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Copier update (pre-commit workflow) (#42)
Pull in upstream changes
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‎.copier-answers.yml

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# Changes here will be overwritten by Copier
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_commit: v0.0.42
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_commit: v0.0.44
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_src_path: gh:LabAutomationAndScreening/copier-base-template.git
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description: Copier template for creating Python libraries and executables
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python_ci_versions:

‎.github/dependabot.yml

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- dependency-name: "boto3" # boto3 gets patch updates way too frequently and they're usually not important
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update-types:
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- "version-update:semver-patch"
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- dependency-name: "sphinx*" # read-the-docs uses specific versions of sphinx, so we generally want to stay tightly pinned unless there's a major version change
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update-types:
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- "version-update:semver-minor"
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- "version-update:semver-patch"
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groups:
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prod-dependencies:

‎.github/workflows/ci.yaml

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pre-commit:
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needs: [ get-values ]
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strategy:
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fail-fast: false
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matrix:
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os:
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- "ubuntu-24.04"
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python-version:
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- 3.12.7
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name: Pre-commit for Py${{ matrix.python-version }} on ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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steps:
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- name: Checkout code
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uses: actions/checkout@v4.2.2
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with:
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ref: ${{ github.ref_name }} # explicitly get the head of
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- name: Install latest versions of python packages
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uses: ./.github/actions/install_deps_uv
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with:
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python-version: ${{ matrix.python-version }}
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- name: Set up mutex # Github concurrency management is horrible, things get arbitrarily cancelled if queued up. So using mutex until github fixes itself. When multiple jobs are modifying cache at once, weird things can happen. possible issue is https://github.com/actions/toolkit/issues/658
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if: ${{ runner.os != 'Windows' }} # we're just gonna have to YOLO on Windows, because this action doesn't support it yet https://github.com/ben-z/gh-action-mutex/issues/14
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uses: ben-z/gh-action-mutex@1ebad517141198e08d47cf72f3c0975316620a65 # v1.0.0-alpha.10
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with:
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branch: mutex-venv-${{ matrix.os }}-${{ matrix.python-version }}
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timeout-minutes: 30 # this is the amount of time this action will wait to attempt to acquire the mutex lock before failing, e.g. if other jobs are queued up in front of it
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- name: Cache Pre-commit hooks
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uses: actions/cache@v4.2.2
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env:
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cache-name: cache-pre-commit-hooks
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with:
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path: ${{ env.PRE_COMMIT_HOME }}
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key: ${{ matrix.os }}-${{ matrix.python-version }}-build-${{ env.cache-name }}-${{ hashFiles('.pre-commit-config.yaml') }}
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restore-keys: |
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${{ matrix.os }}-${{ matrix.python-version }}-build-${{ env.cache-name }}-
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- name: Run pre-commit
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run: pre-commit run -a
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uses: ./.github/workflows/pre-commit.yaml
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with:
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python-version: 3.12.7
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lint-matrix:
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needs: [ pre-commit ]

‎.github/workflows/pre-commit.yaml

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name: Pre-commit
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on:
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workflow_call:
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inputs:
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python-version:
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description: 'What version of python'
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type: string
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required: true
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setup-node:
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description: 'Whether to set up Node'
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type: boolean
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default: false
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node-version:
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description: 'What version of node'
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type: string
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required: false
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default: 'notUsing'
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env:
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PYTHONUNBUFFERED: True
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PRE_COMMIT_HOME: ${{ github.workspace }}/.precommit_cache
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permissions:
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contents: write # needed for mutex
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jobs:
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pre-commit:
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runs-on: ubuntu-24.04
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name: Pre-commit
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steps:
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- name: Checkout code
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uses: actions/checkout@v4.2.2
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with:
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ref: ${{ github.ref_name }} # explicitly get the head of the branch, which will include any new commits pushed if this is a dependabot branch
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- name: Setup node
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uses: actions/setup-node@v4.3.0
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if: ${{ inputs.setup-node }}
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with:
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node-version: ${{ inputs.node-version }}
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- name: Install latest versions of python packages
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uses: ./.github/actions/install_deps_uv
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with:
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python-version: ${{ inputs.python-version }}
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- name: Set up mutex # Github concurrency management is horrible, things get arbitrarily cancelled if queued up. So using mutex until github fixes itself. When multiple jobs are modifying cache at once, weird things can happen. possible issue is https://github.com/actions/toolkit/issues/658
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if: ${{ runner.os != 'Windows' }} # we're just gonna have to YOLO on Windows, because this action doesn't support it yet https://github.com/ben-z/gh-action-mutex/issues/14
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uses: ben-z/gh-action-mutex@1ebad517141198e08d47cf72f3c0975316620a65 # v1.0.0-alpha.10
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with:
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branch: mutex-venv-ubuntu-24.04-py${{ inputs.python-version }}-nodejs-${{ inputs.node-version }}
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timeout-minutes: 30 # this is the amount of time this action will wait to attempt to acquire the mutex lock before failing, e.g. if other jobs are queued up in front of it
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- name: Cache Pre-commit hooks
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uses: actions/cache@v4.2.2
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env:
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cache-name: cache-pre-commit-hooks
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with:
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path: ${{ env.PRE_COMMIT_HOME }}
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key: ubuntu-24.04-py${{ inputs.python-version }}-node-${{ inputs.node-version}}-${{ env.cache-name }}-${{ hashFiles('.pre-commit-config.yaml') }}
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restore-keys: |
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ubuntu-24.04-py${{ inputs.python-version }}-node-${{ inputs.node-version}}-${{ env.cache-name }}-
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- name: Run pre-commit
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run: pre-commit run -a

