What’s new

All notable changes to the codebase are documented in this file.

Version 1.5.10 (2026-07-24)

Bug fixes

• HIV.stop_art now actually sets post_art=True. The post_art BoolState was defined but only ever cleared to False in clear_infection, so downstream cascade-stage attribution (e.g. transmission-source-by-ART-status analyzers) couldn’t distinguish “never on ART” from “on ART, now interrupted”. start_art also clears post_art when re-enrolling a previously-interrupted agent. (#544, #541)
• STITest/SyphTest no longer crash with the default eligibility=None. get_testers treated None as a non-callable UID list instead of falling back to check_eligibility() (which already handles None → everyone), so any test intervention without an explicit eligibility function crashed on its first step. (#537, #562)
• Syphilis: fix new_nnds / new_stillborns (and derived new_congenital_deaths / cum_congenital_deaths) always reading 0 — step_state cleared ti_nnd / ti_stillborn to NaN before update_results could match them against the current timestep. Counts are now stashed before clearing, mirroring the existing _new_congenital_count pattern. (#560)
• ANCTest: fixed a crash under current starsim (ss.dur(1, 'month') → 'months') and a bug where active_diseases was resolved after super().init_pre(sim) had already called init_results(), so per-disease results (n_<disease>_positive) were never created. ANCTest had zero test coverage before this. (#324, #546)

Diseases

• Syphilis: rebalance the mat_active (primary/secondary maternal infection) birth-outcome distribution — miscarriage probability raised (0.10→0.25 early, 0.20→0.25 late) and neonatal death lowered (0.25→0.05) — to better match Gomez 2013 / Cooper 2016, which put most adverse outcomes earlier in pregnancy rather than post-partum. (#543, #541)
• Syphilis: expose per-fetus mtct_from_{mat_active,early,late} flags recording the mother’s disease stage at the moment of mother-to-child transmission, so downstream analyzers can bucket congenital outcomes by maternal stage without reconstructing mother/fetus linkage. (#548)

Demographics

• sti.Migration gains rel_migration (default 1), analogous to ss.Deaths.rel_death: scales both immigration and emigration each timestep. (#542, #545)

Documentation

• Fill in the “Antenatal and infant screening (PMTCT)” stub in the interventions user guide (ANC → ART → newborn-test cascade, maternal_care_scale cross-reference) and add a new gallery example, pmtct_scenario.qmd, comparing MTCT infections and pregnant-women diagnosis rates with/without ANC testing. (#324, #546)
• Document the risk_group/sex/sw-stratified DataFrame format accepted by SyphTest.test_prob_data. (#537, #562)

Tests

• Add tests/test_anc_test.py (smoke test, immediate-ART-scheduling invariant, newborn-test scheduling) and tests/test_sti_interventions.py (default-eligibility regression, stratified test_prob_data) — both interventions had zero coverage before this.
• Add tests/test_demographics.py covering rel_migration.

Version 1.5.9 (2026-07-13)

Bug fixes

• VMMC now hits its coverage as a prevalence (stock) target, not a per-step hazard. The 1.5.6 rewrite computed the per-timestep target over the uncircumcised pool and only in aggregate, so coverage behaved as a per-step uptake rate on the remaining-uncircumcised men: realised circumcision coverage ratcheted toward ~100% regardless of the target, and the age/sex stratification in the input data was ignored (all ages converged to the same level). VMMC.step() now tops up to coverage × (all eligible males) per (age, sex) stratum each step — the denominator includes already-circumcised men, matching cross-sectional survey definitions — and never removes (circumcision is irreversible). Realised coverage converges to the target and preserves the input age gradient. Models calibrated against 1.5.6–1.5.8 VMMC behaviour will need recalibration. (#535)
• HIV.set_prognoses now calls super(), fixing ss.infection_log() for HIV. HIV overrode Disease.set_prognoses() entirely for its natural-history setup and never called super(), so the infection log’s append hook never fired for HIV specifically (other diseases such as SEIS-based Gonorrhea were unaffected). Infection log entries for a 1000-agent HIV sim went from 0 to 259 after the fix, restoring source/target transmission tracking (e.g. attributing onward transmission to a source subgroup). (#536)
• GonorrheaTreatment.set_treat_eff now defends against NaN rel_treat: a small fraction of agents allocated but inactive at sim.init keep an uninitialized slot and read back as NaN when reactivated, which previously propagated to treat_eff and made those agents always fail treatment. NaN entries are now replaced with the declared default (1) before computing treat_eff. (#528)
• art_coverage analyzer plotting no longer produces two identical plots. (#530)

Tests

• Add test_vmmc_hits_target, asserting realised male circumcision prevalence converges to the coverage target. The existing test_vmmc_specs only checked that some circumcisions occurred, which is why the overshoot regression went undetected.
• Regenerate baseline.yaml / benchmark.yaml for starsim 3.5.1 (CRN hash-based random number generation changed the exact values of agent-indexed draws; results are statistically equivalent per starsim’s changelog). test_shorter_sw now uses rand_seed=2 — rand_seed=1 drew zero FSW-sourced HIV transmissions in both arms from the small FSW pool (~9/2000 agents) under the new CRN scheme, making the comparison degenerate.

Diseases

• Syphilis: clear early / late sub-flags when a mother exits the latent state (reactivation to secondary, or progression to tertiary). Previously these BoolStates persisted, so set_congenital’s outcome loop for state in ['mat_active', 'early', 'late'] would overwrite the correct mat_active draw with the (now-stale) early / late table draw — biasing MTCT outcomes for reactivating mothers toward normal (the late table is 80% normal vs mat_active’s 25%). Empirical impact in a hot-seed ANC screening sim: untreated-secondary MTCTs read 67% normal instead of the expected 25%. (#538)

Diseases

• Syphilis: fix new_nnds and new_stillborns (and the derived new_congenital_deaths / cum_congenital_deaths) always reading 0. step_state cleared ti_nnd / ti_stillborn to nan when scheduling the deaths, so the == ti check in update_results (which runs after) never matched. Mirror the existing _new_congenital_count pattern: stash the counts before clearing and read from the stash in update_results.

Version 1.5.8 (2026-06-25)

Logistics

• Add a stisim.logistics package for supply-constrained interventions: Product (cost, delivery mode, time-varying efficacy), Supply/Supplies (quantities and accrued cost), ProductCategory/DeliveryMode enums, and the abstract SuppliedIntervention base that distributes a product across eligible agents subject to available supply. (#492)

Interventions

• PartnerNotification: optional edge-type / partner-sex stratification. step() now walks current-channel edges preserving edge-type info and exposes current_partner_edges ({partner_uid: [edge_type_int, ...]}) to callables on p_notify_current.p / p_attends_current.p. New sti.pn_rates(rates) helper builds such a callable from a dict spec — either {'stable': 0.20, 'casual': 0.10} or per-partner-sex {'stable': {'f': 0.80, 'm': 0.50}, ...}. Per-edge probabilities for multiply-reached partners are summed and capped at 1. Scalar p_notify_current / p_attends_current Bernoullis are unchanged (backward compatible). (#505)

Documentation

• New user-guide pages for analyzers (docs/user_guide/analyzers.md) and care-seeking (docs/user_guide/care_seeking.md).
• Expand the interventions user guide with syndromic management, antenatal/infant (PMTCT) screening, partner notification, and pregnancy-driven risk reduction.
• List all gallery examples in the sidebar; fix syphilis API drift that broke the docs build.

Tests

• Add pn_rates stratification tests.
• Regenerate baseline.yaml / benchmark.yaml for starsim 3.4.0 (n_female).

Version 1.5.7 (2026-06-15)

Diseases

• Syphilis: add treponemal (trep) and non-treponemal (nontrep) serology states with seroconversion/reversion dynamics (window period, ~80% lifelong trep persistence, non-trep titre decline + post-treatment reversion). New trep_prevalence/nontrep_prevalence results (overall, by sex, by age×sex) plus sexually_transmissible/symptomatic/primary stage prevalences. Consolidated the duplicate active property into symptomatic (removed active_prevalence and the *_prevalence_15_64 results). Prevalence denominator age band is now configurable via age_range, exposed as a BaseSTI constructor argument. (#500)

Networks

• Add fsw_mf_conc_mult on StructuredSexual to scale FSW non-sex-work concurrency (values <1 = fewer non-commercial partners). MFNetwork.set_concurrency is now negative-binomial-aware: it reparameterizes the target mean correctly instead of silently no-opping when concurrency_dist is ss.nbinom. (#500)
• Fix the three MSM networks (AgeMatchedMSM, AgeApproxMSM, MSMScaleFreeNetwork): all now honour a participation filter and no longer crash at init. The participation parameter is renamed msm_share → p_msm. (#502)

Interventions

• SyndromicManagement and SymptomaticTesting now take disease names (e.g. diseases=['ng', 'ct']) rather than module objects, resolved against sim.diseases at init. Objects passed at construction were deep-copied into orphans the sim never stepped, giving stale state and dropped result-writes. (#503)

Analyzers

• Add sti.PartnershipFormationAnalyzer. Networks now record the timestep each relationship ends (None if still active at sim end), enabling efficient post-run partnership analysis from a shared results store. (#504)

Results

• Remove the unimplemented partners_12 / n_partners_12m references. (#473, #507)

Version 1.5.6 (2026-06-02)

Networks

• Breaking — default behaviour change. Split stisim/networks.py into a stisim/networks/ sub-package (base.py, mf.py, fsw.py, msm.py, layered_networks.py, matchers.py). Add a match_method string parameter on MFNetwork, dispatched through a MATCHERS registry of pair-formation algorithms (accepts string or callable). The previous default (sort_bisect) collapsed the M-F age gap to ~0 because it didn’t honour age_diff_pars. Eight matchers ship in the registry. Removes stisim/pfa_variants.py and the seven MFNetwork_* subclasses. (#472)
• New closest_age_tapered_seeking matcher, now the default. Orders females by desired_age = age + normal(target_gap, stddev) (drawn each step for under-partnered females) and males by age; uses batch-binary-search to find each female’s closest available match, with a taper that reduces seeking for older females to bring mean age gaps into data alignment. Realised mean age gap is now within <5% of target (was negatively biased and growing); target stddev preserved. Downstream calibrated models will need recalibration: HIV prevalence shifts ~18% in Zimbabwe and ~59% in Eswatini at default settings. (#477)
• Add sti.MSMScaleFreeNetwork: a preferential-attachment MSM sexual network with continuous-time formation/Markovian deletion (Whittles-2019 S2 kernel). Restricted to post-debut males in this first port; subclass hooks (_get_pool, _mix_node_arrays, _mix_weights_row) let you plug in age-/risk-/λ-weighted variants. Documented as not branching-stable under starsim CRN (global weighted-categorical sampling over a pair catalog). Ported from starsim_x/BespokeNet, contributed by Stephen Attwood (Oxford). (#488)

Interventions

• Add sti.PregnancyRiskReduction: during pregnancy, optionally clears FSW status (fsw_redux), drops high-risk-group membership to default_risk_group (high_risk_redux), and/or zeros concurrency (concurrency_redux). Ported from syph_dx_zim. (#482, #484)

Documentation

• New ART state diagram in the docs illustrating how ART intersects the HIV mortality cascade. (#471)

Tests

• Regenerate tests/baseline.yaml for the new default matcher.
• Add tests/update_baseline script (mirroring hpvsim’s pattern) to regenerate both baseline.yaml and benchmark.yaml in one command.

