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Add precommit and run on all files (#1541)
* Add precommit * Use pre-commit * Run precommit * Add EOL
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‎.flake8‎

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[flake8]
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ignore =
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ignore =
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# E*** / W*** pycodestyle codes
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# whitespace before ','
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E203,

‎.github/ISSUE_TEMPLATE/jira_service_desk.md‎

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---
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name: Please file issues in Jira Service Desk
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name: Please file issues in Jira Service Desk
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about: https://sagebionetworks.jira.com/servicedesk/customer/portal/5/group/8/create/87
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title: ''
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labels: ''
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**Describe the bug**
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Please file issues or requests for help with schematic in [Jira Service Desk](https://sagebionetworks.jira.com/servicedesk/customer/portal/5/group/8/create/87).
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These issues are not monitored.
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These issues are not monitored.

‎.github/workflows/api_test.yml‎

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| python3 - --version ${{ env.POETRY_VERSION }};
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poetry config virtualenvs.create true;
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poetry config virtualenvs.in-project true;
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#----------------------------------------------
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# install dependencies and root project
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#----------------------------------------------

‎.github/workflows/docker_build.yml‎

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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Set env variable for version tag
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run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
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labels: ${{ steps.meta.outputs.labels }}
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build-args: |
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TAG=${{ env.RELEASE_VERSION }}
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‎.github/workflows/pdoc.yml‎

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contents: read
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concurrency:
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# cancel the current running workflow from the same branch, PR when a new workflow is triggered
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# cancel the current running workflow from the same branch, PR when a new workflow is triggered
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# when the trigger is not a PR but a push, it will use the commit sha to generate the concurrency group
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# {{ github.workflow }}: the workflow name is used to generate the concurrency group. This allows you to have more than one workflows
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# {{ github.ref_type }}: the type of Git ref object created in the repository. Can be either branch or tag
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# {{ github.event.pull_request.number}}: get PR number
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# {{ github.sha }}: full commit sha
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# {{ github.ref_type }}: the type of Git ref object created in the repository. Can be either branch or tag
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# {{ github.event.pull_request.number}}: get PR number
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# {{ github.sha }}: full commit sha
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# credit: https://github.com/Sage-Bionetworks-Workflows/sagetasks/blob/main/.github/workflows/ci.yml
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group: >-
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${{ github.workflow }}-${{ github.ref_type }}-
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steps:
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#----------------------------------------------
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# check-out repo and set-up python
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# check-out repo and set-up python
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#----------------------------------------------
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- name: Check out repository
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uses: actions/checkout@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ env.PYTHON_VERSION }}
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#----------------------------------------------
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# install & configure poetry
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# install & configure poetry
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#----------------------------------------------
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- name: Install Poetry
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run: |
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curl -sSL https://install.python-poetry.org \
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| python3 - --version ${{ env.POETRY_VERSION }};
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poetry config virtualenvs.create true;
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poetry config virtualenvs.in-project true;
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poetry config virtualenvs.create true;
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poetry config virtualenvs.in-project true;
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#----------------------------------------------
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# install dependencies and root project

‎.github/workflows/publish.yml‎

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with:
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python-version: ${{ env.PYTHON_VERSION }}
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- id: build-package
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run: |
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run: |
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python3 -m pip install --upgrade pip
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python3 -m pip install setuptools
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python3 -m pip install wheel
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echo "sdist-release-url=${RELEASE_URL_PREFIX}${SDIST_PACKAGE_NAME}" >> $GITHUB_OUTPUT
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echo "bdist-release-url=${RELEASE_URL_PREFIX}${BDIST_PACKAGE_NAME}" >> $GITHUB_OUTPUT
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- name: upload-sdist-artifact
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uses: actions/upload-artifact@v4
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with:
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# Post to the `fair-data-tools` slack channel
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channel-id: 'C01ANC02U59'
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slack-message: "A new version of Schematic has been released. Check out the new version: ${{ github.ref_name }}"
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‎.github/workflows/scan_repo.yml‎

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branches:
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- develop
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pull_request:
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workflow_dispatch:
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workflow_dispatch:
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jobs:
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trivy:

‎.github/workflows/test.yml‎

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#----------------------------------------------
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# check formatting
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#----------------------------------------------
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- name: Code formatting with black
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run: |
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# ran only on certain files for now
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# add here when checked
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poetry run black schematic tests schematic_api --check
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- uses: pre-commit/action@v3.0.1
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#----------------------------------------------
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# type checking/enforcement
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SYNAPSE_ACCESS_TOKEN: ${{ secrets.SYNAPSE_ACCESS_TOKEN }}
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SERVICE_ACCOUNT_CREDS: ${{ secrets.SERVICE_ACCOUNT_CREDS }}
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run: >
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poetry run pytest --durations=0 --cov-append --cov-report=term --cov-report=html:htmlcov
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poetry run pytest --durations=0 --cov-append --cov-report=term --cov-report=html:htmlcov
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--cov-report=xml:coverage.xml --cov=schematic/ --reruns 4 -n 8 tests/unit;
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#----------------------------------------------
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LOGGING_EXPORT_FORMAT: ${{ vars.LOGGING_EXPORT_FORMAT }}
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TRACING_SERVICE_NAME: ${{ vars.TRACING_SERVICE_NAME }}
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LOGGING_SERVICE_NAME: ${{ vars.LOGGING_SERVICE_NAME }}
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SERVICE_INSTANCE_ID: ${{ github.head_ref || github.ref_name }}
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SERVICE_INSTANCE_ID: ${{ github.head_ref || github.ref_name }}
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run: >
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poetry run pytest --durations=0 --cov-append --cov-report=term --cov-report=html:htmlcov --cov-report=xml:coverage.xml --cov=schematic/
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-m "not (rule_benchmark or single_process_execution)" --reruns 4 -n 8 --ignore=tests/unit

‎.gitignore‎

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https:*
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# schematic config file
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config.yml
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config.yml

‎.pre-commit-config.yaml‎

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repos:
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# Using this mirror lets us use mypyc-compiled black, which is about 2x faster
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# This is recommended by psf/black: https://github.com/psf/black/blob/main/.pre-commit-hooks.yaml
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- repo: https://github.com/psf/black-pre-commit-mirror
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rev: 23.7.0
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hooks:
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- id: black
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# It is recommended to specify the latest version of Python
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# supported by your project here, or alternatively use
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# pre-commit's default_language_version, see
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# https://pre-commit.com/#top_level-default_language_version
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language_version: python3.10
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files: ^(tests|schematic|schematic_api)/
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- repo: https://github.com/pycqa/isort
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rev: 5.13.2
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hooks:
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- id: isort
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name: isort (python)
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files: ^(tests|schematic|schematic_api)/
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args: ["--profile", "black", "--filter-files"]
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exclude: "^docs/conf.py|^docs/build/"
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.4.0
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hooks:
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- id: trailing-whitespace
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- id: check-added-large-files
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- id: check-ast
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# - id: check-json
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- id: check-merge-conflict
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- id: check-xml
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- id: check-yaml
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exclude: ^mkdocs\.yml$
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- id: debug-statements
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- id: end-of-file-fixer
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- id: requirements-txt-fixer
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- id: mixed-line-ending
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args: ["--fix=auto"] # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
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# - repo: https://github.com/astral-sh/ruff-pre-commit
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# rev: "v0.0.270"
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# hooks:
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# - id: ruff
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# - repo: https://github.com/pycqa/isort
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# rev: 5.13.2
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# hooks:
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# - id: isort
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# name: isort (python)
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- repo: https://github.com/psf/black
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rev: 23.12.1
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hooks:
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- id: black
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language_version: python3
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# - repo: https://github.com/PyCQA/bandit
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# rev: 1.7.5
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# hooks:
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# - id: bandit
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# args: ["-c", "pyproject.toml"]
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# additional_dependencies: ["bandit[toml]"]
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# - repo: https://github.com/asottile/blacken-docs
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# rev: v1.12.0
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# hooks:
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# - id: blacken-docs
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# additional_dependencies: [black]
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# - repo: https://github.com/pre-commit/mirrors-mypy
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# rev: 'v1.0.1'
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# hooks:
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# - id: mypy
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# additional_dependencies: [pydantic~=1.10]
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# Checks for missing docstrings
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# - repo: https://github.com/econchick/interrogate
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# rev: 1.5.0
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# hooks:
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# - id: interrogate
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# exclude: ^(docs/conf.py|setup.py|tests)
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# args: [--config=pyproject.toml]
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# finds dead python code
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# - repo: https://github.com/jendrikseipp/vulture
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# rev: 'v2.7'
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# hooks:
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# - id: vulture

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