From 6528f398dd446d3e16f1139d3951b60bcaffcb63 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]" <github-actions[bot]@users.noreply.github.com>
Date: Wed, 1 Apr 2026 05:25:49 +0000
Subject: [PATCH 1/2] chore: pre-commit autoupdate

---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b9246b5..3b49c31 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -3,7 +3,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: 'v4.5.0'
+    rev: 'v6.0.0'
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
@@ -18,7 +18,7 @@ repos:
       - id: requirements-txt-fixer
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.4.10
+    rev: v0.15.8
     hooks:
       # Run the linter.
       - id: ruff

From 78feffe6ff070efd841eaf2bd665d96a15d50bc5 Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Wed, 8 Apr 2026 19:54:03 -0400
Subject: [PATCH 2/2] appease ruff

---
 .pre-commit-config.yaml                      |  2 +-
 ConservedWaterSearch/hydrogen_orientation.py | 79 ++++++++++----------
 ConservedWaterSearch/utils.py                | 74 +++++++-----------
 ConservedWaterSearch/water_clustering.py     | 16 ++--
 tests/conftest.py                            | 10 +--
 tests/test_hydrogen_orientation.py           | 13 ++--
 6 files changed, 90 insertions(+), 104 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 3b49c31..80cf569 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -21,7 +21,7 @@ repos:
     rev: v0.15.8
     hooks:
       # Run the linter.
-      - id: ruff
+      - id: ruff-check
         types_or: [ python, pyi, jupyter ]
         args: [ --fix ]
       # Run the formatter.
diff --git a/ConservedWaterSearch/hydrogen_orientation.py b/ConservedWaterSearch/hydrogen_orientation.py
index 0fad4e4..bbb8e40 100644
--- a/ConservedWaterSearch/hydrogen_orientation.py
+++ b/ConservedWaterSearch/hydrogen_orientation.py
@@ -2,6 +2,11 @@
 
