Merge pull request #396 from grahamgower/lint

Fix some f-strings; additional linting.

demes/demes.py

@@ -62,7 +62,7 @@ def nonzero_len(self, attribute, value):
 def valid_deme_name(self, attribute, value):
     if not value.isidentifier():
         raise ValueError(
-            "Invalid deme name `{self.name}`. Names must be valid python identifiers. "
+            f"Invalid deme name '{value}'. Names must be valid python identifiers. "
             "We recommend choosing a name that starts with a letter or "
             "underscore, and is followed by one or more letters, numbers, "
             "or underscores."
@@ -1996,7 +1996,7 @@ def fromdict(cls, data: MutableMapping[str, Any]) -> "Graph":
             pop_list(data, "demes", required_type=MutableMapping, scope="toplevel")
         ):
             if "name" not in deme_data:
-                raise KeyError("demes[{i}]: required field 'name' not found")
+                raise KeyError(f"demes[{i}]: required field 'name' not found")
             deme_name = deme_data.pop("name")
             check_allowed(
                 deme_data, allowed_fields_deme_inner, f"demes[{i}] {deme_name}"
@@ -2179,7 +2179,7 @@ def simplify_epochs(data):
             if implied by the deme ancestor(s)'s end time(s).
             """
             for deme in data["demes"]:
-                for j, epoch in enumerate(deme["epochs"]):
+                for epoch in deme["epochs"]:
                     if epoch["size_function"] in ("constant", "exponential"):
                         del epoch["size_function"]
                     if epoch["start_size"] == epoch["end_size"]:
@@ -2276,7 +2276,7 @@ def collapse_demes(pairs):
                                 asymmetric.remove(mig)
                                 pairs.remove(deme_pair)
                             # add to symmetric list
-                            sym_mig = dict(demes=[d for d in deme_set], rate=k[0])
+                            sym_mig = dict(demes=list(deme_set), rate=k[0])
                             if k[1] is not None:
                                 sym_mig["start_time"] = k[1]
                             if k[2] is not None:

demes/ms.py

@@ -26,7 +26,7 @@ class ValueErrorArgumentParser(argparse.ArgumentParser):
     """
 
     def error(self, message):
-        _, exc, traceback = sys.exc_info()
+        _, exc, _ = sys.exc_info()
         raise ValueError(str(exc))
 
 

setup.cfg

@@ -65,3 +65,23 @@ target_version = py36
 [tool:pytest]
 addopts = -n auto
 testpaths = tests
+
+[pylint.messages_control]
+disable =
+    chained-comparison,
+    fixme,
+    invalid-name,
+    missing-docstring,
+    missing-module-docstring,
+    superfluous-parens,
+    protected-access,
+    too-few-public-methods,
+    too-many-arguments,
+    too-many-branches,
+    too-many-instance-attributes,
+    too-many-lines,
+    too-many-locals,
+    too-many-nested-blocks,
+    too-many-statements,
+    unspecified-encoding,
+    unused-argument,

tests/test_ms.py

@@ -122,7 +122,7 @@ def check(command, num_demes: int, migration: bool, N0=1):
                 demes.from_ms(cmd, N0=1)
 
         for bad_sample_configuration in ("50 0 0 2", "2 0 0 0 0 0 2"):
-            cmd = "ms 2 1 -t 1.0 -I {bad_sample_configuration}"
+            cmd = f"ms 2 1 -t 1.0 -I {bad_sample_configuration}"
             with pytest.raises(ValueError):
                 demes.from_ms(cmd, N0=1)
 
@@ -1496,7 +1496,7 @@ def test_li_and_durbin(self):
             N0=N_ref(theta=104693, mu=mu, length=30000000),
         )
 
-    def schiffels_inferring_human_population_size(self):
+    def test_schiffels_inferring_human_population_size(self):
         # Schiffels & Durbin (2014), https://doi.org/10.1038/ng.3015
         mu = 1.25e-8
         # Split simulation