diff --git a/CHANGELOG.rst b/CHANGELOG.rst index db41c8b0..a742e79c 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -8,6 +8,13 @@ All notable changes to the codebase are documented in this file. Changes that ma :local: :depth: 1 + +Version 0.1.5 (2024-01-23) +-------------------------- +- Renamed ``stisim`` to ``starsim``. +- *GitHub info*: PR `200 `_ + + Version 0.1.4 (2024-01-23) -------------------------- - Adds a syphilis module diff --git a/README.rst b/README.rst index bf4bb399..267e07da 100644 --- a/README.rst +++ b/README.rst @@ -1,7 +1,7 @@ -STIsim +Starsim ====== -STIsim is an agent-based model that captures co-transmission of STIs including HIV, HPV, chlamydia, gonorrhea, and syphilis. +Starsim is a agent-based model of disease transmission. It can be used for simulating STIs (including co-transmission of HIV, HPV, chlamydia, gonorrhea, and syphilis), respiratory infections (including tuberculosis), and other diseases (such as Ebola). **WARNING! This library is in the early stages of development. It is being shared solely for transparency and to facilitate collaborative development. It is not ready to be used and any results produced using it will be invalid.** @@ -9,7 +9,7 @@ STIsim is an agent-based model that captures co-transmission of STIs including H Installation ------------ -To install, clone this repository, then run ``pip install -e .`` (don't forget the dot!) in this folder to install ``starsim`` and its dependencies. This will make ``stisim `` available on the Python path. +To install, clone this repository, then run ``pip install -e .`` (don't forget the dot!) in this folder to install ``starsim`` and its dependencies. This will make ``starsim `` available on the Python path. Usage and documentation diff --git a/setup.py b/setup.py index 3fcde7f2..204197a7 100644 --- a/setup.py +++ b/setup.py @@ -4,7 +4,7 @@ # Get version cwd = os.path.abspath(os.path.dirname(__file__)) -versionpath = os.path.join(cwd, 'stisim', 'version.py') +versionpath = os.path.join(cwd, 'starsim', 'version.py') version = runpy.run_path(versionpath)['__version__'] # Get the documentation @@ -25,13 +25,13 @@ ] setup( - name="stisim", + name="starsim", version=version, - author="Romesh Abeysuriya, Robyn Stuart, Jamie Cohen, Cliff Kerr, Daniel Klein", - description="Sexually Transmitted Infections Simulator (STIsim)", + author="Robyn Stuart, Romesh Abeysuriya, Jamie Cohen, Cliff Kerr, Daniel Klein", + description="Starsim", long_description=long_description, long_description_content_type="text/x-rst", - keywords=["agent-based model", "simulation"], + keywords=["agent-based model", "simulation", "disease", "epidemiology"], platforms=["OS Independent"], classifiers=CLASSIFIERS, packages=find_packages(), diff --git a/stisim/__init__.py b/starsim/__init__.py similarity index 100% rename from stisim/__init__.py rename to starsim/__init__.py diff --git a/stisim/analyzers.py b/starsim/analyzers.py similarity index 86% rename from stisim/analyzers.py rename to starsim/analyzers.py index c24a57d3..16a7f468 100644 --- a/stisim/analyzers.py +++ b/starsim/analyzers.py @@ -2,7 +2,7 @@ Define analyzers """ -import stisim as ss +import starsim as ss __all__ = ['Analyzer'] diff --git a/stisim/connectors.py b/starsim/connectors.py similarity index 98% rename from stisim/connectors.py rename to starsim/connectors.py index daad46cd..4cdac665 100644 --- a/stisim/connectors.py +++ b/starsim/connectors.py @@ -2,7 +2,7 @@ Define connections between disease modules ''' -import stisim as ss +import starsim as ss class Connector(ss.Module): diff --git a/stisim/demographics.py b/starsim/demographics.py similarity index 99% rename from stisim/demographics.py rename to starsim/demographics.py index ce34ba53..360ca14f 100644 --- a/stisim/demographics.py +++ b/starsim/demographics.py @@ -3,7 +3,7 @@ """ import numpy as np -import stisim as ss +import starsim as ss import sciris as sc import pandas as pd import scipy.stats as sps diff --git a/stisim/diseases/__init__.py b/starsim/diseases/__init__.py similarity index 100% rename from stisim/diseases/__init__.py rename to starsim/diseases/__init__.py diff --git a/stisim/diseases/disease.py b/starsim/diseases/disease.py similarity index 97% rename from stisim/diseases/disease.py rename to starsim/diseases/disease.py index 3d244a76..2ca20d9c 100644 --- a/stisim/diseases/disease.py +++ b/starsim/diseases/disease.py @@ -4,7 +4,7 @@ import numpy as np import sciris as sc -import stisim as ss +import starsim as ss import scipy.stats as sps import networkx as nx from operator import itemgetter diff --git a/stisim/diseases/examples.py b/starsim/diseases/examples.py similarity index 97% rename from stisim/diseases/examples.py rename to starsim/diseases/examples.py index 1ea1ac0d..39b2f996 100644 --- a/stisim/diseases/examples.py +++ b/starsim/diseases/examples.py @@ -3,7 +3,7 @@ """ import numpy as np -import stisim as ss +import starsim as ss import sciris as sc from .disease import Disease import scipy.stats as sps diff --git a/stisim/diseases/gonorrhea.py b/starsim/diseases/gonorrhea.py similarity index 99% rename from stisim/diseases/gonorrhea.py rename to starsim/diseases/gonorrhea.py index b2953450..fa9028ae 100644 --- a/stisim/diseases/gonorrhea.py +++ b/starsim/diseases/gonorrhea.py @@ -3,7 +3,7 @@ """ import numpy as np -import stisim as ss +import starsim as ss from .disease import STI import scipy.stats as sps diff --git a/stisim/diseases/hiv.py b/starsim/diseases/hiv.py similarity index 99% rename from stisim/diseases/hiv.py rename to starsim/diseases/hiv.py index 94cd2e0a..61e74d8c 100644 --- a/stisim/diseases/hiv.py +++ b/starsim/diseases/hiv.py @@ -4,7 +4,7 @@ import numpy as np import sciris as sc -import stisim as ss +import starsim as ss from .disease import STI import scipy.stats as sps diff --git a/stisim/diseases/syphilis.py b/starsim/diseases/syphilis.py similarity index 99% rename from stisim/diseases/syphilis.py rename to starsim/diseases/syphilis.py index e4158eeb..d2ae48e4 100644 --- a/stisim/diseases/syphilis.py +++ b/starsim/diseases/syphilis.py @@ -8,7 +8,7 @@ from sciris import randround as rr import scipy.stats as sps -import stisim as ss +import starsim as ss from .disease import STI __all__ = ['Syphilis'] diff --git a/stisim/distributions.py b/starsim/distributions.py similarity index 97% rename from stisim/distributions.py rename to starsim/distributions.py index 80f2bd05..d24f5ac9 100644 --- a/stisim/distributions.py +++ b/starsim/distributions.py @@ -5,9 +5,9 @@ """ import numpy as np -from stisim.utils import INT_NAN -from stisim.random import SingleRNG, MultiRNG -from stisim import options, int_ +from starsim.utils import INT_NAN +from starsim.random import SingleRNG, MultiRNG +from starsim import options, int_ from copy import deepcopy from scipy.stats._discrete_distns import bernoulli_gen from scipy.stats import rv_histogram diff --git a/stisim/interventions.py b/starsim/interventions.py similarity index 91% rename from stisim/interventions.py rename to starsim/interventions.py index e3df761f..779f10f0 100644 --- a/stisim/interventions.py +++ b/starsim/interventions.py @@ -2,7 +2,7 @@ Define interventions """ -import stisim as ss +import starsim as ss import sciris as sc import numpy as np import pandas as pd diff --git a/stisim/modules.py b/starsim/modules.py similarity index 99% rename from stisim/modules.py rename to starsim/modules.py index 5fa4d60d..ff349663 100644 --- a/stisim/modules.py +++ b/starsim/modules.py @@ -3,7 +3,7 @@ ''' import