 from typing import TYPE_CHECKING
 
+try:
+    import matplotlib.pyplot as plt
+except ImportError:
+    plt = None
+
 if TYPE_CHECKING:
     try:
         from matplotlib.axes import Axes
@@ -360,7 +365,7 @@ def find_fully_conserved_orientations(
         sk = (
             f"Conserved - kmeans analysis:\n"
             f"angle - mean: {ang:.2f}(calced)<{kmeans_ang_cutoff:.2f};"
-            f" inertia per H: {kmeans.inertia_/len(orientations):.2f}"
+            f" inertia per H: {kmeans.inertia_ / len(orientations):.2f}"
             f"(calced)<{kmeans_inertia_cutoff:.2f}\n"
         )
     if debugH == 2 or (debugH == 1 and len(fully_conserved) > 0):
@@ -372,11 +377,11 @@ def find_fully_conserved_orientations(
             f" buffer:{pct_size_buffer:.2f}\n"
             f"cluster sizes: {counts}; clust labels:{values};biggest: {biggest}"
             f"; secondbiggest: {secondbiggest}\n"
-            f"clusters size: {neioc*pct_size_buffer:.2f}<"
+            f"clusters size: {neioc * pct_size_buffer:.2f}<"
             f"{len(orientations[labels == biggest])},"
             f"{len(orientations[labels == secondbiggest])}"
-            f"(calced)<{neioc*(2-pct_size_buffer):.2f}\n"
-            f"angle mean: {np.abs(np.mean(angs21)-np.mean(angs12)):.2f}(calced)"
+            f"(calced)<{neioc * (2 - pct_size_buffer):.2f}\n"
+            f"angle mean: {np.abs(np.mean(angs21) - np.mean(angs12)):.2f}(calced)"
             f"<{angdiff_cutoff:.2f}); 12 std : {np.std(angs12):.2f};21 std: "
             f"{np.std(angs21):.2f} (both <{angstd_cutoff:.2f})\n"
         )
@@ -391,7 +396,7 @@ def find_fully_conserved_orientations(
         ss,
         (
             f"Reachability of optics plot\n"
-            f"minsamples={int(neioc*pct_size_buffer)}; xi={xi}"
+            f"minsamples={int(neioc * pct_size_buffer)}; xi={xi}"
         ),
         len(fully_conserved) > 0,
         debugH,
@@ -480,8 +485,8 @@ def find_half_conserved_orientations(
         N_elems = len(orientations[labels == bestcand])
         # Debug
         if verbose > 0:
-            sk += f"Cluster {bestcand} has {neioc*pct_size_buffer:.2f}<"
-            sk += f"{N_elems}<{neioc*(2-pct_size_buffer):.2f} elements\n"
+            sk += f"Cluster {bestcand} has {neioc * pct_size_buffer:.2f}<"
+            sk += f"{N_elems}<{neioc * (2 - pct_size_buffer):.2f} elements\n"
         # check if number of elements in hydrogen orientation cluster is
         # between 0.80 and 1.20 elements of Oxygen cluster
         if (
@@ -499,7 +504,7 @@ def find_half_conserved_orientations(
             # Debug
             if verbose > 0 or debugH > 0:
                 sk += "result angles: mean= "
-                sk += f"{np.abs(np.mean(angs1all)-104.5):.2f}(Calced)<"
+                sk += f"{np.abs(np.mean(angs1all) - 104.5):.2f}(Calced)<"
                 sk += f"{angdiff_cutoff:.2f}; std dev={np.std(angs1all):.2f}"
                 sk += f"(Calced)<{angstd_cutoff:.2f}\n"
             # check if angle and its std deviation is satisfactory
@@ -522,10 +527,10 @@ def find_half_conserved_orientations(
         ss = (
             f"Half Conserved - OPTICS analysis;xi={xi}"
             f"best: {bestcand}; N_hyd_cls (w/o -1): "
-            f"{len(np.unique(labels[labels!=-1]))};\n N elem in biggest:"
-            f"{neioc*(2-pct_size_buffer):.2f}>"
-            f"{len(orientations[labels==bestcand])}>"
-            f"{neioc*pct_size_buffer:.2f}\n"
+            f"{len(np.unique(labels[labels != -1]))};\n N elem in biggest:"
+            f"{neioc * (2 - pct_size_buffer):.2f}>"
+            f"{len(orientations[labels == bestcand])}>"
+            f"{neioc * pct_size_buffer:.2f}\n"
         )
     # Printing
     if verbose == 2 or (verbose == 1 and len(half_conserved) > 0):
@@ -538,7 +543,7 @@ def find_half_conserved_orientations(
         ss + sk,
         (
             f"Reachability of optics plot\n minsamples="
-            f"{int(neioc*min_samp_data_size_pct)}; xi={xi}"
+            f"{int(neioc * min_samp_data_size_pct)}; xi={xi}"
         ),
         len(half_conserved) > 0,
         debugH,
@@ -645,8 +650,8 @@ def find_weakly_conserved_orientations(
             N_elems = len(orientations[labels == ii])
             # Debug
             if verbose > 0 or debugH > 0:
-                sk += f"Cluster {ii} has {neioc*lower_bound_pct_buffer:.2f}<"
-                sk += f"{N_elems}<{neioc*(2-pct_size_buffer):.2f} elements\n"
+                sk += f"Cluster {ii} has {neioc * lower_bound_pct_buffer:.2f}<"
+                sk += f"{N_elems}<{neioc * (2 - pct_size_buffer):.2f} elements\n"
             # check if size of hydorgen orientation cluster is between 1.20
             # and lower_bound_pct_buffer times number of elements in oxygen cluster
             if (
@@ -675,11 +680,11 @@ def find_weakly_conserved_orientations(
                         maxcomp = np.max([N_elems, N_elems_jj])
                         calcedcomp = (1 - pct_size_buffer) * maxcomp
                         sk += f"cluster combo:{ii} & {jj}size:{N_elems},"
-                        sk += f"{neioc*lower_bound_pct_buffer:.2f}<{N_elems_jj}<"
-                        sk += f"{neioc*(2-pct_size_buffer):.2f}\n"
-                        sk += f"size comparison {np.abs(N_elems -N_elems_jj)}"
+                        sk += f"{neioc * lower_bound_pct_buffer:.2f}<{N_elems_jj}<"
+                        sk += f"{neioc * (2 - pct_size_buffer):.2f}\n"
+                        sk += f"size comparison {np.abs(N_elems - N_elems_jj)}"
                         sk += f"(calced) < {calcedcomp} \n"
-                        sk += f"ang diff={np.abs(np.mean(angs1j)-104.5):.2f}"
+                        sk += f"ang diff={np.abs(np.mean(angs1j) - 104.5):.2f}"
                         sk += f"(calced)<{angdiff_cutoff:.2f},std dev:"
                         sk += f"{angstd_cutoff:.2f}>{np.std(angs1j):.2f}(calced)\n"
                     # check if size of new cluster and check if size of clusters
@@ -796,20 +801,20 @@ def find_weakly_conserved_orientations(
                         sk += "size check "
                         sk += f"{np.abs(N_elems - (N_elems_jj + N_elems_kk))}"
                         sk += f"(calced)< {sizeingprint}\n"
-                        sk += f"ang diff={np.abs(np.mean(angs1jk)-104.5):.2f}"
+                        sk += f"ang diff={np.abs(np.mean(angs1jk) - 104.5):.2f}"
                         sk += f"(calced)<{angdiff_cutoff:.2f},std dev:"
                         sk += f"{angstd_cutoff:.2f}>{np.std(angs1jk):.2f}"
                         sk += "(calced)\n"
-                        sk += f"ij {ii},{jj}, {np.abs(np.mean(angs1j)-104.5)},"
+                        sk += f"ij {ii},{jj}, {np.abs(np.mean(angs1j) - 104.5)},"
                         sk += f"<,angdiff_cutoff,and std {np.std(angs1j)}<"
                         sk += f"{angstd_cutoff} \n"
-                        sk += f"ik {ii},{kk}, {np.abs(np.mean(angs1k)-104.5)},"
+                        sk += f"ik {ii},{kk}, {np.abs(np.mean(angs1k) - 104.5)},"
                         sk += f"<,angdiff_cutoff,and std {np.std(angs1k)}<"
                         sk += f"{angstd_cutoff} \n"
-                        sk += f"kj {kk},{jj}, {np.abs(np.mean(angskj)-104.5)},"
+                        sk += f"kj {kk},{jj}, {np.abs(np.mean(angskj) - 104.5)},"
                         sk += f"<,angdiff_cutoff,and std {np.std(angskj)}<"
                         sk += f"{angstd_cutoff} \n"
-                        sk += f"jk {jj},{kk}, {np.abs(np.mean(angsjk)-104.5)},"
+                        sk += f"jk {jj},{kk}, {np.abs(np.mean(angsjk) - 104.5)},"
                         sk += f"<,angdiff_cutoff,and std {np.std(angsjk)}<"
                         sk += f"{angstd_cutoff} \n"
                     # check if size of clusters is about equal ii==jj+kk
@@ -981,8 +986,8 @@ def find_weakly_conserved_orientations(
             f"weakly Conserved - OPTICS analysis;xi={xi}\n"
             f"Number of hydrogen clusters : {len(np.unique(labels))};\n"
             f"number of elements : {counts}; range needed for best cluster:"
-            f"(depends on numbpct) {neioc*(2-pct_size_buffer):.2f},"
-            f"{neioc*lower_bound_pct_buffer:.2f}\n"
+            f"(depends on numbpct) {neioc * (2 - pct_size_buffer):.2f},"
+            f"{neioc * lower_bound_pct_buffer:.2f}\n"
         )
     # Debug Printing
     if verbose == 2 or (verbose == 1 and len(weakly_conserved) > 0):
@@ -995,7 +1000,7 @@ def find_weakly_conserved_orientations(
         ss,
         (
             f"Reachability of optics plot\n"
-            f"minsamples={int(neioc*min_samp_data_size_pct)}; xi={xi}"
+            f"minsamples={int(neioc * min_samp_data_size_pct)}; xi={xi}"
         ),
         len(weakly_conserved) > 0,
         debugH,
@@ -1026,11 +1031,9 @@ def __plot3Dorients(subplot, labels: int, orientations: np.ndarray, tip: str) ->
     For debuging only.
 
     """
-    try:
-        import matplotlib.pyplot as plt
-    except ModuleNotFoundError as err:
+    if plt is None:
         msg = "install matplotlib"
-        raise Exception(msg) from err
+        raise Exception(msg)
 
     fig = plt.figure()
     if isinstance(labels, int):
@@ -1043,7 +1046,7 @@ def __plot3Dorients(subplot, labels: int, orientations: np.ndarray, tip: str) ->
             jaba[:, 0],
             jaba[:, 1],
             jaba[:, 2],
-            label=f"{j} ({len(labels[labels==j])})",
+            label=f"{j} ({len(labels[labels == j])})",
         )
         if j > -1:
             ax.quiver(
@@ -1075,15 +1078,13 @@ def __plotreachability(
     For debuging purposes only.
 
     """
-    try:
-        import matplotlib.pyplot as plt
-    except ModuleNotFoundError as err:
+    if plt is None:
         msg = "install matplotlib"
-        raise Exception(msg) from err
+        raise Exception(msg)
 
     if fig is None:
         fig: Figure = plt.figure()
-    if type(cc) != OPTICS:
+    if not isinstance(cc, OPTICS):
         return fig
     lblls = cc.labels_[cc.ordering_]
     labels = cc.labels_
@@ -1100,7 +1101,7 @@ def __plotreachability(
             ax2.plot(
                 space[lblls == clst],
                 reachability[lblls == clst],
-                label=f"{clst} ({len(space[lblls==clst])}), avg reach={label}",
+                label=f"{clst} ({len(space[lblls == clst])}), avg reach={label}",
                 color="blue",
             )
         else:
@@ -1108,7 +1109,7 @@ def __plotreachability(
             ax2.plot(
                 space[lblls == clst],
                 reachability[lblls == clst],
-                label=f"{clst} ({len(space[lblls==clst])}), avg reach={label}",
+                label=f"{clst} ({len(space[lblls == clst])}), avg reach={label}",
             )
     ax2.legend()
     return fig
diff --git a/ConservedWaterSearch/utils.py b/ConservedWaterSearch/utils.py
index 869d9bd..a9e797a 100644
--- a/ConservedWaterSearch/utils.py
+++ b/ConservedWaterSearch/utils.py
@@ -3,33 +3,43 @@
 
 import os
 import platform
+import warnings
 from typing import TYPE_CHECKING
 
 import numpy as np
 
+try:
+    import matplotlib.pyplot as plt
+except ImportError:
+    plt = None
+
+try:
+    import pymol
+    from pymol import cmd
+except ImportError:
+    pymol = None
+    cmd = None
+
+try:
+    import nglview as ngl
+except ImportError:
+    ngl = None
+
 if TYPE_CHECKING:
     try:
         from nglview import NGLWidget
     except ImportError:
         NGLWidget = None
-    try:
-        import pymol
-        from pymol import cmd
-    except ImportError:
-        pymol = None
-        cmd = None
 
 
 def _check_mpl_installation():
     """Check if matplotlib is installed."""
-    try:
-        import matplotlib.pyplot as plt
-    except ModuleNotFoundError as err:
+    if plt is None:
         msg = (
             "install matplotlib using conda install -c conda-forge"
             "matplotlib or pip install matplotlib"
         )
-        raise Exception(msg) from err
+        raise Exception(msg)
     return plt
 
