hpvsim 2.2.0__tar.gz → 2.2.4__tar.gz

hpvsim-2.2.4/.github/workflows/pypi_release.yaml

@@ -0,0 +1,37 @@
+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - 'v*'
+
+jobs:
+  build-and-publish:
+    name: Build and publish
+    runs-on: ubuntu-latest
+
+    permissions:
+      id-token: write
+      contents: read
+
+    environment:
+      name: pypi
+      url: https://pypi.org/project/hpvsim/
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      - name: Install build backend
+        run: python -m pip install build
+
+      - name: Build sdist and wheel
+        run: python -m build
+
+      - name: Publish
+        uses: pypa/gh-action-pypi-publish@release/v1

{hpvsim-2.2.0 → hpvsim-2.2.4}/CHANGELOG.rst

@@ -8,11 +8,36 @@ All notable changes to the codebase are documented in this file. Changes that ma
    :local:
    :depth: 1
 
+
+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 `653 <https://github.com/starsimhub/hpvsim_orig/pull/673>`__
+- *Github info* PR `673 <https://github.com/starsimhub/hpvsim_orig/pull/673>`__
 
 
 Version 2.1.0 (2025-03-25)

{hpvsim-2.2.0/hpvsim.egg-info → hpvsim-2.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: hpvsim
-Version: 2.2.0
+Version: 2.2.4
 Summary: HPVsim: Human Papillomavirus Simulator
 Author: Robyn Stuart, Jamie Cohen, Cliff Kerr, Romesh Abeysuriya, Mariah Boudreau, Daniel Klein, Hao Hu
 Maintainer-email: HPVsim Team <info@hpvsim.org>
@@ -31,6 +31,9 @@ Dynamic: license-file
 Human papillomavirus simulator (HPVsim)
 =======================================
 
+.. image:: https://badgen.net/pypi/v/hpvsim/?color=blue
+ :target: https://pypi.org/project/hpvsim
+
 .. image:: https://github.com/institutefordiseasemodeling/hpvsim/actions/workflows/tests.yaml/badge.svg
     :target: https://github.com/institutefordiseasemodeling/hpvsim/actions/workflows/tests.yaml
     :alt: pipeline status

{hpvsim-2.2.0 → hpvsim-2.2.4}/README.rst

@@ -1,6 +1,9 @@
 Human papillomavirus simulator (HPVsim)
 =======================================
 
+.. image:: https://badgen.net/pypi/v/hpvsim/?color=blue
+ :target: https://pypi.org/project/hpvsim
+
 .. image:: https://github.com/institutefordiseasemodeling/hpvsim/actions/workflows/tests.yaml/badge.svg
     :target: https://github.com/institutefordiseasemodeling/hpvsim/actions/workflows/tests.yaml
     :alt: pipeline status

{hpvsim-2.2.0 → hpvsim-2.2.4}/hpvsim/analysis.py

@@ -785,9 +785,9 @@ class age_results(Analyzer):
                 if rdict.result_type == 'flow':
                     if not rdict.by_genotype:  # Results across all genotypes
                         if rdict.by_hiv:
-                            if rdict.hiv_attr:
+                            if rdict.hiv_attr == 'with':
                                 inds = ((ppl[rdict.date_attr] == sim.t) * (ppl[rdict.attr]) * (ppl['hiv'])).nonzero()[-1]
-                            else:
+                            elif rdict.hiv_attr == 'no':
                                 inds = ((ppl[rdict.date_attr] == sim.t) * (ppl[rdict.attr]) * (~ppl['hiv'])).nonzero()[-1]
                         else:
                             inds = ((ppl[rdict.date_attr] == sim.t) * (ppl[rdict.attr])).nonzero()[-1]
@@ -1111,6 +1111,7 @@ class age_causal_infection(Analyzer):
         if self.start_year is None:
             self.start_year = sim['start']
         self.age_causal = []
+        self.age_cin = []
         self.age_cancer = []
         self.dwelltime = dict()
         for state in ['precin', 'cin', 'total']:
@@ -1127,6 +1128,7 @@ class age_causal_infection(Analyzer):
                 cin_time = (sim.t - date_cin) * sim['dt']
                 total_time = (sim.t - date_exposed) * sim['dt']
                 self.age_causal += (current_age - total_time).tolist()
+                self.age_cin += (current_age - cin_time).tolist()
                 self.age_cancer += current_age.tolist()
                 self.dwelltime['precin'] += hpv_time.tolist()
                 self.dwelltime['cin'] += cin_time.tolist()

