Make Delphi-Epidata tests Pytest compatible.

docs/epidata_development.md

@@ -143,6 +143,15 @@ The final line of output should be similar to the following:
 All 48 tests passed! 68% (490/711) coverage.
 ```
 
+You can also run tests using pytest like this:
+```
+docker run --rm delphi_python pytest repos/delphi/delphi-epidata/tests/
+```
+and with pdb enabled like this:
+```
+docker run -it --rm delphi_python pytest repos/delphi/delphi-epidata/tests/ --pdb
+```
+
 ## manual tests
 
 You can test your changes manually by:
@@ -284,6 +293,15 @@ More concretely, you can run Epidata API integration tests like this:
   ✔ All 3 tests passed! [coverage unavailable]
   ```
 
+  You can also run tests using pytest like this:
+  ```
+  docker run --network delphi-net --rm delphi_python pytest repos/delphi/delphi-epidata/integrations/
+  ```
+  and with pdb enabled like this:
+  ```
+  docker run --network delphi-net -it --rm delphi_python pytest repos/delphi/delphi-epidata/integrations/ --pdb
+  ```
+
 5. Bring down the servers, for example with the `docker stop` command.
 
 # rapid iteration

docs/new_endpoint_tutorial.md

@@ -267,6 +267,15 @@ If all succeeds, output should look like this:
 ✔ All 48 tests passed! 69% (486/704) coverage.
 ```
 
+You can also run tests using pytest like this:
+```
+docker run --rm delphi_python pytest repos/delphi/delphi-epidata/tests/
+```
+and with pdb enabled like this:
+```
+docker run -it --rm delphi_python pytest repos/delphi/delphi-epidata/tests/ --pdb
+```
+
 ## integration
 
 Integration tests require more effort and take longer to set up and run.
@@ -317,6 +326,14 @@ delphi.delphi-epidata.integrations.server.test_fluview_meta.FluviewMetaTests.tes
 
 ✔ All 16 tests passed! 48% (180/372) coverage.
 ```
+You can also run tests using pytest like this:
+```
+docker run --network delphi-net --rm delphi_python pytest repos/delphi/delphi-epidata/integrations/
+```
+and with pdb enabled like this:
+```
+docker run --network delphi-net -it --rm delphi_python pytest repos/delphi/delphi-epidata/integrations/ --pdb
+```
 
 # code review and submission
 

integrations/__init__.py

@@ -0,0 +1,4 @@
+import sys
+import os
+
+sys.path.append(os.getcwd())

integrations/acquisition/covid_hosp/facility/__init__.py

@@ -0,0 +1,4 @@
+import sys
+import os
+
+sys.path.append(os.getcwd())

integrations/acquisition/covid_hosp/facility/test_scenarios.py

@@ -8,6 +8,7 @@
 from delphi.epidata.acquisition.covid_hosp.common.database import Database
 from delphi.epidata.acquisition.covid_hosp.common.test_utils import TestUtils
 from delphi.epidata.client.delphi_epidata import Epidata
+from delphi.epidata.acquisition.covid_hosp.facility.update import Update
 import delphi.operations.secrets as secrets
 
 # py3tester coverage target (equivalent to `import *`)

integrations/acquisition/covid_hosp/state_timeseries/__init__.py

@@ -0,0 +1,4 @@
+import sys
+import os
+
+sys.path.append(os.getcwd())

integrations/acquisition/covid_hosp/state_timeseries/test_scenarios.py

@@ -8,6 +8,7 @@
 from delphi.epidata.acquisition.covid_hosp.common.database import Database
 from delphi.epidata.acquisition.covid_hosp.common.test_utils import TestUtils
 from delphi.epidata.client.delphi_epidata import Epidata
+from delphi.epidata.acquisition.covid_hosp.state_timeseries.update import Update
 import delphi.operations.secrets as secrets
 
 # py3tester coverage target (equivalent to `import *`)

integrations/acquisition/covidcast/__init__.py

@@ -0,0 +1,4 @@
+import sys
+import os
+
+sys.path.append(os.getcwd())

integrations/acquisition/covidcast/test_covidcast_meta_caching.py

@@ -12,6 +12,7 @@
 from delphi.epidata.client.delphi_epidata import Epidata
 import delphi.operations.secrets as secrets
 import delphi.epidata.acquisition.covidcast.database as live
+from delphi.epidata.acquisition.covidcast.covidcast_meta_cache_updater import main
 
 # py3tester coverage target (equivalent to `import *`)
 __test_target__ = (

integrations/acquisition/covidcast/test_csv_uploading.py

@@ -11,6 +11,7 @@
 
 # first party
 from delphi.epidata.client.delphi_epidata import Epidata
+from delphi.epidata.acquisition.covidcast.csv_to_database import main
 import delphi.operations.secrets as secrets
 
 # py3tester coverage target (equivalent to `import *`)

integrations/acquisition/covidcast/test_fill_is_latest_issue.py

@@ -8,6 +8,7 @@
 
 # first party
 from delphi.epidata.client.delphi_epidata import Epidata
+from delphi.epidata.acquisition.covidcast.fill_is_latest_issue import main
 import delphi.operations.secrets as secrets
 
 # py3tester coverage target (equivalent to `import *`)

integrations/acquisition/covidcast_nowcast/__init__.py

@@ -0,0 +1,4 @@
+import sys
+import os
+
+sys.path.append(os.getcwd())

integrations/client/__init__.py

@@ -0,0 +1,4 @@
+import sys
+import os
+
+sys.path.append(os.getcwd())

integrations/server/__init__.py

@@ -0,0 +1,4 @@
+import sys
+import os
+
+sys.path.append(os.getcwd())

tests/acquisition/covid_hosp/common/__init__.py

@@ -0,0 +1,4 @@
+import sys
+import os
+
+sys.path.append(os.getcwd())

tests/acquisition/covid_hosp/common/test_database.py

@@ -9,6 +9,8 @@
 # third party
 import pandas as pd
 
+from delphi.epidata.acquisition.covid_hosp.common.database import Database
+
 # py3tester coverage target
 __test_target__ = 'delphi.epidata.acquisition.covid_hosp.common.database'
 

tests/acquisition/covid_hosp/common/test_network.py

@@ -5,6 +5,8 @@
 from unittest.mock import MagicMock
 from unittest.mock import sentinel
 
+from delphi.epidata.acquisition.covid_hosp.common.network import Network
+
 # py3tester coverage target
 __test_target__ = 'delphi.epidata.acquisition.covid_hosp.common.network'
 

tests/acquisition/covid_hosp/common/test_utils.py

@@ -7,6 +7,7 @@
 
 # first party
 from delphi.epidata.acquisition.covid_hosp.common.test_utils import TestUtils
+from delphi.epidata.acquisition.covid_hosp.common.utils import Utils, CovidHospException
 
 # py3tester coverage target
 __test_target__ = 'delphi.epidata.acquisition.covid_hosp.common.utils'

tests/acquisition/covid_hosp/facility/__init__.py

@@ -0,0 +1,4 @@
+import sys
+import os
+
+sys.path.append(os.getcwd())

tests/acquisition/covid_hosp/facility/test_database.py

@@ -7,6 +7,7 @@
 
 # first party
 from delphi.epidata.acquisition.covid_hosp.common.test_utils import TestUtils
+from delphi.epidata.acquisition.covid_hosp.facility.database import Database
 
 # py3tester coverage target
 __test_target__ = 'delphi.epidata.acquisition.covid_hosp.facility.database'

tests/acquisition/covid_hosp/facility/test_network.py

@@ -5,6 +5,8 @@
 from unittest.mock import patch
 from unittest.mock import sentinel
 
+from delphi.epidata.acquisition.covid_hosp.facility.network import Network
+
 # py3tester coverage target
 __test_target__ = 'delphi.epidata.acquisition.covid_hosp.facility.network'
 

tests/acquisition/covid_hosp/facility/test_update.py

@@ -7,6 +7,7 @@
 
 # first party
 from delphi.epidata.acquisition.covid_hosp.common.utils import Utils
+from delphi.epidata.acquisition.covid_hosp.facility.update import Update
 
 # py3tester coverage target
 __test_target__ = 'delphi.epidata.acquisition.covid_hosp.facility.update'

tests/acquisition/covid_hosp/state_timeseries/__init__.py

@@ -0,0 +1,4 @@
+import sys
+import os
+
+sys.path.append(os.getcwd())

tests/acquisition/covid_hosp/state_timeseries/test_database.py

@@ -7,6 +7,7 @@
 
 # first party
 from delphi.epidata.acquisition.covid_hosp.common.test_utils import TestUtils
+from delphi.epidata.acquisition.covid_hosp.state_timeseries.database import Database
 
 # py3tester coverage target
 __test_target__ = \

tests/acquisition/covid_hosp/state_timeseries/test_network.py

@@ -5,6 +5,9 @@
 from unittest.mock import patch
 from unittest.mock import sentinel
 
+from delphi.epidata.acquisition.covid_hosp.state_timeseries.network import Network
+
+
 # py3tester coverage target
 __test_target__ = \
     'delphi.epidata.acquisition.covid_hosp.state_timeseries.network'

tests/acquisition/covid_hosp/state_timeseries/test_update.py

@@ -7,6 +7,7 @@
 
 # first party
 from delphi.epidata.acquisition.covid_hosp.common.utils import Utils
+from delphi.epidata.acquisition.covid_hosp.state_timeseries.update import Update
 
 # py3tester coverage target
 __test_target__ = \

tests/acquisition/covidcast/__init__.py

@@ -0,0 +1,4 @@
+import sys
+import os
+
+sys.path.append(os.getcwd())

tests/acquisition/covidcast/test_covidcast_meta_cache_updater.py

@@ -8,6 +8,8 @@
 # third party
 import pandas
 
+from delphi.epidata.acquisition.covidcast.covidcast_meta_cache_updater import get_argument_parser, \
+  main
 # py3tester coverage target
 __test_target__ = (
   'delphi.epidata.acquisition.covidcast.'

