Fix PT006, PT007, PT018, PT030 prek violations

Remove PT006/PT007 from ignore list and fix all violations: convert
list/string parametrize args to tuples, convert tuple-of-tuples values
to list-of-tuples, split compound assertions, and add match= to
pytest.warns calls.

Author: jeromekelleher

pyproject.toml

@@ -154,11 +154,7 @@ ignore = [
     "PT009", # pytest.raises(ValueError) too broad
     "PT011", # pytest.raises(ValueError) too broad
     "PT012", # pytest.raises() block should contain a single simple statement
-    "PT006", # Wrong type passed to first argument of `pytest.mark.parametrize`
-    "PT007", # Wrong type pytest.mark.parametrize` expected `list` of `tuple
     "B018", # Found useless expression. Either assign it
-    "PT018", # Assertion should be broken down into multiple parts 
-    "PT030", # `pytest.warns(UserWarning)` is too broad, set the 
     "B028", # No stacklevel for warnings
 ]
 

tests/test_algorithms.py

@@ -372,7 +372,7 @@ def test_from_ts(self):
             assert ts.sequence_length == 100
 
     @pytest.mark.parametrize(
-        ["num_founders", "num_generations", "r"],
+        ("num_founders", "num_generations", "r"),
         [
             (4, 5, 0),
             (4, 5, 0.1),

tests/test_cli.py

@@ -1346,7 +1346,7 @@ def test_simulate_short_args(self, tmp_path):
     def test_compress_warns(self, tmp_path):
         cmd = "simulate"
         tree_sequence_file = str(tmp_path / "out.ts")
-        with pytest.warns(UserWarning):
+        with pytest.warns(UserWarning, match="--compress option is no longer supported"):
             capture_output(cli.msp_main, [cmd, "10", tree_sequence_file, "--compress"])
         tree_sequence = tskit.load(tree_sequence_file)
         assert tree_sequence.get_sample_size() == 10
@@ -1450,7 +1450,7 @@ def test_run_yaml(self, tmp_path):
 
 class TestSampleParsing:
     @pytest.mark.parametrize(
-        ["param", "result"], [("1", 1), ("1000", 1000), ("1_000", 1000), ("1e3", 1000)]
+        ("param", "result"), [("1", 1), ("1000", 1000), ("1_000", 1000), ("1e3", 1000)]
     )
     def test_parse_sample_size(self, param, result):
         value = cli.parse_sample_size(param)
@@ -1462,7 +1462,7 @@ def test_parse_sample_size_error(self, param):
             cli.parse_sample_size(param)
 
     @pytest.mark.parametrize(
-        ["param", "result"],
+        ("param", "result"),
         [
             (["A:1"], {"A": 1}),
             (["A:2", "B:1"], {"A": 2, "B": 1}),
@@ -1484,7 +1484,7 @@ def test_parse_sample_spec_malformed_token(self, param):
 
 
 @pytest.mark.parametrize(
-    ["verbosity", "log_level"],
+    ("verbosity", "log_level"),
     [("", "WARN"), ("-v", "INFO"), ("-vv", "DEBUG"), ("-vvv", "DEBUG")],
 )
 def test_setup_logging(verbosity, log_level):

tests/test_demes.py

@@ -594,7 +594,8 @@ def test_activate_ghost_split(self):
         assert "B" == dbg.epochs[0].active_populations[0].name
         assert len(dbg.epochs[1].active_populations) == 2
         active_pops = [_.name for _ in dbg.epochs[1].active_populations]
-        assert "B" in active_pops and "C" in active_pops
+        assert "B" in active_pops
+        assert "C" in active_pops
         assert len(dbg.epochs[2].active_populations) == 1
         assert "A" in dbg.epochs[2].active_populations[0].name
 
@@ -628,10 +629,12 @@ def test_activate_ghost_admixture(self):
         assert "D" == dbg.epochs[0].active_populations[0].name
         assert len(dbg.epochs[1].active_populations) == 2
         active_pops = [_.name for _ in dbg.epochs[1].active_populations]
-        assert "B" in active_pops and "D" in active_pops
+        assert "B" in active_pops
+        assert "D" in active_pops
         assert len(dbg.epochs[2].active_populations) == 2
         active_pops = [_.name for _ in dbg.epochs[2].active_populations]
-        assert "B" in active_pops and "C" in active_pops
+        assert "B" in active_pops
+        assert "C" in active_pops
         assert len(dbg.epochs[3].active_populations) == 1
         assert "A" in dbg.epochs[3].active_populations[0].name
 
@@ -775,7 +778,7 @@ def test_admixture_via_mass_migration(self):
             assert epoch.end_size == 1000
 
     @pytest.mark.parametrize(
-        "time_lo,time_hi", [(0, math.inf), (0, 20), (10, math.inf), (10, 20)]
+        ("time_lo", "time_hi"), [(0, math.inf), (0, 20), (10, math.inf), (10, 20)]
     )
     def test_asymmetric_migration_via_rate_change(self, time_lo, time_hi):
         demog = msprime.Demography.isolated_model([1000] * 2)
@@ -928,8 +931,8 @@ def test_bad_pulse(self):
             demog.to_demes()
 
     @pytest.mark.parametrize(
-        "sizes,times",
-        (([1000], [0]), ([1000, 500], [0, 20]), ([1000, 50, 1000], [0, 20, 30])),
+        ("sizes", "times"),
+        [([1000], [0]), ([1000, 500], [0, 20]), ([1000, 50, 1000], [0, 20, 30])],
     )
     def test_piecewise_constant_sizes(self, sizes, times):
         assert len(sizes) == len(times)
@@ -953,13 +956,13 @@ def test_piecewise_constant_sizes(self, sizes, times):
             assert epochs[j].end_time == times[len(times) - j - 1]
 
     @pytest.mark.parametrize(
-        "sizes,growth_rates,times",
-        (
+        ("sizes", "growth_rates", "times"),
+        [
             ([1000, 500], [0.1, 0], [0, 20]),
             ([1000, None, 1000], [0.1, -0.1, 0], [0, 20, 30]),
             ([1000, 5000, 1000], [0.1, None, 0], [0, 20, 30]),
             ([1000, 5000, None], [0.1, None, 0], [0, 20, 30]),
-        ),
+        ],
     )
     def test_piecewise_exponential_sizes(self, sizes, growth_rates, times):
         assert growth_rates[-1] == 0  # can't convert to demes graph otherwise

tests/test_demography.py

@@ -1731,7 +1731,7 @@ def test_double_step_validation(self):
         )
         ddb = model.debug()
         steps = np.linspace(0, 400, 2)
-        with pytest.warns(UserWarning):
+        with pytest.warns(UserWarning, match="Doubling the number of steps"):
             ddb.coalescence_rate_trajectory(steps=steps, lineages={"A": 2})
         # Test coalescence rates without double step validation
         steps = np.linspace(0, 400, 401)

tests/test_mutations.py

@@ -367,7 +367,7 @@ def test_SMM(self):
         sys.platform.startswith("win"), reason="Windows BLAS issue #2349"
     )
     @pytest.mark.parametrize(
-        "p, m, lo, hi",
+        ("p", "m", "lo", "hi"),
         [
             (0.9, 0.9, 2, 50),
             (0.5, 0.25, 50, 500),
@@ -428,7 +428,7 @@ def test_EL2(self):
                 assert np.abs(exp - a_ratio) < 1e-6
 
     @pytest.mark.parametrize(
-        "m, u, v, p, s, lo, hi",
+        ("m", "u", "v", "p", "s", "lo", "hi"),
         [
             (1.0, 0.62, 0.015, 0, 0.88, 1, 10.0),
             (0.43, 0.68, 0.037, 1.0, 0.5, 3.0, 10),
@@ -444,7 +444,7 @@ def test_MicrosatMutationModel(self, m, u, v, p, s, lo, hi):
 
 class TestMicrosatModels:
     @pytest.mark.parametrize(
-        "m, u, v, p, s",
+        ("m", "u", "v", "p", "s"),
         [
             (1.0, 0.62, 0.015, 0, 0.88),
             (0.43, 0.68, 0.037, 0, 0.88),
@@ -468,7 +468,7 @@ def test_transition_matrix(self, m, u, v, p, s):
             assert ((d[0] / d[j]) - exp) < 1e-6
 
     @pytest.mark.parametrize(
-        "m, u, v, p, s, lo, hi",
+        ("m", "u", "v", "p", "s", "lo", "hi"),
         [
             (1.0, 0.62, 0.015, 0, 0.88, 1, np.inf),
             (0.43, 0.68, 0.037, 0, 0.88, np.inf, 10),

tests/test_python_c.py

@@ -934,7 +934,8 @@ def test_demographic_events(self):
                     migration_matrix[:] = rate
                     np.fill_diagonal(migration_matrix, 0)
                 else:
-                    assert source >= 0 and dest >= 0
+                    assert source >= 0
+                    assert dest >= 0
                     migration_matrix[source, dest] = rate
             elif event_type == "mass_migration":
                 source = event["source"]