Merge pull request #37 from virtualcell/simpler-apis

Session-based remote API, notebook testing, and usability improvements

Author: jcschaff

.gitignore

@@ -178,6 +178,8 @@ test_output_1/
 examples/test_output/SimID_*
 /examples/notebooks/*.py
 /examples/solver_output/zarr/
+/examples/solver_output/*.vtu
+/examples/solver_output/*.json
 
 examples/notebooks/workspace/
 

CLAUDE.md

@@ -28,6 +28,14 @@ Run `make check`, which does:
 
 Then run tests: `poetry run pytest tests -v`
 
+For changes to remote/session code, also prompt the developer to run authenticated integration tests manually:
+
+```bash
+poetry run pytest tests/vcml/test_remote_integration.py -v --run-remote
+```
+
+This requires interactive browser login and a live VCell server.
+
 ## Project structure
 
 ```
@@ -58,8 +66,10 @@ scripts/
 
 The main entry point is `import pyvcell.vcml as vc`. Key functions:
 
-- **Load models**: `vc.load_vcml_file()`, `vc.load_vcml_url()`, `vc.load_biomodel(id)`, `vc.load_sbml_file()`, `vc.load_antimony_str()`
-- **Simulate**: `vc.simulate(biomodel, sim_name)` (local), `vc.run_remote(...)` (server)
+- **Load models (local)**: `vc.load_vcml_file()`, `vc.load_vcml_url()`, `vc.load_sbml_file()`, `vc.load_antimony_str()`
+- **Simulate (local)**: `vc.simulate(biomodel, sim_name)`
+- **Remote (anonymous)**: `session = vc.connect()`, `session.load_biomodel(id)`, `session.list_biomodels()`
+- **Remote (authenticated)**: `session = vc.connect(login=True)`, `session.run_sim(...)`, `session.start_sim(...)`
 - **Results**: `result.plotter.plot_concentrations()`, `result.plotter.plot_slice_3d()`
 
 ## Code conventions

docs/getting-started/quickstart.md

@@ -11,28 +11,20 @@ biomodel = vc.load_vcml_file("path/to/model.vcml")
 print(biomodel)
 ```
 
-You can also load public models directly from the VCell database by ID:
+You can also load public models from the VCell server. Use `vc.connect()` to create a session for remote access:
 
 ```python
-biomodel = vc.load_biomodel("279851639")
-```
-
-To browse or search models by name, authenticate first:
-
-```python
-from pyvcell._internal.api.vcell_client.auth.auth_utils import login_interactive
+session = vc.connect()
 
-api_client = login_interactive()  # opens a browser for login
+# Load by database ID
+biomodel = session.load_biomodel("279851639")
 
-# List available models (public, shared, and your private models)
-for m in vc.list_biomodels(api_client=api_client)[:2]:
+# List available models
+for m in session.list_biomodels()[:2]:
     print(m)
 
 # Load by name and owner
-biomodel = vc.load_biomodel(name="Tutorial_MultiApp", owner="tutorial", api_client=api_client)
-
-# Load by database ID
-biomodel = vc.load_biomodel("279851639", api_client=api_client)
+biomodel = session.load_biomodel(name="Tutorial_MultiApp", owner="tutorial")
 ```
 
 Output: