Initial commit

.github/dependabot.yml

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+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    target-branch: "main"
+    labels:
+      - "dependencies"
+    schedule:
+      interval: "daily"
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    target-branch: "main"
+    schedule:
+      interval: "daily"

.github/workflows/bot-auto-merge.yml

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+---
+name: bot-auto-merge
+
+on:
+  workflow_run:
+    types: [completed]
+    workflows: ["tox-pytest"]
+
+jobs:
+  bot-auto-merge:
+    name: Auto-merge passing bot PRs
+    runs-on: ubuntu-latest
+    steps:
+      - name: Auto-merge passing dependabot PRs
+        if: ${{ github.event.workflow_run.conclusion == 'success' }}
+        uses: ridedott/merge-me-action@v2
+        with:
+          # For clarity only. dependabot is default.
+          GITHUB_LOGIN: dependabot
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          ENABLED_FOR_MANUAL_CHANGES: "true"
+      - name: Auto-merge passing pre-commit-ci PRs
+        if: ${{ github.event.workflow_run.conclusion == 'success' }}
+        uses: ridedott/merge-me-action@v2
+        with:
+          GITHUB_LOGIN: pre-commit-ci
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          ENABLED_FOR_MANUAL_CHANGES: "true"

.github/workflows/docs-to_gh-pages.yml

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+name: docs
+on: [push, pull_request, workflow_dispatch]
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Get history and tags for SCM versioning to work
+        run: |
+          git fetch --prune --unshallow
+          git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          pip install ./[doc]
+      - name: Sphinx build
+        run: |
+          sphinx-build -b html docs _build
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: _build/
+          force_orphan: true
+      - name: Deploy dev
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/dev' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: _build/
+          force_orphan: true

.github/workflows/tox-pytest.yml

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+name: tox-pytest
+
+on: [push, pull_request]
+
+jobs:
+  ci-test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 2
+
+      - name: Set up conda environment for testing
+        uses: conda-incubator/[email protected]
+        with:
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          use-mamba: true
+          mamba-version: "*"
+          channels: conda-forge,defaults
+          channel-priority: true
+          python-version: ${{ matrix.python-version }}
+          activate-environment: cheshire
+          environment-file: environment.yml
+      - shell: bash -l {0}
+        run: |
+          conda info
+          conda list
+          conda config --show-sources
+          conda config --show
+          printenv | sort
+
+      - name: Run PyTest with Tox
+        run: |
+          conda run -n cheshire tox
+
+      - name: Coveralls
+        uses: coverallsapp/github-action@master
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          path-to-lcov: ./coverage.info
+
+  finish:
+    needs: ci-test
+    runs-on: ubuntu-latest
+    steps:
+      - name: Coveralls Finished
+        uses: coverallsapp/github-action@master
+        with:
+          github-token: ${{ secrets.github_token }}
+          parallel-finished: true

.gitignore

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+# Catalyst specific files
+*.swp
+commit.txt
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+coverage.info
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env_tox/
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# annoying mac stuff
+.DS_Store
+.DS_Store?
+~$*
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# PyCharm
+/.idea
+*.iml
+
+# ================= R related =================
+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+.RDataTmp
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+#*.Rproj  # do want to share these files, for now
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
+# translation temp files
+po/*~
+
+# RStudio Connect folder
+rsconnect/