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‎.flake8‎

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[flake8]
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exclude =
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.git,
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__pycache__,
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build,
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.venv,
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venv,
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.conda
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max-complexity = 10

‎.github/ISSUE_TEMPLATE/bug_report.md‎

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---
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name: Bug report
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about: Create a report to help us improve
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title: ''
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labels: ''
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assignees: ''
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---
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**Describe the bug**
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A clear and concise description of what the bug is.
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**To Reproduce**
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Steps to reproduce the behavior:
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1. Go to '...'
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2. Click on '....'
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3. Scroll down to '....'
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4. See error
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**Expected behavior**
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A clear and concise description of what you expected to happen.
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**Screenshots**
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If applicable, add screenshots to help explain your problem.
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**Desktop (please complete the following information):**
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- OS: [e.g. iOS]
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- Browser [e.g. chrome, safari]
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- Version [e.g. 22]
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**Smartphone (please complete the following information):**
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- Device: [e.g. iPhone6]
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- OS: [e.g. iOS8.1]
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- Browser [e.g. stock browser, safari]
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- Version [e.g. 22]
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**Additional context**
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Add any other context about the problem here.

‎.github/ISSUE_TEMPLATE/feature_request.md‎

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---
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name: Feature request
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about: Suggest an idea for this project
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title: ''
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labels: ''
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assignees: ''
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---
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**Is your feature request related to a problem? Please describe.**
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A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
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**Describe the solution you'd like**
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A clear and concise description of what you want to happen.
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**Describe alternatives you've considered**
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A clear and concise description of any alternative solutions or features you've considered.
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**Additional context**
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Add any other context or screenshots about the feature request here.

‎.github/ISSUE_TEMPLATE/user-story.md‎

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---
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name: User story
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about: This template provides a basic structure for user story issues.
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title: ''
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labels: ''
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assignees: ''
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---
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# User story
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As a ..., I want to ..., so I can ...
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*Ideally, this is in the issue title, but if not, you can put it here. If so, delete this section.*
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# Acceptance criteria
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- [ ] This is something that can be verified to show that this user story is satisfied.
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# Sprint Ready Checklist
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- [ ] 1. Acceptance criteria defined
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- [ ] 2. Team understands acceptance criteria
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- [ ] 3. Team has defined solution / steps to satisfy acceptance criteria
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- [ ] 4. Acceptance criteria is verifiable / testable
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- [ ] 5. External / 3rd Party dependencies identified
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- [ ] 6. Ticket is prioritized and sized
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# Notes
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*Add any helpful notes here.*

‎.github/dependabot.yml‎

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# To get started with Dependabot version updates, you'll need to specify which
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# package ecosystems to update and where the package manifests are located.
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# Please see the documentation for all configuration options:
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# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
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version: 2
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updates:
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- package-ecosystem: "pip"
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directory: "/"
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schedule:
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interval: "weekly"
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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interval: "weekly"

‎.github/workflows/init.yml‎

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# Workflow runs only once when the template is first used.
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# File can be safely deleted after repo is initialized.
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name: Initialize repository
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on:
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push:
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branches:
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- main
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jobs:
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initialize-package:
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name: Initialize the package
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if: ${{github.event.repository.name != 'aind-library-template'}}
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runs-on: ubuntu-latest
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env:
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REPO_NAME: ${{ github.event.repository.name }}
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GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Rename package
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run: |
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current_date=$(date '+%Y-%m-%d')
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pkg_name=$(echo "${REPO_NAME}" | tr - _)
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current_description='description = "Prints messages to stdout. Simple boilerplate for libraries."'
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new_description='description = "Generated from aind-library-template"'
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readme_description='Template for a minimal, basic repository for an AIND library.'
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new_readme_description='Generated from aind-library-template'
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echo "Package Name ${pkg_name}"
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mkdir src/${pkg_name}
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touch src/${pkg_name}/__init__.py
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echo '"""Init package"""' >> src/${pkg_name}/__init__.py
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sed -i "s/aind_library_template/${pkg_name}/" pyproject.toml
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sed -i "s/aind-library-template/${REPO_NAME}/" pyproject.toml
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sed -i "s/aind-library-template/${REPO_NAME}/" CITATION.cff
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sed -i "s/^version:.*/version: \"v0.0.0\"/" CITATION.cff
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sed -i "s/^date-released:.*/date-release: $current_date/" CITATION.cff
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sed -i "s/aind_library_template/${pkg_name}/" docs/source/conf.py
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sed -i "s/aind-library-template/${REPO_NAME}/" docs/source/conf.py
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sed -i "s/${current_description}/${new_description}/" pyproject.toml
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sed -i "/pandas/d" pyproject.toml
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sed -i "s/aind-library-template/${REPO_NAME}/" README.md
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sed -i "s/${readme_description}/${new_readme_description}/" README.md
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- name: Set up uv
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uses: astral-sh/setup-uv@v7
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- name: Reset version and lockfile
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run: |
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uv version 0.0.0
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uv lock
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- name: Commit changes
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uses: EndBug/add-and-commit@v9
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with:
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default_author: github_actions
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message: "ci: version bump [skip actions]"
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add: '["pyproject.toml", "uv.lock", "README.md", "CITATION.cff", "src/*", "docs/source/conf.py"]'
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remove: '["-r src/aind_library_template", "tests/test_message_handler.py"]'
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- name: Add first tag
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run: |
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git tag v0.0.0
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git push origin v0.0.0
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- name: Disable workflow
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run: |
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gh workflow disable -R $GITHUB_REPOSITORY "${{ github.workflow }}"

