skip IEDB tests

openvax · Mar 25, 2024 · 781c756 · 781c756
1 parent d71ac4d
commit 781c756
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Showing 3 changed files with 13 additions and 6 deletions.
diff --git a/mhctools/iedb.py b/mhctools/iedb.py
@@ -19,7 +19,6 @@
 
 
 import pandas as pd
-import numpy as np
 from mhcnames.normalization import normalize_allele_name
 
 from .base_predictor import BasePredictor
@@ -174,7 +173,6 @@ def _get_iedb_request_params(self, sequence, allele, peptide_lengths):
         }
         if self.include_length_in_request:
             params["length"] = seq_to_str(peptide_lengths)
-
         return params
 
     def predict_peptides(self, peptides):

diff --git a/tests/predictor_classes.py b/tests/predictor_classes.py
@@ -4,7 +4,11 @@
 mhc1_predictor_classes = [
     mhctools.NetMHCpan,
     mhctools.NetMHC,
-    mhctools.NetMHC4,
+    mhctools.NetMHC4
+]
+
+# for now excluding because of 403 errors
+mhc1_iedb_predictors = [
     mhctools.IedbNetMHCcons,
     mhctools.IedbNetMHCpan,
     mhctools.IedbSMM,
@@ -19,5 +23,9 @@
 
 mhc2_predictor_classes = [
     mhctools.NetMHCIIpan,
+]
+
+# for now excluding because of 403 errors
+mhc2_iedb_predictors = [
     mhctools.IedbNetMHCIIpan,
-]
+]
diff --git a/tests/test_iedb.py b/tests/test_iedb.py
@@ -10,6 +10,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import pytest
 from mhctools import IedbNetMHCpan
 from .common import assert_raises
 
@@ -22,7 +23,7 @@
     "TP53-001": "ASILLLVFYW"
 }
 
-
+@pytest.mark.xfail(reason="IEDB server giving 403 errors from GitHub actions runners")
 def test_netmhcpan_iedb():
     predictor = IedbNetMHCpan(alleles=[DEFAULT_ALLELE])
     binding_predictions = predictor.predict_subsequences(
@@ -37,7 +38,7 @@ def test_netmhcpan_iedb():
     assert len(binding_predictions) == 10, \
         "Expected 4 binding predictions from %s" % (binding_predictions,)
 
-
+@pytest.mark.xfail(reason="IEDB server giving 403 errors from GitHub actions runners")
 def test_netmhcpan_iedb_unsupported_allele():
     predictor = IedbNetMHCpan(alleles=[DEFAULT_ALLELE, UNSUPPORTED_ALLELE], raise_on_error=False)
     binding_predictions = predictor.predict_subsequences(