Version 1.5.5 (2026-05-15)

Sim / parameter routing

• Add sti.route_pars utility (in stisim/utils.py) that auto-discovers par categories (sim, sti, nw, dem) from the par-class registry and routes flat kwargs accordingly. Cross-category clashes broadcast to all matches with a printed note; unknown keys raise when strict=True. sti.Sim.separate_pars now delegates to it and shrinks from ~95 to ~30 lines. (#451, #452)
• Auto-add coinfection connectors when diseases=[...] is supplied without an explicit connectors=. Lookup tries sti.<d1>_<d2> then sti.<d2>_<d1>; pairs with no registered class are silently skipped. Replaces the previous NotImplementedError stub. (#442, #453)
• Route flat connector pars (e.g. rel_sus_hiv_syph=3.5) through to the matching connector instance. (#442, #453)

Interventions

• Replace PartnerNotification with a PriorPartners-based implementation. Two channels (current sexual network, optional prior-partner recall network) each with separate notification × attendance probabilities. Tracks notifications and attendance per-channel. The previous transmission-graph-based version is removed. New gallery example docs/examples/partner_notification.qmd. (#457)
• Add dur_dx2tx parameter to HIVTest (default ss.constant(0)) for the delay between HIV diagnosis and ART start. HIVTest now schedules hiv.ti_art = ti + delay on positive results; ART becomes passive and starts agents whose ti_art == ti & ~on_art. ANCTest and initially-diagnosed cases schedule with no delay (backward compatible). (#398, #464)
• Fix ART stratified coverage to allocate per-(age, sex) stratum independently. Previously, stratified coverage data was parsed correctly but then collapsed to a single aggregate target before correction, washing out the age/sex differentials in the input. New compute_stratum_targets helper in interventions/utils.py. (#463)

HIV

• new_agents_on_art result now gates on on_art (since ti_art may also hold a scheduled future start). (#464)

Documentation

• New gallery example docs/examples/vmmc_costing.qmd: attach unit costs to sim.results, discount, and compute an ICER for VMMC vs no-VMMC, framed as a quick STIsim analog of Bansi-Matharu et al., Lancet Global Health 2023;11(2):e244–e255. (#455, #465)

Version 1.5.4 (2026-05-04)

Networks

• Split StructuredSexual into reusable MFNetwork (heterosexual) and SWNetwork (sex-work) networks built on a new BaseNetwork. StructuredSexual is preserved as the combined default. (#307, #445)
• Window sex-work participation by per-agent age_sw_start + dur_sw instead of lifetime; fsw / client / age_sw_stop are now derived properties. (#307, #445)
• Add condom_smoothness parameter forwarded to sc.smoothinterp for time-varying condom data. (#445)
• Replace shared debut / debut_pars_f / debut_pars_m with per-sex debut_f / debut_m distributions; supports scalar shortcuts, full ss.Dist instances, and callables. (#397, #420, #423)

Interventions

• Add SyndromicManagement to core stisim, consolidating duplicated implementations from anc_sti_screening and stisim_vddx_zim. cervical_diseases parameter generalises the cervical-symptom check. (#369, #443)
• Add ANCTest for single-visit ANC screening (auto-detects HIV + syphilis; per-disease sensitivity; routes to treatment maps). Raises if disease names are mistyped. (#370, #444)
• Add InfantHIVTest for newborn/infant testing scheduled by ANCTest or by HIVTest via the maternal network. (#370, #444)
• Decouple Prep eligibility from clinical filters: user-supplied eligibility= callables now express targeting only; ~hiv.infected and ~on_prep are applied unconditionally. (#330, #441)
• Refactor Prep legacy years= handling: pop from kwargs before update_pars instead of reading back from self.pars. (#444)

