test: suppress some warnings

deeprank2/dataset.py

@@ -430,9 +430,11 @@ def save_hist(
         else:
             raise ValueError("Please provide valid features names. They must be present in the current :class:`DeeprankDataset` children instance.")
 
-        fig.tight_layout()
-        fig.savefig(fname)
-        plt.close(fig)
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore")
+            fig.tight_layout()
+            fig.savefig(fname)
+            plt.close(fig)
 
     def _compute_mean_std(self):
         means = {

tests/features/test_secondary_structure.py

@@ -1,3 +1,5 @@
+import warnings
+
 import numpy as np
 
 from deeprank2.domain import nodestorage as Nfeat
@@ -19,7 +21,9 @@ def test_secondary_structure_residue():
         influence_radius=10,
         max_edge_length=10,
     )
-    add_features(pdb_path, graph)
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore")
+        add_features(pdb_path, graph)
 
     # Create a list of node information (residue number, chain ID, and secondary structure features)
     node_info_list = [[node.id.number, node.id.chain.id, node.features[Nfeat.SECSTRUCT]] for node in graph.nodes]

tests/tools/test_target.py

@@ -2,6 +2,7 @@
 import shutil
 import tempfile
 import unittest
+import warnings
 
 from pdb2sql import StructureSimilarity
 
@@ -34,25 +35,27 @@ def test_add_target(self):
             os.remove(graph_path)
 
     def test_compute_ppi_scores(self):
-        scores = compute_ppi_scores(
-            os.path.join(self.pdb_path, "1ATN_1w.pdb"),
-            os.path.join(self.ref, "1ATN.pdb"),
-        )
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore")
 
-        sim = StructureSimilarity(
-            os.path.join(self.pdb_path, "1ATN_1w.pdb"),
-            os.path.join(self.ref, "1ATN.pdb"),
-            enforce_residue_matching=False,
-        )
-        lrmsd = sim.compute_lrmsd_fast(method="svd")
-        irmsd = sim.compute_irmsd_fast(method="svd")
-        fnat = sim.compute_fnat_fast()
-        dockq = sim.compute_DockQScore(fnat, lrmsd, irmsd)
-        binary = irmsd < 4.0
-        capri = 4
-        for thr, val in zip([6.0, 4.0, 2.0, 1.0], [4, 3, 2, 1], strict=True):
-            if irmsd < thr:
-                capri = val
+            scores = compute_ppi_scores(
+                os.path.join(self.pdb_path, "1ATN_1w.pdb"),
+                os.path.join(self.ref, "1ATN.pdb"),
+            )
+            sim = StructureSimilarity(
+                os.path.join(self.pdb_path, "1ATN_1w.pdb"),
+                os.path.join(self.ref, "1ATN.pdb"),
+                enforce_residue_matching=False,
+            )
+            lrmsd = sim.compute_lrmsd_fast(method="svd")
+            irmsd = sim.compute_irmsd_fast(method="svd")
+            fnat = sim.compute_fnat_fast()
+            dockq = sim.compute_DockQScore(fnat, lrmsd, irmsd)
+            binary = irmsd < 4.0
+            capri = 4
+            for thr, val in zip([6.0, 4.0, 2.0, 1.0], [4, 3, 2, 1], strict=True):
+                if irmsd < thr:
+                    capri = val
 
         assert scores["irmsd"] == irmsd
         assert scores["lrmsd"] == lrmsd