Init

.copier-answers.yml

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+# Changes here will be overwritten by Copier
+_commit: 69236c7
+_src_path: gh:alleninstitute/copier-pdm-npc
+add_requirements_txt: true
+author_email: [email protected]
+author_fullname: Ben Hardcastle
+author_username: bjhardcastle
+build_doc: true
+copyright_date: '2024'
+copyright_holder: Allen Institute for Neural Dynamics
+copyright_holder_email: ''
+copyright_license: MIT
+package_version: 0.1.0
+project_description: Tools for accessing and processing stim data, compatible with
+    data in the cloud.
+project_name: npc_stim
+python_package_distribution_name: npc-stim
+python_package_import_name: npc_stim
+python_package_requires_python: '>=3.9'
+repository_name: npc_stim
+repository_namespace: AllenInstitute
+

.github/workflows/docs.yml

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+name: Build docs
+
+on:
+  push:
+    paths:
+      - "**.md"
+      - docs/**
+      - .github/workflows/docs.yml
+    tags:        
+      - '*'        
+  release:
+    types: [published]
+  workflow_dispatch:
+
+
+concurrency:
+  group: ${{ '{{' }} github.ref {{ '}}' }}
+
+
+jobs:
+  build-doc:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: pdm-project/setup-pdm@main
+        with:
+          python-version: 3.x
+          cache: true
+      - name: Build pages
+        run: |
+          pdm install -G docs
+          cd docs && pdm run mkdocs build
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ '{{' }} secrets.GITHUB_TOKEN {{ '}}' }}
+          publish_dir: ./docs/site

.github/workflows/publish.yml

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+# This workflow will install Python dependencies, run tests and lint/formatting - possibly with a variety of Python versions - bump version, re-commit  publish to PYPI
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Publish Python package
+
+on:
+  push:
+    branches: [ "main" ] 
+    paths: # pushing any files/folders marked ! will not trigger the workflow
+      - '**'
+      - '!**.ipynb'
+      - '!**.json'
+      - '!.vscode'
+      - '!scripts/**'
+      - '!tests/**'
+      - '!notebooks/**'
+      - '!**.md'
+      - '!**.yml'
+      - '.github/workflows/publish.yml'
+  workflow_dispatch:  # adds a 'Run Workflow' button for manual launching
+
+concurrency: # jobs currently running will be cancelled when this workflow starts
+  group: ${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/master' }}
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+      matrix:
+        python-version: ["3.9", "3.11"]
+        os: [ubuntu-latest, macOS-latest, windows-latest]
+    permissions: write-all
+
+    steps:
+    - uses: actions/checkout@v4
+      env:
+        GITHUB_TOKEN: ${{ secrets.PAT }}
+        # use PAT, or push comes from `github-actions` bot, which can't trigger
+        # other workflows   
+
+    - uses: pdm-project/setup-pdm@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+        update-python: true
+        cache: true # speeds-up setup by caching downloaded packages 
+
+    - name: Install dependencies
+      run: |
+        pdm install -G dev
+        
+    - name: Test, format, lint
+      env:
+        AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+        AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }}
+        AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+        DBHUB_API_KEY: ${{ secrets.DBHUB_API_KEY }}
+        CODE_OCEAN_API_TOKEN: ${{ secrets.CODE_OCEAN_API_TOKEN }}
+        CODE_OCEAN_DOMAIN: ${{ secrets.CODE_OCEAN_DOMAIN }}
+      run: |
+        mkdir .mypy_cache   
+        pdm run test
+    
+  publish:
+    needs: test
+    runs-on: ubuntu-latest
+    permissions: write-all
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0    # get all commits (on default branch)
+        fetch-tags: true  
+
+    - uses: pdm-project/setup-pdm@v4
+      with:
+        python-version: '3.11'
+        cache: true # speeds-up setup by caching downloaded packages 
+
+    - name: Publish with bump & tag
+      # actions/checkout 
+      run: |
+        pdm install -G dev
+        git config --global user.email "${{ github.actor }}@users.noreply.github.com"
+        git config --global user.name "${{ github.actor }}"
+        pdm publish
+        git push
+        git push --tags
+      env:
+        GITHUB_TOKEN: ${{ secrets.PAT }}
+        # use PAT, or push comes from `github-actions` bot, which can't trigger
+        # other workflows   
+
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v3
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+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/
+cover/
+
+# 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
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .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
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__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/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+*.sqlite
+.misc
+.ruff_cache
+
+.sandbox.py

.vscode/extensions.json

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+{   
+   "recommendations": [
+    "ms-python.python",
+    "ms-python.vscode-pylance",
+    "ms-python.black-formatter",
+    "ms-python.mypy-type-checker",
+    "donjayamanne.python-environment-manager",
+    "ms-toolsai.jupyter",
+    "eamodio.gitlens"
+  ]
+} 

.vscode/settings.json

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+{
+    "python.linting.mypyEnabled": true,
+    "python.linting.enabled": true,
+    "python.linting.pylintEnabled": false,
+    "python.analysis.inlayHints.functionReturnTypes": true,
+    "python.analysis.typeCheckingMode": "off"
+}

CHANGELOG.md

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+# Changelog
+
+<!-- insertion marker -->