Modifying 'meaning' to match LinkML prefix

.copier-answers.yml

@@ -0,0 +1,16 @@
+# Changes here will be overwritten by Copier
+_commit: v0.5.0
+_src_path: https://github.com/linkml/linkml-project-copier
+add_example: false
+copyright_year: '2026'
+email: yelena.cox@vumc.org
+existing_license_file: ''
+full_name: Yelena Cox
+gh_action_docs_preview: true
+gh_action_pypi: false
+github_org: include-dcc
+license: MIT
+project_description: Source enumerations for the INCLUDE Common Access Model
+project_name: cam-source-enums
+project_slug: cam_source_enums
+

.github/dependabot.yml

@@ -0,0 +1,13 @@
+# Please see the documentation for all configuration options:
+# https://docs.github.com/en/code-security/dependabot/working-with-dependabot/dependabot-options-reference
+
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: "/"
+    schedule:
+      interval: monthly
+    groups:
+      github-actions:
+        patterns:
+          - "*"

.github/workflows/deploy-docs.yaml

@@ -0,0 +1,62 @@
+---
+name: Deploy docs
+on:  # yamllint disable-line rule:truthy
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+permissions: {}
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        pyversion: ["3.13"]
+
+    # Grant GITHUB_TOKEN the permissions required to make a gh-pages deployment
+    permissions:
+      contents: write  # to let mkdocs write the new docs
+      pages: write     # to deploy to Pages
+      id-token: write  # allow to generate an OpenID Connect (OIDC) token
+
+    steps:
+      # https://github.com/actions/checkout
+      - name: Checkout
+        uses: actions/checkout@v6.0.2
+        with:
+          fetch-depth: 0  # otherwise, you will fail to push refs to dest repo
+
+      - name: Configure git for the bot
+        # Gives the bot that commits to gh-pages a name & email address
+        # so that the commits have an author in the commit log.
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email github-actions[bot]@users.noreply.github.com
+
+      # https://github.com/astral-sh/setup-uv
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.1.0
+        with:
+          python-version: ${{ matrix.pyversion }}
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      # https://github.com/actions/setup-python
+      - name: Set up Python
+        uses: actions/setup-python@v6.2.0
+        with:
+          python-version: ${{ matrix.pyversion }}
+
+      - name: Install just
+        run: |
+          uv tool install rust-just
+
+      - name: Install dependencies
+        run: uv sync --group dev --no-progress
+
+      - name: Generate schema documentation
+        run: |
+          just gen-doc
+          uv run mkdocs gh-deploy --force

.github/workflows/main.yaml

@@ -0,0 +1,55 @@
+# Built from:
+# https://docs.github.com/en/actions/guides/building-and-testing-python
+---
+name: Build and test
+
+on:  # yamllint disable-line rule:truthy
+  push:
+    branches: [main]
+  pull_request:
+
+env:
+  FORCE_COLOR: "1"  # Make tools pretty.
+
+permissions: {}
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
+      fail-fast: false
+
+    steps:
+
+      # https://github.com/actions/checkout
+      - name: Check out repository
+        uses: actions/checkout@v6.0.2
+        with:
+          persist-credentials: false
+
+      # https://github.com/astral-sh/setup-uv
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.1.0
+        with:
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      # https://github.com/actions/setup-python
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6.2.0
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install just
+        run: |
+          uv tool install rust-just
+
+      - name: Install project
+        run: uv sync --group dev
+
+      - name: Run test suite
+        run: just test

.github/workflows/test_pages_build.yaml

@@ -0,0 +1,71 @@
+name: Preview documentation build
+
+on:  # yamllint disable-line rule:truthy
+  pull_request:
+    types:
+      - opened
+      - reopened
+      - synchronize
+
+env:
+  CLICOLOR: 1
+
+concurrency: preview-${{ github.ref }}
+
+permissions: {}
+
+jobs:
+  run:
+    # Don't run for PRs from forks which fails due to lack of permissions.
+    if: github.event.pull_request.head.repo.full_name == github.repository
+    # Grant GITHUB_TOKEN the permissions required to make a gh-pages deployment
+    permissions:
+      contents: write  # to let mkdocs write the new docs
+      pages: write     # to deploy to Pages
+      id-token: write  # allow to generate an OpenID Connect (OIDC) token
+      pull-requests: write  # add comment on the PR with the preview URL
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        pyversion: ["3.13"]
+
+    steps:
+      # https://github.com/actions/checkout
+      - name: Checkout
+        uses: actions/checkout@v5.0.0
+        with:
+          fetch-depth: 0
+
+      # https://github.com/actions/setup-python
+      - name: Set up Python
+        uses: actions/setup-python@v6.0.0
+        with:
+          python-version: ${{ matrix.pyversion }}
+      # https://github.com/astral-sh/setup-uv
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7.1.2
+        with:
+          python-version: ${{ matrix.pyversion }}
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      - name: Install just
+        run: |
+          uv tool install rust-just
+
+      - name: Install dependencies
+        run: uv sync --dev --no-progress
+
+      - name: Build documentation
+        run: |
+          just gen-doc
+          uv run mkdocs build -d site
+          touch site/.nojekyll
+
+      # https://github.com/rossjrw/pr-preview-action
+      - name: Deploy preview
+        uses: rossjrw/pr-preview-action@v1.6.2
+        with:
+          source-dir: site/
+          preview-branch: gh-pages

docs/term-expansion.md

@@ -12,4 +12,4 @@ This is the source of the enumeration files to be materialized by the [Term-Weav
 - include_self
     - true/false
 
-* It does not currently support 'traverse_up'
+*It does not currently support 'traverse_up'

src/README.md

@@ -0,0 +1,4 @@
+# The linkML model and its Python representations
+
+This directory holds the schema, its Python representations
+and optionally also additional Python code for the project.

src/cam_source_enums/schema/EnumConsanguinityAssertion.yaml

@@ -8,16 +8,16 @@ enums:
       not_suspected:
         title: not-suspected
         description: Not suspected
-        meaning: snomed_ct:428263003
+        meaning: snomedct:428263003
       suspected:
         title: suspected
         description: Suspected
-        meaning: snomed_ct:415684004
+        meaning: snomedct:415684004
       known_present:
         title: known-present
         description: Known Present
-        meaning: snomed_ct:410515003
+        meaning: snomedct:410515003
       unknown:
         title: unknown
         description: Unknown
-        meaning: snomed_ct:261665006
+        meaning: snomedct:261665006