tests/acquisition/covidcast/test_csv_importer.py

@@ -3,9 +3,14 @@
 # standard library
 import unittest
 from unittest.mock import MagicMock
+from datetime import date
 
 # third party
 import pandas
+import epiweeks as epi
+
+from delphi.epidata.acquisition.covidcast.csv_importer import CsvImporter
+from delphi.utils.epiweek import delta_epiweeks
 
 # py3tester coverage target
 __test_target__ = 'delphi.epidata.acquisition.covidcast.csv_importer'

tests/acquisition/covidcast/test_csv_to_database.py

@@ -5,6 +5,9 @@
 import unittest
 from unittest.mock import MagicMock
 
+from delphi.epidata.acquisition.covidcast.csv_to_database import get_argument_parser, main, \
+  collect_files, upload_archive, make_handlers
+
 # py3tester coverage target
 __test_target__ = 'delphi.epidata.acquisition.covidcast.csv_to_database'
 

tests/acquisition/covidcast/test_database.py

@@ -4,6 +4,8 @@
 import unittest
 from unittest.mock import MagicMock
 
+from delphi.epidata.acquisition.covidcast.database import Database
+
 # py3tester coverage target
 __test_target__ = 'delphi.epidata.acquisition.covidcast.database'
 

tests/acquisition/covidcast/test_file_archiver.py

@@ -5,6 +5,8 @@
 import unittest
 from unittest.mock import MagicMock
 
+from delphi.epidata.acquisition.covidcast.file_archiver import FileArchiver
+
 # py3tester coverage target
 __test_target__ = 'delphi.epidata.acquisition.covidcast.file_archiver'
 

tests/acquisition/covidcast_nowcast/__init__.py

@@ -0,0 +1,4 @@
+import sys
+import os
+
+sys.path.append(os.getcwd())

tests/acquisition/flusurv/__init__.py

@@ -0,0 +1,4 @@
+import sys
+import os
+
+sys.path.append(os.getcwd())

tests/acquisition/flusurv/test_flusurv.py

@@ -5,6 +5,8 @@
 from unittest.mock import MagicMock
 from unittest.mock import sentinel
 
+from delphi.epidata.acquisition.flusurv.flusurv import fetch_json
+
 # py3tester coverage target
 __test_target__ = 'delphi.epidata.acquisition.flusurv.flusurv'
 

tests/acquisition/fluview/__init__.py

@@ -0,0 +1,4 @@
+import sys
+import os
+
+sys.path.append(os.getcwd())

tests/acquisition/fluview/test_impute_missing_values.py

@@ -7,6 +7,8 @@
 
 # first party
 from delphi.utils.geo.locations import Locations
+from delphi.epidata.acquisition.fluview.impute_missing_values import get_argument_parser, \
+  get_lag_and_ili, impute_missing_values, StatespaceException
 
 # py3tester coverage target
 __test_target__ = 'delphi.epidata.acquisition.fluview.impute_missing_values'
@@ -29,7 +31,7 @@ def test_get_lag_and_ili(self):
     for args, expected in samples:
       with self.subTest(args=args):
         actual = get_lag_and_ili(*args)
-        self.assertEquals(actual, expected)
+        self.assertEqual(actual, expected)
 
   def test_impute_missing_values(self):
     """Atoms are imputed and stored."""
@@ -48,23 +50,23 @@ def test_impute_missing_values(self):
 
     impute_missing_values(db, test_mode=True)
 
-    self.assertEquals(db.connect.call_count, 1)
+    self.assertEqual(db.connect.call_count, 1)
     self.assertTrue(db.count_rows.call_count >= 1)
     self.assertTrue(db.find_missing_rows.call_count >= 1)
-    self.assertEquals(db.add_imputed_values.call_count, 1)
-    self.assertEquals(db.close.call_count, 1)
+    self.assertEqual(db.add_imputed_values.call_count, 1)
+    self.assertEqual(db.close.call_count, 1)
     self.assertFalse(db.close.call_args[0][0])
 
     imputed = db.add_imputed_values.call_args[0][-1]
     self.assertTrue(unknown_set <= set(imputed.keys()))
     for loc, (lag, n_ili, n_pat, n_prov, ili) in imputed.items():
       with self.subTest(loc=loc):
         num = len(Locations.region_map[loc])
-        self.assertEquals(lag, 0)
-        self.assertEquals(n_ili, num)
-        self.assertEquals(n_pat, num)
-        self.assertEquals(n_prov, num)
-        self.assertEquals(ili, 100)
+        self.assertEqual(lag, 0)
+        self.assertEqual(n_ili, num)
+        self.assertEqual(n_pat, num)
+        self.assertEqual(n_prov, num)
+        self.assertEqual(ili, 100)
 
   def test_impute_missing_values_vipr(self):
     """PR and VI are imputed only when appropriate."""

tests/client/__init__.py

@@ -0,0 +1,4 @@
+import sys
+import os
+
+sys.path.append(os.getcwd())

tests/server/__init__.py

@@ -0,0 +1,4 @@
+import sys
+import os
+
+sys.path.append(os.getcwd())