This folder is a handy place to put Jupyter notebooks or other documents which help to demonstrate the state of the project at a particular point in time. Because these are point-in-time demos, there's no guarantee they will continue to be runnable as changes are made to the project. That's expected. (If you really need to run a Notebook in its original context, you can git-checkout back to the commit that added the Notebook and run it there; caveat emptor).
Notable Devlogs: Some devlogs are more than mere experiments, acting like documentation -- demoing new features of the project or novel approaches to problem solving. These devlogs are check-marked as Maintained in the index below (indicating that they are intended to be kept up to date as the project changes).
| Filename | Author | Maintained? | Description |
|---|---|---|---|
| 2023-05-03.ipynb | Tyler | An obsolete demo, running different movement models with the Pei IPM/Geo. | |
| 2023-05-04.ipynb | Tyler | An experiment in running epymorph simulations in parallel using multiprocessing. |
|
| 2023-05-16.ipynb | Tyler | An attempt to simplify project organization by turning then-hard-coded examples into Jupyter notebooks. | |
| 2023-05-17.ipynb | Tyler | Demo of the newly-added .toml file input scheme for providing parameter values for CLI simulations. | |
| 2023-05-31-mm.ipynb | Alex | Movement model experimentation. | |
| 2023-05-31-sirh.ipynb | Alex | SIRH IPM experimentation. | |
| 2023-06-01-pei-example.ipynb | Frank | Demonstration of the 'pei' movement model. | |
| 2023-06-01-sparsemod-example.ipynb | Frank | Demonstration of the 'sparsemod' movement model. | |
| 2023-06-28.ipynb | Tyler | Proving validity of the newly-added declarative compartment model IPM implementation. | |
| 2023-06-30.ipynb | Tyler | ✓ | Demonstrating the newly-added declarative compartment model IPM system. (This is a good reference for building custom IPMs, so we're keeping it current.) |
| 2023-07-06.ipynb | Tyler | Creates the Pei Geo. (Maintained until such a time as the ADRIO system can replace it.) | |
| 2023-07-07.ipynb | Tyler | Creates the 2015 US States and US Counties Geos. (Maintained until such a time as the ADRIO system can replace them.) | |
| 2023-07-12.ipynb | Tyler | Creates the 2019 Maricopa County CBGs Geo. (Maintained until such a time as the ADRIO system can replace it.) | |
| 2023-07-13.ipynb | Tyler | Implements a compatibility matrix test: are all possible combinations of IPM/MM/GEO valid? | |
| 2023-07-14.ipynb | Tyler | Demonstrates filtering a geo down to a subset of its nodes. (While the motivation to do this still exists, recent changes have made this exact approach obsolete.) | |
| 2023-07-20-movement-probs.ipynb | Tyler | Analyzing statistical correctness of our movement processing algorithms. | |
| 2023-07-24.ipynb | Tyler | Experiments with adapting an IPM by "attaching" a function to an IPM parameter. This approach has been superseded by a design for direct support for functional parameters. | |
| 2023-08-11.ipynb | Tyler | Demonstrates performance differences between the Basic and Hypercube movement engines. A pending refactor will make the concept of movement engines obsolete. | |
| 2023-08-17.ipynb | Tyler | (Obsolete) Demonstrates the newly-added Initializer functions, including library examples and custom initializers. | |
| 2023-08-23.ipynb | Tyler | Describes what IPM attribute broadcasting is and why it's useful. Introduces our concept of data shapes. | |
| 2023-09-22-adrio-demo.ipynb | Trevor | Demonstrates the newly-added ADRIOs functionality by fetching data from the US Census ACS5. | |
| 2023-09-29.ipynb | Tyler | Experiments in representing exogenous births and deaths in the existing compartment IPM system. | |
| 2023-10-05.ipynb | Tyler | Demonstrates the newly-added first-class support for exogenous births and deaths in the compartment IPM system. | |
| 2023-10-10.ipynb | Tyler | A demo of various epymorph workflows in a Notebook environment, designed for a live presentation. | |
| 2023-10-26.ipynb | Tyler | Describes a major Geo system refactor and introduces new systems. | |
| 2023-11-03-seirs-example.ipynb | Ajay | Demonstrates the building and running of an SEIRS model. | |
| 2023-11-08.ipynb | Ajay | Demonstration of using proxy geo to access data in parameter functions. | |
