init

.github/ISSUE_TEMPLATE/bug-report.md

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+---
+name: Bug Report
+about: 'Use this template for issues relating to unexpected / non-functioning behavior '
+title: "[BUG]"
+labels: bug
+assignees: ''
+
+---
+
+### Summary
+<!-- Provide a clear and concise description of what the bug is -->
+
+#### Expected Behavior
+<!-- Provide a description of what the expected behavior should be -->
+
+
+### To Reproduce
+<!-- Provide steps to reproduce the behavior -->
+
+
+
+### Environment Details
+#### Desktop (please complete the following information):
+- **OS**: [e.g. iOS]
+- **GCS Version** [e.g. 0.0.1 or commit ID]
+- **Python Version** [e.g. python 3.9.16]

.github/ISSUE_TEMPLATE/feature-request.md

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+---
+name: Feature Request
+about: 'Use this template for requesting new features'
+title: "[FEATURE]"
+labels: enhancement
+assignees: ''
+---
+
+### Summary
+<!-- Provide a clear and concise description of the feature request. -->
+
+#### Justification
+<!-- Provide a justification for taking on this request. Why do we **need** this? -->
+
+#### Solution
+<!-- If there is a solution, please add any details below -->

.github/PULL_REQUEST_TEMPLATE/default.md

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+# Details
+
+## Type of Change
+- [ ] Refactor
+- [ ] Bug fix
+- [ ] New Feature
+- [ ] Breaking change
+
+
+## Problem
+
+<!-- Please describe the problem -->
+
+Fixes # (issue)
+
+## Solution
+
+### Summary of Changes
+
+<!-- Provide a summary of the changes -->
+
+### Change List
+
+<!-- Please add list of changes in itemized form -->
+- 
+- 
+- 
+
+
+### Additional Details
+
+
+## Testing
+
+### Automated Tests
+
+<!-- TBD -->
+
+### Manual Tests
+
+<!-- Add any manual test steps that you have run to confirm the changes -->
+

.github/PULL_REQUEST_TEMPLATE/simple.md

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+## What's in this Change?
+
+<!-- Please describe the problem in bullet points -->
+
+
+## Testing
+
+<!-- Add any automated/manual test steps that you have run to confirm the changes -->
+

.github/actions/setup-ai-github-urls/action.yml

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+name: AllenInstitute Repo Setup
+
+description: |
+  Configures all credentials to use AllenInstitute Repos in GitHub.
+inputs:
+  token:
+    required: false
+  ssh_private_key:
+    required: false
+  ssh_auth_sock:
+    required: false
+    default: "/tmp/ssh_agent.sock"
+
+runs: 
+  using: "composite"
+  steps:
+    - name: Configure AllenInstitute Repo URLs with PAT Authorization
+      if: ${{ inputs.token != '' }}
+      run: |
+        git config --global url."https://${{ github.actor }}:${{ inputs.token }}@github.com/AllenInstitute".insteadOf https://github.com/AllenInstitute
+      shell: bash
+    - name: Configure AllenInstitute Repo URLs with SSH Authorization
+      if: ${{ inputs.ssh_private_key != '' }}
+      uses: webfactory/[email protected]
+      with:
+        ssh-private-key: ${{ inputs.ssh_private_key }}

.github/scripts/release.py

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+#!/usr/bin/env python3
+import json
+import subprocess
+
+
+def get_last_version() -> str:
+    """Return the version number of the last release."""
+    json_string = (
+        subprocess.run(
+            ["gh", "release", "view", "--json", "tagName"],
+            check=True,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+        )
+        .stdout.decode("utf8")
+        .strip()
+    )
+
+    return json.loads(json_string)["tagName"]
+
+
+def bump_patch_number(version_number: str) -> str:
+    """Return a copy of `version_number` with the patch number incremented."""
+    major, minor, patch = version_number.split(".")
+    return f"{major}.{minor}.{int(patch) + 1}"
+
+
+def create_new_patch_release():
+    """Create a new patch release on GitHub."""
+    try:
+        last_version_number = get_last_version()
+    except subprocess.CalledProcessError as err:
+        if err.stderr.decode("utf8").startswith("HTTP 404:"):
+            # The project doesn't have any releases yet.
+            new_version_number = "0.0.1"
+        else:
+            raise
+    else:
+        new_version_number = bump_patch_number(last_version_number)
+
+    subprocess.run(
+        ["gh", "release", "create", "--generate-notes", new_version_number],
+        check=True,
+    )
+
+
+if __name__ == "__main__":
+    create_new_patch_release()

.github/workflows/build.yml

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+name: Build and Test
+
+on:
+  pull_request:
+    branches: [ main ]
+  push:
+    branches: [ main ]
+
+jobs:
+  test:
+    name: Build and Test
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4        
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+      - name: Set up AllenInstitute Repo Authorization
+        uses: ./.github/actions/setup-ai-github-urls
+        with:
+          token: ${{ secrets.AI_PACKAGES_TOKEN }}
+      - name: Run Release
+        run: |
+          make release
+        shell: bash

.gitignore

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+# Config copies
+config_local.py
+config_orig.py
+
+# VS Code workspace config
+*.code-workspace
+.vscode/
+
+# JetBrains stuff
+.idea/
+
+# Mac OS
+.DS_Store
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Some large files used for building docker
+cellranger*tar.gz
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# IntelliJ
+.idea/