{hpvsim-2.2.0 → hpvsim-2.2.4}/hpvsim/calibration.py

@@ -133,7 +133,7 @@ class Calibration(sc.prettyobj):
         self.sim['analyzers'] += [ar]
         if hiv_pars is not None:
             self.sim['model_hiv'] = True # if calibrating HIV parameters, make sure model is running HIV
-        self.sim.initialize()
+        self.sim.initialize(init_intvs=False)
         if self.sim['model_hiv']:
             self.sim.results = sc.mergedicts(self.sim.results, self.sim.hivsim.results)
         for rkey in sim_results.keys():
@@ -715,6 +715,7 @@ class Calibration(sc.prettyobj):
                     # Set title and labels
                     ax.set_xlabel('Age group')
                     ax.set_title(f'{self.result_args[resname].name}, {date}')
+                    sc.setylim(data=[ydata, modeldf['values']], ax=ax)
                     ax.legend()
                     ax.set_xticks(x, age_labels[resname], rotation=45)
                     plot_count += 1

{hpvsim-2.2.0 → hpvsim-2.2.4}/hpvsim/data/loaders.py

@@ -314,6 +314,8 @@ def get_birth_rates(location=None):
         raise ValueError(errormsg) from E
 
     raw_df = map_entries(birth_rate_data, location)
+    raw_df = raw_df.dropna()
     df = sc.dataframe(raw_df).reset_index().rename(columns={'Time':'year', 'CBR':'cbr'})
+
     return df
 

{hpvsim-2.2.0 → hpvsim-2.2.4}/hpvsim/hiv.py

@@ -45,15 +45,11 @@ class HIVsim(hpb.ParsObj):
             "rel_reactivation_prob": 3,  # Unused for now
             "model_hiv_death": True,  # whether or not to model HIV mortality. Typically only set to False for testing purposes
             "time_to_hiv_death_shape": 2,  # shape parameter for weibull distribution, based on https://royalsocietypublishing.org/action/downloadSupplement?doi=10.1098%2Frsif.2013.0613&file=rsif20130613supp1.pdf
-            "time_to_hiv_death_scale": lambda a: 21.182
-            - 0.2717
-            * a,  # scale parameter for weibull distribution, based on https://royalsocietypublishing.org/action/downloadSupplement?doi=10.1098%2Frsif.2013.0613&file=rsif20130613supp1.pdf
+            "time_to_hiv_death_scale_pars": dict(m=21.182, b=-0.2717),  # scale parameter for weibull distribution, based on https://royalsocietypublishing.org/action/downloadSupplement?doi=10.1098%2Frsif.2013.0613&file=rsif20130613supp1.pdf
             "hiv_death_adj": 1,
             "cd4_start": dict(dist="normal", par1=594, par2=20),
-            "cd4_trajectory": lambda f: (24.363 - 16.672 * f)
-            ** 2,  # based on https://docs.idmod.org/projects/emod-hiv/en/latest/hiv-model-healthcare-systems.html?highlight=art#art-s-impact-on-cd4-count
-            "cd4_reconstitution": lambda m: 15.584 * m
-            - 0.2113 * m**2,  # growth in CD4 count following ART initiation
+            "cd4_pars": dict(m=24.363, b=-16.672),  # based on https://docs.idmod.org/projects/emod-hiv/en/latest/hiv-model-healthcare-systems.html?highlight=art#art-s-impact-on-cd4-count
+            "cd4_reconstitution_pars": dict(b1=15.584, b2=-0.2113),  # growth in CD4 count following ART initiation
             "art_failure_prob": 0.0,  # Percentage of people on ART who will fail treatment
             "dt_art": 1.0,  # Timestep for art updates (in years)
         }
@@ -63,7 +59,9 @@ class HIVsim(hpb.ParsObj):
         self.init_results(sim)
 
