Running Unit Tests¶
Unit tests can run from either the root directory or
pytest. Note the following useful options for pytest. The first
couple are custom flags we created.
pytest --ihmeThis is a flag we created that enables those tests which we would run within the IHME environment. If you write a test that calls IHME databases, you must include the ihme fixture in order for that unit test to run. This guarantees that when Jenkins runs without the –ihme flag, none of the tests it runs require the IHME databases.
pytest --dismodThis is a flag we created that enables those tests which require having a command-line Dismod-AT running. Using
pytest --signalsThis is a flag we created that enables those tests which turns off tests that send UNIX signals to test failure modes. It’s useful on the Mac, which helpfully offers to inform Apple of application failure.
The rest are standard options, but they are so important that I’m listing them here.
pytest ---log-cli-level debugCaptures log messages nicely within unit tests.
pytest --pdbThis flag asks to drop into the debugger when an exception happens in a unit test. Very helpful when using tests for test-driven development.
pytest --capture=noThis allows stdout, stderr, and logging to be printed when running tests.
pytest -k partial_nameThis picks out all tests whose names contain the letters “partial_name”.
pytest --lfRun the last set of failing tests.
pytest --ffRun the last set of failing tests, and then run the rest of the tests.
pytest -xDie on the first failure.
In order to make a test that relies on IHME databases, use the global fixture
def test_get_ages(ihme): gbd_round = 12 ages = get_gbd_age_groups(gbd_round)
This test will automatically be disabled until the
--ihme flag is on.
Running Acceptance Tests¶
There is a separate directory for acceptance tests. It’s called
in the unit directory. Here, too, run
pytest, but it will take longer
and do thread tests, which are tests from one interaction to a response.
Unit and acceptance tests are run with the
turned on, just before the end of installation. If they fail, then
installation fails. Be sure to run unit tests on the cluster
--ihme, even if they pass in Tox, which runs a subset
Structure of Tests¶
Testing structure follows the component structure of the code, but there are a few tests that outweigh others in importance because they are system integration tests. If we look at the larger architectural parts, those system integration tests mock out different pieces. The larger architectural parts are:
Main success scenario (MSS), that does a fit and simulate with Dismod-AT.
Input data of various kinds
Bundle data records
IHME databases of mortality.
Interface with the Dismod-AT db file
Main Success Scenario¶
There is a single file that runs the core set of steps for the wrapper, using no inputs from external sources. It does the first two of these steps. As we work through the main success scenario, we should make it do all of the steps.
Generate input data with Dismod-AT predict.
Fit that data.
Fit those simulations.
Summarize simulation outputs.
Create posterior data.
It’s set up to run through different types of models
and different combinations of input parameters. It does
a fractional-factorial experiment on those parameters, working
up to seeing how two parameters interact, and whether the
code still runs.
This same script generates files with timings on how long it takes Dismod-AT to do a fit, for a given set of parameters and data.
Test Settings Parsing¶
This mocks the creation of EpiViz-AT settings and
then runs stochastically-generated settings through
the builder for models, all the way to writing a Dismod-AT db file.
Live Tests against Database¶
These use a real MVID, and pull settings and data
for it in order to build a database, in
Testing the Dismod-AT DB File Interface¶
These tests skip any IHME database interaction.
The redo the extensive tests included with Dismod-AT,
but they do it using the internal interface.
This is what tells us our internal interface works.
There should be a test that creates settings and input data, and runs completely through the main scenario. This would save us from waiting for the IHME databases to send data and would exercise the later part of the main success scenario, which isn’t covered enough yet.