hpvsim 2.2.6__tar.gz → 2.3.0__tar.gz

{hpvsim-2.2.6 → hpvsim-2.3.0}/.gitignore

@@ -2,6 +2,15 @@
 *.obj
 files/
 
+# Quarto
+_freeze/
+_inv/
+api/
+.jupyter_cache/
+
+# Regression baselines (regenerate via tests/generate_v2_baselines.py)
+tests/regression_baselines/
+
 # Other files
 .idea
 .vscode
@@ -79,9 +88,11 @@ instance/
 # Scrapy stuff:
 .scrapy
 
-# Sphinx documentation
+# Sphinx (legacy) / Quarto documentation
 docs/_build/
 docs/api/_autosummary
+docs/_site/
+objects.json
 
 # PyBuilder
 target/

hpvsim-2.3.0/CHANGELOG.md

@@ -0,0 +1,490 @@
+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 2.3.0 (2026-04-20)
+
+- Fixes dt-dependent results by scaling partnership formation rates to
+  per-timestep probabilities; `layer_probs` and cross-layer defaults
+  converted to annual probabilities.
+- *Regression information*: If workflows from v2.2.6 or earlier override default `layer_probs`, `f_cross_layer`, or `m_cross_layer` values
+  and have timesteps not equal to 1 year, then the probabilities must be converted to annual probabilities instead of per-timestep probabilities using this formula: `1 - (1 - prob) ** dt`
+- *Regression information:* baseline model outputs change; baselines have been regenerated.
+- Fixes `precins` flow never being incremented; removes redundant `dysplasias` flow (was an alias of `cins`).
+- Adds test coverage for previously untested code paths.
+- Vaccine immunity is now sterilizing (all-or-nothing) rather than leaky (per-contact). `imm_init` sets the probability of sterilizing immunity; non-sterilizing recipients get leaky protection at the `imm_init` level. Default is 0.95.
+- Adds per-timestep transmission logging (`sim._transmission_log`) for downstream analysis of transmission chains.
+- Calibration now supports resuming from an existing database via `keep_db=True`, running only the remaining trials.
+- Calibration workers catch exceptions instead of crashing the entire run.
+- Fixes `res_to_plot` indexing bug in `Calibration.plot()`.
+- *Regression information*: vaccine efficacy will differ from previous versions due to the immunity model change.
+
+## Version 2.2.7 (2026-04-22)
+
+- Fix cancer treatment results always being blank: `BaseTreatment.check_eligibility` was excluding cancer patients (preventing radiation from running), `BaseTreatment.apply` was writing to CIN fields for cancer treatment, and `cum_cancer_treated` cumsum used the wrong source array
+- *Github info* PR [94](https://github.com/starsimhub/hpvsim/pull/94), issue [91](https://github.com/starsimhub/hpvsim/issues/91)
+
+## Version 2.2.6 (2026-04-17)
+
+- Reconcile different copies of repository
+- *Github info* PR [75](https://github.com/starsimhub/hpvsim/pull/75)
+
+## Version 2.2.5 (2025-10-27)
+
+- Small bugfix for campaign vaccination
+- *Github info* PR
+  [689](https://github.com/starsimhub/hpvsim_orig/pull/689)
+
+## Version 2.2.4 (2025-08-20)
+
+- Fixes a bug in analyzer results for cancer by age and HIV status
+- *Github info* PR
+  [687](https://github.com/starsimhub/hpvsim_orig/pull/687)
+
+## Version 2.2.3 (2025-06-27)
+
+- Small bugfixes and changes to HIV module parameterization
+- *Github info* PR
+  [685](https://github.com/starsimhub/hpvsim_orig/pull/685)
+
+## Version 2.2.2 (2025-06-20)
+
+- Bugfix to allow running simulations beyond 2100
+- *Github info* PR
+  [681](https://github.com/starsimhub/hpvsim_orig/pull/681)
+
+## Version 2.2.1 (2025-05-29)
+
+- Bugfix for running calibrations to prevent interventions being
+  reinitialized
+- *Github info* PR
+  [678](https://github.com/starsimhub/hpvsim_orig/pull/678)
+
+## Version 2.2.0 (2025-05-23)
+
+- Refresh results: ensure all main results are populated, remove cancer
+  detection results, and fix bug with HPV prevalence calculations
+- Updates to docs
+- *Github info* PR
+  [673](https://github.com/starsimhub/hpvsim_orig/pull/673)
+
+## Version 2.1.0 (2025-03-25)
+
+- Updates how HPV prognoses are re-evaluated for WLWH
+- Fixes CD4 reconstitution trajectory so that it plateaus before
+  quadratic starts decreasing
+- Fixes ART coverage so that it's now by age, sex, and time
+- Fixes assignment of HIV mortality based upon ART coverage
+- Removes HIV-mortality from background mortality
+- Small fix to enable calibration to HIV-stratified data
+- Adds a more robust data downloading method and renamed `get_data()` to
+  `download_data()`; updated data version to 1.4
+- *Github info* PR [652](https://github.com/amath-idm/hpvsim/pull/652)
+
+## Version 2.0.2 (2024-03-05)
+
+- Modifies DALY analyzer to output YLLL, YLD and DALYs
+- *Github info* PR [659](https://github.com/amath-idm/hpvsim/pull/659)
+
+## Version 2.0.1 (2024-02-14)
+
+- Adds in relative transmissibility attribute to people that can be
+  modified by vaccination or treatment
+- *Github info* PR [643](https://github.com/amath-idm/hpvsim/pull/658)
+
+## Version 2.0.0 (2023-11-29)
+
+- Simplifies natural history model by compressing CIN grades
+- Changes the way HPV progression is modeled so that there is a
+  probability of developing CIN based upon duration of precin and
+  probability of cancer based upon duration of cancer (based upon
+  Rodriguez et al.
+  <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3705579/>)
+- Adds support for pre-calibration explorations
+- Improvements to networks, including clustering functionality, support
+  for different distributions for male and female partners and for
+  differing concurrency rates, and changes to default partnership
+  durations
+- Exposes a parameter for specifying the sex ratio of a population
+- Fixes plotting issue with tutorial
+- Updates filtering for tests that are not genotype-specific
+- *Github info* PR [643](https://github.com/amath-idm/hpvsim/pull/643)
+
+## Version 1.2.7 (2023-09-22)
+
+- Updates `sim.summary` to have more useful information
+- *Github info* PR [618](https://github.com/amath-idm/hpvsim/pull/618)
+
+## Version 1.2.6 (2023-09-22)
+
+- Fixes plotting issue with MultiSims and Jupyter notebooks
+- Allows scenarios to be run fully in parallel
+- *Github info* PR [614](https://github.com/amath-idm/hpvsim/pull/614)
+
+## Version 1.2.5 (2023-09-21)
+
+- Fixes file path when run via Jupyter
+- *Github info* PR [610](https://github.com/amath-idm/hpvsim/pull/610)
+
+## Version 1.2.4 (2023-09-19)
+
+- Fixes Matplotlib regression in plotting
+- *Github info* PR [609](https://github.com/amath-idm/hpvsim/pull/609)
+
+## Version 1.2.3 (2023-08-30)
+
+- Updates data loading to be much more efficient
+- *Github info* PR [604](https://github.com/amath-idm/hpvsim/pull/604)
+
+## Version 1.2.2 (2023-08-11)
+
+- Improved tests and included `conda` environment specification
+- *Github info* PR [598](https://github.com/amath-idm/hpvsim/pull/598)
+
+## Version 1.2.1 (2023-07-09)
+
+- Updated data files being used
+- *Github info* PR [586](https://github.com/amath-idm/hpvsim/pull/586)
+
+## Version 1.2.0 (2023-05-31)
+
+- Changes to improve run speed, most notably changes to how migration is
+  applied
+- Additional tests to ensure consistency between calibration results,
+  age analyzer results, and sim results
+- Updates to natural history to prevent people progressing too quickly
+  to cancer
+- *Github info* PR [576](https://github.com/amath-idm/hpvsim/pull/576)
+
+## Version 1.1.5 (2023-03-23)
+
+- Adds cross-protection functionality to t-cell immunity and adds
+  <span class="title-ref">sev_imm</span> attribute to people
+- *Github info* PR [564](https://github.com/amath-idm/hpvsim/pull/564)
+
+## Version 1.1.4 (2023-03-15)
+
+- Fixes bug that caused location data to be loaded twice
+- *Github info* PR [546](https://github.com/amath-idm/hpvsim/pull/546)
+
+## Version 1.1.3 (2023-03-14)
+
+- Fixes bug that misses some ways you can specify sex for vaccination
+- *Github info* PR [555](https://github.com/amath-idm/hpvsim/pull/555)
+
+## Version 1.1.2 (2023-03-13)
+
+- Fixes bug that never computed cancer deaths by age
+- *Github info* PR [554](https://github.com/amath-idm/hpvsim/pull/554)
+
+## Version 1.1.1 (2023-03-01)
+
+- Sets time to and date of HIV death for those not on ART and who fail
+  on ART
+- Moves all HIV attributes, parameters, and results into hivsim class
+  instance
+- Merges HIV results with sim.results at conclusion of simulation
+- Adds HIV pars as an argument to calibration as well as HIV-specific
+  results to age-results analyzer
+- Allows for flexible severity growth functions
+- *Github info* PR [542](https://github.com/amath-idm/hpvsim/pull/542)
+
+## Version 1.1.0 (2023-02-16)
+
+- Moves all HIV functionality into hiv.py
+- Establishes new class HIVsim, which is defined by a set of parameters