         y = np.linspace(0, 1, 101)
-        cd4_decline = self["hiv_pars"]["cd4_trajectory"](y)
+        # Calculate the CD4 trajectory based on the parameters
+        m, b = self["hiv_pars"]["cd4_pars"]["m"], self["hiv_pars"]["cd4_pars"]["b"]
+        cd4_decline = m + b* y  # CD4 decline trajectory
         self.cd4_decline_diff = np.diff(cd4_decline)
         sim.pars["hiv_pars"]["mortality_rates"] = self.pars["mortality_rates"]
         return
@@ -235,7 +233,8 @@ class HIVsim(hpb.ParsObj):
         shape = self["hiv_pars"]["time_to_hiv_death_shape"]
         dt = people.pars["dt"]
         if self["hiv_pars"]["model_hiv_death"]:
-            scale = self["hiv_pars"]["time_to_hiv_death_scale"](people.age[inds])
+            m, b = self["hiv_pars"]["time_to_hiv_death_scale_pars"]["m"], self["hiv_pars"]["time_to_hiv_death_scale_pars"]["b"]
+            scale = m + b*people.age[inds]
             adjust = self["hiv_pars"]["hiv_death_adj"]
             scale = np.maximum(scale, 0)
             time_to_hiv_death = adjust * weibull_min.rvs(
@@ -300,7 +299,8 @@ class HIVsim(hpb.ParsObj):
             # Now take care of people successfully on ART (CD4 reconstitutes)
             mpy = 12
             months_on_ART = (people.t - people.date_art[art_success_inds]) * mpy
-            cd4_change = self["hiv_pars"]["cd4_reconstitution"](months_on_ART)
+            b1, b2 = self["hiv_pars"]["cd4_reconstitution_pars"]["b1"], self["hiv_pars"]["cd4_reconstitution_pars"]["b2"]
+            cd4_change = b1*months_on_ART + b2*months_on_ART**2
             cd4_change[cd4_change < 0] = 0
             people.cd4[art_success_inds] += cd4_change
 

{hpvsim-2.2.0 → hpvsim-2.2.4}/hpvsim/immunity.py

@@ -212,7 +212,7 @@ def check_immunity(people):
     Now suppose we have 3 people, whose immunity levels are
 
         people.nab_imm = np.array([[0.9, 0.0, 0.0],
-                               [0.0, 0.7, 0.0]])
+                                   [0.0, 0.7, 0.0]])
 
     This indicates that person 1 has a prior HPV16 infection, person 2 has a prior HPV18
     infection, and person 3 has no history of infection.

{hpvsim-2.2.0 → hpvsim-2.2.4}/hpvsim/interventions.py

@@ -651,7 +651,6 @@ class BaseVaccination(Intervention):
         accept_inds = np.array([])
 
         if do_apply:
-
             # Select people for screening and then record the number of screens
             eligible_inds   = self.check_eligibility(sim) # Check eligibility
             if len(self.timepoints)==0: # No timepoints provided
@@ -717,10 +716,10 @@ class campaign_vx(BaseVaccination, CampaignDelivery):
     '''
 
     def __init__(self, product=None, prob=None, age_range=None, sex=0, eligibility=None,
-                 years=None, interpolate=True, **kwargs):
+                 years=None, interpolate=True, annual_prob=None, **kwargs):
 
