From 6e0002ab7902146898bfa7e485fc4fb138ff8cd9 Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Tue, 9 Apr 2024 13:20:23 -0400
Subject: [PATCH] more ruff fixes

---
 ConservedWaterSearch/utils.py      |  2 +-
 tests/test_hydrogen_orientation.py | 10 ++++++----
 tests/test_utils.py                |  2 +-
 tests/test_water_clustering.py     |  6 +++---
 4 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/ConservedWaterSearch/utils.py b/ConservedWaterSearch/utils.py
index 36492f2..869d9bd 100644
--- a/ConservedWaterSearch/utils.py
+++ b/ConservedWaterSearch/utils.py
@@ -693,7 +693,7 @@ def visualise_nglview(
 ) -> NGLWidget:
     """Creates a nglview visualisation widget for results.
 
-    Starts a `nglview <https://github.com/nglviewer/nglview>`__ visualisation 
+    Starts a `nglview <https://github.com/nglviewer/nglview>`__ visualisation
     instance from clustering results.
 
     Args:
diff --git a/tests/test_hydrogen_orientation.py b/tests/test_hydrogen_orientation.py
index 65e8cc9..94b8325 100644
--- a/tests/test_hydrogen_orientation.py
+++ b/tests/test_hydrogen_orientation.py
@@ -25,7 +25,7 @@ def test_orientation_normalization():
 
 def test_orientation_shape():
     orientations = np.asarray([[[1]]])
-    with pytest.raises(ValueError):
+    with pytest.raises(ValueError, match="Input array must be 2-dimensional"):
         ConservedWaterSearch.hydrogen_orientation.hydrogen_orientation_analysis(
             orientations
         )
@@ -33,7 +33,7 @@ def test_orientation_shape():
 
 def test_orientation_dimensions():
     orientations = np.asarray([[1, 0], [0, 1]])
-    with pytest.raises(ValueError):
+    with pytest.raises(ValueError, match="Input array must have shape (N, 3)"):
         ConservedWaterSearch.hydrogen_orientation.hydrogen_orientation_analysis(
             orientations
         )
@@ -48,7 +48,7 @@ def test_orientation_valid_input():
 
 def test_orientation_size():
     orientations = np.asarray([[1, 0, 0]])
-    with pytest.raises(ValueError):
+    with pytest.raises(ValueError, match="Input array must have shape (N, 3)"):
         ConservedWaterSearch.hydrogen_orientation.hydrogen_orientation_analysis(
             orientations
         )
@@ -56,7 +56,9 @@ def test_orientation_size():
 
 def test_orientation_array_odd():
     orientations = np.asarray([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
-    with pytest.raises(ValueError):
+    with pytest.raises(
+        ValueError, match="Input array must have an even number of rows"
+    ):
         ConservedWaterSearch.hydrogen_orientation.hydrogen_orientation_analysis(
             orientations
         )
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 0829d83..5e1a661 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -14,7 +14,7 @@
 
 
 @pytest.fixture(autouse=True)
-def pymol_skip():
+def _pymol_skip():
     pytest.importorskip("pymol")
 
 
diff --git a/tests/test_water_clustering.py b/tests/test_water_clustering.py
index 6d5ddaa..15b0ad1 100644
--- a/tests/test_water_clustering.py
+++ b/tests/test_water_clustering.py
@@ -3,6 +3,7 @@
 
 import numpy as np
 import numpy.testing as npt
+import pytest
 
 from ConservedWaterSearch.utils import (
     get_orientations_from_positions,
@@ -140,10 +141,9 @@ def test_create_from_file():
 
 def test_read_and_set_water_clust_options_file_not_found():
     wc = WaterClustering(9)
-    try:
+    with pytest.raises(FileNotFoundError, match="output file not found") as e:
         wc.read_and_set_water_clust_options("tests/data/nonexistent.dat")
-    except Exception as e:
-        assert str(e) == "output file not found"
+    assert str(e.value) == "output file not found"
 
 
 def test_restart_cluster_onlyO():