+  and methods for updating a people object
+- Bug fix for setting people.sev wrong on day of infection
+- *Github info* PR [526](https://github.com/amath-idm/hpvsim/pull/526)
+
+## Version 1.0.1 (2023-02-09)
+
+- Fixes computation of dur_episomal by adjusting for dt
+- *GitHub info*: PR [527](https://github.com/amath-idm/hpvsim/pull/527)
+
+## Version 1.0.0 (2023-01-31)
+
+- Official release!
+- *GitHub info*: PR [521](https://github.com/amath-idm/hpvsim/pull/521)
+
+## Version 0.4.17 (2023-01-31)
+
+- Adds a tutorial on calibration
+- Small changes to parameter values
+- *GitHub info*: PR [520](https://github.com/amath-idm/hpvsim/pull/520)
+
+## Version 0.4.16 (2023-01-30)
+
+- Change to natural history, including computation of transformation
+  based upon time with dysplasia
+- Addition of cellular immunity to moderate progression in a secondary
+  infection
+- Default parameter changes and some small typo/bug fixes
+- *GitHub info*: PR [513](https://github.com/amath-idm/hpvsim/pull/513)
+
+## Version 0.4.15 (2023-01-13)
+
+- Fixed bug in intervention and analyzer initialization
+- *GitHub info*: PR [511](https://github.com/amath-idm/hpvsim/pull/511)
+
+## Version 0.4.14 (2023-01-11)
+
+- Add Sweep class
+- *GitHub info*: PR [431](https://github.com/amath-idm/hpvsim/pull/431)
+
+## Version 0.4.13 (2023-01-09)
+
+- Dysplasia percentages are now tracked throughout agent lifetimes, and
+  CIN grades are defined as properties based on these percentages
+- Removes all genotypes aside from HPV 16, 18 and a composite 'other
+  high risk' genotype from the defaults
+- *GitHub info*: PR [507](https://github.com/amath-idm/hpvsim/pull/507)
+
+## Version 0.4.12 (2023-01-02)
+
+- Adds documentation and examples for screening algorithms.
+- *GitHub info*: PR [505](https://github.com/amath-idm/hpvsim/pull/505)
+
+## Version 0.4.11 (2022-12-21)
+
+- Adds colposcopy and cytology testing options, along with default
+  values for screening sensitivity and specificity.
+- Adds a clearance probability for treatment to control the % of treated
+  women who also clear their infection
+- Removes use_multiscale parameter and sets ms_agent_ratio to 1 by
+  default
+- *GitHub info*: PR [497](https://github.com/amath-idm/hpvsim/pull/497)
+
+## Version 0.4.10 (2022-12-19)
+
+- Change the seed used for running simulations to avoid having random
+  processes in the model run sometimes being correlated with population
+  attributes
+- Deprecate `Sim.set_seed()` - use `hpu.set_seed()` instead
+- Added `hpvsim.rootdir` to provide a convenient absolute path to the
+- Added equality operator for <span class="title-ref">Result</span>
+  objects
+- Exporting simulation results to JSON now includes 2D results (e.g., by
+  genotype)
+- `age_pyramid` and `age_results` analyzer argument changed from
+  `datafile` to `data` since this input supports both passing in a
+  filename or a dataframe
+- *GitHub info*: PR [485](https://github.com/amath-idm/hpvsim/pull/485)
+
+## Version 0.4.9 (2022-12-16)
+
+- Added in high- and low-grade lesions to type distribution results
+- Changes default duration and rate of dysplasia for hr HPVs
+- *GitHub info*: PR [479](https://github.com/amath-idm/hpvsim/pull/482)
+
+## Version 0.4.8 (2022-12-14)
+
+- Small bug fix to re-enable plots of cytology outcomes by genotype
+- *GitHub info*: PR [484](https://github.com/amath-idm/hpvsim/pull/484)
+
+## Version 0.4.7 (2022-12-13)
+
+- Migration is now modeled by finding mismatches between the modeled
+  population size by age and data on population sizes by age
+  (previously, this adjustment was done for the overall population
+  rather than by age bucket).
+- *GitHub info*: PR [479](https://github.com/amath-idm/hpvsim/pull/479)
+
+## Version 0.4.6 (2022-12-12)
+
+- Changes to several default parameters: default genotypes are now 16,
+  18, and other high-risk; and default hpv control prob is now 0.
+- Results now capture infections by age and type distributions.
+- Adds age of cancer to analyzer
+- Changes to default plotting styles
+- Various bugfixes: prevents immunity values from exceeding 1, ensures
+  people with cancer aren't given second cancers
+- *GitHub info*: PR [458](https://github.com/amath-idm/hpvsim/pull/458)
+
+## Version 0.4.5 (2022-12-06)
+
+- Removes default screening products pending review