         BaseVaccination.__init__(self, product=product, age_range=age_range, sex=sex, eligibility=eligibility, **kwargs)
-        CampaignDelivery.__init__(self, prob=prob, years=years, interpolate=interpolate)
+        CampaignDelivery.__init__(self, prob=prob, annual_prob=annual_prob, years=years, interpolate=interpolate)
 
     def initialize(self, sim):
         CampaignDelivery.initialize(self, sim) # Initialize this first, as it ensures that prob is interpolated properly
@@ -873,9 +872,9 @@ class routine_screening(BaseScreening, RoutineDelivery):
         screen3 = hpv.routine_screening(product='hpv', prob=np.linspace(0.005,0.025,5), years=np.arange(2020,2025)) # Scale up screening over 5 years starting in 2020
     '''
     def __init__(self, product=None, prob=None, eligibility=None, age_range=None,
-                         years=None, start_year=None, end_year=None, **kwargs):
+                         years=None, start_year=None, end_year=None, annual_prob=None, **kwargs):
         BaseScreening.__init__(self, product=product, age_range=age_range, eligibility=eligibility, **kwargs)
-        RoutineDelivery.__init__(self, prob=prob, start_year=start_year, end_year=end_year, years=years)
+        RoutineDelivery.__init__(self, prob=prob, start_year=start_year, end_year=end_year, annual_prob=annual_prob, years=years)
 
     def initialize(self, sim):
         RoutineDelivery.initialize(self, sim) # Initialize this first, as it ensures that prob is interpolated properly
@@ -892,9 +891,9 @@ class campaign_screening(BaseScreening, CampaignDelivery):
         screen2 = hpv.campaign_screening(product='hpv', prob=0.02, years=[2025,2030]) # Screen 20% of the eligible population in 2025 and again in 2030
     '''
     def __init__(self, product=None, age_range=None, eligibility=None,
-                 prob=None, years=None, interpolate=None, **kwargs):
+                 prob=None, years=None, interpolate=None, annual_prob=None, **kwargs):
         BaseScreening.__init__(self, product=product, age_range=age_range, eligibility=eligibility, **kwargs)
-        CampaignDelivery.__init__(self, prob=prob, years=years, interpolate=interpolate)
+        CampaignDelivery.__init__(self, prob=prob, years=years, interpolate=interpolate, annual_prob=annual_prob)
 
     def initialize(self, sim):
         CampaignDelivery.initialize(self, sim) # Initialize this first, as it ensures that prob is interpolated properly
@@ -936,9 +935,9 @@ class campaign_triage(BaseTriage, CampaignDelivery):
         screened_pos = lambda sim: sim.get_intervention('screening').outcomes['positive']
         triage1 = hpv.campaign_triage(product='pos_screen_assessment', eligibility=screen_pos, prob=0.9, years=2030)
     '''
-    def __init__(self, product=None, age_range=None, sex=None, eligibility=None,
+    def __init__(self, product=None, age_range=None, eligibility=None,
                  prob=None, years=None, interpolate=None, annual_prob=None, **kwargs):
-        BaseTriage.__init__(self, product=product, age_range=age_range, sex=sex, eligibility=eligibility, **kwargs)
+        BaseTriage.__init__(self, product=product, age_range=age_range, eligibility=eligibility, **kwargs)
         CampaignDelivery.__init__(self, prob=prob, years=years, interpolate=interpolate, annual_prob=annual_prob)
 
     def initialize(self, sim):
@@ -1386,13 +1385,12 @@ class tx(Product):
                         people[f'date_{state}'][g, eff_treat_inds] = np.nan
                         people[f'date_cancerous'][g, eff_treat_inds] = np.nan
                         people['date_clearance'][g, eff_treat_inds] = people.t + 1
-                        # Determine whether women also clear infection
+                        # # Determine whether women also clear infection
                         # clearance_probs = np.full(len(eff_treat_inds), self.clearance, dtype=hpd.default_float)
                         # to_clear = hpu.binomial_arr(clearance_probs)  # Determine who will have effective treatment
                         # clear_inds = eff_treat_inds[to_clear]
                         # if len(clear_inds):
                         #     # If so, set date of clearance of infection on next timestep
-                        #
                         #     people.dur_infection[g, clear_inds] = (people.t - people.date_infectious[g, clear_inds]) * people.pars['dt']
 
         tx_successful = np.array(list(set(tx_successful)))

