Changelog

1.4.0 - August 14th 2020

  • MetaWards now includes ward-local parameters (e.g. cutoff and scale_uv), plus supports custom user ward-local parameters. This supports modelling of different ward-local behaviour, e.g. local control measures or local lockdowns. Examples of a local lockdown model is in chapter 7 and chapter 8 of part 3 of the tutorial, plus chapter 5 of part 8. This can also be used to model ward-local vaccination strategies.

  • We have re-worked the go_functions. We have added go_ward() that can be used with MoveGenerator to specify moves between any and all combinations of demographics, disease stages and wards (for players) and ward links (for workers). Individuals can move from worker to player, player to worker, move around the network, move to different networks in different demographics, move between different disease stages, move from susceptible to infected or infected to susceptible etc. etc. This enables some advanced modelling, e.g. of vaccinated or recovered individuals who gradually lose immunity and become susceptible again, movements associated with, e.g. start of university, and movements and quarantine associated with holidays.

  • Added a Ward.bg_foi per-ward parameter to set a background force of infection that can be used to drive (or suppress) infections regardless of the number of infecteds in each ward.

  • Added a global Parameters.bg_foi to set a per-network background force of infection. This is useful as a way to model holiday destinations as different networks.

  • Added a global Parameters.scale_uv <metawards.Parameters.scale_uv() make it easier to set and control the scale_uv parameter via a design file, parameter or via an adjustment in a demographic.

  • Finalised demographic adjustment support, enabling you to create demographics with adjusted parameters, e.g. see the holiday destinations example.

  • Added MoveRecord that can be used to record all moves performed by a mover or go_function. Added go_record() that can move specific individuals according to specific moves indicated in the MoveRecord. As there is a MoveRecord.invert you can use this to reverse moves.

  • Added is_infected parameter to Disease to mark whether a disease stage is classed as being an infected stage. This is useful for non-recovered, non-susceptible and non-infected stages, e.g. vaccinated (V) stages. For example see this tutorial.

  • MetaWards now has a proper R package. You can now install and update MetaWards directly from within R. See the updated installation instructions and the R quickstart guide.

  • Added a --UV-max command line parameter so that you can specify the date in the year when disease transmission is highest (if UV is not equal to 1.0, and thus disease transmission is seasonal). This defaults to the first day of the outbreak.

  • Optimised advance_foi() to skip calculations of FOI for a stage if beta[stage] is zero. This changes the order of random numbers, so meaning that this version of metawards will give different output than older versions for the same input and same random number seed. We’ve made a similar change to the original C code to make sure that this has not invalidated the results.

  • Added a “null” or “scratch” ward that can be used to temporarily store individuals during a day. This is useful when implementing more complex moves that involve gathering and scattering populations.

  • Removed all parameters and dead code that were ported from the original C code but are unused.

1.3.0 - July 22nd 2020

  • Added a new quick start guide that quickly showcases the main features of MetaWards. A Python, R and command line version is available, so this should suit a range of audiences.

  • Added support for different demographics to use different networks. This is described partially in the Part 8 - Creating your own models / networks, but mostly in the new quick start guide. This will be documented further in the tutorial in a future release (e.g. 1.3.1 or 1.4.0).

  • Added a metawards.run() function to run MetaWards jobs from the API. This enables jobs to be run from within Python or R scripts, or to run interactively from within, e.g. RStudio or Jupyter.

  • Added in R support via reticulate. You can now use the MetaWards API within R, plus, via the new metawards.run() function you can write nice tutorials or vignettes that include running the jobs. Aim to create a CRAN MetaWards package in a future release.

  • Cleaned up the Python API so that this is as flexible as the R API. Made sure that key classes, like Disease, InputFiles and Demographics are easy to use and can serialised to/from JSON.

  • New Ward / Wards API to let you easily create new networks in Python or R. You can convert Network to and from a Wards, and these can be saved and loaded from JSON. You can harmonise multiple Wards objects, which enables different demographics to use different networks. Also can now refer to wards in a network by name rather than index.

