import biocommons.example

.github/.github/CODEOWNERS

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+* @biocommons/maintainers

.github/.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.
+
+**Additional context**
+Add any other context about the problem here.

.github/.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/.github/ISSUE_TEMPLATE/project-proposal.md

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+---
+name: Project Proposal
+about: Create a proposal for an intern or GSoC project
+title: 'Project: ...'
+labels: 'project'
+assignees: ''
+
+---
+
+### Summary
+
+1-3 sentence summary of project.
+
+See <a href="#background">Background</a>.
+
+## Value
+
+Why is this project meaningful?
+
+## Required and Desired Skills
+
+- Python
+- Relational database design, SQL
+
+## Expected Outcomes
+
+- **Headline**. Description...
+- **Headline**. Description...
+
+## Potential Mentors
+
+- @reece
+
+## Background

.github/.github/labels.yml

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+- name: "bug"
+  color: "d73a4a"
+  description: "Something isn't working"
+
+- name: "documentation"
+  color: "0075ca"
+  description: "Improvements or additions to documentation"
+
+- name: "duplicate"
+  color: "cfd3d7"
+  description: "This issue or pull request already exists"
+
+- name: "enhancement"
+  color: "a2eeef"
+  description: "New feature or request"
+
+- name: "good first issue"
+  color: "7057ff"
+  description: "Good for newcomers"
+
+- name: "help wanted"
+  color: "008672"
+  description: "Extra attention is needed"
+
+- name: "invalid"
+  color: "e4e669"
+  description: "This doesn't seem right"
+
+- name: "keep alive"
+  color: "666666"
+  description: "exempt issue from staleness checks"
+  from_name: "keep alive"
+
+- name: "project proposal"
+  color: "d876e3"
+  description: "project proposal for interns and GSoC students"
+
+- name: "question"
+  color: "d876e3"
+  description: "Further information is requested"
+
+- name: "rfc"
+  color: "d876e3"
+  description: "Request for comments"
+
+- name: "stale"
+  color: "777777"
+  description: "Issue is stale and subject to automatic closing"
+  from_name: "Stale"
+
+- name: "stale closed"
+  color: "444444"
+  description: "Issue was closed automatically due to inactivity"
+  from_name: "stale-closed"
+
+- name: "won't fix"
+  color: "ffffff"
+  description: "This will not be worked on"
+  from_name: wontfix

.github/.github/workflows/labels.yml

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+name: Synchronize labels
+
+on:
+  push:
+    branches:
+      - 'main'
+    paths:
+      - '.github/labels.yml'
+      - '.github/workflows/labels.yml'
+
+jobs:
+  labeler:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Checkout
+        uses: actions/checkout@v3
+      -
+        name: Run Labeler
+        uses: crazy-max/ghaction-github-labeler@v4
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          yaml-file: .github/labels.yml

.github/.github/workflows/python-package.yml

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+name: Python package
+
+on:
+  push:
+    tags:
+      - '[0-9]+.[0-9]+.[0-9]+'
+  pull_request:
+
+jobs:
+  cqa:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+        cache: pip
+        cache-dependency-path: '**/setup.cfg'
+
+    - name: Install test dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install --use-deprecated=legacy-resolver -e .[dev]
+
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+    - name: Format check with isort
+      run: |
+        isort --check src
+
+    - name: Format check with black
+      run: |
+        black --check src
+
+    - name: Security check with bandit
+      run: |
+        bandit -ll -r src
+
+  test:
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: pip
+        cache-dependency-path: '**/setup.cfg'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        make develop
+
+    - name: Test with pytest
+      run: |
+        make test
+
+    - name: Upload coverage data to Codecov
+      run: |
+        # Verify integrity of codecov download
+        curl https://uploader.codecov.io/verification.gpg | gpg --no-default-keyring --keyring trustedkeys.gpg --import
+        curl -Os https://uploader.codecov.io/latest/linux/codecov
+        curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM
+        curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM.sig
+        gpgv codecov.SHA256SUM.sig codecov.SHA256SUM
+        shasum -a 256 -c codecov.SHA256SUM
+        # Upload coverage report
+        chmod +x codecov
+        ./codecov        
+        
+  deploy:
+    needs:
+    - cqa
+    - test
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Environment
+      run: |
+        echo "::group::Environment info"
+        echo github.event_name = ${{ github.event_name }}
+        echo refs = ${{ github.ref }}
+        echo tags = ${{ startsWith(github.ref, 'refs/tags') }}
+        echo "::endgroup::"
+
+    - uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+        cache: pip
+        cache-dependency-path: '**/setup.cfg'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build twine
+
+    - name: Build package
+      run: python -m build
+
+    - name: Publish package
+      if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/.github/workflows/stale.yml

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+# https://github.com/actions/stale
+
+name: 'Close stale issues and PRs'
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '1 1 * * *'
+
+jobs:
+  stale:
+    uses: biocommons/actions/.github/workflows/stale.yml@main

.github/CODEOWNERS

@@ -0,0 +1 @@
+* @biocommons/maintainers

.github/ISSUE_TEMPLATE/bug-report.md

@@ -0,0 +1,24 @@
+---
+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.
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature-request.md

@@ -0,0 +1,20 @@
+---
+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/project-proposal.md

@@ -0,0 +1,34 @@
+---
+name: Project Proposal
+about: Create a proposal for an intern or GSoC project
+title: 'Project: ...'
+labels: 'project'
+assignees: ''
+
+---
+
+### Summary
+
+1-3 sentence summary of project.
+
+See <a href="#background">Background</a>.
+
+## Value
+
+Why is this project meaningful?
+
+## Required and Desired Skills
+
+- Python
+- Relational database design, SQL
+
+## Expected Outcomes
+
+- **Headline**. Description...
+- **Headline**. Description...
+
+## Potential Mentors
+
+- @reece
+
+## Background