Reenable more tests (#4770)

* Reenable more tests
* Update comments

Co-authored-by: Michael Osthege <[email protected]>

Author: ricardoV94

.github/workflows/pytest.yml

@@ -13,32 +13,25 @@ jobs:
         floatx: [float32, float64]
         test-subset:
         # Tests are split into multiple jobs to accelerate the CI.
-        # The first job (starting in the next block) shouldn't run any tests, but
-        # just ignores tests because that don't work at all, or run in other jobs.'
+        #
+        # How this works:
+        # 1st block: Only passes --ignore parameters to pytest.
+        # → pytest will run all test_*.py files that are NOT ignored.
+        # Other blocks: Only pass paths to test files.
+        # → pytest will run only these files
+        #
         # Any test that was not ignored runs in the first job.
-        # A pre-commit hook (scripts/check_all_tests_are_covered.py) enforces that
-        # test run just once.
-
-        # Because YAML doesn't allow comments in the blocks below, here they are..
-        # 1st block: These tests are temporarily disabled, because they are _very_ broken
-        # 2nd block: The JAX tests run through their own workflow: jaxtests.yml
-        # 3nd & 4rd: These tests are covered by other matrix jobs
-        # 5th block: These tests PASS without a single XFAIL
-        # 6th block: These have some XFAILs
+        # A pre-commit hook (scripts/check_all_tests_are_covered.py)
+        # enforces that test run just once.
           - |
             --ignore=pymc3/tests/test_distributions_timeseries.py
-            --ignore=pymc3/tests/test_missing.py
             --ignore=pymc3/tests/test_mixture.py
             --ignore=pymc3/tests/test_model_graph.py
             --ignore=pymc3/tests/test_modelcontext.py
             --ignore=pymc3/tests/test_parallel_sampling.py
             --ignore=pymc3/tests/test_profile.py
-            --ignore=pymc3/tests/test_random.py
-            --ignore=pymc3/tests/test_shared.py
             --ignore=pymc3/tests/test_smc.py
-            --ignore=pymc3/tests/test_starting.py
             --ignore=pymc3/tests/test_step.py
-            --ignore=pymc3/tests/test_tracetab.py
             --ignore=pymc3/tests/test_tuning.py
             --ignore=pymc3/tests/test_types.py
             --ignore=pymc3/tests/test_variational_inference.py

pymc3/tests/test_missing.py

@@ -121,7 +121,12 @@ def test_interval_missing_observations():
 
         assert {"theta1", "theta2"} <= set(prior_trace.keys())
 
-        trace = sample(chains=1, draws=50, compute_convergence_checks=False)
+        trace = sample(
+            chains=1,
+            draws=50,
+            compute_convergence_checks=False,
+            return_inferencedata=False,
+        )
 
         assert np.all(0 < trace["theta1_missing"].mean(0))
         assert np.all(0 < trace["theta2_missing"].mean(0))

pymc3/tests/test_starting.py

@@ -13,8 +13,7 @@
 #   limitations under the License.
 
 import numpy as np
-
-from pytest import raises
+import pytest
 
 from pymc3 import (
     Beta,
@@ -47,6 +46,7 @@ def test_accuracy_non_normal():
         close_to(newstart["x"], mu, select_by_precision(float64=1e-5, float32=1e-4))
 
 
+@pytest.mark.xfail(reason="find_MAP fails with derivatives")
 def test_find_MAP_discrete():
     tol = 2.0 ** -11
     alpha = 4
@@ -68,12 +68,15 @@ def test_find_MAP_discrete():
     assert map_est2["ss"] == 14
 
 
+@pytest.mark.xfail(reason="find_MAP fails with derivatives")
 def test_find_MAP_no_gradient():
     _, model = simple_arbitrary_det()
     with model:
         find_MAP()
 
 
+@pytest.mark.skip(reason="test is slow because it's failing")
+@pytest.mark.xfail(reason="find_MAP fails with derivatives")
 def test_find_MAP():
     tol = 2.0 ** -11  # 16 bit machine epsilon, a low bar
     data = np.random.randn(100)
@@ -106,8 +109,8 @@ def test_find_MAP_issue_4488():
         map_estimate = find_MAP()
 
     assert not set.difference({"x_missing", "x_missing_log__", "y"}, set(map_estimate.keys()))
-    assert np.isclose(map_estimate["x_missing"], 0.2)
-    np.testing.assert_array_equal(map_estimate["y"], [2.0, map_estimate["x_missing"][0] + 1])
+    np.testing.assert_allclose(map_estimate["x_missing"], 0.2, rtol=1e-5, atol=1e-5)
+    np.testing.assert_allclose(map_estimate["y"], [2.0, map_estimate["x_missing"][0] + 1])
 
 
 def test_allinmodel():
@@ -120,11 +123,16 @@ def test_allinmodel():
         x2 = Normal("x2", mu=0, sigma=1)
         y2 = Normal("y2", mu=0, sigma=1)
 
+    x1 = model1.rvs_to_values[x1]
+    y1 = model1.rvs_to_values[y1]
+    x2 = model2.rvs_to_values[x2]
+    y2 = model2.rvs_to_values[y2]
+
     starting.allinmodel([x1, y1], model1)
     starting.allinmodel([x1], model1)
-    with raises(ValueError, match=r"Some variables not in the model: \['x2', 'y2'\]"):
+    with pytest.raises(ValueError, match=r"Some variables not in the model: \['x2', 'y2'\]"):
         starting.allinmodel([x2, y2], model1)
-    with raises(ValueError, match=r"Some variables not in the model: \['x2'\]"):
+    with pytest.raises(ValueError, match=r"Some variables not in the model: \['x2'\]"):
         starting.allinmodel([x2, y1], model1)
-    with raises(ValueError, match=r"Some variables not in the model: \['x2'\]"):
+    with pytest.raises(ValueError, match=r"Some variables not in the model: \['x2'\]"):
         starting.allinmodel([x2], model1)