugin add jq https://github.com/lsanwick/asdf-jq.git
       - asdf plugin add uv https://github.com/asdf-community/asdf-uv.git
       - asdf install jq latest
       - asdf install uv latest
       - asdf global jq latest
       - asdf global uv latest
-      # Turn `python -m virtualenv` into `python -c pass`
-      - truncate --size 0 $( dirname $( uv python find ) )/../lib/python3*/site-packages/virtualenv/__main__.py
-    post_create_environment:
-      - uv venv $READTHEDOCS_VIRTUALENV_PATH
-      # Turn `python -m pip` into `python -c pass`
-      - truncate --size 0 $( ls -d $READTHEDOCS_VIRTUALENV_PATH/lib/python3* )/site-packages/pip.py
-    # post_install replaces the top-level {python: {install: [{requirements: requirements.txt}]}}
-    post_install:
-      # Use a cache dir in the same mount to halve the install time
-      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install --cache-dir $READTHEDOCS_VIRTUALENV_PATH/../../uv_cache -r requirements.txt
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv venv
+    install:
+      - >
+        VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH
+        UV_CACHE_DIR=$READTHEDOCS_VIRTUALENV_PATH/../../uv_cache
+        uv sync --active --locked
     # Normal pre-build step to inject schema.json into the source directory
     # so schema.json is hosted alongside the specification documents
     pre_build:

requirements.txt

@@ -595,8 +595,7 @@
             },
             "required": ["level"],
             "additionalProperties": false
-          },
-          { "type": "string", "pattern": "recommended.*" }
+          }
         ]
       },
       "issue": {

src/metaschema.json

@@ -161,7 +161,7 @@ A guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
 {{ MACROS___make_sidecar_table([
-     "mri.MRIB0FieldIdentifier",
+     "fmap.MRIFieldmapB0FieldIdentifier",
      "mri.MRIEchoPlanarImagingAndB0FieldSource",
    ])
 }}

src/modality-specific-files/magnetic-resonance-imaging-data.md

@@ -167,7 +167,7 @@ references (the cases in which they are used will be presented later):
     (which are in turn references to individual values), and the references inside `GeneticLevel.anyOf` indicate that there may be a single
     such value or a list of values.
 
-1.  In [`rules.files.deriv.preprocessed_data`](./rules/files/deriv/preprocessed_data.yaml):
+1.  In [`rules.files.deriv.preprocessed_data`][preprocessed_data]:
     ```YAML
     anat_nonparametric_common:
       $ref: rules.files.raw.anat.nonparametric
@@ -1071,4 +1071,5 @@ ensuring consistency across the entire schema directory. Validation of the schem
 incorporated into the CI, so any changes that are inconsistent will be flagged before
 inclusion.
 
+[preprocessed_data]: https://github.com/bids-standard/bids-specification/tree/master/src/schema/rules/files/deriv/preprocessed_data.yaml
 [tabular files]: https://bids-specification.readthedocs.io/en/stable/common-principles.html#tabular-files