From c60e8ec4f6fa263ac68dbffef333802291a462f4 Mon Sep 17 00:00:00 2001
From: James Gaboardi <jgaboardi@gmail.com>
Date: Sat, 21 Oct 2023 21:22:36 -0400
Subject: [PATCH] handle warnings and linting more granularly

---
 giddy/tests/test_ergodic.py |  4 +++-
 pyproject.toml              | 40 +++++++++++++++++++++++--------------
 2 files changed, 28 insertions(+), 16 deletions(-)

diff --git a/giddy/tests/test_ergodic.py b/giddy/tests/test_ergodic.py
index e180e37..434d88d 100644
--- a/giddy/tests/test_ergodic.py
+++ b/giddy/tests/test_ergodic.py
@@ -1,3 +1,4 @@
+import pytest
 import unittest
 from .. import ergodic
 import numpy as np
@@ -58,7 +59,8 @@ def test_mfpt(self):
         )
         np.testing.assert_array_almost_equal(exp, obs)
 
-        obs = ergodic.fmpt(self.p2)
+        with pytest.warns(DeprecationWarning, match="fmpt is deprecated."):
+            obs = ergodic.fmpt(self.p2)
         exp = np.array(
             [
                 [2.66666667, 2.0, np.inf],
diff --git a/pyproject.toml b/pyproject.toml
index a276cea..fbe5ff6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -77,33 +77,33 @@ extend-exclude = '''
 line-length = 88
 select = ["E", "F", "W", "I", "UP", "N", "B", "A", "C4", "SIM", "ARG"]
 target-version = "py39"
-ignore = [
-    "B006",
-    "B008",
-    "B009",
-    "B010",
-    "C408",
-    "E731",
-    "F401",
-    "F403",
-    "N803",
-    "N806",
-    "N999",
-    "UP007"
-]
 exclude = ["giddy/tests/*", "docs/*"]
 [tool.ruff.per-file-ignores]
+"__init__.py" = ["F401"] # imported but unused
 "giddy/directional.py" = [
     "ARG002",  # Unused method argument
+    "N803",  # Argument name should be lowercase
+    "N806",  # Variable in function should be lowercase
+]
+"giddy/ergodic.py" = [
+    "N803",  # Argument name should be lowercase
+    "N806",  # Variable in function should be lowercase
 ]
 "giddy/markov.py" = [
+    "B006",  # Do not use mutable data structures for argument defaults
     "N801",  # Class name should use CapWords convention
     "N802",  # Function name should be lowercase
+    "N803",
+    "N806",
 ]
 "giddy/rank.py" = [
-    "N801",
     "ARG002",
+    "N801",
+    "N803",
+    "N806",
 ]
+"giddy/sequence.py" = ["N806"]
+"giddy/util.py" = ["N803"]
 
 [tool.coverage.run]
 source = ["./giddy"]
@@ -118,3 +118,13 @@ exclude_lines = [
 ]
 ignore_errors = true
 omit = ["giddy/tests/*", "docs/conf.py"]
+
+[tool.pytest.ini_options]
+filterwarnings = [
+    "ignore:The weights matrix is not fully connected",             # libpysal
+    "ignore:Objects based on the `Geometry` class will deprecated", # libpysa
+    "ignore:divide by zero encountered",
+    "ignore:invalid value encountered",
+    "ignore:numba.generated_jit is deprecated.",                    # numba/quantecon
+    "ignore:::.*quantecon.lss:19",                                  # numba/quantecon
+]
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