cookiecutter commit

.cookiecutter.yaml

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+default_context:
+    author_name: "bioio-devs"
+    author_email: "[email protected]"
+    hosting_github_username_or_org: "bioio-devs"
+    project_name: "bioio-nd2"
+    project_slug: "bioio-nd2"
+    python_slug: "bioio_nd2"
+    project_short_description: "A BioIO reader plugin for reading ND2 images."
+    hosting_pypi_username: "bioio-devs"
+    license: "MIT License"

.editorconfig

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+# http://editorconfig.org
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+insert_final_newline = true
+charset = utf-8
+end_of_line = lf
+
+[*.yml]
+indent_size = 2
+
+[*.bat]
+indent_style = tab
+end_of_line = crlf
+
+[LICENSE]
+insert_final_newline = false
+
+[Makefile]
+indent_style = tab

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug Report
+about: Create a report to help us improve bioio-nd2
+labels: bug
+---
+
+<!--
+  ⚠️⚠️ Please do the following before submitting: ⚠️⚠️
+
+  📖 Please read our Code of Conduct.
+  🔎 Please search existing issues to avoid creating duplicates.
+-->
+
+### Describe the Bug
+
+<!-- A clear and concise description of the bug. -->
+
+### Expected Behavior
+
+<!-- What did you expect to happen instead? -->
+
+### Reproduction
+
+<!-- Steps to reproduce the behavior and/or a minimal example that exhibits the behavior. -->
+
+### Environment
+
+<!-- Any additional information about your environment. -->
+
+-   OS Version: _[e.g. macOS 11.3.1]_
+-   bioio-nd2 Version: _[e.g. 0.5.0]_

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature Request
+about: Suggest a feature for bioio-nd2
+labels: enhancement
+---
+
+<!--
+  ⚠️⚠️ Please do the following before submitting: ⚠️⚠️
+
+  📖 Please read our Code of Conduct.
+  🔎 Please search existing issues to avoid creating duplicates.
+-->
+
+### Feature Description
+
+<!-- A clear and concise description of the feature you're requesting. -->
+
+### Use Case
+
+<!-- Please provide a use case to help us understand your request in context. -->
+
+### Solution
+
+<!-- Please describe your ideal solution. -->
+
+### Alternatives
+
+<!-- Please describe any alternatives you've considered, even if you've dismissed them. -->

.github/PULL_REQUEST_TEMPLATE.md

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+<!--
+  Thank you for submitting a pull request!
+
+  ⚠️⚠️ Please do the following before submitting: ⚠️⚠️
+
+  - Read the CONTRIBUTING.md guide and make sure you've followed all the steps given.
+  - Ensure that the code is up-to-date with the `main` branch.
+  - Provide or update documentation for any feature added by your pull request.
+  - Provide relevant tests for your feature or bug fix.
+
+  ❗️ Also: ❗️
+
+  Please name your pull request {development-type}/{short-description}.
+  For example: feature/read-tiff-files
+-->
+
+### Link to Relevant Issue
+
+This pull request resolves #
+
+### Description of Changes
+
+<!-- Include a description of the proposed changes. -->

.github/dependabot.yml

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+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    commit-message:
+      prefix: "ci(dependabot):"

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+    branches:
+      - main
+  schedule:
+    # <minute [0,59]> <hour [0,23]> <day of the month [1,31]>
+    # <month of the year [1,12]> <day of the week [0,6]>
+    # https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07
+    # Run every Monday at 10:24:00 PST
+    # (Since these CRONs are used by a lot of people -
+    # let's be nice to the servers and schedule it _not_ on the hour)
+    - cron: "24 18 * * 1"
+  workflow_dispatch:
+
+jobs:
+  # Check that all files listed in manifest make it into build
+  check-manifest:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+      - run: pip install check-manifest && check-manifest
+
+  # Check tests pass on multiple Python and OS combinations
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.9, 3.10, 3.11]
+        os: [ubuntu-latest, macOS-latest, windows-latest]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - uses: extractions/setup-just@v1
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    - name: Install Dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[test]
+    - name: Run Tests
+      run: just test
+    - name: Upload Codecov
+      uses: codecov/codecov-action@v3
+
+  # Check linting, formating, types, etc.
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.11"
+    - uses: extractions/setup-just@v1
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    - name: Install Dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[lint]
+    - name: Lint
+      run: just lint
+
+  # Publish to PyPI if test, lint, and manifest checks passed
+  publish:
+    if: "success() && startsWith(github.ref, 'refs/tags/')"
+    needs: [check-manifest, test, lint]
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.11"
+    - name: Install Dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build wheel
+    - name: Build Package
+      run: |
+        python -m build
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: bioio-devs
+        password: ${{ secrets.PYPI_TOKEN }}
+

.github/workflows/docs.yml

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+name: Documentation
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - uses: extractions/setup-just@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Install Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[docs]
+      - name: Generate Docs
+        run: |
+          just generate-docs
+          touch docs/_build/.nojekyll
+      - name: Publish Docs
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: docs/_build/

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# OS generated files
+.DS_Store
+
+# 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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/bioio_nd2.*rst
+docs/modules.rst
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# Dask
+dask-worker-space
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# VSCode
+.vscode