 
@@ -154,8 +164,6 @@ def get_orientations_from_positions(
 
 
 def _make_protein_surface_with_ligand():
-    from pymol import cmd
-
     protein = cmd.get_unused_name("only_protein_")
     cmd.select(protein, "polymer", state=1)
     povrsina = cmd.get_unused_name("protein_surface_")
@@ -171,8 +179,6 @@ def _make_protein_surface_with_ligand():
 
 
 def _add_polar_contacts(waters: str, aminokis_u_am: str | None = None):
-    from pymol import cmd
-
     if aminokis_u_am is not None:
         sele = aminokis_u_am + " or " + waters + " or organic"
     else:
@@ -187,8 +193,6 @@ def _add_polar_contacts(waters: str, aminokis_u_am: str | None = None):
 
 
 def _fix_pymol_camera(active_site_center: str | None = None, waters: str | None = None):
-    from pymol import cmd
-
     # reset camera
     cmd.reset()
     if active_site_center is not None:
@@ -198,8 +202,6 @@ def _fix_pymol_camera(active_site_center: str | None = None, waters: str | None
 
 
 def _determine_active_site_ids(active_site_ids: list[int]):
-    from pymol import cmd
-
     selection = ""
     for i in active_site_ids:
         selection += str(i) + "+"
@@ -220,17 +222,13 @@ def _determine_active_site_ids(active_site_ids: list[int]):
 
 
 def _add_density_map(density_map: str):
-    from pymol import cmd
-
     cmd.load(density_map)
-    cmd.volume("water_density", density_map.split(".")[0])
+    cmd.volume("water_density", density_map.split(".", maxsplit=1)[0])
 
 
 def _add_crystal_waters(
     crystal_waters, protein, ligand_resname, dist, active_site_ids, active_site_center
 ):
-    from pymol import cmd
-
     cmd.fetch(crystal_waters)
     cmd.hide("everything", crystal_waters)
     cmd.align(
@@ -264,8 +262,6 @@ def _add_crystal_waters(
 
 
 def _add_hydrogen_and_bond(wname, Hpos, Hname, resn, resi):
-    from pymol import cmd
-
     cmd.pseudoatom(
         wname,
         pos=[Hpos[0], Hpos[1], Hpos[2]],
@@ -279,8 +275,6 @@ def _add_hydrogen_and_bond(wname, Hpos, Hname, resn, resi):
 
 
 def _make_water_objects(water_type, waterO, waterH1, waterH2, output_file):
-    from pymol import cmd
-
     cntr = {
         name: (
             len(cmd.get_names("objects", False, f"model {name}*"))
@@ -340,7 +334,7 @@ def _make_water_objects(water_type, waterO, waterH1, waterH2, output_file):
                     _add_hydrogen_and_bond(
                         wname,
                         waterH2[ind + add_ind + 1],
-                        f"H{add_ind+3}",
+                        f"H{add_ind + 3}",
                         resn,
                         highest_resi + 1,
                     )
@@ -367,7 +361,7 @@ def _make_water_objects(water_type, waterO, waterH1, waterH2, output_file):
                         _add_hydrogen_and_bond(
                             wname,
                             waterH1[ind + add_ind + 1],
-                            f"H{add_ind+ghind+3}",
+                            f"H{add_ind + ghind + 3}",
                             resn,
                             highest_resi + 1,
                         )
@@ -387,7 +381,7 @@ def _make_water_objects(water_type, waterO, waterH1, waterH2, output_file):
                         _add_hydrogen_and_bond(
                             wname,
                             waterH2[ind + add_ind + 1],
-                            f"H{add_ind+hind+ghind+3}",
+                            f"H{add_ind + hind + ghind + 3}",
                             resn,
                             highest_resi + 1,
                         )
@@ -491,8 +485,6 @@ def visualise_pymol(
         lunch_pymol = False
     _initialize_pymol(reinitialize, lunch_pymol)
     if platform.system() == "Darwin" and output_file is None:
-        import warnings
-
         warnings.warn(
             (
                 "mac OS detected interactive pymol session cannot be lunched."
@@ -503,8 +495,6 @@ def visualise_pymol(
             stacklevel=2,
         )
         output_file = "pymol_water_visualization.pse"
-    from pymol import cmd
-
     cmd.hide("everything")
     active_site_center = None
     aminokis_u_am = None
@@ -599,7 +589,6 @@ def visualise_pymol_from_pdb(
     if platform.system() == "Darwin":
         lunch_pymol = False
     _initialize_pymol(reinitialize, lunch_pymol)
-    from pymol import cmd
 