| 2023-11-08-age-ipm.ipynb | Jarom | Initial prototyping of age-class IPMs. | |
| 2023-11-15.ipynb | Ajay | Detailed description of parameter functions functionality. | |
| 2023-11-20-adrio-phase-2-demo.ipynb | Trevor | Demonstrates the refactor work on DynamicGeos and the ADRIO system, and geo cache handling. | |
| 2023-11-22-ipm-probs.ipynb | Tyler | Analyzing statistical correctness of our IPM processing algorithms. | |
| 2023-12-05.ipynb | Tyler | A brief tour of changes to epymorph due to the refactor effort. | |
| 2024-01-08.ipynb | Tyler | Another functional parameters demonstration, revisiting the Bonus Example from 2023-10-10. | |
| 2024-02-06-adrio-demo.ipynb | Trevor | Demonstrates the ADRIO system using code updated for latest changes. | |
| 2024-02-06.ipynb | Tyler | Revisiting age-class IPMs, and thinking about modularity of approach. | |
| 2024-02-12.ipynb | Tyler | Continued age-class IPM work, this time in more than one geo node. | |
| 2024-02-14.ipynb | Tyler | Prep work related to the "Z-virus" workshop. (Not very organized.) | |
| 2024-03-01.ipynb | Tyler | Getting the indices of IPM events and compartments by name with wildcard support. | |
| 2024-03-13.ipynb | Tyler | Showing off movement data collection (NEW!) | |
| 2024-03-19.ipynb | Tyler | Create and save the us_sw_counties_2015.geo spec file. |
|
| 2024-04-04-draw-demo.ipynb | Izaac | Showing the new draw module for visualising IPMs (NEW!) | |
| 2024-04-16.ipynb | Izaac | Showing error handling for common ipm errors (NEW!) | |
| 2024-04-25.ipynb | Tyler | Integration test: epymorph cache utilities | |
| 2024-05-03.ipynb | Tyler | ✓ | Integration test: loading US Census geography from TIGER |
| 2024-05-09-lodes-adrio-demo.ipynb | Meaghan | A full geo spec for testing LODES ADRIOs | |
| 2024-05-22.ipynb | Sachin | Integrating particle filter with epymorph. Propagating the particles using epymorph simulation and plot the infection rates | |
| 2024-06-03.ipynb | Trevor | ✓ | Integration test: using dynamic geos to fetch Census data |
| 2024-06-05.ipynb | Meaghan | ✓ | A user manual and basic demonstrations of calling LODES ADRIOs |
| 2024-06-12.ipynb | Trevor | ✓ | Integration test: CSV file ADRIOs |
| 2024-07-03.ipynb | Trevor | ✓ | Demonstration of CDC ADRIO functionality and attributes. |
| 2024-07-08.ipynb | Tyler | ✓ | Demonstrates the updated Initializers system, including library examples and custom initializers. |
| 2024-07-10.ipynb | Trevor | ✓ | Integration test: Census ADRIOs |
| 2024-07-12-v0.4.ipynb | Tyler | Comparing v0.4 to v0.5 via example. (See next also.) | |
| 2024-07-12-v0.5.ipynb | Tyler | Comparing v0.4 to v0.5 via example. (See previous also.) | |
| 2024-07-12-v0.6.ipynb | Tyler | Comparing v0.5 to v0.6 via example. (See previous also.) | |
| 2024-07-16.ipynb | Meaghan | Testing the space and runtime for downloading and interpreting PRISM data | |
| 2024-07-18.ipynb | Tyler | A simple demo of ADRIOs "version 2". | |
| 2024-08-13.ipynb | Tyler | Demo @adrio_cache. | |
| 2024-08-26-prism-adrio-demo.ipynb | Meaghan | ✓ | Demo and usage manual for PRISM ADRIO. |
| 2024-08-28.ipynb | Trevor | ✓ | Demo of numpy ADRIOs. |
| 2024-08-30.ipynb | Tyler | Testing non-returner movement support. | |
| 2024-09-24.ipynb | Tyler | Demonstrating ADRIO with simulated download activity. | |
| 2024-09-25.ipynb | Meaghan | ✓ | Demo of humidity ADRIO. |
| 2024-10-09.ipynb | Tyler | Comparing methods for group-and-aggregate on time-series data. | |
| 2024-10-11.ipynb | Tyler | Comparing methods for group-and-aggregate on geo-series data. | |
| 2024-12-03-v0.7.ipynb | Tyler | Comparing v0.6 to v0.7 via example. (See others in this series.) | |
| 2024-12-06.ipynb | Tyler | Visualizing movement models. | |
| 2024-12-16.ipynb | Tyler | Demonstrates table output tools with time-axis group-and-aggregate. |
When adding a devlog, checking in the .ipynb file is sufficient as long as it has been fully rendered. (GitHub even knows how to display them as-is!)
Jupyter notebooks can be exported to HTML if needed using VS Code (CTRL+SHIFT+P, Jupyter: Export to HTML) or from the command line, for example:
# make sure .venv is activated
python -m jupyter nbconvert ./doc/devlog/2023-05-03.ipynb --to html --output <your_absolute_path>/Epymorph/doc/devlog/2023-05-03.html