Update pre-commit

Author: benjeffery

.pre-commit-config.yaml

@@ -1,14 +1,14 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
       - id: check-merge-conflict
       - id: debug-statements
       - id: mixed-line-ending
       - id: check-case-conflict
       - id: check-yaml
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.5
+    rev: v0.11.0
     hooks:
       - id: ruff
         args: [  "--fix", "--config", "ruff.toml" ]

tests/test_accuracy.py

@@ -41,7 +41,7 @@ class TestAccuracy:
     Test for some of the basic functions used in tsdate
     """
 
-    @pytest.mark.makefiles()
+    @pytest.mark.makefiles
     def test_make_static_files(self, request):
         """
         The function used to create the tree sequences for accuracy testing.

tests/test_cli.py

@@ -389,8 +389,7 @@ def test_probability_space(self, tmp_path):
         params = f"-n {self.popsize} --probability-space linear --method inside_outside"
         self.verify(tmp_path, input_ts, params)
         params = (
-            f"-n {self.popsize} --probability-space logarithmic "
-            "--method inside_outside"
+            f"-n {self.popsize} --probability-space logarithmic --method inside_outside"
         )
         self.verify(tmp_path, input_ts, params)
 

tests/test_functions.py

@@ -101,7 +101,7 @@ def test_one_tree_n2(self):
         span_data = self.verify_spans(ts)
         # with a single tree there should only be one span
         for node in span_data.nodes_to_date:
-            assert len(span_data.get_spans(node)), 1
+            assert len(span_data.get_spans(node)) == 1
         assert 2 in span_data.get_spans(2)[ts.num_samples]["descendant_tips"]
 
     def test_one_tree_n3(self):
@@ -110,7 +110,7 @@ def test_one_tree_n3(self):
         span_data = self.verify_spans(ts)
         # with a single tree there should only be one span
         for node in span_data.nodes_to_date:
-            assert len(span_data.get_spans(node)), 1
+            assert len(span_data.get_spans(node)) == 1
         for nd, expd_tips in [
             (4, 3),  # Node 4 (root) expected to have 3 descendant tips
             (3, 2),
@@ -123,7 +123,7 @@ def test_one_tree_n4(self):
         span_data = self.verify_spans(ts)
         # with a single tree there should only be one span
         for node in span_data.nodes_to_date:
-            assert len(span_data.get_spans(node)), 1
+            assert len(span_data.get_spans(node)) == 1
         for nd, expd_tips in [
             (6, 4),  # Node 6 (root) expected to have 4 descendant tips
             (5, 3),  # Node 5 (1st internal node) expected to have 3 descendant tips

tests/test_inference.py

@@ -453,7 +453,7 @@ class TestVariational:
     """
 
     @pytest.fixture(autouse=True)
-    def ts(self):  # noqa PT004
+    def ts(self):
         ts = msprime.sim_ancestry(
             samples=10,
             recombination_rate=1e-8,

tsdate/cli.py

@@ -72,8 +72,7 @@ def tsdate_cli_parser():
     parser = subparsers.add_parser(
         "date",
         help=(
-            "Takes an inferred tree sequence topology and "
-            "returns a dated tree sequence."
+            "Takes an inferred tree sequence topology and returns a dated tree sequence."
         ),
     )
 
@@ -87,8 +86,7 @@ def tsdate_cli_parser():
     parser.add_argument(
         "output",
         help=(
-            "The path and name of output file where the dated tree "
-            "sequence will saved."
+            "The path and name of output file where the dated tree sequence will saved."
         ),
     )
     parser.add_argument(

tsdate/discrete.py

@@ -207,12 +207,12 @@ def get_mut_lik_fixed_node(self, edge):
         that are equal to or older than the child age. This is not cached, as it is
         likely to be unique for each edge
         """
-        assert (
-            edge.child in self.fixednodes
-        ), "Wrongly called fixed node function on non-fixed node"
-        assert (
-            self.mut_rate is not None
-        ), "Cannot calculate mutation likelihoods with no mutation_rate set"
+        assert edge.child in self.fixednodes, (
+            "Wrongly called fixed node function on non-fixed node"
+        )
+        assert self.mut_rate is not None, (
+            "Cannot calculate mutation likelihoods with no mutation_rate set"
+        )
 
         mutations_on_edge = self.mut_edges[edge.id]
         child_time = self.ts.node(edge.child).time
@@ -235,12 +235,12 @@ def get_mut_lik_lower_tri(self, edge):
 
         """
         # Debugging asserts - should probably remove eventually
-        assert (
-            edge.child not in self.fixednodes
-        ), "Wrongly called lower_tri function on fixed node"
-        assert hasattr(
-            self, "unfixed_likelihood_cache"
-        ), "Must call `precalculate_mutation_likelihoods()` before getting likelihoods"
+        assert edge.child not in self.fixednodes, (
+            "Wrongly called lower_tri function on fixed node"
+        )
+        assert hasattr(self, "unfixed_likelihood_cache"), (
+            "Must call `precalculate_mutation_likelihoods()` before getting likelihoods"
+        )
 
         mutations_on_edge = self.mut_edges[edge.id]
         return self.unfixed_likelihood_cache[mutations_on_edge, edge.span]
@@ -598,9 +598,9 @@ def inside_pass(self, *, standardize=True, cache_inside=False, progress=None):
                 (self.ts.num_edges, self.lik.grid_size), self.lik.identity_constant
             )
         denominator = np.full(self.ts.num_nodes, np.nan)
-        assert (
-            self.lik.standardize is False
-        ), "Marginal likelihood requires unstandardized mutation likelihoods"
+        assert self.lik.standardize is False, (
+            "Marginal likelihood requires unstandardized mutation likelihoods"
+        )
         marginal_lik = self.lik.identity_constant
         # Iterate through the nodes via groupby on parent node
         for parent, edges in tqdm(

tsdate/evaluation.py

@@ -726,7 +726,7 @@ def allele_frequency_spectra(
             ax.text(
                 0.02,
                 0.98,
-                f"{i+1}:{j+1}",
+                f"{i + 1}:{j + 1}",
                 ha="left",
                 va="top",
                 transform=ax.transAxes,

tsdate/hypergeo.py

@@ -25,7 +25,7 @@
 """
 
 import ctypes
-from math import erf, exp, lgamma, log, pi, pow, sqrt
+from math import erf, exp, lgamma, log, pi, pow, sqrt  # noqa: A004
 
 import numba
 import numpy as np