Quick Test with Modern LinkML Template

.copier-answers.yml

@@ -0,0 +1,15 @@
+# Changes here will be overwritten by Copier
+_commit: v0.4.1
+_src_path: https://github.com/linkml/linkml-project-copier
+add_example: false
+copyright_year: '2025'
+email: eric.s.torstenson@vumc.org
+full_name: Eric S Torstenson
+gh_action_docs_preview: false
+gh_action_pypi: false
+github_org: include-dcc
+license: MIT
+project_description: TBD
+project_name: INCLUDE LinkML Data Model
+project_slug: include_linkml_data_model
+

.editorconfig

@@ -0,0 +1,18 @@
+# Check http://editorconfig.org for more information
+# This is the main config file for this project:
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+indent_style = space
+indent_size = 2
+trim_trailing_whitespace = true
+
+[*.py]
+indent_style = space
+indent_size = 4
+
+[*.md]
+trim_trailing_whitespace = false

.github/dependabot.yml

@@ -0,0 +1,9 @@
+# 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

.github/workflows/deploy-docs.yaml

@@ -1,33 +1,58 @@
-name: Auto-deployment of Documentation
-on:
+---
+name: Deploy docs
+on:  # yamllint disable-line rule:truthy
   push:
-    branches: [ main ]
+    branches: [main]
+  workflow_dispatch:
+
+permissions: {}
 
 jobs:
   build-docs:
     runs-on: ubuntu-latest
+
+    # 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:
-    - name: Checkout
-      uses: actions/checkout@main
-      with:
-        fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
-
-    - name: Set up Python 3.
-      uses: actions/setup-python@v3
-      with:
-        python-version: 3.9
-
-    - name: Install Poetry.
-      uses: snok/install-poetry@v1.3
-
-    - name: Install dependencies.
-      run: poetry install -E docs
-
-    - name: Build documentation.
-      run: |
-        mkdir -p docs
-        touch docs/.nojekyll
-        cp src/docs/*md docs
-        poetry run gen-erdiagram src/linkml/include_schema.yaml > docs/erdiagram.md
-        poetry run gen-doc -d docs --template-directory src/doc_templates src/linkml/include_schema.yaml        
-        poetry run mkdocs gh-deploy
+      # https://github.com/actions/checkout
+      - name: Checkout
+        uses: actions/checkout@v4.2.2
+        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@v6.4.3
+        with:
+          python-version: 3.13
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      # https://github.com/actions/setup-python
+      - name: Set up Python
+        uses: actions/setup-python@v5.6.0
+        with:
+          python-version: 3.13
+
+      - name: Install just
+        run: |
+          uv tool install rust-just
+
+      - name: Install dependencies
+        run: uv sync --dev --no-progress
+
+      - name: Generate schema documentation
+        run: |
+          just gen-doc
+          uv run mkdocs gh-deploy

.github/workflows/main.yaml

@@ -1,53 +1,55 @@
 # Built from:
 # https://docs.github.com/en/actions/guides/building-and-testing-python
-# https://github.com/snok/install-poetry#workflows-and-tips
+---
+name: Build and test
 
-name: Build and test linkml-runtime
+on:  # yamllint disable-line rule:truthy
+  push:
+    branches: [main]
+  pull_request:
 
-on: [pull_request]
+env:
+  FORCE_COLOR: "1" # Make tools pretty.
+
+permissions: {}
 
 jobs:
   test:
 
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+      fail-fast: false
 
     steps:
 
-      #----------------------------------------------
-      #       check-out repo and set-up python
-      #----------------------------------------------
+      # https://github.com/actions/checkout
       - name: Check out repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4.2.2
+        with:
+          persist-credentials: false
+
+      # https://github.com/astral-sh/setup-uv
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6.4.3
+        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@v2
+        uses: actions/setup-python@v5.6.0
         with:
           python-version: ${{ matrix.python-version }}
 
-      #----------------------------------------------
-      #          install & configure poetry
-      #----------------------------------------------
-      - name: Install Poetry
-        uses: snok/install-poetry@v1.3
-
-      #----------------------------------------------
-      # install dependencies if cache does not exist 
-      #----------------------------------------------
-      - name: Install dependencies
-        run: poetry install --no-interaction --no-root
-
-      #----------------------------------------------
-      #    install your root project, if required 
-      #----------------------------------------------      
-      - name: Install library
-        run: poetry install --no-interaction
-
-      #----------------------------------------------
-      #              run test suite   
-      #----------------------------------------------
-      - name: Run tests
-        run: make test
+      - name: Install just
+        run: |
+          uv tool install rust-just
+
+      - name: Install project
+        run: uv sync --dev
 
+      - name: Run test suite
+        run: just test

.gitignore

@@ -1,10 +1,21 @@
+# generated part of documentation
+/docs/elements/*.md
+# linkml-run-examples output (not useful to have in git in its current form)
+/examples/output/
+
+# Derived schemas, generated from the schema.yaml
+tmp/
+project/
+!project/README.md
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
 *$py.class
+
 # C extensions
 *.so
-poetry.lock
+
 # Distribution / packaging
 .Python
 build/
@@ -69,23 +80,16 @@ instance/
 
 # Sphinx documentation
 docs/_build/
-site/
-docs/*md
-docs/types/
-project/
+
 # PyBuilder
 target/
 
 # Jupyter Notebook
 .ipynb_checkpoints
 
-# Pycharm
-.idea
-
 # IPython
 profile_default/
 ipython_config.py
-*.ipynb
 
 # pyenv
 .python-version
@@ -134,13 +138,7 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
-#local dev environment
-/local_data
-.DS_Store
-#cogs
-.cogs/
-
-config.yml
-great_expectations/
-harmonized_data/
-schematic_service_account_creds.json
+# pycharm
+.idea
+# Local vscode editor config
+.vscode

.pre-commit-config.yaml

@@ -0,0 +1,45 @@
+---
+# https://pre-commit.com/
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-toml
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+
+  - repo: https://github.com/adrienverge/yamllint.git
+    rev: v1.37.0
+    hooks:
+      - id: yamllint
+        args: [-c=.yamllint.yaml]
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.4.1
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli
+
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.31.1
+    hooks:
+      - id: typos
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.11.3
+    hooks:
+      # Run the linter.
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+      # Run the formatter.
+      - id: ruff-format
+
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    # uv version.
+    rev: 0.6.12
+    hooks:
+      - id: uv-lock

.yamllint.yaml

@@ -0,0 +1,12 @@
+# Configuration for https://github.com/adrienverge/yamllint
+
+extends: default
+
+rules:
+  document-start: disable  # Don't check if document has a start marker (---).
+  line-length:
+    max: 80
+    level: warning
+    allow-non-breakable-words: true
+    allow-non-breakable-inline-mappings: true
+  new-lines: disable  # Don't check for type of new line characters.