HIV

• Update acute HIV defaults to Bellan 2015 central estimates: rel_trans_acute=N(5.3, 0.5), dur_acute=LogNorm(1.7 mo, 1 mo). EHM drops from 15 to ~7.3. (#396, #426)
• Add rel_sus_age: list of (age_lo, age_hi, sex, multiplier) tuples for age/sex-stratified susceptibility. Default None preserves existing behaviour. (#395, #427)
• Remove BaseSTI.infect() override; inherits parent ss.Infection.infect() for free mixing-pool compatibility. (#412, #421, #422)

Sim / parameter routing

• process_networks / process_stis / process_demographics now raise on collisions instead of silently winning; separate_pars raises on pars ∩ kwargs collisions in both sti.Sim and hivsim.Sim. (#423)
• Improve “ambiguous parameter” error messages to name the offending par. (#423)
• hivsim.Sim pulls network-level kwargs from user input into the default StructuredSexual instance. (#423)
• Remove BreastfeedingNet from sti.Sim default networks; only relevant for diseases with postnatal transmission (HIV, syphilis). (#406, #444)

Bug fixes

• Fix birth data key mismatches in process_demographics when use_pregnancy=False: 'births' → 'cbr'/'birth' keys, file path, and metadata columns. (#411, #428)

Documentation

• Switch docs build from MkDocs to Quarto; convert tutorials from .ipynb to .qmd. (#439)
• Documentation audit and uplift via IDM standards plugin (folder READMEs, API reference, navigation polish). (#435)
• Add new publication entry: Stuart et al., “Estimating the value of novel tests for active syphilis in Zimbabwe…” forthcoming in STD. (#447, #448)

Tests

• Add tests/devtests/devtest_sw_networks.py with 10 integration tests covering MF only, SW only, MF+SW modular, StructuredSexual, implicit-SW thresholds, windowed entry/exit, and all sti.Sim / hivsim.Sim / hivsim.demo creation patterns. (#445)
• Add test_shorter_sw: shorter SW participation window → fewer FSW-attributable transmissions. (#445)
• Remove fragile len(sim.diseases/networks/interventions) count assertions in test_sim. (#444)
• Remove fragile test_doubling_hiv_sexual_beta. (#445)
• Regenerate baseline.yaml to reflect default behaviour changes (windowed SW, BreastfeedingNet removal, Bellan acute pars). (#426, #444, #445)

Version 1.5.3 (2026-04-17)

Interventions

• Extract shared coverage-targeting logic into interventions/utils.py: parse_coverage, age_sex_mask, compute_coverage_target (#328)
• Replace _parse_age_bin with starsim’s ss.parse_age_range and ss.apply_age_range (#326)
• Expose smoothness parameter for coverage interpolation (default 0 = linear) (#327)
• Support mixed n/p coverage format: historical absolute numbers transitioning to projected proportions within a single DataFrame or dict (#383)
• Remove deprecated coverage_data and future_coverage parameters; use coverage instead (#383)
• Refactor PrEP to use parse_coverage (#327)
• Add pmtct_efficacy parameter to ART (default 0.96), replacing hardcoded rel_sus=0 for prenatal MTCT protection (#404)
• Extend PMTCT protection to breastfed infants via BreastfeedingNet (#407)
• Add ANC HIV testing pattern using HIVTest with pregnancy eligibility (#322)

HIV / MTCT

• Add new_infections_mtct, new_infections_sex, new_infections_prenatal, new_infections_postnatal results to BaseSTI (#325)
• Implement breastfeeding HIV transmission via BreastfeedingNet with beta_breastfeed parameter (#323)
• Add p_diagnosed_pregnant result tracking ANC testing coverage (#322)
• Include BreastfeedingNet in hivsim.Sim defaults (conditional on Pregnancy module)

Bug fixes

• Fix chlamydia eff_condom default: updated to 0.4 based on linked citation (#391)
• Fix hivsim.Sim: conditionally add BreastfeedingNet only when Pregnancy is present (#413)
• Fix disease count assertion in test_sim_creation (#413)