+- *GitHub info*: PR [464](https://github.com/amath-idm/hpvsim/pull/464)
+
+## Version 0.4.4 (2022-12-05)
+
+- Changes to progression to cancer -- no longer based on clinical
+  cutoffs, now stochastically applied by genotype to CIN3 agents
+- *GitHub info*: PR [430](https://github.com/amath-idm/hpvsim/pull/430)
+
+## Version 0.4.3 (2022-12-01)
+
+- Fixes bug with population growth function
+- *GitHub info*: PR [459](https://github.com/amath-idm/hpvsim/pull/459)
+
+## Version 0.4.2 (2022-11-21)
+
+- Changes to parameterization of immunity
+- *GitHub info*: PR [425](https://github.com/amath-idm/hpvsim/pull/425)
+
+## Version 0.4.1 (2022-11-21)
+
+- Fixes age of migration
+- Adds scale parameter for vital dynamics
+- *GitHub info*: PR [423](https://github.com/amath-idm/hpvsim/pull/423)
+
+## Version 0.4.0 (2022-11-16)
+
+- Adds merge method for scenarios and fixes printing bugs
+- *GitHub info*: PR [422](https://github.com/amath-idm/hpvsim/pull/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](https://github.com/amath-idm/hpvsim/pull/421)
+  and [420](https://github.com/amath-idm/hpvsim/pull/420)
+
+## Version 0.3.8 (2022-11-02)
+
+- Store treatment properties as part of sim.people
+- *GitHub info*: PR [413](https://github.com/amath-idm/hpvsim/pull/413)
+
+## Version 0.3.7 (2022-11-01)
+
+- Fix to ensure consistent results for the number of txvx doses
+- *GitHub info*: PR [411](https://github.com/amath-idm/hpvsim/pull/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](https://github.com/amath-idm/hpvsim/pull/396)
+
+## Version 0.3.5 (2022-10-31)
+
+- Store stocks related to interventions
+- *GitHub info*: PR [395](https://github.com/amath-idm/hpvsim/pull/395)
+
+## Version 0.3.4 (2022-10-31)
+
+- Bugfixes for therapeutic vaccination
+- *GitHub info*: PR [394](https://github.com/amath-idm/hpvsim/pull/394)
+
+## Version 0.3.3 (2022-10-30)
+
+- Changes to therapeautic vaccine efficacy assumptions
+- *GitHub info*: PR [393](https://github.com/amath-idm/hpvsim/pull/393)
+
+## Version 0.3.2 (2022-10-26)
+
+- Additional tutorials and minor release tidying
+- *GitHub info*: PR [380](https://github.com/amath-idm/hpvsim/pull/380)
+
+## Version 0.3.1 (2022-10-26)
+
+- Fixes bug with screening
+- Increases coverage of baseline test
+- *GitHub info*: PR [373](https://github.com/amath-idm/hpvsim/pull/373)
+
+## Version 0.3.0 (2022-10-26)
+
+- Implements multiscale modeling
+- Minor release tidying
+- *GitHub info*: PR [365](https://github.com/amath-idm/hpvsim/pull/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](https://github.com/amath-idm/hpvsim/pull/374)
+
+## Version 0.2.10 (2022-10-24)
+
+- Fixes bug with treatment
+- *GitHub info*: PR [354](https://github.com/amath-idm/hpvsim/pull/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](https://github.com/amath-idm/hpvsim/pull/345)
+
+## 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](https://github.com/amath-idm/hpvsim/pull/338)
+
+## Version 0.2.7 (2022-10-14)
+
+- Adds robust relative paths via `hpv.datadir`
+- *GitHub info*: PR [333](https://github.com/amath-idm/hpvsim/pull/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](https://github.com/amath-idm/hpvsim/pull/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](https://github.com/amath-idm/hpvsim/pull/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](https://github.com/amath-idm/hpvsim/pull/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](https://github.com/amath-idm/hpvsim/pull/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](https://github.com/amath-idm/hpvsim/pull/255)
+
+## Version 0.2.1 (2022-08-19)
+
+- Improves calibration to enable support for MySQL.
+- Fixes plotting bug.
+- *GitHub info*: PR [253](https://github.com/amath-idm/hpvsim/pull/253)
+
+## Version 0.2.0 (2022-08-19)
+
+- Fixed tests and data loading logic.
+- *GitHub info*: PR [251](https://github.com/amath-idm/hpvsim/pull/251)
+
+## Version 0.1.0 (2022-08-01)
+
+- Updated calibration.
+- *GitHub info*: PR [215](https://github.com/amath-idm/hpvsim/pull/215)
+
+## Version 0.0.3 (2022-07-18)
+
+- Updated data loading scripts.
+- *GitHub info*: PR [156](https://github.com/amath-idm/hpvsim/pull/156)
+
+## Version 0.0.2 (2022-06-15)
+
+- Made into a Python module.
+- *GitHub info*: PR [64](https://github.com/amath-idm/hpvsim/pull/64)
+
+## Version 0.0.1 (2022-04-04)
+
+- Initial version.