{hpvsim-2.2.0 → hpvsim-2.2.4}/hpvsim/people.py

@@ -761,6 +761,7 @@ class People(hpb.BasePeople):
         if new_births is None:
             years = self.pars['birth_rates']['year']
             rates = self.pars['birth_rates']['cbr']
+
             this_birth_rate = (
                 self.pars['rel_birth']
                 * np.interp(year, years, rates)

{hpvsim-2.2.0 → hpvsim-2.2.4}/hpvsim/sim.py

@@ -74,7 +74,7 @@ class Sim(hpb.BaseSim):
         return
 
 
-    def initialize(self, reset=True, init_states=True, init_analyzers=True, **kwargs):
+    def initialize(self, reset=True, init_states=True, init_intvs=True, init_analyzers=True, **kwargs):
         '''
         Perform all initializations on the sim.
         '''
@@ -85,7 +85,7 @@ class Sim(hpb.BaseSim):
         hpu.set_seed(self['rand_seed']) # Reset the random seed before the population is created
         self.init_genotypes() # Initialize the genotypes
         self.init_results() # After initializing the genotypes and people, create the results structure
-        self.init_interventions()  # Initialize the interventions BEFORE the people, because then vaccination interventions get counted in immunity structures
+        if init_intvs: self.init_interventions()  # Initialize the interventions BEFORE the people, because then vaccination interventions get counted in immunity structures
         self.init_immunity() # Includes immunity matrices and cumulative dysplasia arrays
         self.init_people(reset=reset, init_states=init_states, **kwargs) # Create all the people (the heaviest step)
         if init_analyzers: self.init_analyzers()  # ...and the analyzers...

{hpvsim-2.2.0 → hpvsim-2.2.4}/hpvsim/version.py

@@ -4,6 +4,6 @@ Version and license information.
 
 __all__ = ['__version__', '__versiondate__', '__license__']
 
-__version__ = '2.2.0'
-__versiondate__ = '2025-05-23'
+__version__ = '2.2.4'
+__versiondate__ = '2025-08-20'
 __license__ = f'HPVsim {__version__} ({__versiondate__}) — © 2023-2025 by IDM'

{hpvsim-2.2.0 → hpvsim-2.2.4/hpvsim.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: hpvsim
-Version: 2.2.0
+Version: 2.2.4
 Summary: HPVsim: Human Papillomavirus Simulator
 Author: Robyn Stuart, Jamie Cohen, Cliff Kerr, Romesh Abeysuriya, Mariah Boudreau, Daniel Klein, Hao Hu
 Maintainer-email: HPVsim Team <info@hpvsim.org>
@@ -31,6 +31,9 @@ Dynamic: license-file
 Human papillomavirus simulator (HPVsim)
 =======================================
 
+.. image:: https://badgen.net/pypi/v/hpvsim/?color=blue
+ :target: https://pypi.org/project/hpvsim
+
 .. image:: https://github.com/institutefordiseasemodeling/hpvsim/actions/workflows/tests.yaml/badge.svg
     :target: https://github.com/institutefordiseasemodeling/hpvsim/actions/workflows/tests.yaml
     :alt: pipeline status

{hpvsim-2.2.0 → hpvsim-2.2.4}/hpvsim.egg-info/SOURCES.txt

@@ -6,6 +6,7 @@ LICENSE
 MANIFEST.in
 README.rst
 pyproject.toml
+.github/workflows/pypi_release.yaml
 .github/workflows/tests.yaml
 docs/Makefile
 docs/README.md