Documentation

• Add examples gallery with first entry: Modeling ART interruptions (#394)
• Add PMTCT section to HIV user guide (ANC testing, prenatal/postnatal protection)
• Document HIV transmission route results (MTCT, prenatal, postnatal)
• Add docstrings across interventions, diseases, networks, and analyzers (#409)

Tests

• Add test_pmtct: 8-sim combinatorial test for ANC testing, PMTCT efficacy, and breastfeeding duration
• Add test_mtct: prenatal + postnatal MTCT consistency checks

Version 1.5.2 (2026-04-06)

Bug fixes

• Fix default_build_fn to apply rand_seed when reseed=True, so each calibration trial uses its own seed
• Fix timepar handling in data loaders (remove unnecessary TimePar catch)
• Fix stray plot appearing when running pytest (test_zimbabwe called hivsim.demo with plot=True)

Improvements

• Add HIV.plot() with curated 6-panel view (new infections, deaths, prevalence, prevalence 15-49, diagnoses, proportion on ART)
• Pin starsim>=3.3.1 and sciris>=3.2.9

Tests

• Add baseline regression test and benchmark test using Zimbabwe HIV example
• Refactor test suite with clear file responsibilities: test_sim.py (constructor/routing), test_hiv.py (HIV scientific validation), test_stis.py (non-HIV STI validation), test_networks.py (network dynamics)
• Add hivsim.Sim constructor tests (defaults, parameter routing, custom modules)
• Add HIV sensitivity tests: test_par_ranges checks beta_m2f, init_prev, dur_falling, and art_efficacy against both cum_infections and cum_deaths
• Add test_prevalence_by_sex verifying female > male HIV prevalence under defaults
• Add MSM network test
• Rename test_diseases.py to test_stis.py, test_hiv_natural_history_verification.py to test_hiv.py
• Merge test_examples.py into test_sim.py

Documentation

• Fix calibration tutorial to use disease instances instead of strings
• Add note about scikit-learn requirement for plot_param_importances

Version 1.5.1 (2026-03-27)

Bug fixes

• Fix VMMC eligibility: pass eligibility to parent class and use check_eligibility() in step(), so user-supplied eligibility functions are no longer silently ignored (#353)
• Fix starsim compatibility: convert ss.years/ss.date to int in get_age_distribution() for newer starsim __len__ behavior
• Fix rand_seed placement in beta transmission test (#354)

Parameter handling

• Remove parameters from SimPars that duplicate starsim’s Sim (label, verbose, total_pop, pop_scale, birth_rate, death_rate, use_aging) (#351)
• Add get_valid_pars() to detect ambiguous parameters across namespaces (#351)
• Improve error messages for unrecognized parameters with suggestions via sc.suggest() (#351)
• Handle location/demographics conflict in remap_pars() (#351)
• mergepars() now returns sc.objdict for dot-notation access (#351)

Other changes

• Delete legacy setup.py (use pyproject.toml)
• Relax sc.require to only check starsim, with die=False
• Comment out unused dt parameter in Migration

Tests

• Add VMMC tests: reduces male infections, male-only targeting, eligibility targeting (#251, #355)
• Add ART dropout tests: CD4 decline and rel_trans increase after stopping ART (#244)
• Add exponential early-phase epidemic growth test (#260)
• Add increased testing speeds diagnosis test (#253)
• Add no-HIV-without-seeding test (#271)

Documentation

• Fix sti.Pregnancy → ss.Pregnancy in Getting Started tutorial (#343)
• Fix tutorials and user guide nav nesting
• Update syphilis docs: exposed stage, treatment/reinfection, key properties
• Fix HIV dur_on_art default in docs

Version 1.5.0 (2026-03-13)

Interventions

• Refactor ART and VMMC coverage input: accept scalar, dict, or DataFrame formats with flexible column names (#126)
• Add art_coverage analyzer for tracking ART coverage by age and sex
• Simplify art_initiation: accept plain number, drop init_prob backward compat
• Guard pregnancy/maternalnet access in HIV and syphilis interventions so they work without a pregnancy module (#319)
• Document HIV intervention pipeline and ordering (#314)