hpvsim-2.3.0/CODE_OF_CONDUCT.md

@@ -0,0 +1,82 @@
+# Code of conduct
+
+## Our pledge
+
+We believe that a diverse, equitable, and inclusive environment is
+essential for producing the best quality software. In the interest of
+fostering an open and welcoming environment, we as contributors and
+maintainers pledge to making participation in HPVsim development and the
+HPVsim community a harassment-free experience for everyone, regardless
+of age, body size, disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic
+status, nationality, personal appearance, race, religion, or sexual
+identity and orientation.
+
+## Our standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+- Using welcoming and inclusive language
+- Being respectful of differing viewpoints and experiences
+- Gracefully accepting constructive criticism
+- Focusing on what is best for the community
+- Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+- The use of sexualized language or imagery and unwelcome sexual
+  attention or advances
+- Trolling, insulting/derogatory comments, and personal or political
+  attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or
+  electronic address, without explicit permission
+- Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our responsibilities
+
+HPVsim maintainers are responsible for clarifying the standards of
+acceptable behavior and will take appropriate and fair corrective action
+in response to any instances of unacceptable behavior.
+
+HPVsim maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other
+contributions that are not aligned to this Code of Conduct, or to ban
+temporarily or permanently any contributor for other behaviors that they
+deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public
+spaces when an individual is representing HPVsim or its community.
+Examples of representing the HPVsim project or community include using
+an official project e-mail address, posting via an official social media
+account, or acting as an appointed representative at an online or
+offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may
+be reported by contacting the project team at
+<robyn.stuart@gatesfoundation.org>. All complaints will be reviewed and
+investigated and will result in a response that is deemed necessary and
+appropriate to the circumstances. The HPVsim team is obligated to
+maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted
+separately.
+
+HPVsim maintainers who do not follow or enforce the Code of Conduct in
+good faith may face temporary or permanent repercussions as determined
+by other members of HPVsim's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor
+Covenant](https://www.contributor-covenant.org), version 1.4, available
+at
+<https://www.contributor-covenant.org/version/1/4/code-of-conduct.html>.
+
+For answers to common questions about this code of conduct, see the
+[FAQ](https://www.contributor-covenant.org/faq).

{hpvsim-2.2.6 → hpvsim-2.3.0}/MANIFEST.in

@@ -1,6 +1,6 @@
 include LICENSE
 global-include requirements*.txt
-global-include *.rst
+global-include *.md
 recursive-include hpvsim *.py
 recursive-include hpvsim *.csv
 recursive-include hpvsim *.json