  • Fixed issues with the “single” ward model. This did not assign any player weights, so outbreaks were incorrect. This is now fixed, and the single-ward model now matches a manually-created single ward model.

  • Added convenience executables (metawards-python, metawards-jupyter and metawards-reticulate) to make it easier for users to use the right Python executable if many are installed on the system.

  • Cleaned up the output and changed “UV” to “scale_uv” as this clashed with the UV command-line parameter (and confused people).

  • Fixed a bug where the “population” parameter was ignored for repeated single-ward network runs.

  • More robust reading of the traditional network file format

  • Added progress bars for slow operations :-)

  • Better support for sequential naming of output directories for repeated runs

  • “master” branch was renamed to “main”

1.2.0 - June 26th 2020

  • Added the ability to use custom-named disease stages. You can now run any type of model, and are not limited to S, E, I and R. Learn more in the tutorial here.

  • Improved formatting out information output to the user regarding different disease stages. This includes better console output and also more informative output data files. Again, this is all detailed in the above tutorial.

  • Updated all output files to support the summary data for custom named disease stages. Now you can collect the data you want directly without needing to build a custom extractor - just say which mapping stage you want. Again, this is described in the above tutorial.

  • Added really flexible support for reading in different formats of additional seeds. See the tutorial here and the new fileformats documentation. This includes being able to read extra seeds from the command line, rather than needing to always write a file.

  • Added in the ability to seed infections by date as well as day. Also seeding wards by name as well as index (e.g. Clifton/Bristol).

  • Added in metawards.Interpret to consolidate all of the code used to interpret strings into data types. This increases the power and flexibility of the data parsers, and adds in new features such as reading in random data, or adding math functions to the expression support, e.g. pi * sqrt(3.5) now works.

  • Added cython support for plugins. If your plugin ends with .pyx and you have cython installed, then it will be compiled at run time. This should enable you to write plugin that are both powerful and fast.

  • Fixed a deadlock on Linux when using multiprocessing and OpenMP together

  • Removed the unused .err file.

  • Removed TotalInfections.dat.bz2 file (and similar) as these were difficult to work with and not well understood. Replaced with total_infections.csv.bz2 (and similar) files, which have more information and are easier to work with (e.g. have column names).

1.1.0 - June 11th 2020

  • Different demographics can now follow different disease pathways. This supports modelling of super-spreaders and hospitals, as described in part 7 of the tutorial.

  • Variables in demographic sub-networks can be scanned independently from the overal network or other sub-networks. This means you can, e.g. enact lock-downs in specific demographics, or scan disease parameters for different demographics.

  • Added a go_stage() function that moves individuals from and to specific disease stages in different demographics. This is used to support conditional branching, e.g. 20% of I2 infecteds go to hospital.

  • Added “–star-as-E”, “–star-as-R” and “–disable-star” command line arguments to control how the “*” state is counted in the summary outputs. This enables it to be counted as an extra “E” state, which makes the output more meaningful and more easily interpretable.

  • Clarified the meaning the “day 0” and “day 1”. Now “day 0” is before the model run starts (i.e. setup). The first iteration of the model run is “day 1”. This is a change from previous versions, which called the first half of the first iteration “day 0” and the second half “day 1”. Since seeding happens in the first half, this means that we now seed one day earlier than previous versions, so outbreaks are now one day ahead.

  • Fixed a major bug in calculation of the demographic sub-networks denominators. These have not been used in production yet. If you are going to use demographic sub-networks then please make sure you use this version (1.1.0) or above.

  • Added database support to OutputFiles, so that you can now write data to SQLite3 databases. This is described in a new part of tutorial chapter 4.

  • Added in extra output to Workspace so that you can get the populations of all disease stages for all demographics. This is demonstrated in a rate calculation, also in the new tutorial chapter 4.

  • Fixed a directory permissions bug that appeared sometimes on windows.