HIV

• Add aids property to HIV module (cd4 < 200)
• Fix dur_on_art being silently scaled by dur_on_art_trend: default is now None (#336)
• Add time-varying ART duration and wider care-seeking distribution
• Add custom module support to Sim constructor (#318)

Syphilis dynamics

• Fix Syphilis.infect(): use rel_trans=1 for maternal transmission, stage-specific for sexual
• Fix NewbornTreatment to detect MTC-infected babies (susceptible=False, congenital not yet fired)
• Fix congenital syphilis over-counting: clear ti_* after events fire, mark babies non-susceptible after MTC
• Add step_die to Syphilis to clear states on death
• Add n_infections counter and new_reinfections result

Calibration API

• New dot-notation parameter routing: 'hiv.beta_m2f' automatically finds and sets the right module parameter via sim.get_module() (requires Starsim 3.2.0+)
• Support nested parameter format: dict(hiv=dict(beta_m2f=dict(low=..., high=...))) alongside flat {'hiv.beta_m2f': dict(...)}
• Add flatten_calib_pars() to normalize between nested and flat formats
• Add set_sim_pars(sim, pars) for setting calibrated parameters on any sim (pre- or post-init)
• Add Calibration.get_pars(n) to extract top-N parameter sets as flat dicts
• Add make_calib_sims() for creating and running sims from calibrated parameters, with filtering (check_fn) and seed replication (seeds_per_par)
• Add Calibration.save() method for shrink/save workflow (replaces manual shrink + saveobj boilerplate)
• No custom build_fn needed – default_build_fn handles all module types automatically

Documentation

• Add calibration tutorial with ABC philosophy, custom analyzer fitting, production workflow
• Update co-transmission tutorial: HIV-syphilis example with epidemiological explanation of connector effects
• Add custom results section to results tutorial
• Cross-link calibration and results tutorials

Tests

• Add HIV natural history verification test suite: CD4 decline, transmission doubling, MTCT, AIDS property (#178, #226, #227, #228, #237, #238, #295)
• Add HIV intervention tests: ART coverage formats, duration, effects, parameter sensitivity
• Add testlib.py with shared build_testing_sim() helper

Version 1.4.9 (2026-02-24)

• Add default_build_fn for calibration: routes parameters by prefix (hiv_*, syph_*, nw_*) to diseases and networks automatically, removing need for custom build_fn
• sti.Calibration now uses default_build_fn when no build_fn is provided
• Fix make_df() time column to use years from timevec instead of integer index
• Fix parse_study() to guard sim_results reordering when save_results=False
• Fix calibration data column names to use dot notation (hiv.prevalence)
• Standardize import conventions: import stisim as sti, import hivsim (no alias)

Version 1.4.8 (2026-02-23)

• Add hivsim_examples package with simple and zimbabwe pre-configured examples
• Add hs.demo() function for quickly running example HIV simulations (e.g. hs.demo('zimbabwe'))
• Add Sim.plot() override that auto-selects curated HIV result keys when HIV is present
• Add data parameter to sti.Sim for passing comparison data (e.g. UNAIDS estimates) to starsim’s plot overlay
• Fix process_demographics() to use total_pop from sim_pars when set, and correctly scale age data (values in thousands)
• Fix separate_pars() so kwargs override sim_pars defaults (e.g. stop=1995 overrides sim_pars=dict(stop=2025))
• Fix get_age_distribution() to handle CSV files without a year column

Version 1.4.7 (2026-02-20)

• Fix bugs in coinfection analyzer: age limit typo, variable name errors for male results
• Remove STIsim Pregnancy module, now superseded by the Starsim Pregnancy module
• Add exposed/incubation period for syphilis (dur_exposed), and allow maternal transmission during this stage
• Rename syphilis birth outcome key active to mat_active to reflect inclusion of exposed stage
• Add .vscode/ and *.code-workspace to .gitignore

