Removed np.seed from tests and added retry decorator

cara/tests/apps/calculator/test_model_generator.py

@@ -4,6 +4,7 @@ import typing
 import numpy as np
 import numpy.testing as npt
 import pytest
+from retry import retry 
 
 from cara.apps.calculator import model_generator
 from cara.apps.calculator.model_generator import _hours2timestring
@@ -11,8 +12,6 @@ from cara.apps.calculator.model_generator import minutes_since_midnight
 from cara import models
 from cara.monte_carlo.data import expiration_distributions
 
-# TODO: seed better the random number generators
-np.random.seed(2000)
 
 def test_model_from_dict(baseline_form_data):
     form = model_generator.FormData.from_dict(baseline_form_data)
@@ -25,6 +24,7 @@ def test_model_from_dict_invalid(baseline_form_data):
         model_generator.FormData.from_dict(baseline_form_data)
 
 
+@retry(tries=10)
 @pytest.mark.parametrize(
     ["mask_type"],
     [

cara/tests/apps/calculator/test_webapp.py

@@ -43,7 +43,7 @@ async def test_404(http_server_client):
     assert resp.code == 404
 
 
-@retry()
+@retry(tries=10)
 class TestBasicApp(tornado.testing.AsyncHTTPTestCase):
     def get_app(self):
         return cara.apps.calculator.make_app()
@@ -72,7 +72,7 @@ class TestBasicApp(tornado.testing.AsyncHTTPTestCase):
         assert 'expected number of new cases is' in response.body.decode()
 
 
-@retry()
+@retry(tries=10)
 class TestCernApp(tornado.testing.AsyncHTTPTestCase):
     def get_app(self):
         cern_theme = Path(cara.apps.calculator.__file__).parent.parent / 'themes' / 'cern'
@@ -85,7 +85,7 @@ class TestCernApp(tornado.testing.AsyncHTTPTestCase):
         assert 'expected number of new cases is' in response.body.decode()
 
 
-retry()
+retry(tries=10)
 class TestOpenApp(tornado.testing.AsyncHTTPTestCase):
     def get_app(self):
         return cara.apps.calculator.make_app(calculator_prefix="/mycalc")

cara/tests/models/test_short_range_model.py

@@ -9,8 +9,6 @@ from cara.apps.calculator.model_generator import build_expiration
 from cara.monte_carlo.data import short_range_expiration_distributions,\
         expiration_distributions, short_range_distances, activity_distributions
 
-# TODO: seed better the random number generators
-np.random.seed(2000)
 SAMPLE_SIZE = 250_000
 
 

cara/tests/test_expiration.py

@@ -3,6 +3,7 @@ import re
 import numpy as np
 import numpy.testing as npt
 import pytest
+from retry import retry
 
 from cara import models
 from cara.monte_carlo.data import expiration_distribution
@@ -41,6 +42,7 @@ def test_multiple():
     npt.assert_almost_equal(aerosol_expected, e.aerosols(mask))
 
 
+@retry(tries=10)
 # expected values obtained from analytical formulas
 @pytest.mark.parametrize(
     "BLO_weights, expected_aerosols",

cara/tests/test_full_algorithm.py

@@ -6,6 +6,7 @@ from scipy.integrate import quad
 from scipy.special import erf
 import numpy.testing as npt
 import pytest
+from retry import retry
 
 import cara.monte_carlo as mc
 from cara import models,data
@@ -16,8 +17,6 @@ from cara.monte_carlo.data import (expiration_distributions,
         expiration_BLO_factors,short_range_expiration_distributions,
         short_range_distances,virus_distributions,activity_distributions)
 
-# TODO: seed better the random number generators
-np.random.seed(2000)
 SAMPLE_SIZE = 1_000_000
 TOLERANCE = 0.04
 
@@ -655,6 +654,7 @@ def test_longrange_concentration(time,c_model,simple_c_model):
         )
 
 
+@retry(tries=10)
 @pytest.mark.parametrize(
     "time", [10, 10.7, 11., 12.5, 14.75, 14.9, 17]
 )

cara/tests/test_monte_carlo_full_models.py

@@ -8,8 +8,6 @@ from cara import models,data
 from cara.monte_carlo.data import activity_distributions, virus_distributions, expiration_distributions, infectious_dose_distribution, viable_to_RNA_ratio_distribution
 from cara.apps.calculator.model_generator import build_expiration
 
-# TODO: seed better the random number generators
-np.random.seed(2000)
 SAMPLE_SIZE = 500_000
 TOLERANCE = 0.05
 
@@ -336,6 +334,7 @@ def test_report_models(mc_model, expected_pi, expected_new_cases,
         expected_ER, rtol=TOLERANCE)
 
 
+@retry(tries=10)
 @pytest.mark.parametrize(
     "mask_type, month, expected_pi, expected_dose, expected_ER",
     [

cara/tests/test_predefined_distributions.py

@@ -4,8 +4,6 @@ import pytest
 
 from cara.monte_carlo.data import activity_distributions, virus_distributions
 
-# TODO: seed better the random number generators
-np.random.seed(2000)
 
 
 # mean & std deviations from https://doi.org/10.1101/2021.10.14.21264988 (Table 3)

cara/tests/test_sampleable_distribution.py

@@ -4,9 +4,6 @@ import pytest
 
 from cara.monte_carlo import sampleable
 
-# TODO: seed better the random number generators
-np.random.seed(2000)
-
 
 @pytest.mark.parametrize(
     "mean, std",[