  • Fixed an existing bug from the C code whereby user-set values of contrib_foi are ignored. This had no impact as these values are always 1.0.

  • Fixed a bug in distribute_remainders that meant that individuals could sometimes still be added to a demographic even if the desired percentage was zero.

1.0.0 - May 23rd 2020

  • Improved “go_to” and “go_isolate” functions, which now support modelling self-isolation and quarantine. This is all demonstrated in a new part 6 of the tutorial.

  • Added an InteractionMatrix class to make it easier to create more sophisticated interaction matricies.

  • Added ability for any plugin to signal that the model run should end after the current iteration by raising a StopIteration exception

  • Added a “–model single” mode that uses a single-ward model for debugging and validation purposes.

  • Updated parallel runners (multiprocessing, scoop and MPI) to return results as they are available, so that the Console can report summaries and live progress.

  • Added a developer’s “debug” mode to the Console, complete with nice variable printing.

  • Lots of file and text encoding fixes, particularly to fix unicode issues on windows.

  • Finally fixed the issue on windows where the wrong plugin would sometimes be loaded.

  • Updated all tutorial outputs to the new format.

  • Fixed a runtime check exception that occurred on rare occasions on Windows. This didn’t cause any errors in data, but did stop runs from continuing when the run-time test was failed.

0.12.0 - May 18th 2020

  • Switched to configargparse to have better management of command line options, plus adding the ability to set options using a config file. This is now written to the output directory of each job to support reproducibility.

  • metawards-plot defaults to png output if pillow (and jpeg) are not available

  • Got basic movers working and added half of the sixth part of the tutorial, where self-isolation is modelled.

  • Added rich-console support, which has significantly altered the look and feel of metawards. Output is now more robust, with more info given in real time for parallel jobs, plus all output now also being recorded to output/console.txt.bz2, so that no output is lost.

  • Added theming support and a “simple” theme activated using “–theme simple” for those that don’t like colour ;-)

  • Added support for setting the number of repeats for a VariableSet into the output file. Also can specify different number of repeats for different adjustable variable sets on the command line.

  • Cleaned up the design file and user custom variable file parsing to use csv and support a wide range of formats, variable types and inputs. Can now directly work with dates, ints, floats, bools and strings. This is intelligent, and will use the best type it thinks, but it can be forced by the user via a d”3.4” numpy-type syntax

  • Improved the robustness of the parallel runners (multiprocessing, scoop and mpi4py) such that errors in one job don’t break all jobs. These are now handled individually and recorded properly. Jobs are run async so that results are processed and feedback is given to the user as soon as it is available.

  • Updated all of the tutorial to use lurgy3 - accidentally had gone back to lurgy2 in part 5.

0.11.2 - May 11th 2020

  • Minor bugfixes

  • Use last matching custom function rather than first, so that the examples in the tutorial work and behaviour is more natural

  • Caching network builds so that they are more thoroughly tested, fixed bug in networks.copy that meant that independent copies weren’t made. This bug did not impact any past results or runs.

  • Added more validation tests of the mixers

  • Cleaned up website typos and fixed the version switcher

  • Fixed packaging problems that caused broken builds when pip installing from a .tgz sdist package.

0.11.1 - May 10th 2020

  • Fixed CI/CD to produce working sdist and bdist packages

0.11.0 - May 10th 2020

  • Code now fully works and has been tested on Windows :-)

  • Major update of the API to support a Networks of multiple Network objects

  • This has been used to support modelling multiple demographics

  • Added in movers and mixers to enable a user to customise how individuals are moved between demographics and how the FOIs of demographics are merged together (e.g. via an interaction matrix). This is demonstrated in part 5 of the tutorial which shows how this can be used to model shielding

  • Allow compilation using compilers that don’t support OpenMP - now compiles even on stock OS X.

  • Added more extractors and can now output files that are needed for graphics

  • Added a special random number seed to support debugging

  • Moved random number files to a separate library which is now properly compiled and linked.

