Script to Pull Descendants from OLS

.copier-answers.yml

@@ -0,0 +1,17 @@
+# 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: false
+gh_action_pypi: false
+github_org: include-dcc
+license: MIT
+project_description: This project is a LinkML model containing expanded enumerations
+    from the Common Access Model.
+project_name: cam-expanded-enums
+project_slug: cam_expanded_enums
+

.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 +1,13 @@
+# 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

.gitignore

@@ -1,16 +1,18 @@
+# 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[codz]
+*.py[cod]
 *$py.class
 
-# Help with managing local environments
-.envrc
-.bash_history_local
-.direnv
-
-# Temp place for script to turn the design into MD
-scripts
-
 # C extensions
 *.so
 
@@ -28,15 +30,16 @@ parts/
 sdist/
 var/
 wheels/
+pip-wheel-metadata/
 share/python-wheels/
 *.egg-info/
 .installed.cfg
 *.egg
 MANIFEST
 
 # 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.
+#  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.
 *.manifest
 *.spec
 
@@ -54,10 +57,9 @@ htmlcov/
 nosetests.xml
 coverage.xml
 *.cover
-*.py.cover
+*.py,cover
 .hypothesis/
 .pytest_cache/
-cover/
 
 # Translations
 *.mo
@@ -80,7 +82,6 @@ instance/
 docs/_build/
 
 # PyBuilder
-.pybuilder/
 target/
 
 # Jupyter Notebook
@@ -91,73 +92,27 @@ profile_default/
 ipython_config.py
 
 # pyenv
-#   For a library or package, you might want to ignore these files since the code is
-#   intended to run in multiple environments; otherwise, check them in:
-# .python-version
+.python-version
 
 # pipenv
 #   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
 #   However, in case of collaboration, if having platform-specific dependencies or dependencies
 #   having no cross-platform support, pipenv may install dependencies that don't work, or not
 #   install all needed dependencies.
-# Pipfile.lock
-
-# UV
-#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-# uv.lock
-
-# poetry
-#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-# poetry.lock
-# poetry.toml
-
-# pdm
-#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
-#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
-# pdm.lock
-# pdm.toml
-.pdm-python
-.pdm-build/
-
-# pixi
-#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
-# pixi.lock
-#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
-#   in the .venv directory. It is recommended not to include this directory in version control.
-.pixi
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
 __pypackages__/
 
 # Celery stuff
 celerybeat-schedule
 celerybeat.pid
 
-# Redis
-*.rdb
-*.aof
-*.pid
-
-# RabbitMQ
-mnesia/
-rabbitmq/
-rabbitmq-data/
-
-# ActiveMQ
-activemq-data/
-
 # SageMath parsed files
 *.sage.py
 
 # Environments
 .env
-.envrc
 .venv
 env/
 venv/
@@ -183,44 +138,7 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
-# pytype static type analyzer
-.pytype/
-
-# Cython debug symbols
-cython_debug/
-
-# PyCharm
-#   JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-#   be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-#   and can be added to the global gitignore or merged into this file.  For a more nuclear
-#   option (not recommended) you can uncomment the following to ignore the entire idea folder.
-# .idea/
-
-# Abstra
-#   Abstra is an AI-powered process automation framework.
-#   Ignore directories containing user credentials, local state, and settings.
-#   Learn more at https://abstra.io/docs
-.abstra/
-
-# Visual Studio Code
-#   Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
-#   that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
-#   and can be added to the global gitignore or merged into this file. However, if you prefer,
-#   you could uncomment the following to ignore the entire vscode folder
-# .vscode/
-# Temporary file for partial code execution
-tempCodeRunnerFile.py
-
-# Ruff stuff:
-.ruff_cache/
-
-# PyPI configuration file
-.pypirc
-
-# Marimo
-marimo/_static/
-marimo/_lsp/
-__marimo__/
-
-# Streamlit
-.streamlit/secrets.toml
+# pycharm
+.idea
+# Local vscode editor config
+.vscode