sciris as sc -import stisim as ss +import starsim as ss from scipy.stats._distn_infrastructure import rv_frozen __all__ = ['Module'] diff --git a/stisim/networks/__init__.py b/starsim/networks/__init__.py similarity index 100% rename from stisim/networks/__init__.py rename to starsim/networks/__init__.py diff --git a/stisim/networks/networks.py b/starsim/networks/networks.py similarity index 99% rename from stisim/networks/networks.py rename to starsim/networks/networks.py index aba1d72e..d14e9f28 100644 --- a/stisim/networks/networks.py +++ b/starsim/networks/networks.py @@ -5,7 +5,7 @@ # %% Imports import numpy as np import sciris as sc -import stisim as ss +import starsim as ss import scipy.optimize as spo import scipy.stats as sps import scipy.spatial as spsp @@ -889,18 +889,18 @@ def add_pairs(self, mother_inds, unborn_inds, dur): class static(Network): """ A network class of static partnerships converted from a networkx graph. There's no formation of new partnerships - and initialized partnerships only end when one of the partners dies. The networkx graph can be created outside STIsim - if population size is known. Or the graph can be created by passing a networkx generator function to STIsim. + and initialized partnerships only end when one of the partners dies. The networkx graph can be created outside Starsim + if population size is known. Or the graph can be created by passing a networkx generator function to Starsim. **Examples**:: - # Generate a networkx graph and pass to STIsim + # Generate a networkx graph and pass to Starsim import networkx as nx - import stisim as ss + import starsim as ss g = nx.scale_free_graph(n=10000) ss.static(graph=g) - # Pass a networkx graph generator to STIsim + # Pass a networkx graph generator to Starsim ss.static(graph=nx.erdos_renyi_graph, p=0.0001) """ diff --git a/stisim/networks/randnet.py b/starsim/networks/randnet.py similarity index 96% rename from stisim/networks/randnet.py rename to starsim/networks/randnet.py index 67cb07ed..e1bb0ba5 100644 --- a/stisim/networks/randnet.py +++ b/starsim/networks/randnet.py @@ -1,6 +1,6 @@ """Random networks""" -import stisim as ss +import starsim as ss import numpy as np import numba as nb from .networks import Network diff --git a/stisim/parameters.py b/starsim/parameters.py similarity index 99% rename from stisim/parameters.py rename to starsim/parameters.py index 218e2046..e26ef1d1 100644 --- a/stisim/parameters.py +++ b/starsim/parameters.py @@ -3,7 +3,7 @@ """ import sciris as sc -import stisim as ss +import starsim as ss __all__ = ['Parameters', 'make_pars'] diff --git a/stisim/people.py b/starsim/people.py similarity index 99% rename from stisim/people.py rename to starsim/people.py index 9da92e24..9bf3b54a 100644 --- a/stisim/people.py +++ b/starsim/people.py @@ -6,7 +6,7 @@ import numpy as np import pandas as pd import sciris as sc -import stisim as ss +import starsim as ss import scipy.stats as sps __all__ = ['BasePeople', 'People'] diff --git a/stisim/random.py b/starsim/random.py similarity index 99% rename from stisim/random.py rename to starsim/random.py index 930395d8..d894b7a8 100644 --- a/stisim/random.py +++ b/starsim/random.py @@ -1,6 +1,6 @@ import hashlib import numpy as np -import stisim as ss +import starsim as ss __all__ = ['RNGContainer', 'MultiRNG', 'SingleRNG', 'RNG'] @@ -106,7 +106,7 @@ class MultiRNG(np.random.Generator): rng and ultimately ask for randomly distributed random numbers for agents with UIDs 1 and 4: - >>> import stisim as ss + >>> import starsim as ss >>> import numpy as np >>> rng = ss.MultiRNG('Test') # The hashed name determines the seed offset. >>> rng.initialize(container=None, slots=5) # In practice, slots will be sim.people.slots. When scalar (for testing), an