Changelog

0.11.0 (unreleased)

• Update to laser-core~=1.0 (namespace package laser.core)

• Switch to uv_build build system

• Migrate namespace package laser_cholera to laser.cholera

• Update pyproject.toml for additional package data files

• Remove MANIFEST.in (uv build does not use it)

• Dependency updates: setuptools, h11, requests, tornado, jupyterlab, urllib3, fonttools

0.10.1 (2026-01-16)

• Add tests for new IFR implementation

0.10.0 (2026-01-15)

• New IFR model (Infection Fatality Ratio)

• Update observation process with rho and chi based on infectious prevalence and diagnostic rates

• Update default_parameters.json and LICENSE copyright dates

• Test fixes for NumPy scalar serialization

• Remove MacOS x86_64 from test matrix

• Linter issues and GitHub runner fixes

0.9.1 (2025-10-02)

• Fix typo infective -> ineffective

• Add checks against populations going negative

• Expose new_symptomatic

• Only print if verbose is True in parameters

• Skip likelihood check unless “calc_likelihood” is in parameters

• Address linter issues

• Bugfix for parameter constraints (alphas)

0.9.0 (2025-08-19)

• Support single location configuration

0.8.0 (2025-07-24)

• Spatial hazard computation fix (don’t transpose pi_ij in model.results)

0.7.11 (2025-07-11)

• Trim and transpose for convenience in MOSAIC

0.7.10 (2025-07-10)

• Fix bug in double counting Vxinf

• Fix bug in suitability to decay calculations

• Update default parameters

• Fix indexing for human daily seasonality

0.7.9 (2025-06-06)

• Rename beta_env to beta_jt_env

• Rename beta_j_seasonality to beta_jt_human and use directly in spatial hazard calculation

• Update pre-commit

• Fix handling of pi_ij matrix math

• Track vaccine doses delivered

• Births should be Poisson rather than binomial

• Rename estimated to simulated for clarity

• Switch from ‘agents’ to ‘people’ terminology

• Fix coupling calculation for denominator == 0

0.7.8 (2025-05-16)

• Likelihood cleanup for NaNs and all zeros

0.7.7 (2025-05-13)

• Calculate log likelihood at end of simulation

0.7.6 (2025-05-13)

• Fix logging setup and np.var() usage

0.7.5 (2025-05-13)

• Add Python implementation of R tests for likelihood functions

0.7.4 (2025-05-07)

• Fix up reading JSON files back into memory (handle actual NaN vs “NA” or “NaN”)

• Record incidence (total and per source)

• Adding likelihood functions

• Adding likelihood function tests

• More consistent variable names

0.7.3 (2025-04-30)

• Gate file output on hdf5_output and “return” config parameters

• Clean up console output with logging infrastructure

• Add “quiet” parameter to suppress console progress bar (defaults to False for CLI, True for programmatic interface)

• Update GHA to run tests on push to main

• Support params from R (numeric values come in as doubles, but we need an integer for p)

0.7.2 (2025-04-24)

• Support for passing dict to get_parameters()

• Tests for run_model() function

• Additional tests for tracking vital statistics (births, non-disease deaths, disease deaths)

0.7.1 (2025-04-24)

• Minor version bump

0.7.0 (2025-04-23)

• Initial alpha release

• Support passing parameter dictionary to run_model()

• Fix mapping of environmental suitability (psi_jt) to decay parameter (delta_jt)

• Update default_parameters.json with matrices

• Update parameter loading for matrices

• Clean up plotting and fix seasonality phase

• Handle command line parameter overrides

• Enable parameter overrides correctly

• Allow test parameter sets to skip validation

• Pin numpy, numba, and llvmlite versions

• Remove subpackages

• Update laser-core dependency

• Return model from run_model()

• Require Numba that supports NumPy>=2.0

• Update shedding to environment based on theta_j

• Updated parameters including switch from delta_min/delta_max to decay_days_fast/decay_days_slow

• Use decay_shape_1 and decay_shape_2 to parameterize scipy.stats.beta.cdf

• Add version bump, build, and release GHA

• Metapop implementation work-in-progress commits

0.0.0 (2024-09-30)

• First release on PyPI