     cmd.load(pdbfile)
     cmd.hide("everything")
@@ -640,7 +629,7 @@ def visualise_pymol_from_pdb(
     if crystal_waters is not None:
         _add_crystal_waters(
             crystal_waters,
-            pdbfile.split(".")[0],
+            pdbfile.split(".", maxsplit=1)[0],
             ligand_resname,
             dist,
             active_site_ids,
@@ -669,12 +658,9 @@ def _initialize_pymol(reinitialize: bool, finish: bool):
             in interactive mode. If `False` pymol will be
             imported without lunching. Defaults to True.
     """
-    try:
-        import pymol
-        from pymol import cmd
-    except ModuleNotFoundError as err:
+    if pymol is None or cmd is None:
         msg = "pymol not installed. Either install pymol or use nglview"
-        raise Exception(msg) from err
+        raise Exception(msg)
     if finish:
         pymol.finish_launching(["pymol", "-q"])
     if reinitialize:
@@ -734,11 +720,9 @@ def visualise_nglview(
         # initialise widget
         view
     """
-    try:
-        import nglview as ngl
-    except ModuleNotFoundError as err:
+    if ngl is None:
         msg = "nglview not installed. Either install pymol or nglview"
-        raise Exception(msg) from err
+        raise Exception(msg)
 
     if aligned_protein is not None:
         view: NGLWidget = ngl.show_file(aligned_protein, default_representation=False)
diff --git a/ConservedWaterSearch/water_clustering.py b/ConservedWaterSearch/water_clustering.py
index 9c9f10d..ec5c336 100644
--- a/ConservedWaterSearch/water_clustering.py
+++ b/ConservedWaterSearch/water_clustering.py
@@ -835,15 +835,15 @@ def _scan_clustering_params(
                         if self.debugO > 0:
                             dbgt: str = ""
                             if self.verbose > 0:
-                                (aa, bb) = np.unique(clusters, return_counts=True)
+                                (_aa, bb) = np.unique(clusters, return_counts=True)
                                 dbgt = (
                                     f"Oxygen clustering {type(clust)} "
                                     f"minsamp={i}, xi={j}, "
-                                    f"{len(np.unique(clusters[clusters!=-1]))} "
+                                    f"{len(np.unique(clusters[clusters != -1]))} "
                                     f"clusters \n"
                                     f"Required N(elem) range:"
-                                    f"{self.nsnaps*self.numbpct_oxygen:.2f} to "
-                                    f"{(2-self.numbpct_oxygen)*self.nsnaps}; "
+                                    f"{self.nsnaps * self.numbpct_oxygen:.2f} to "
+                                    f"{(2 - self.numbpct_oxygen) * self.nsnaps}; "
                                     f"(tar cls size={self.nsnaps} and numbpct="
                                     f"{self.numbpct_oxygen:.2f})\n"
                                     f"N(elements) for each cluster: {bb}\n"
@@ -932,7 +932,7 @@ def _analyze_oxygen_clustering(
             # Nsnap*0.85<Nelem<Nsnap*1.15 then ignore
             if min_neioc < neioc < max_neioc:
                 if self.verbose > 0:
-                    print(f"O clust {k}, size {len(clusters[clusters==k])}\n")
+                    print(f"O clust {k}, size {len(clusters[clusters == k])}\n")
                 O_center = np.mean(Odata[mask], axis=0)
                 if "onlyO" not in self.water_types_to_find:
                     # Construct array of hydrogen orientations
@@ -1214,7 +1214,7 @@ def _oxygen_clustering_plot(
                 jaba[:, 0],
                 jaba[:, 1],
                 jaba[:, 2],
-                label=f"{k} ({len(cc.labels_[cc.labels_==k])})",
+                label=f"{k} ({len(cc.labels_[cc.labels_ == k])})",
                 s=s,
             )
         ax.set_xlabel("X")
@@ -1234,14 +1234,14 @@ def _oxygen_clustering_plot(
                     ax.plot(
                         space[lblls == clst],
                         cc.reachability_[lblls == clst],
-                        label=f"{clst} ({len(space[lblls==clst])})",
+                        label=f"{clst} ({len(space[lblls == clst])})",
                         color="blue",
                     )
                 else:
                     ax.plot(
                         space[lblls == clst],
                         cc.reachability_[lblls == clst],
-                        label=f"{clst} ({len(space[lblls==clst])})",
+                        label=f"{clst} ({len(space[lblls == clst])})",
                     )
             ax.legend()
     if debugO == 2:
diff --git a/tests/conftest.py b/tests/conftest.py
index a774c44..b4cf5ee 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -99,12 +99,12 @@ def generate_water_network(
     return np.asarray(Opos), np.asarray(Hpos), base_oxygens
 
