Merge pull request #200 from amath-idm/starsim-rename

Starsim rename

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 <https://github.com/amath-idm/stisim/pull/200>`_
+
+
 Version 0.1.4 (2024-01-23)
 --------------------------
 - Adds a syphilis module

README.rst

@@ -1,15 +1,15 @@
-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.** 
 
 
 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

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(),

stisim/analyzers.py → starsim/analyzers.py

@@ -2,7 +2,7 @@
 Define analyzers
 """
 
-import stisim as ss
+import starsim as ss
 
 
 __all__ = ['Analyzer']

stisim/connectors.py → starsim/connectors.py

@@ -2,7 +2,7 @@
 Define connections between disease modules
 '''
 
-import stisim as ss
+import starsim as ss
 
 
 class Connector(ss.Module):

stisim/demographics.py → 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

stisim/diseases/disease.py → 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

stisim/diseases/examples.py → 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

stisim/diseases/gonorrhea.py → 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
 

stisim/diseases/hiv.py → 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
 

stisim/diseases/syphilis.py → 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']

stisim/distributions.py → 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

stisim/interventions.py → 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

stisim/modules.py → 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']

stisim/networks/networks.py → 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)
 
     """

stisim/networks/randnet.py → 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

stisim/parameters.py → starsim/parameters.py

@@ -3,7 +3,7 @@
 """
 
 import sciris as sc
-import stisim as ss
+import starsim as ss
 
 
 __all__ = ['Parameters', 'make_pars']

stisim/people.py → 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']

stisim/random.py → 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.

stisim/settings.py → 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)

stisim/sim.py → 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'])

stisim/states.py → 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
 

stisim/utils.py → 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

stisim/version.py → 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'

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

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

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

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

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