  • Updated CI to CI/CD and now build the OS X, Windows and ManyLinux wheels

  • Updated URLs to metawards.org

  • Allow multiple multi-node jobs to run from a single directory (they now have their own hostfiles)

  • Updated metawards-plot to render multi-demographic trajectories and to make better animations.

  • General bug fixes and speed-ups :-)

0.10.0 - April 27th 2020

  • Created all of the extract framework to support customising the output and analysis during a run.

  • Created a better Workspace class for holding accumulated data during extract

  • Completed most of the extractor tutorial

  • Added in WardInfo(s) to get metadata about wards, and to support searching for wards via their name, code, authority and region

0.9.0 - April 24th 2020

  • Merged in latest changes from the C code. Now gives complete agreement, including via a custom iterator that repeats the lockdown model.

  • Support x/y and lat/lon coordinates and distances. Now works properly with the 2011UK model data

  • Added an example of a lockdown parameter set scan

0.8.5 - April 22nd 2020

  • Small bugfixes to support the loading of the 2011UK model data

  • Cleaned up the website and added the version combo box

0.8.3 - April 21st 2020

  • Fixing CI/CD so that I can build and deploy on a new tag (hopefully 0.8.2)

0.8.0 - April 21st 2020

  • Automated github actions for building a versioned website plus automating building the packages.

  • Switched default for UV parameter to 0.0, as this should not normally be 1.0

  • Added custom user variables both for scanning and to act as inputs that may be used by custom advance and iterate functions. Detailed tutorial now shows how these can be used to model a lockdown.

  • Improved speed of custom iterators

0.7.1 - April 17th 2020

  • Small bugfixes to support all of the examples in part 3 of the tutorial

0.7.0 - April 17th 2020

  • Lots of progress with the project website, including a detailed tutorial

  • Support fully customisable disease models, and can adjust any disease parameter using a more flexible input file format

  • Can record the date in a model run, plus set the starting day and date

  • Broken up the iterate function into metawards.iterators, and can now have the user create their own custom iterators. Tutorial on how to do this will appear soon.

  • Broken up the extract_data function into metawards.extractors, and will soon enable a user to create their own. Tutorial on how to do this will appear soon.

  • Added metawards-plot to create simple plots and animations. This is particularly useful when working through the tutorial.

  • General code cleaning, documentation improvements and nice-to-haves that make the code easier to use.

0.6.0 - April 9th 2020

  • Wrote an initial draft of the complete project website

  • Fixed packaging problems that prevented installation of older packages on some systems

0.5.0 - April 8th 2020

  • Support running multiple model runs in serial or in parallel

  • Support aggregation and writing of model multiple model run outputs to the same directory, including to a single shared CSV data file.

  • Support for parallel running via multiprocessing, mpi4py or scoop

0.4.0 - April 7th 2020

  • Parallelisation of individual model runs using OpenMP

  • Parallel code scales to large numbers of cores and can complete individual runs in 10-15 seconds.

0.3.1 - April 5th 2020

  • Minor bug fixes in packaging and misplaced commits caused by move of repository

0.3.0 - April 5th 2020

  • Adding in a simple profiler to support optimisation of the code

  • Replaced GSL random number generator with a more liberally licensed and easily bundled generator extracted from numpy.

  • Switched code to the https://github.com/metawards organisation

  • Optimised more using cython and raw C for file reading

  • Added automatic versioning of packages and files using versioneer

  • Cleaned up the repository and added status badges

0.2.0 - March 31st 2020

  • Cythonizing the bottleneck code to bring the python code up to a comparable performance as the original C code.

  • Added in packaging information and general repository and file cleaning.

0.1.0 - March 29th 2020

  • Fully working Python port of the original C code that completely reproduces the results of the C code when given the same random number seed. However, it is significantly slower! Python port has promise, so worth exploring different options for speeding the code up.

Start of the Python port - March 25th 2020

  • Imported code from https://github.com/ldanon/metawards and began thinking about what the code was and trying to understand it. Decided to write a port as I find that if I can translate something, then I can understand it.