‎template/.github/workflows/ci.yaml.jinja

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lint:
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needs: [ get-values ]
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name: Pre-commit
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runs-on: {% endraw %}{{ gha_linux_runner }}{% raw %}
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steps:
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- name: Checkout code
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uses: actions/checkout@{% endraw %}{{ gha_checkout }}{% raw %}
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- name: Install latest versions of python packages
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uses: ./.github/actions/install_deps_uv
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with:
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python-version: {% endraw %}{{ python_version }}{% raw %}{% endraw %}{% if python_package_registry == "AWS CodeArtifact" %}{% raw %}
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code-artifact-auth-role-name: CoreInfraBaseAccess
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code-artifact-auth-role-account-id: {% endraw %}{{ aws_central_infrastructure_account_id }}{% raw %}
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code-artifact-auth-region: {% endraw %}{{ aws_org_home_region }}{% endif %}{% raw %}
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- name: Set up mutex # Github concurrency management is horrible, things get arbitrarily cancelled if queued up. So using mutex until github fixes itself. When multiple jobs are modifying cache at once, weird things can happen. possible issue is https://github.com/actions/toolkit/issues/658
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if: ${{ runner.os != 'Windows' }} # we're just gonna have to YOLO on Windows, because this action doesn't support it yet https://github.com/ben-z/gh-action-mutex/issues/14
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uses: ben-z/gh-action-mutex@{% endraw %}{{ gha_mutex }}{% raw %}
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with:
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branch: mutex-venv-{% endraw %}{{ gha_linux_runner }}{% raw %}-py{% endraw %}{{ python_version }}{% raw %}
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timeout-minutes: 30 # this is the amount of time this action will wait to attempt to acquire the mutex lock before failing, e.g. if other jobs are queued up in front of it
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- name: Cache Pre-commit hooks
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uses: actions/cache@{% endraw %}{{ gha_cache }}{% raw %}
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env:
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cache-name: cache-pre-commit-hooks
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with:
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path: ${{ env.PRE_COMMIT_HOME }}
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key: {% endraw %}{{ gha_linux_runner }}{% raw %}-py{% endraw %}{{ python_version }}{% raw %}-build-${{ env.cache-name }}-${{ hashFiles('.pre-commit-config.yaml') }}
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restore-keys: |
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{% endraw %}{{ gha_linux_runner }}{% raw %}-py{% endraw %}{{ python_version }}{% raw %}-build-${{ env.cache-name }}-
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- name: Run pre-commit
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run: pre-commit run -a
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uses: ./.github/workflows/pre-commit.yaml
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with:
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python-version: {% endraw %}{{ python_version }}{% raw %}
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test:
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needs: [ lint ]

‎template/.github/workflows/pre-commit.yaml

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name: Pre-commit
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on:
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workflow_call:
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inputs:
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python-version:
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description: 'What version of python'
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type: string
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required: true
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setup-node:
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description: 'Whether to set up Node'
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type: boolean
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default: false
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node-version:
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description: 'What version of node'
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type: string
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required: false
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default: 'notUsing'
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env:
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PYTHONUNBUFFERED: True
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PRE_COMMIT_HOME: ${{ github.workspace }}/.precommit_cache
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permissions:
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contents: write # needed for mutex
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jobs:
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pre-commit:
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runs-on: ubuntu-24.04
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name: Pre-commit
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steps:
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- name: Checkout code
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uses: actions/checkout@v4.2.2
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with:
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ref: ${{ github.ref_name }} # explicitly get the head of the branch, which will include any new commits pushed if this is a dependabot branch
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- name: Setup node
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uses: actions/setup-node@v4.3.0
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if: ${{ inputs.setup-node }}
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with:
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node-version: ${{ inputs.node-version }}
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- name: Install latest versions of python packages
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uses: ./.github/actions/install_deps_uv
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with:
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python-version: ${{ inputs.python-version }}
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- name: Set up mutex # Github concurrency management is horrible, things get arbitrarily cancelled if queued up. So using mutex until github fixes itself. When multiple jobs are modifying cache at once, weird things can happen. possible issue is https://github.com/actions/toolkit/issues/658
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if: ${{ runner.os != 'Windows' }} # we're just gonna have to YOLO on Windows, because this action doesn't support it yet https://github.com/ben-z/gh-action-mutex/issues/14
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uses: ben-z/gh-action-mutex@1ebad517141198e08d47cf72f3c0975316620a65 # v1.0.0-alpha.10
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with:
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branch: mutex-venv-ubuntu-24.04-py${{ inputs.python-version }}-nodejs-${{ inputs.node-version }}
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timeout-minutes: 30 # this is the amount of time this action will wait to attempt to acquire the mutex lock before failing, e.g. if other jobs are queued up in front of it
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- name: Cache Pre-commit hooks
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uses: actions/cache@v4.2.2
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env:
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cache-name: cache-pre-commit-hooks
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with:
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path: ${{ env.PRE_COMMIT_HOME }}
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key: ubuntu-24.04-py${{ inputs.python-version }}-node-${{ inputs.node-version}}-${{ env.cache-name }}-${{ hashFiles('.pre-commit-config.yaml') }}
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restore-keys: |
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ubuntu-24.04-py${{ inputs.python-version }}-node-${{ inputs.node-version}}-${{ env.cache-name }}-
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- name: Run pre-commit
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run: pre-commit run -a

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