Prettier updates

.codespell-ignore.txt

@@ -0,0 +1 @@
+# This is a test

.pre-commit-config.yaml

@@ -2,35 +2,46 @@
 # https://pre-commit.com/
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-toml
       - id: check-yaml
+        # mkdocs.yml uses !!python/name tags unsupported by the safe YAML loader
+        exclude: ^mkdocs\.yml$
       - id: end-of-file-fixer
+        exclude: ^\.copier-answers\.yml$
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
 
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.37.0
+    rev: v1.38.0
     hooks:
       - id: yamllint
         args: [-c=.yamllint.yaml]
+        exclude: |
+                  (?x)^(
+                    \.copier-answers\.yml|
+                    docs/schema/.*\.yaml|
+                    src/include_access_model/schema/upstream-models/.*\.yaml
+                  )$
+        verbose: true  # Show warnings.
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.4.1
+    rev: v2.4.2
     hooks:
       - id: codespell
         additional_dependencies:
           - tomli
+        exclude: ^src/include_access_model/schema/upstream-models/.*\.yaml$
 
   - repo: https://github.com/crate-ci/typos
-    rev: v1.31.1
+    rev: v1.46.3
     hooks:
       - id: typos
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.11.3
+    rev: v0.15.14
     hooks:
       # Run the linter.
       - id: ruff
@@ -40,6 +51,6 @@ repos:
 
   - repo: https://github.com/astral-sh/uv-pre-commit
     # uv version.
-    rev: 0.6.12
+    rev: 0.11.16
     hooks:
       - id: uv-lock

.yamllint.yaml

@@ -2,6 +2,14 @@
 
 extends: default
 
+# Specify files to ignore.
+ignore:
+  # Ignore autogenerated file that does not conform to yamllint rules.
+  - .copier-answers.yml
+  # Ignore schema files that may not conform due to imports.
+  - docs/schema/*.yaml
+  - src/include_access_model/schema/upstream-models/*.yaml
+
 rules:
   document-start: disable  # Don't check if document has a start marker (---).
   line-length:

COLLABORATORS.md

@@ -3,7 +3,7 @@
 This repository serves as a downstream model designed to specialize the
 [Common Access Model](https://github.com/include-dcc/common-access-model). A
 pinned version of this upstream model is captured in
-src/kf_access_model/schema/upstream-models/common_access_model*.yaml.
+src/include_access_model/schema/upstream-models/common_access_model*.yaml.
 
 The purpose of this model is to build out a program-specific extension (or
 profile) by importing the core elements and layering the INCLUDE unique data
@@ -36,10 +36,10 @@ just update-cam
 ```
 
 This recipe will download the newest version to the directory,
-src/kf_access_model/schema/upstream-models and create a symbolic link from the
-common name, common_access_model.yaml. As a result, once that one entry has been
-made to the local model, subsequent updates should work without further updates
-to the model itself.
+src/include_access_model/schema/upstream-models and create a symbolic link from
+the common name, common_access_model.yaml. As a result, once that one entry has
+been made to the local model, subsequent updates should work without further
+updates to the model itself.
 
 ```model-yaml
 imports:

_typos.toml

@@ -0,0 +1,15 @@
+[files]
+extend-exclude = [
+  "_typos.toml",
+  ".git*",
+]
+
+# These were caught as typos
+[default.extend-words]
+NAMD = "NAMD"
+BA = "BA"
+
+# Real typos that are encountered from other sources
+# (currently one from OBI, specify) and an unrecognized acronym, NAMD
+[default.extend-identifiers]
+specificy = "specificy"

justfile

@@ -61,7 +61,7 @@ _setup_part2: gen-project gen-doc
 
 # Install project dependencies
 [group('project management')]
-install:
+install: precommit
   uv sync --group dev
 
 # Updates project template and LinkML package

project.justfile

@@ -37,3 +37,7 @@ expand:
 [group('model development')]
 clear file_path:
   uv run weaver --clear src/common_access_model/schema/enums/{{file_path}}.yaml
+
+[group('project management')]
+precommit:
+  pre-commit install

pyproject.toml

@@ -54,7 +54,7 @@ testpaths = ["tests"]
 # https://docs.astral.sh/ruff/configuration/
 [tool.ruff]
 exclude = [
-    "src/kf_access_model/_version.py",
+    "src/include_access_model/_version.py",
 ]
 
 # Ref.: https://github.com/codespell-project/codespell
@@ -63,10 +63,12 @@ skip = [
   "LICENSE",
   "pyproject.toml",
   "uv.lock",
+  "_typos.toml",
   "project/*",
   "src/include_access_model/datamodel/include_access_model_pydantic.py",
   "src/include_access_model/datamodel/include_access_model_sqla.py",
   "src/include_access_model/datamodel/include_access_model.py",
+  "./src/include_access_model/schema/upstream-models/*.yaml"
 ]
 
 # Reminder: words have to be lowercased for the ignore-words-list

src/include_access_model/schema/include_access_model.yaml

@@ -4,11 +4,11 @@ title: INCLUDE DCC Access Model
 description: LinkML Schema for the internal INCLUDE DCC Access Model
 license: MIT
 see_also:
-- https://includedcc.github.io/include-access-model
+  - https://includedcc.github.io/include-access-model
 
 prefixes:
   includedcc: https://includedcc.org/include-access-model/
- # subset of CDC Race and Ethnicity Code Set Version 1.0
+  # subset of CDC Race and Ethnicity Code Set Version 1.0
   cdc_race_eth: urn:oid:2.16.840.1.113883.6.238/
   ig_dob_method: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-date-of-birth-method/
   igcondtype: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/condition-type/
@@ -84,14 +84,14 @@ default_prefix: includedcc
 default_range: linkml:string
 
 imports:
-- upstream-models/common_access_model-0.0.7
+  - upstream-models/common_access_model-0.2.0
 classes:
   IncludeParticipant:
     title: INCLUDE Participant
     description: Information specific to INCLUDE participants
     is_a: Demographics
     slots:
-    - down_syndrome_status
+      - down_syndrome_status
 
 slots:
   down_syndrome_status: