Prepare pyvcell for 2026 workshop: docs, remote simulation API, and client regeneration

.github/workflows/main.yml

@@ -43,8 +43,11 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
+      - name: Install xvfb
+        run: sudo apt-get update && sudo apt-get install -y xvfb
+
       - name: Run tests
-        run: poetry run pytest tests --cov --cov-config=pyproject.toml --cov-report=xml
+        run: xvfb-run poetry run pytest tests --cov --cov-config=pyproject.toml --cov-report=xml
 
       - name: Check typing
         run: poetry run mypy

.gitignore

@@ -183,3 +183,5 @@ examples/notebooks/workspace/
 
 examples/scripts/workspace/
 workspace
+
+docs/guides/notebooks/workspace/

.openapi-generator/FILES

@@ -0,0 +1,207 @@
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.openapi-generator/VERSION

@@ -0,0 +1 @@
+7.20.0

Makefile

@@ -41,6 +41,11 @@ publish: ## publish a release to pypi.
 .PHONY: build-and-publish
 build-and-publish: build publish ## Build and publish.
 
+.PHONY: docs-execute-notebooks
+docs-execute-notebooks: ## Execute guide notebooks and save outputs
+	@echo "🚀 Executing guide notebooks"
+	@poetry run jupyter nbconvert --to notebook --execute --inplace $(filter-out docs/guides/notebooks/remote-simulations.ipynb,$(wildcard docs/guides/notebooks/*.ipynb))
+
 .PHONY: docs-test
 docs-test: ## Test if documentation can be built without warnings or errors
 	@poetry run mkdocs build -s

docs/getting-started/installation.md

@@ -0,0 +1,56 @@
+# Installation
+
+## Requirements
+
+- Python 3.11 or later
+
+## Install from PyPI
+
+```bash
+pip install pyvcell
+```
+
+## Install with Poetry (for development)
+
+```bash
+git clone https://github.com/virtualcell/pyvcell.git
+cd pyvcell
+poetry install
+```
+
+## Verify the installation
+
+```python
+import pyvcell.vcml as vc
+print("pyvcell imported successfully")
+```
+
+## Workspace directory
+
+pyvcell stores simulation output in a **workspace directory**. By default this is `./workspace` relative to your current working directory. You can change it:
+
+```python
+import pyvcell.vcml as vc
+
+# Check the current workspace
+print(vc.get_workspace_dir())
+
+# Set a custom workspace
+vc.set_workspace_dir("/path/to/my/workspace")
+```
+
+The workspace directory is created automatically if it doesn't exist.
+
+## Optional dependencies
+
+pyvcell includes visualization tools that depend on:
+
+- **Matplotlib** — 2D plots and concentration time series
+- **VTK / PyVista** — 3D volume rendering and mesh visualization
+- **Trame** — Interactive browser-based 3D widgets (for Jupyter notebooks)
+
+All of these are installed automatically with `pip install pyvcell`.
+
+## Next steps
+
+- [Quick Start](quickstart.md) — Load a model, simulate, and plot results