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🚀 Launch INCLUDE version of the Model
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‎.copier-answers.yml‎

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# Changes here will be overwritten by Copier
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_commit: v0.4.1
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_src_path: https://github.com/linkml/linkml-project-copier
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add_example: false
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copyright_year: '2025'
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email: robert.carroll@vumc.org
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full_name: Robert Carroll
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gh_action_docs_preview: true
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gh_action_pypi: false
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github_org: include-dcc
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license: MIT
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project_description: Internal Access model for the INCLUDE DCC.
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project_name: include-access-model
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project_slug: include_access_model
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‎.editorconfig‎

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

‎.github/dependabot.yml‎

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# Please see the documentation for all configuration options:
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# https://docs.github.com/en/code-security/dependabot/working-with-dependabot/dependabot-options-reference
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version: 2
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updates:
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- package-ecosystem: github-actions
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directory: "/"
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schedule:
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interval: monthly

‎.github/workflows/deploy-docs.yaml‎

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---
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name: Deploy docs
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on: # yamllint disable-line rule:truthy
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push:
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branches: [main]
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workflow_dispatch:
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permissions: {}
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jobs:
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build-docs:
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runs-on: ubuntu-latest
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# Grant GITHUB_TOKEN the permissions required to make a gh-pages deployment
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permissions:
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contents: write # to let mkdocs write the new docs
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pages: write # to deploy to Pages
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id-token: write # allow to generate an OpenID Connect (OIDC) token
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steps:
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# https://github.com/actions/checkout
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- name: Checkout
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uses: actions/checkout@v6.0.2
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with:
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fetch-depth: 0 # otherwise, you will fail to push refs to dest repo
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- name: Configure git for the bot
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# Gives the bot that commits to gh-pages a name & email address
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# so that the commits have an author in the commit log.
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run: |
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git config user.name github-actions[bot]
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git config user.email github-actions[bot]@users.noreply.github.com
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# https://github.com/astral-sh/setup-uv
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- name: Install uv
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uses: astral-sh/setup-uv@v8.0.0
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with:
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python-version: 3.13
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enable-cache: true
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cache-dependency-glob: "uv.lock"
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# https://github.com/actions/setup-python
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- name: Set up Python
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uses: actions/setup-python@v6.2.0
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with:
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python-version: 3.13
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- name: Install just
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run: |
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uv tool install rust-just
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- name: Install dependencies
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run: uv sync --dev --no-progress
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- name: Generate schema documentation
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run: |
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just gen-doc
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uv run mkdocs gh-deploy

‎.github/workflows/main.yaml‎

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# Built from:
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# https://docs.github.com/en/actions/guides/building-and-testing-python
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---
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name: Build and test
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on: # yamllint disable-line rule:truthy
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push:
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branches: [main]
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pull_request:
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env:
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FORCE_COLOR: "1" # Make tools pretty.
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permissions: {}
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jobs:
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test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
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fail-fast: false
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steps:
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# https://github.com/actions/checkout
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- name: Check out repository
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uses: actions/checkout@v6.0.2
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with:
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persist-credentials: false
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# https://github.com/astral-sh/setup-uv
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- name: Install uv
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uses: astral-sh/setup-uv@v8.0.0
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with:
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python-version: ${{ matrix.python-version }}
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enable-cache: true
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cache-dependency-glob: "uv.lock"
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# https://github.com/actions/setup-python
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v6.2.0
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install just
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run: |
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uv tool install rust-just
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- name: Install project
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run: uv sync --dev
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- name: Run test suite
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run: just test

‎.github/workflows/test_pages_build.yaml‎

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name: Preview documentation build
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on: # yamllint disable-line rule:truthy
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pull_request:
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types:
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- opened
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- reopened
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- synchronize
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env:
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CLICOLOR: 1
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concurrency: preview-${{ github.ref }}
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permissions: {}
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jobs:
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run:
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# Grant GITHUB_TOKEN the permissions required to make a gh-pages deployment
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permissions:
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contents: write # to let mkdocs write the new docs
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pages: write # to deploy to Pages
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id-token: write # allow to generate an OpenID Connect (OIDC) token
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pull-requests: write # add comment on the PR with the preview URL
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runs-on: ubuntu-latest
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steps:
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# https://github.com/actions/checkout
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- name: Checkout
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uses: actions/checkout@v6.0.2
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with:
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fetch-depth: 0
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# https://github.com/astral-sh/setup-uv
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- name: Install uv
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uses: astral-sh/setup-uv@v8.0.0
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with:
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python-version: 3.13
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enable-cache: true
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cache-dependency-glob: "uv.lock"
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# https://github.com/actions/setup-python
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- name: Set up Python 3
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uses: actions/setup-python@v6.2.0
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with:
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python-version: 3.13
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- name: Install just
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run: |
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uv tool install rust-just
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- name: Install dependencies
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run: uv sync --dev --no-progress
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- name: Build documentation
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run: |
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just gen-doc
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uv run mkdocs build -d site
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touch site/.nojekyll
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# https://github.com/rossjrw/pr-preview-action
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- name: Deploy preview
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uses: rossjrw/pr-preview-action@v1.8.1
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with:
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source-dir: site/
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preview-branch: gh-pages

‎.gitignore‎

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# generated part of documentation
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/docs/elements/*.md
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/docs/schema/*.yaml
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# generated pydantic model
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/src/include_access_model/datamodel/include_access_model_pydantic.py
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/src/include_access_model/datamodel/include_access_model.py
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# linkml-run-examples output (not useful to have in git in its current form)
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/examples/output/
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# Derived schemas, generated from the schema.yaml
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tmp/
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project/
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!project/README.md
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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pip-wheel-metadata/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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.python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pycharm
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.idea
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# Local vscode editor config
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.vscode

‎.gitmodules‎

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[submodule "common-access-model"]
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path = common-access-model
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url = https://github.com/include-dcc/common-access-model
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[submodule "src/include_access_model/schema/common-access-model"]
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path = src/include_access_model/schema/common-access-model
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url = https://github.com/include-dcc/common-access-model

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