merged with master

.github/workflows/ubuntu.yaml

@@ -0,0 +1,33 @@
+name: Covasim CI workflow
+on: [push, pull_request]
+
+jobs:
+  install_and_test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      max-parallel: 3
+      matrix:
+        python-version: [ '3.7' ]
+    name: Install and test
+    steps:
+      - name: Checkout sources
+        uses: actions/checkout@v1
+      - uses: actions/setup-python@master
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: x64
+      - name: Install Covasim
+        run: python setup.py develop
+      - name: Run tests
+        working-directory: ./tests
+        run: |
+          pip install pytest
+          pytest test_* unittest_* --junitxml=test-results.xml
+
+      - name: Upload test results
+        uses: actions/upload-artifact@v1
+        if: failure()
+        with:
+          name: test_results
+          path: tests/test-results.xml

.gitignore

@@ -1,6 +1,8 @@
 # Custom
+covasim/cova_cdc/results_2020mar14/
 covasim/cova_oregon/received/
 covasim/cova_oregon/results_2020mar14/
+covasim/cova_oregon/results_2020mar15/
 covasim/cova_seattle/capacity_analysis
 covasim/cova_seattle/school_analysis
 covasim/cova_seattle/seattle_analysis

LICENSE

@@ -1,21 +1,3 @@
-MIT License
+COVASim is licensed under the Creative Commons Attribution-Noncommercial-ShareAlike 4.0 License.
 
-Copyright (c) 2020 Institute for Disease Modeling
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+To view a copy of this license, visit https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode

covasim/cova_base/model.py

@@ -145,24 +145,6 @@ def likelihood(self):
     def plot(self):
         '''
         Plot the results -- can supply arguments for both the figure and the plots.
-
-        Parameters
-        ----------
-        do_save : bool or str
-            Whether or not to save the figure. If a string, save to that filename.
-
-        fig_args : dict
-            Dictionary of kwargs to be passed to pl.figure()
-
-        plot_args : dict
-            Dictionary of kwargs to be passed to pl.plot()
-
-        as_days : bool
-            Whether to plot the x-axis as days or time points
-
-        Returns
-        -------
-        Figure handle
         '''
         raise NotImplementedError
 
@@ -172,16 +154,19 @@ def plot_people(self):
         raise NotImplementedError
 
 
-def single_run(sim=None, ind=0, noise=0.0, noisepar=None, verbose=None, **kwargs):
+def single_run(sim=None, ind=0, noise=0.0, noisepar=None, verbose=None, sim_args=None, **kwargs):
     '''
     Convenience function to perform a single simulation run. Mostly used for
     parallelization, but can also be used directly:
         import covid_abm
         sim = covid_abm.single_run() # Create and run a default simulation
     '''
 
+    if sim_args is None:
+        sim_args = {}
+
     if sim is None:
-        new_sim = Sim(**kwargs)
+        new_sim = Sim(**sim_args)
     else:
         new_sim = sc.dcp(sim) # To avoid overwriting it; otherwise, use
 
@@ -191,44 +176,73 @@ def single_run(sim=None, ind=0, noise=0.0, noisepar=None, verbose=None, **kwargs
     new_sim['seed'] += ind # Reset the seed, otherwise no point of parallel runs
     new_sim.set_seed()
 
+    # If the noise parameter is not found, guess what it should be
+    if noisepar is None:
+        guesses = ['r_contact', 'r0', 'beta']
+        found = [guess for guess in guesses if guess in sim.pars.keys()]
+        if len(found)!=1:
+            raise KeyError(f'Cound not guess noise parameter since out of {guesses}, {found} were found')
+        else:
+            noisepar = found[0]
+
     # Handle noise -- normally distributed fractional error
     noiseval = noise*np.random.normal()
     if noiseval > 0:
         noisefactor = 1 + noiseval
     else:
         noisefactor = 1/(1-noiseval)
+    new_sim[noisepar] *= noisefactor
 
     if verbose>=1:
         print(f'Running a simulation using {new_sim["seed"]} seed and {noisefactor} noise')
 
-    new_sim[noisepar] *= noisefactor
+    # Handle additional arguments
+    for key,val in kwargs.items():
+        print(f'Processing {key}:{val}')
+        if key in new_sim.pars.keys():
+            if verbose>=1:
+                print(f'Setting key {key} from {new_sim[key]} to {val}')
+                new_sim[key] = val
+            pass
+        else:
+            raise KeyError(f'Could not set key {key}: not a valid parameter name')
+
+    # Run
     new_sim.run(verbose=verbose)
 
     return new_sim
 
 
-def multi_run(sim=None, n=4, noise=0.0, noisepar=None, verbose=None, combine=False, **kwargs):
+def multi_run(sim=None, n=4, noise=0.0, noisepar=None, iterpars=None, verbose=None, sim_args=None, combine=False, **kwargs):
     '''
     For running multiple runs in parallel. Example:
         import covid_seattle
         sim = covid_seattle.Sim()
         sims = covid_seattle.multi_run(sim, n=6, noise=0.2)
     '''
+
+    # Create the sims
+    if sim_args is None:
+        sim_args = {}
     if sim is None:
-        sim = Sim(**kwargs)
+        sim = Sim(**sim_args)
 
-    # If the noise parameter is not found, guess what it should be
-    if noisepar is None:
-        guesses = ['r_contact', 'r0', 'beta']
-        found = [guess for guess in guesses if guess in sim.pars.keys()]
-        if len(found)!=1:
-            raise KeyError(f'Cound not guess noise parameter since out of {guesses}, {found} were found')
-        else:
-            noisepar = found[0]
+    # Handle iterpars
+    if iterpars is None:
+        iterpars = {}
+    else:
+        n = None # Reset and get from length of dict instead
+        for key,val in iterpars.items():
+            new_n = len(val)
+            if n is not None and new_n != n:
+                raise ValueError(f'Each entry in iterpars must have the same length, not {n} and {len(val)}')
+            else:
+                n = new_n
 
     # Copy the simulations
     iterkwargs = {'ind':np.arange(n)}
-    kwargs = {'sim':sim, 'noise':noise, 'noisepar':noisepar, 'verbose':verbose}
+    iterkwargs.update(iterpars)
+    kwargs = {'sim':sim, 'noise':noise, 'noisepar':noisepar, 'verbose':verbose, 'sim_args':sim_args}
     sims = sc.parallelize(single_run, iterkwargs=iterkwargs, kwargs=kwargs)
 
     if not combine:

covasim/cova_base/version.py

@@ -1,4 +1,4 @@
 __all__ = ['__version__', '__versiondate__']
 
-__version__ = '0.4'
-__versiondate__ = '2020-03-12'
+__version__ = '0.5'
+__versiondate__ = '2020-03-15'