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emod-demo's Issues

Figure out why local docker+jupyter command fails 

ewenger@Edwards-MBP ~ % docker run -it --name test-emod -p 8888:8888 edwenger/emod-demo jupyter lab --ip 0.0.0.0
/srv/conda/envs/notebook/lib/python3.8/subprocess.py:848: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
  self.stdout = io.open(c2pread, 'rb', bufsize)
[I 2021-09-09 17:39:33.894 ServerApp] jupyter_offlinenotebook | extension was successfully linked.
[I 2021-09-09 17:39:33.894 ServerApp] jupyter_resource_usage | extension was successfully linked.
[I 2021-09-09 17:39:33.907 ServerApp] jupyterlab | extension was successfully linked.
[I 2021-09-09 17:39:33.921 ServerApp] Writing notebook server cookie secret to /home/jovyan/.local/share/jupyter/runtime/jupyter_cookie_secret
[I 2021-09-09 17:39:34.361 ServerApp] nteract_on_jupyter | extension was found and enabled by nbclassic. Consider moving the extension to Jupyter Server's extension paths.
[I 2021-09-09 17:39:34.361 ServerApp] nteract_on_jupyter | extension was successfully linked.
[I 2021-09-09 17:39:34.361 ServerApp] nbclassic | extension was successfully linked.
[I 2021-09-09 17:39:34.478 ServerApp] jupyter_offlinenotebook | extension was successfully loaded.
[I 2021-09-09 17:39:34.479 ServerApp] jupyter_resource_usage | extension was successfully loaded.
[I 2021-09-09 17:39:34.481 LabApp] JupyterLab extension loaded from /srv/conda/envs/notebook/lib/python3.8/site-packages/jupyterlab
[I 2021-09-09 17:39:34.481 LabApp] JupyterLab application directory is /srv/conda/envs/notebook/share/jupyter/lab
[I 2021-09-09 17:39:34.486 ServerApp] jupyterlab | extension was successfully loaded.
[I 2021-09-09 17:39:34.497 ServerApp] nbclassic | extension was successfully loaded.
[I 2021-09-09 17:39:34.497 ServerApp] nteract extension loaded from /srv/conda/envs/notebook/lib/python3.8/site-packages/nteract_on_jupyter
[I 2021-09-09 17:39:34.499 ServerApp] nteract_on_jupyter | extension was successfully loaded.
[I 2021-09-09 17:39:34.499 ServerApp] Serving notebooks from local directory: /home/jovyan
[I 2021-09-09 17:39:34.499 ServerApp] Jupyter Server 1.4.1 is running at:
[I 2021-09-09 17:39:34.499 ServerApp] http://df86cb91de6c:8888/lab?token=2328a7fe990dee0e62eefa1672ff062d89e30edabdf9949a
[I 2021-09-09 17:39:34.499 ServerApp]  or http://127.0.0.1:8888/lab?token=2328a7fe990dee0e62eefa1672ff062d89e30edabdf9949a
[I 2021-09-09 17:39:34.499 ServerApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[W 2021-09-09 17:39:34.505 ServerApp] No web browser found: could not locate runnable browser.

Expand demo set for Codespaces

  1. compare_timesteps -> add more context as markdown + devcontainer for repro
  2. sweep on infectious reservoir by age statistics (sweep over incidence + treatment rate)
  3. more realistic prevalence/incidence vs. age calibration workflow
  4. extend voila webapp? (w/ challenge, treat, step, reset buttons; seasonal challenge + treat-on-fever toggles; emodlib/examples/naive_infection.py plotting style + antibody capacity/concentration histograms)
  5. investigating antibody capacity/concentration in relation to immune initialization?
  6. pass infections among objects in simple numpy container?

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