np.arange will be used. diff --git a/stisim/regression/pars_v0.1.0.json b/starsim/regression/pars_v0.1.0.json similarity index 100% rename from stisim/regression/pars_v0.1.0.json rename to starsim/regression/pars_v0.1.0.json diff --git a/stisim/results.py b/starsim/results.py similarity index 100% rename from stisim/results.py rename to starsim/results.py diff --git a/stisim/settings.py b/starsim/settings.py similarity index 93% rename from stisim/settings.py rename to starsim/settings.py index dd60282f..3feebd15 100644 --- a/stisim/settings.py +++ b/starsim/settings.py @@ -1,5 +1,5 @@ """ -Define options for STIsim. +Define options for Starsim. All options should be set using set() or directly, e.g.:: ss.options(verbose=False) @@ -16,7 +16,7 @@ # Not public to avoid confusion with ss.options class Options(sc.objdict): """ - Set options for STIsim. + Set options for Starsim. Use ``ss.options.set('defaults')`` to reset all values to default, or ``ss.options.set(dpi='default')`` to reset one parameter to default. See ``ss.options.help(detailed=True)`` for @@ -48,7 +48,7 @@ def __init__(self): @staticmethod def get_orig_options(): """ - Set the default options for STIsim -- not to be called by the user, use + Set the default options for Starsim -- not to be called by the user, use ``ss.options.set('defaults')`` instead. """ @@ -63,16 +63,16 @@ def get_orig_options(): options.multirng = False optdesc.verbose = 'Set default level of verbosity (i.e. logging detail): e.g., 0.1 is an update every 10 simulated timesteps.' - options.verbose = float(os.getenv('STISIM_VERBOSE', 0.1)) + options.verbose = float(os.getenv('STARSIM_VERBOSE', 0.1)) optdesc.warnings = 'How warnings are handled: options are "warn" (default), "print", and "error"' - options.warnings = str(os.getenv('STISIM_WARNINGS', 'warn')) + options.warnings = str(os.getenv('STARSIM_WARNINGS', 'warn')) optdesc.sep = 'Set thousands seperator for text output' - options.sep = str(os.getenv('STISIM_SEP', ',')) + options.sep = str(os.getenv('STARSIM_SEP', ',')) optdesc.precision = 'Set arithmetic precision -- 32-bit by default for efficiency' - options.precision = int(os.getenv('STISIM_PRECISION', 32)) + options.precision = int(os.getenv('STARSIM_PRECISION', 32)) return optdesc, options @@ -84,7 +84,7 @@ def __call__(self, *args, **kwargs): def __repr__(self): """ Brief representation """ output = sc.objectid(self) - output += 'STIsim options (see also ss.options.disp()):\n' + output += 'Starsim options (see also ss.options.disp()):\n' output += sc.pp(self.to_dict(), output=True) return output @@ -108,7 +108,7 @@ def __exit__(self, *args, **kwargs): def disp(self): """ Detailed representation """ - output = 'STIsim options (see also ss.options.help()):\n' + output = 'Starsim options (see also ss.options.help()):\n' keylen = 10 # Maximum key length -- "interactive" for k, v in self.items(): keystr = sc.colorize(f' {k:>{keylen}s}: ', fg='cyan', output=True) diff --git a/stisim/sim.py b/starsim/sim.py similarity index 99% rename from stisim/sim.py rename to starsim/sim.py index c921e606..ef6b08e6 100644 --- a/stisim/sim.py +++ b/starsim/sim.py @@ -5,7 +5,7 @@ # Imports import numpy as np import sciris as sc -import stisim as ss +import starsim as ss import itertools import numba as nb @@ -134,7 +134,7 @@ def validate_pars(self): # Handle n_agents if self.people is not None: self.pars['n_agents'] = len(self.people) - #elif self.popdict is not None: # STIsim does not currenlty support self.popdict + #elif self.popdict is not None: # Starsim does not currenlty support self.popdict #self.pars['n_agents'] = len(self.popdict) elif self.pars['n_agents'] is not None: self.pars['n_agents'] = int(self.pars['n_agents']) diff --git a/stisim/states.py b/starsim/states.py