Init commit

.devcontainer/devcontainer.json

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+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/python
+{
+    "name": "pyvcell",
+    // Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+    "image": "mcr.microsoft.com/devcontainers/python:1-3.11-bullseye",
+    "features": {
+        "ghcr.io/devcontainers-contrib/features/poetry:2": {}
+    },
+
+    // Use 'postCreateCommand' to run commands after the container is created.
+    "postCreateCommand": "./.devcontainer/postCreateCommand.sh",
+
+    // Configure tool-specific properties.
+    "customizations": {
+        "vscode": {
+            "extensions": [
+                "ms-python.python",
+                "editorconfig.editorconfig",
+            ],
+            "settings": {
+                "python.testing.pytestArgs": ["tests"],
+                "python.testing.unittestEnabled": false,
+                "python.testing.pytestEnabled": true,
+                "python.defaultInterpreterPath": "/workspaces/pyvcell/.venv/bin/python",
+                "python.testing.pytestPath": "/workspaces/pyvcell/.venv/bin/pytest"
+            }
+        }
+    }
+}

.devcontainer/postCreateCommand.sh

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+#! /usr/bin/env bash
+
+# Install Dependencies
+poetry install --with dev
+
+# Install pre-commit hooks
+poetry run pre-commit install --install-hooks

.editorconfig

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+max_line_length = 120
+
+[*.json]
+indent_style = space
+indent_size = 4

.github/actions/setup-poetry-env/action.yml

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+name: "setup-poetry-env"
+description: "Composite action to setup the Python and poetry environment."
+
+inputs:
+   python-version:
+     required: false
+     description: "The python version to use"
+     default: "3.11"
+
+runs:
+  using: "composite"
+  steps:
+    - name: Set up python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - name: Install Poetry
+      env:
+        POETRY_VERSION: "1.7.1"
+      run: curl -sSL https://install.python-poetry.org | python - -y
+      shell: bash
+
+    - name: Add Poetry to Path
+      run: echo "$HOME/.local/bin" >> $GITHUB_PATH
+      shell: bash
+
+    - name: Configure Poetry virtual environment in project
+      run: poetry config virtualenvs.in-project true
+      shell: bash
+
+    - name: Load cached venv
+      id: cached-poetry-dependencies
+      uses: actions/cache@v4
+      with:
+        path: .venv
+        key: venv-${{ runner.os }}-${{ inputs.python-version }}-${{ hashFiles('poetry.lock') }}
+
+    - name: Install dependencies
+      if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+      run: poetry install --no-interaction
+      shell: bash

.github/workflows/main.yml

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+name: Main
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+
+jobs:
+  quality:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - uses: actions/cache@v4
+        with:
+          path: ~/.cache/pre-commit
+          key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-poetry-env
+
+      - name: Run checks
+        run: make check
+
+  tests-and-type-check:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+      fail-fast: false
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-poetry-env
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Run tests
+        run: poetry run pytest tests --cov --cov-config=pyproject.toml --cov-report=xml
+
+      - name: Check typing
+        run: poetry run mypy
+
+
+      - name: Upload coverage reports to Codecov with GitHub Action on Python 3.11
+        uses: codecov/codecov-action@v4
+        if: ${{ matrix.python-version == '3.11' }}
+
+  check-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-poetry-env
+
+      - name: Check if documentation can be built
+        run: poetry run mkdocs build -s

.github/workflows/on-release-main.yml

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+name: release-main
+
+on:
+  release:
+    types: [published]
+    branches: [main]
+
+jobs:
+
+  publish:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-poetry-env
+
+      - name: Export tag
+        id: vars
+        run: echo tag=${GITHUB_REF#refs/*/} >> $GITHUB_OUTPUT
+
+      - name: Build and publish
+        run: |
+          source .venv/bin/activate
+          poetry version $RELEASE_VERSION
+          make build-and-publish
+        env:
+          PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
+          RELEASE_VERSION: ${{ steps.vars.outputs.tag }}
+
+  deploy-docs:
+    needs: publish
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-poetry-env
+
+      - name: Deploy documentation
+        run: poetry run mkdocs gh-deploy --force
+

.github/workflows/validate-codecov-config.yml

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+name: validate-codecov-config
+
+on:
+  pull_request:
+    paths: [codecov.yaml]
+  push:
+    branches: [main]
+
+jobs:
+  validate-codecov-config:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+      - name: Validate codecov configuration
+        run: curl -sSL --fail-with-body --data-binary @codecov.yaml https://codecov.io/validate

.gitignore

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+docs/source
+
+# From https://raw.githubusercontent.com/github/gitignore/main/Python.gitignore
+
+# 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
+
+# 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/
+
+# Vscode config files
+.vscode/
+
+# 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/