What’s new

All notable changes to the codebase are documented in this file. Changes that may result in differences in model output, or are required in order to run an old parameter set with the current version, are flagged with the term “Regression information”.

Version 0.4.0 (2022-11-16)

  • Adds merge method for scenarios and fixes printing bugs

  • GitHub info: PRs 422

Version 0.3.9 (2022-11-15)

  • Simplifies genotype initialization, adds checks for HIV runs.

  • Since the last release, changes were also made to virological clearance rates for people receiving treatment - previously all treated people would clear infection, but now some may control latently instead.

  • GitHub info: PRs 421 and 420

Version 0.3.8 (2022-11-02)

  • Store treatment properties as part of sim.people

  • GitHub info: PR 413

Version 0.3.7 (2022-11-01)

  • Fix to ensure consistent results for the number of txvx doses

  • GitHub info: PR 411

Version 0.3.6 (2022-11-01)

  • Fix bug related to screening eligibility. NB, this has a sizeable impact on results - screening strategies will be much more effective after this fix.

  • GitHub info: PR 396

Version 0.3.5 (2022-10-31)

  • Store stocks related to interventions

  • GitHub info: PR 395

Version 0.3.4 (2022-10-31)

  • Bugfixes for therapeutic vaccination

  • GitHub info: PR 394

Version 0.3.3 (2022-10-30)

  • Changes to therapeautic vaccine efficacy assumptions

  • GitHub info: PR 393

Version 0.3.2 (2022-10-26)

  • Additional tutorials and minor release tidying

  • GitHub info: PR 380

Version 0.3.1 (2022-10-26)

  • Fixes bug with screening

  • Increases coverage of baseline test

  • GitHub info: PR 373

Version 0.3.0 (2022-10-26)

  • Implements multiscale modeling

  • Minor release tidying

  • GitHub info: PR 365

Version 0.2.11 (2022-10-25)

  • Changes the way dates of HPV clearance are assigned to use durations sampled

  • GitHub info: PR 374

Version 0.2.10 (2022-10-24)

  • Fixes bug with treatment

  • GitHub info: PR 354

Version 0.2.9 (2022-10-18)

  • Prevents infectious people from being passed to People.infect()

  • Fixes bugs with initialization within scenario runs

  • Remove ununsed prevalence results

  • GitHub info: PR 338

Version 0.2.8 (2022-10-17)

  • Fixes bug with intervention year interpolation

  • Changes reactivation probabilities to annual, not per time step

  • Refactor prognoses calls

  • GitHub info: PR 338

Version 0.2.7 (2022-10-14)

  • Adds robust relative paths via hpv.datadir

  • GitHub info: PR 333

Version 0.2.6 (2022-10-12)

  • Removes Numba since slower for small sims and only 10% faster for large sims.

  • Moves functions from utils.py into people.py, sim.py, and population.py.

  • GitHub info: PR 326

Version 0.2.5 (2022-10-07)

  • Adds people filtering (NB: not used, and later removed).

  • Fixes bug with print(sim) not working.

  • Adds baseline tests.

  • GitHub info: PR 310

Version 0.2.4 (2022-10-07)

  • Changes to dysplasia progression parameterization

  • Adds a new implementation of HPV natural history for HIV positive women

  • Note: HIV was added since the previous version

  • GitHub info: PR 304

Version 0.2.3 (2022-09-01)

  • Adds a use_migration parameter that activates immigration/emigration to ensure population sizes line up with data.

  • Adds simple data versioning.

  • GitHub info: PR 279

Version 0.2.2 (2022-08-22)

  • Separates out the Calibration class into a separate file and to no longer inherit from Analyzer. Functionality is unchanged.

  • GitHub info: PR 255

Version 0.2.1 (2022-08-19)

  • Improves calibration to enable support for MySQL.

  • Fixes plotting bug.

  • GitHub info: PR 253

Version 0.2.0 (2022-08-19)

  • Fixed tests and data loading logic.

  • GitHub info: PR 251

Version 0.1.0 (2022-08-01)

  • Updated calibration.

  • GitHub info: PR 215

Version 0.0.3 (2022-07-18)

  • Updated data loading scripts.

  • GitHub info: PR 156

Version 0.0.2 (2022-06-15)

  • Made into a Python module.

  • GitHub info: PR 64

Version 0.0.1 (2022-04-04)

  • Initial version.