similarity index 97% rename from stisim/states.py rename to starsim/states.py index 75100089..fce06231 100644 --- a/stisim/states.py +++ b/starsim/states.py @@ -2,9 +2,9 @@ import numpy as np import sciris as sc import numba as nb -from stisim.utils import INT_NAN -from stisim.distributions import ScipyDistribution -from stisim.utils import warn +from starsim.utils import INT_NAN +from starsim.distributions import ScipyDistribution +from starsim.utils import warn from numpy.lib.mixins import NDArrayOperatorsMixin # Inherit from this to automatically gain operators like +, -, ==, <, etc. from scipy.stats._distn_infrastructure import rv_frozen diff --git a/stisim/utils.py b/starsim/utils.py similarity index 99% rename from stisim/utils.py rename to starsim/utils.py index d63b04b5..7c8a8776 100644 --- a/stisim/utils.py +++ b/starsim/utils.py @@ -7,7 +7,7 @@ import warnings import numpy as np import sciris as sc -import stisim as ss +import starsim as ss import numba as nb import scipy.stats as sps import pandas as pd diff --git a/stisim/version.py b/starsim/version.py similarity index 90% rename from stisim/version.py rename to starsim/version.py index fd039558..265871a3 100644 --- a/stisim/version.py +++ b/starsim/version.py @@ -4,6 +4,6 @@ __all__ = ['__version__', '__versiondate__', '__license__'] -__version__ = '0.1.4' +__version__ = '0.1.5' __versiondate__ = '2024-01-23' __license__ = f'STIsim {__version__} ({__versiondate__}) — © 2024 by IDM' diff --git a/tests/.coveragerc b/tests/.coveragerc index a2a446ca..05a86f00 100644 --- a/tests/.coveragerc +++ b/tests/.coveragerc @@ -1,7 +1,7 @@ # .coveragerc to control coverage.py [run] branch = True -source = stisim +source = starsim [report] # Regexes for lines to exclude from consideration diff --git a/tests/check_coverage b/tests/check_coverage index 4d4b4db7..a777e72c 100755 --- a/tests/check_coverage +++ b/tests/check_coverage @@ -4,7 +4,7 @@ export SCIRIS_BACKEND='agg' # Don't open up figures echo 'Running tests...' -pytest -v test_*.py -n auto --cov-config=.coveragerc --cov=../stisim --durations=0 +pytest -v test_*.py -n auto --cov-config=.coveragerc --cov=../starsim --durations=0 echo 'Creating HTML report...' coverage html diff --git a/tests/conftest.py b/tests/conftest.py index 3af303b5..19ee91d8 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,6 +1,6 @@ # Fixtures defined in this file will be used by all tests -import stisim as ss +import starsim as ss import pytest # Run all tests with both single and multi RNG streams diff --git a/tests/devtests/devtest_art_impact_viz.py b/tests/devtests/devtest_art_impact_viz.py index 84a16b2f..7691a928 100644 --- a/tests/devtests/devtest_art_impact_viz.py +++ b/tests/devtests/devtest_art_impact_viz.py @@ -3,7 +3,7 @@ """ # %% Imports and settings -import stisim as ss +import starsim as ss import matplotlib.pyplot as plt import pandas as pd import numpy as np diff --git a/tests/devtests/devtest_births.py b/tests/devtests/devtest_births.py index ae05b31d..af9987a3 100644 --- a/tests/devtests/devtest_births.py +++ b/tests/devtests/devtest_births.py @@ -3,7 +3,7 @@ """ # %% Imports and settings -import stisim as ss +import starsim as ss import matplotlib.pyplot as plt import pandas as pd diff --git a/tests/devtests/devtest_connectors.py b/tests/devtests/devtest_connectors.py index f557542f..e30d7189 100644 --- a/tests/devtests/devtest_connectors.py +++ b/tests/devtests/devtest_connectors.py @@ -3,7 +3,7 @@ """ # %% Imports and settings -import stisim as ss +import starsim as ss import matplotlib.pyplot as plt ng = ss.Gonorrhea() diff --git a/tests/devtests/devtest_dists.py b/tests/devtests/devtest_dists.py index 600e160a..542da457 100644 --- a/tests/devtests/devtest_dists.py +++ b/tests/devtests/devtest_dists.py @@ -3,7 +3,7 @@ """ # %% Imports and settings -import stisim as ss +import starsim as ss import matplotlib.pyplot as plt import numpy as np diff --git a/tests/devtests/devtest_networks.py b/tests/devtests/devtest_networks.py index 536623fb..769be881 100644 --- a/tests/devtests/devtest_networks.py +++ b/tests/devtests/devtest_networks.py @@ -3,7 +3,7 @@ """ # %% Imports and settings -import stisim as ss +import starsim as ss import matplotlib.pyplot as plt diff --git a/tests/devtests/devtest_orientation.py b/tests/devtests/devtest_orientation.py index 80fd9782..44176b70 100644 --- a/tests/devtests/devtest_orientation.py +++ b/tests/devtests/devtest_orientation.py @@ -2,7 +2,7 @@ Experimenting with a sexual orentation class """ -import stisim as ss +import starsim as ss import numpy as np ######################################################### diff --git a/tests/devtests/devtest_remove_people.py b/tests/devtests/devtest_remove_people.py index 4458a69b..1c50a342 100644 --- a/tests/devtests/devtest_remove_people.py +++ b/tests/devtests/devtest_remove_people.py @@ -3,7 +3,7 @@ """ # %% Imports and settings -import stisim as ss +import starsim as ss import matplotlib.pyplot as plt import pandas as pd import numpy as np diff --git a/tests/devtests/devtest_rng.py b/tests/devtests/devtest_rng.py index 379c1bcb..71c4e9ba 100644 --- a/tests/devtests/devtest_rng.py +++ b/tests/devtests/devtest_rng.py @@ -4,7 +4,7 @@ # %% Imports and settings import os -import stisim as ss +import starsim as ss import sciris as sc import pandas as pd import seaborn as sns diff --git a/tests/devtests/devtest_sensitivity.py b/tests/devtests/devtest_sensitivity.py index 973631d5..da4ce03a 100644 --- a/tests/devtests/devtest_sensitivity.py +++ b/tests/devtests/devtest_sensitivity.py @@ -4,7 +4,7 @@ # %% Imports and settings import os -import stisim as ss +import starsim as ss import sciris as sc import pandas as pd import seaborn as sns diff --git a/tests/devtests/devtest_simple.py b/tests/devtests/devtest_simple.py index 95ca23e4..3faca5d1 100644 --- a/tests/devtests/devtest_simple.py +++ b/tests/devtests/devtest_simple.py @@ -3,7 +3,7 @@ """ # %% Imports and settings -import stisim as ss +import starsim as ss import matplotlib.pyplot as plt diff --git a/tests/devtests/devtest_static_networks.py b/tests/devtests/devtest_static_networks.py index 0fc5fa41..419a1b54 100644 --- a/tests/devtests/devtest_static_networks.py +++ b/tests/devtests/devtest_static_networks.py @@ -3,7 +3,7 @@ """ # %% Imports and settings -import stisim as ss +import starsim as ss import matplotlib.pyplot as plt import networkx as nx diff --git a/tests/removing_people.py b/tests/removing_people.py index 8dc4e61d..b2008deb 100644 --- a/tests/removing_people.py +++ b/tests/removing_people.py @@ -1,7 +1,7 @@ import pandas as pd import numpy as np import sciris as sc -from stisim.states import State, DynamicView +from starsim.states import State, DynamicView INT_NAN = np.iinfo(int).max # Value to use to flag removed UIDs (i.e., an integer value we are treating like NaN, since NaN can't be stored in an integer array) diff --git a/tests/removing_people_demo.ipynb b/tests/removing_people_demo.ipynb index d9eade57..21d9552d 100644 --- a/tests/removing_people_demo.ipynb +++ b/tests/removing_people_demo.ipynb @@ -38,7 +38,7 @@ "outputs": [], "source": [ "import numpy as np\n", - "from stisim.states import State, DynamicView\n", + "from starsim.states import State, DynamicView\n", "from removing_people import DynamicPeople" ] }, diff --git a/tests/simple_benchmark.py b/tests/simple_benchmark.py index 479c6e9e..ed98a476 100644 --- a/tests/simple_benchmark.py +++ b/tests/simple_benchmark.py @@ -1,6 +1,6 @@ import sciris as sc import pylab as pl -import stisim as