Initial commit

.flake8

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

.github/ISSUE_TEMPLATE/bug_report.md

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

.github/ISSUE_TEMPLATE/feature_request.md

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

.github/ISSUE_TEMPLATE/user-story.md

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

.github/workflows/init.yml

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+# Workflow runs only once when the template is first used.
+# File can be safely deleted after repo is initialized.
+name: Initialize repository
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  initialize-package:
+    name: Initialize the package
+    if: ${{github.event.repository.name != 'aind-library-template'}}
+    runs-on: ubuntu-latest
+    env:
+      REPO_NAME: ${{ github.event.repository.name }}
+      GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+    - name: Rename package
+      run: |
+        pkg_name=$(echo "${REPO_NAME}" | tr - _)
+        current_description='description = "Prints messages to stdout. Simple boilerplate for libraries."'
+        new_description='description = "Generated from aind-library-template"'
+        readme_description='Template for a minimal, basic repository for an AIND library.'
+        new_readme_description='Generated from aind-library-template'
+        echo "Package Name ${pkg_name}"
+        mkdir src/${pkg_name}
+        touch src/${pkg_name}/__init__.py
+        echo '"""Init package"""' >> src/${pkg_name}/__init__.py
+        echo '__version__ = "0.0.0"' >> src/${pkg_name}/__init__.py
+        sed -i "s/aind_library_template/${pkg_name}/" pyproject.toml
+        sed -i "s/aind-library-template/${REPO_NAME}/" pyproject.toml
+        sed -i "s/aind_library_template/${pkg_name}/" doc_template/source/conf.py
+        sed -i "s/${current_description}/${new_description}/" pyproject.toml
+        sed -i "/pandas/d" pyproject.toml
+        sed -i "s/aind-library-template/${REPO_NAME}/" README.md
+        sed -i "s/${readme_description}/${new_readme_description}/" README.md
+    - name: Commit changes
+      uses: EndBug/add-and-commit@v9
+      with:
+        default_author: github_actions
+        message: "ci: version bump [skip actions]"
+        add: '["pyproject.toml", "README.md", "src/*", "doc_template/source/conf.py"]'
+        remove: '["-r src/aind_library_template", "tests/test_message_handler.py"]'
+    - name: Add first tag
+      run: |
+        git tag v0.0.0
+        git push origin v0.0.0
+    - name: Disable workflow
+      run: |
+        gh workflow disable -R $GITHUB_REPOSITORY "${{ github.workflow }}"

.github/workflows/tag_and_publish.yml

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+name: Tag and publish
+on:
+  push:
+    branches:
+      - main
+# Remove line 61 to enable automated semantic version bumps.
+# Change line 67 from "if: false" to "if: true" to enable PyPI publishing. 
+# Requires that svc-aindscicomp be added as an admin to repo.
+jobs:
+  update_badges:
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        ref: ${{ env.DEFAULT_BRANCH }}
+        fetch-depth: 0
+        token: ${{ secrets.SERVICE_TOKEN }}
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v3
+      with:
+        python-version: 3.8
+    - name: Install dependencies
+      run: | 
+        python -m pip install -e .[dev] --no-cache-dir
+    - name: Get Python version and Update README.md
+      run: |
+        python_version=$(grep "requires-python" pyproject.toml | grep -o ">=[^\"]*")
+        python_badge=$(grep -o 'python-[^)]*' README.md)
+        new_python_badge="python-$python_version-blue?logo=python"
+        sed -i "s/$python_badge/$new_python_badge/g" README.md
+    - name: Get interrogate values and Update README.md
+      run: |
+        interrogate_val=$(interrogate . | grep -o 'actual: [0-9]*\.[0-9]*' | awk '{print $2}')
+        interrogate_badge=$(grep -o 'interrogate-[^)]*' README.md)
+        if (( $(echo "$interrogate_val >= 90.00" | bc -l) )); then
+            new_interrogate_badge="interrogate-$interrogate_val%25-brightgreen"
+        elif (( $(echo "$interrogate_val < 80.00" | bc -l) )); then
+            new_interrogate_badge="interrogate-$interrogate_val%25-red"
+        else
+            new_interrogate_badge="interrogate-$interrogate_val%25-yellow"
+        fi
+        sed -i "s/$interrogate_badge/$new_interrogate_badge/g" README.md
+    - name: Get Coverage values and Update README.md
+      run: |
+        coverage run -m unittest discover
+        coverage_val=$(coverage report | grep "^TOTAL" | grep -o '[0-9]\+%' | grep -o '[0-9]\+')
+        coverage_badge=$(grep -o "coverage-[^?]*" README.md)
+        if (( $(echo "$coverage_val >= 90.00" | bc -l) )); then 
+            new_coverage_badge="coverage-$coverage_val%25-brightgreen"
+        elif (( $(echo "$coverage_val < 80.00" | bc -l) )); then
+            new_coverage_badge="coverage-$coverage_val%25-red"
+        else
+            new_coverage_badge="coverage-$coverage_val%25-yellow"
+        fi
+        sed -i "s/$coverage_badge/$new_coverage_badge/g" README.md
+    - name: Commit changes
+      uses: EndBug/add-and-commit@v9
+      with:
+        default_author: github_actions
+        message: "ci: update badges [skip actions]"
+        add: '["README.md"]'
+  tag:
+    needs: update_badges
+    if: ${{github.event.repository.name == 'aind-library-template'}}
+    uses: AllenNeuralDynamics/aind-github-actions/.github/workflows/tag.yml@main
+    secrets:
+      SERVICE_TOKEN: ${{ secrets.SERVICE_TOKEN }}
+  publish:
+    needs: tag
+    if: false
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Pull latest changes
+        run: git pull origin main
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - name: Install dependencies
+        run: |
+          pip install --upgrade setuptools wheel twine build
+          python -m build
+          twine check dist/*
+      - name: Publish on PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.AIND_PYPI_TOKEN }}

.github/workflows/test_and_lint.yml

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+name: Lint and run tests
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  ci:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ '3.8', '3.9', '3.10' ]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: | 
+        python -m pip install -e .[dev]
+    - name: Run linter checks
+      run: flake8 . && interrogate --verbose .
+    - name: Run tests and coverage
+      run: coverage run -m unittest discover && coverage report