Version 1.4.6 (2026-02-20)

• Add sensible beta_m2f defaults for all diseases (NG: 0.06, CT: 0.06, TV: 0.1, HIV: 0.05, syphilis: 0.1)
• Add rel_trans_hiv_ng parameter to the HIV-NG connector
• Fix connector handling in Sim.init() when a single connector is passed
• Set auto_plot=False on subpopulation, care-seeking, and detail results so sim.plot() shows only high-level results
• Add tutorials: intro (gonorrhea), co-transmission, results/plotting, and interventions
• Add user guide pages for interventions (testing, treatment, ART, VMMC, PrEP)
• Update disease docs with beta_m2f defaults and per-act description
• Pre-build font cache in docs CI workflow

Version 1.4.5 (2026-02-20)

• Fix BV trimester KeyError during initialization
• Add documentation: intro tutorial, disease reference pages, and network guide
• Configure mkdocs to execute notebooks and add user guide structure
• Update README with Python/R install instructions and example repos
• Move devtests to tests/devtests/ and rename test_hiv to devtest_hiv

Version 1.4.3 (2025-12-08)

• Patch to add super calls to init_results for analyzers
• GitHub info: PR 160

Version 1.4.2 (2025-11-28)

• Patch to ensure that products have different names
• Add ti_exposed attribute to HIV module
• GitHub info: PR 150

Version 1.4 (2025-08-12)

• Add location arg and Sim class
• Update to work with Starsim v3.
• GitHub info: PR 148

Version 1.3 (2025-06-27)

• Fixes to the pair-matching algorithm within the sexual network to better align partner ages
• Improvements to networks, including analyzers for debut age and partner age differences
• GitHub info: PR 143

Version 1.2 (2025-06-10)

• Improvements to networks, including analyzers for relationship duration and network degree
• Adds a PriorPartners network for recalling past relationships - for use in partner notification
• GitHub info: PR 135

Version 1.1.2 (2025-06-03)

• Bugfix to calibration class for multisims
• GitHub info: PR 138

Version 1.1.1 (2025-05-23)

• Bugfixes to calibration class and BV connector
• Replaces the match_pairs method of the StructuredSexual network with the faster option that was previously in the FastStructuredSexual network (now removed).
• GitHub info: PR 124

Version 1.1.0 (2025-05-13)

• Improvements to the Calibration class: this class now inherits directly from the Starsim calibration class, so users will have access to easier parameter constraints, plotting, flexible fit functions, etc
• Generalization of the coinfection class to handle any two diseases
• Addition of a more detailed BV model
• GitHub info: PR 119

Version 1.0.5 (2025-05-08)

• Adds results for syphilis transmission by disease stage
• GitHub info: PR 112

Version 1.0.4 (2025-05-07)

• Adds results for overtreatment among pregnant women
• GitHub info: PR 111

Version 1.0.3 (2025-04-30)

• Bugfixes for congenital syphilis
• GitHub info: PR 85

Version 1.0.2 (2025-04-14)

• Bugfixes for syphilis and GUD
• GitHub info: PR 83

Version 1.0.1 (2025-03-31)

• Track HIV prevalence for 15-49 year olds
• GitHub info: PR 79

Version 1.0.0 (2024-12-11)

• Updates to work with Starsim v2.2.1
• GitHub info: PR 63

Version 0.2.0 (2024-11-01)

• Updates to work with Starsim v2.0
• GitHub info: PR 62

Version 0.1.0 (2024-10-02)

• Collection of updates related to the NG/CT/TV work
• GitHub info: PR 59

Version 0.0.2 (2024-06-07)

• Initial version of STIsim with structured sexual networks, models of HIV and syphilis, worksflows for model calibration, and interventions for testing and treatment.
• GitHub info: PR 22

Version 0.0.1 (2024-05-15)

• Pre-release version