ss +import starsim as ss do_plot = False diff --git a/tests/test_base.py b/tests/test_base.py index 8b7b329e..4ca263fe 100644 --- a/tests/test_base.py +++ b/tests/test_base.py @@ -5,7 +5,7 @@ # %% Imports and settings import sciris as sc import numpy as np -import stisim as ss +import starsim as ss import matplotlib.pyplot as plt import scipy.stats as sps diff --git a/tests/test_baselines.py b/tests/test_baselines.py index 6bdf74ad..853e2b72 100644 --- a/tests/test_baselines.py +++ b/tests/test_baselines.py @@ -5,7 +5,7 @@ import numpy as np import sciris as sc -import stisim as ss +import starsim as ss do_plot = 1 do_save = 0 diff --git a/tests/test_demographics.py b/tests/test_demographics.py index d59209da..81429c3b 100644 --- a/tests/test_demographics.py +++ b/tests/test_demographics.py @@ -3,7 +3,7 @@ """ # %% Imports and settings -import stisim as ss +import starsim as ss import pandas as pd import matplotlib.pyplot as plt import numpy as np diff --git a/tests/test_distributions.py b/tests/test_distributions.py index 7c1fe33e..61b44905 100644 --- a/tests/test_distributions.py +++ b/tests/test_distributions.py @@ -5,10 +5,10 @@ # %% Imports and settings import numpy as np import sciris as sc -import stisim as ss -from stisim.random import RNG +import starsim as ss +from starsim.random import RNG import scipy.stats as sps -from stisim.distributions import ScipyDistribution +from starsim.distributions import ScipyDistribution import pytest import matplotlib.pyplot as plt diff --git a/tests/test_examples.py b/tests/test_examples.py index e660d8ac..3201aa59 100644 --- a/tests/test_examples.py +++ b/tests/test_examples.py @@ -3,7 +3,7 @@ """ # %% Imports and settings -import stisim as ss +import starsim as ss import matplotlib.pyplot as plt import scipy.stats as sps import numpy as np diff --git a/tests/test_random.py b/tests/test_random.py index c0021d4e..52042c23 100644 --- a/tests/test_random.py +++ b/tests/test_random.py @@ -5,8 +5,8 @@ # %% Imports and settings import numpy as np import sciris as sc -import stisim as ss -from stisim.random import RNG +import starsim as ss +from starsim.random import RNG import pytest @pytest.fixture diff --git a/tests/test_rngcontainer.py b/tests/test_rngcontainer.py index 8bf21707..c4b67ff7 100644 --- a/tests/test_rngcontainer.py +++ b/tests/test_rngcontainer.py @@ -5,9 +5,9 @@ # %% Imports and settings import numpy as np import sciris as sc -import stisim as ss -from stisim.random import NotInitializedException, SeedRepeatException, RepeatNameException -from stisim.random import SingleRNG, MultiRNG +import starsim as ss +from starsim.random import NotInitializedException, SeedRepeatException, RepeatNameException +from starsim.random import SingleRNG, MultiRNG import scipy.stats as sps import pytest diff --git a/tests/test_syphilis.py b/tests/test_syphilis.py index e00fb1f2..f28c6f78 100644 --- a/tests/test_syphilis.py +++ b/tests/test_syphilis.py @@ -4,7 +4,7 @@ # %% Imports and settings import numpy as np -import stisim as ss +import starsim as ss import pandas as pd import matplotlib.pyplot as plt import scipy.stats as sps @@ -24,7 +24,7 @@ def make_syph_sim(): # Make people and networks ss.set_seed(1) - ppl = ss.People(5000, age_data=pd.read_csv(ss.root / 'tests/test_data/nigeria_age.csv')) + ppl = ss.People(500, age_data=pd.read_csv(ss.root / 'tests/test_data/nigeria_age.csv')) # CK: temporary small pop size mf = ss.mf( pars=dict(duration_dist=ss.lognorm(mean=0.1, stdev=0.5)) ) @@ -32,7 +32,7 @@ def make_syph_sim(): ppl.networks = ss.ndict(mf, maternal) sim_kwargs = dict( - dt=1/12, + dt=1/2, # CK: temporary long dt total_pop=93963392, start=1990, n_years=40, diff --git a/tests/update_baseline.py b/tests/update_baseline.py old mode 100755 new mode 100644