hpvsim-2.2.4/tests/baseline.json

@@ -0,0 +1,60 @@
+{
+  "summary": {
+    "infections": 25928375.0,
+    "cins": 991155.375,
+    "cancers": 37402.08984375,
+    "cancer_deaths": 21194.517578125,
+    "reinfections": 19583733.0,
+    "reactivations": 0.0,
+    "n_susceptible": 586726464.0,
+    "n_infectious": 33513516.0,
+    "n_inactive": 250594.0,
+    "n_normal": 307198304.0,
+    "n_cin": 2878714.0,
+    "n_cancerous": 250594.0,
+    "n_infected": 33764108.0,
+    "n_abnormal": 3129308.0,
+    "n_latent": 0.0,
+    "n_precin": 12741644.0,
+    "n_screened": 2716638.25,
+    "n_cin_treated": 0.0,
+    "n_cancer_treated": 0.0,
+    "n_vaccinated": 1174425.5,
+    "n_tx_vaccinated": 11397662.0,
+    "hpv_incidence": 0.022095794710906374,
+    "cin_incidence": 0.006756010901715178,
+    "cancer_incidence": 25.045710785848303,
+    "births": 7966644.8931,
+    "other_deaths": 2701677.5,
+    "migration": -162075.7177,
+    "asr_cancer_incidence": 30.200933504294884,
+    "asr_cancer_mortality": 20.74842122892415,
+    "new_vaccinated": 87271.54296875,
+    "cum_vaccinated": 1246736.328125,
+    "new_doses": 87271.54296875,
+    "cum_doses": 1246736.328125,
+    "new_txvx_doses": 11784151.25,
+    "new_tx_vaccinated": 11408883.0,
+    "cum_txvx_doses": 11784151.25,
+    "cum_tx_vaccinated": 11408883.0,
+    "new_screens": 2777728.6875,
+    "new_screened": 2726612.4375,
+    "new_cin_treatments": 0.0,
+    "new_cin_treated": 0.0,
+    "new_cancer_treatments": 0.0,
+    "new_cancer_treated": 0.0,
+    "cum_screens": 2777728.6875,
+    "cum_screened": 2726612.4375,
+    "cum_cin_treatments": 0.0,
+    "cum_cin_treated": 0.0,
+    "cum_cancer_treatments": 0.0,
+    "cum_cancer_treated": 0.0,
+    "cancer_mortality": 14.168793323015917,
+    "n_alive": 307198304.0,
+    "cdr": 0.00879457166534357,
+    "cbr": 0.025933232017778328,
+    "hpv_prevalence": 0.109094078852727,
+    "precin_prevalence": 0.04258972155558187,
+    "cin_prevalence": 0.01924455395208896
+  }
+}

{hpvsim-2.2.0 → hpvsim-2.2.4}/tests/benchmark.json

@@ -1,7 +1,7 @@
 {
   "time": {
-    "initialize": 0.048,
-    "run": 2.113
+    "initialize": 0.015,
+    "run": 1.809
   },
   "parameters": {
     "n_agents": 10000,
@@ -10,5 +10,5 @@
     "n_interventions": 7,
     "n_analyzers": 0
   },
-  "cpu_performance": 0.1865387682627365
+  "cpu_performance": 0.3104645325856668
 }

{hpvsim-2.2.0 → hpvsim-2.2.4}/tests/test_sim.py

@@ -401,7 +401,6 @@ def test_resuming():
     return s1
 
 
-
 #%% Run as a script
 if __name__ == '__main__':
 

hpvsim-2.2.0/tests/baseline.json

@@ -1,60 +0,0 @@
-{
-  "summary": {
-    "infections": 26122864.5,
-    "cins": 978687.96875,
-    "cancers": 37402.08984375,
-    "cancer_deaths": 21194.517578125,
-    "reinfections": 19906639.0,
-    "reactivations": 0.0,
-    "n_susceptible": 586950912.0,
-    "n_infectious": 33458658.0,
-    "n_inactive": 250594.0,
-    "n_normal": 307255648.0,
-    "n_cin": 2840065.5,
-    "n_cancerous": 250594.0,
-    "n_infected": 33709256.0,
-    "n_abnormal": 3090659.0,
-    "n_latent": 0.0,
-    "n_precin": 12789020.0,
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