‎.github/workflows/link-issues-by-milestone.yml‎

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name: Link Issue to Milestone Parent
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on:
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issues:
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types: [milestoned]
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jobs:
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link-issue:
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if: github.event.issue.milestone != null
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uses: AllenNeuralDynamics/.github/.github/workflows/util-link-issues-by-milestone.yml@main
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with:
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issue-number: ${{ github.event.issue.number }}
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issue-id: ${{ github.event.issue.id }}
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milestone-description: ${{ github.event.issue.milestone.description }}
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secrets:
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service-token: ${{ secrets.SERVICE_TOKEN }}

‎.github/workflows/tag_and_publish.yml‎

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name: Tag and publish
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on:
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push:
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branches:
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- main
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# Remove line 67 to enable automated semantic version bumps.
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# Requires that svc-aindscicomp be added to the repo with "write" role.
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# Change line 73 from "if: false" to "if: true" to enable PyPI publishing.
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# Requires that the repo has been added as a Trusted Publisher in the PyPI.
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# Please submit a request to Scientific Computing to add the Trusted Publisher.
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jobs:
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update_badges:
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runs-on: ubuntu-latest
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continue-on-error: true
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steps:
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- uses: actions/checkout@v6
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with:
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ref: ${{ env.DEFAULT_BRANCH }}
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fetch-depth: 0
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token: ${{ secrets.SERVICE_TOKEN }}
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- name: Set up Python 3.10
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uses: astral-sh/setup-uv@v7
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with:
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python-version: '3.10'
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- name: Install dependencies
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run: uv sync
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- name: Get Python version and Update README.md
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run: |
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python_version=$(grep "requires-python" pyproject.toml | grep -o ">=[^\"]*")
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python_badge=$(grep '^\!\[Python\]' README.md | sed -n 's/.*\(python-[^)]*\).*/\1/p')
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new_python_badge="python-$python_version-blue?logo=python"
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sed -i "s/$python_badge/$new_python_badge/g" README.md
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- name: Get interrogate values and Update README.md
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run: |
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interrogate_val=$(uv run interrogate . | grep -o 'actual: [0-9]*\.[0-9]*' | awk '{print $2}')
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interrogate_badge=$(grep '^\!\[Interrogate\]' README.md | sed -n 's/.*\(interrogate-[^)]*\).*/\1/p')
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if (( $(echo "$interrogate_val >= 90.00" | bc -l) )); then
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new_interrogate_badge="interrogate-$interrogate_val%25-brightgreen"
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elif (( $(echo "$interrogate_val < 80.00" | bc -l) )); then
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new_interrogate_badge="interrogate-$interrogate_val%25-red"
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else
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new_interrogate_badge="interrogate-$interrogate_val%25-yellow"
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fi
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sed -i "s/$interrogate_badge/$new_interrogate_badge/g" README.md
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- name: Get Coverage values and Update README.md
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run: |
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uv run coverage run -m unittest discover
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coverage_val=$(uv run coverage report | grep "^TOTAL" | grep -o '[0-9]\+%' | grep -o '[0-9]\+')
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coverage_badge=$(grep '^\!\[Coverage\]' README.md | sed -n 's/.*\(coverage-[^)]*\).*/\1/p')
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if (( $(echo "$coverage_val >= 90.00" | bc -l) )); then
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new_coverage_badge="coverage-$coverage_val%25-brightgreen"
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elif (( $(echo "$coverage_val < 80.00" | bc -l) )); then
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new_coverage_badge="coverage-$coverage_val%25-red"
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else
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new_coverage_badge="coverage-$coverage_val%25-yellow"
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fi
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sed -i "s/$coverage_badge/$new_coverage_badge/g" README.md
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- name: Commit changes
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uses: EndBug/add-and-commit@v9
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with:
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default_author: github_actions
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message: "ci: update badges [skip actions]"
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add: '["README.md"]'
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tag:
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needs: update_badges
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if: ${{github.event.repository.name == 'aind-library-template'}}
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uses: AllenNeuralDynamics/.github/.github/workflows/release-bump-version-uv.yml@main
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secrets:
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repo-token: ${{ secrets.SERVICE_TOKEN }}
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publish:
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needs: tag
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if: false
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runs-on: ubuntu-latest
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permissions:
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contents: read
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# IMPORTANT: this permission is mandatory for Trusted Publishing
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id-token: write
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steps:
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- uses: actions/checkout@v6
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- name: Pull latest changes
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run: git pull origin main
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- name: Set up Python 3.10
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uses: astral-sh/setup-uv@v7
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with:
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python-version: '3.10'
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- name: Build and validate package
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run: |
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uv build
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uvx twine check dist/*
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- name: Publish on PyPI
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uses: pypa/gh-action-pypi-publish@release/v1

‎.github/workflows/test_and_lint.yml‎

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name: Lint and run tests
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on:
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pull_request:
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branches:
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- main
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jobs:
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ci:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [ '3.10', '3.11', '3.12' ]
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steps:
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- uses: actions/checkout@v6
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- name: Set up Python ${{ matrix.python-version }}
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uses: astral-sh/setup-uv@v7
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: uv sync
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- name: Run linter checks
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run: uv run flake8 . && uv run interrogate --verbose .
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- name: Run tests and coverage
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run: uv run coverage run -m unittest discover && uv run coverage report

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