 
-@pytest.fixture()
+@pytest.fixture
 def orientations_normalized():
     return np.asarray([[1, 0, 0], [-0.25038 * 2, 0.96814764 * 2, 0]])
 
 
-@pytest.fixture()
+@pytest.fixture
 def orientations_not_normalized():
     return np.asarray([[1, 0, 0], [-0.25038, 0.96814764, 0]])
 
@@ -123,7 +123,7 @@ def water_data(request):
     return generate_orientation_sample(kind, nsnaps=24, rng=rng), expected
 
 
-@pytest.fixture()
+@pytest.fixture
 def _pymol_skip():
     pytest.importorskip("pymol")
 
@@ -151,7 +151,7 @@ def water_clustering_setup(request):
     return wc, request.param["onlyO"]
 
 
-@pytest.fixture()
+@pytest.fixture
 def water_clustering_setup_for_deletion():
     with tempfile.NamedTemporaryFile(
         mode="w+", delete=True
@@ -163,7 +163,7 @@ def water_clustering_setup_for_deletion():
         yield wc, dat.name, Odata, H1, H2
 
 
-@pytest.fixture()
+@pytest.fixture
 def water_clustering_data():
     rng = np.random.default_rng(2024)
     Opos, Hpos, centers = generate_water_network(nsnaps=12, n_waters=2, rng=rng)
diff --git a/tests/test_hydrogen_orientation.py b/tests/test_hydrogen_orientation.py
index 7dbf748..990ea8f 100644
--- a/tests/test_hydrogen_orientation.py
+++ b/tests/test_hydrogen_orientation.py
@@ -1,6 +1,11 @@
 """Unit and regression test for the ConservedWaterSearch package."""
 
 # Import package, test suite, and other packages as needed
+try:
+    import matplotlib.pyplot as plt
+except ImportError:
+    plt = None
+
 import numpy as np
 import pytest
 
@@ -33,9 +38,7 @@ def test_water_types_from_files(data_file):
     res = ConservedWaterSearch.hydrogen_orientation.hydrogen_orientation_analysis(
         orientations, debugH=make_ho_plots
     )
-    if make_ho_plots > 0:
-        import matplotlib.pyplot as plt
-
+    if make_ho_plots > 0 and plt is not None:
         plt.show()
     if "not_conserved" in data_label:
         assert len(res) == 0
@@ -49,9 +52,7 @@ def test_water_types(water_data):
     res = ConservedWaterSearch.hydrogen_orientation.hydrogen_orientation_analysis(
         orientations, debugH=make_ho_plots
     )
-    if make_ho_plots > 0:
-        import matplotlib.pyplot as plt
-
+    if make_ho_plots > 0 and plt is not None:
         plt.show()
     if expected is None:
         assert len(res) == 0