Merge pull request #854 from bashtage/fix-853-freebsd-tests

TST: Run the IVJIVE docstring examples quietly under pytest -v

Author: bashtage

README.md

@@ -125,6 +125,47 @@ python -m pip install -r requirements.txt -r requirements-dev.txt
 python -m pip install -e . --no-build-isolation
 ```
 
+## Running the tests
+
+The tests are installed with linearmodels. They need pytest 9 and xarray, and
+pytest-xdist to run in parallel.
+
+```bash
+python -c "import linearmodels; linearmodels.test(['--skip-slow', '-n', 'auto'])"
+```
+
+`--skip-slow` skips the slow tests and `--skip-examples` the example notebooks.
+
+pytest loads every plugin that is installed in the environment, and the test
+configuration of linearmodels is strict, so that, for example, a marker that is
+not registered is an error. A plugin that uses such a marker makes tests fail
+with a message such as `'gpu' not found in markers configuration option`. To run
+the tests without the other plugins, turn off their automatic loading and load
+pytest-xdist explicitly. This works with `python -m pytest` too.
+
+```bash
+PYTEST_DISABLE_PLUGIN_AUTOLOAD=1 python -c "import linearmodels; linearmodels.test(['-p', 'xdist', '-n', 'auto'])"
+```
+
+When the tests run in several processes with pytest-xdist, limit the BLAS
+libraries to one thread in each process. Otherwise every process starts as many
+threads as there are cores, and excessive context switching makes the tests run
+very slow. This problem is particularly acute on machines with high CPU counts.
+
+```bash
+export MKL_NUM_THREADS=1
+export OPENBLAS_NUM_THREADS=1
+export OMP_NUM_THREADS=1
+```
+
+or, in PowerShell,
+
+```powershell
+$env:MKL_NUM_THREADS = 1
+$env:OPENBLAS_NUM_THREADS = 1
+$env:OMP_NUM_THREADS = 1
+```
+
 ## Documentation
 
 [Stable Documentation](https://bashtage.github.io/linearmodels/) is
@@ -173,6 +214,8 @@ Python, NumPy and the other dependencies.
 ### Testing
 
 -   pytest (9.0+)
+-   xarray (0.16+)
+-   pytest-xdist (optional, to run the tests in parallel)
 
 ### Documentation
 

linearmodels/tests/iv/test_new_feature_hardening.py

@@ -88,7 +88,9 @@ def run_docstring_examples(obj, name):
     failures = []
     with_examples = set()
     for test in finder.find(obj, name, globs={}):
-        runner = doctest.DocTestRunner(optionflags=doctest.ELLIPSIS)
+        # verbose=None, the default, is verbose when "-v" is in sys.argv, as it is in
+        # "pytest -v", and the examples that pass are then written to out as well
+        runner = doctest.DocTestRunner(verbose=False, optionflags=doctest.ELLIPSIS)
         with warnings.catch_warnings():
             warnings.simplefilter("ignore", MissingValueWarning)
             runner.run(test, out=failures.append)

linearmodels/tests/test_kernel_bandwidth_few_observations.py

@@ -874,6 +874,29 @@ def system_equations(nobs, endogenous=False):
     }
 
 
+def gmm_equations(nobs):
+    """
+    Two equations, each with one endogenous regressor and one instrument
+
+    IVSystemGMM inverts the covariance of the moment conditions, in the robust and
+    the kernel weights. The equations of system_equations(nobs, True) are exactly
+    identified, so that their 4 moment conditions sum to zero at the estimates and have
+    rank nobs - 1 or less: their covariance is singular with 4 or fewer observations,
+    and inverting it only works up to rounding (it raised "Singular matrix" on FreeBSD,
+    #853). These equations have no constant and 2 moment conditions, whose covariance
+    has full rank from 3 observations.
+    """
+    first, second = iv_data(nobs, seed=11), iv_data(nobs, seed=111)
+    return {
+        f"eq{i}": {
+            "dependent": data.y,
+            "endog": data[["xn"]],
+            "instruments": data[["z1"]],
+        }
+        for i, data in enumerate((first, second))
+    }
+
+
 @pytest.mark.parametrize("kernel", CANONICAL)
 @pytest.mark.parametrize(("model", "endogenous"), [(SUR, False), (IV3SLS, True)])
 def test_system_models_raise_when_fit_with_too_few_observations(
@@ -914,7 +937,7 @@ def test_system_models_explicit_bandwidth_works_with_the_observations_that_raise
 def test_system_gmm_weights_raise_when_fit_with_too_few_observations(kernel):
     nobs = fewest_observations(kernel) - 1
     mod = IVSystemGMM(
-        system_equations(nobs, True),
+        gmm_equations(nobs),
         weight_type="kernel",
         kernel=kernel,
         optimal_bw=True,
@@ -923,20 +946,24 @@ def test_system_gmm_weights_raise_when_fit_with_too_few_observations(kernel):
         mod.fit()
 
 
-# The robust weights of the two equations need 4 observations before the covariance
-# gets to the bandwidth: the Bartlett kernel is reached with 4
-SYSTEM_GMM_COVARIANCE_FEW = [("parzen", 4), ("qs", 4), ("qs", 5)]
+# Every number of observations from 3, where the robust weights of gmm_equations can
+# be estimated, to one less than the kernel needs
+SYSTEM_GMM_COVARIANCE_FEW = [
+    (kernel, nobs)
+    for kernel in CANONICAL
+    for nobs in range(3, fewest_observations(kernel))
+]
 
 
 @pytest.mark.parametrize(("kernel", "nobs"), SYSTEM_GMM_COVARIANCE_FEW)
 def test_system_gmm_covariance_raises_when_fit_with_too_few_observations(kernel, nobs):
-    mod = IVSystemGMM(system_equations(nobs, True))
+    mod = IVSystemGMM(gmm_equations(nobs))
     with pytest.raises(ValueError, match=re.escape(too_few_message(kernel, nobs))):
         mod.fit(cov_type="kernel", kernel=kernel)
 
 
 def test_system_gmm_default_bandwidth_raises_when_fit_with_too_few_observations():
-    mod = IVSystemGMM(system_equations(3, True), weight_type="kernel")
+    mod = IVSystemGMM(gmm_equations(3), weight_type="kernel")
     with pytest.warns(DefaultBandwidthWarning):
         with pytest.raises(ValueError, match=re.escape(too_few_message("bartlett", 3))):
             mod.fit()
@@ -945,7 +972,7 @@ def test_system_gmm_default_bandwidth_raises_when_fit_with_too_few_observations(
 @pytest.mark.parametrize("kernel", CANONICAL)
 def test_system_gmm_explicit_bandwidth_works_with_the_observations_that_raise(kernel):
     nobs = fewest_observations(kernel) - 1
-    equations = system_equations(nobs, True)
+    equations = gmm_equations(nobs)
     explicit = IVSystemGMM(
         equations, weight_type="kernel", kernel=kernel, bandwidth=1
     ).fit()
@@ -959,7 +986,7 @@ def test_system_gmm_explicit_bandwidth_works_with_the_observations_that_raise(ke
 @pytest.mark.parametrize("kernel", CANONICAL)
 def test_system_gmm_with_the_fewest_observations(kernel):
     nobs = fewest_observations(kernel)
-    equations = system_equations(nobs, True)
+    equations = gmm_equations(nobs)
     res = IVSystemGMM(
         equations, weight_type="kernel", kernel=kernel, optimal_bw=True
     ).fit(cov_type="kernel", kernel=kernel)