got rid of yield in unit tests

openvax · Mar 13, 2024 · e829942 · e829942
1 parent 65a0205
commit e829942
Show file tree

Hide file tree

Showing 6 changed files with 9 additions and 9 deletions.
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -68,6 +68,7 @@ jobs:
           echo `which netMHCcons` && netMHCcons -h
           echo `which netMHCstab` && netMHCstab -h
           echo `which netMHCstabpan` && netMHCstabpan -h
+
           ./test.sh
       - name: Publish coverage to Coveralls
         uses: coverallsapp/[email protected]
diff --git a/setup.py b/setup.py
@@ -54,7 +54,7 @@
             'Topic :: Scientific/Engineering :: Bio-Informatics',
         ],
         install_requires=[
-            'numpy>=1.7',
+            'numpy>=1.7,<2.0',
             'pandas>=0.13.1',
             'varcode>=0.5.9',
             'pyensembl>=1.0.3',

diff --git a/tests/test_known_class1_epitopes.py b/tests/test_known_class1_epitopes.py
@@ -48,11 +48,11 @@ def test_MAGE_epitope():
     #   T Cells
     for mhc_class in mhc_classes:
         mhc_model = make_mhc_model(mhc_class, "HLA-A*01:01")
-        yield (expect_binder, mhc_model, "ESDPIVAQY")
+        expect_binder(mhc_model, "ESDPIVAQY")
 
 def test_HIV_epitope():
     # Test the A2 HIV epitope SLYNTVATL from
     #    The HIV-1 HLA-A2-SLYNTVATL Is a Help-Independent CTL Epitope
     for mhc_class in mhc_classes:
         mhc_model = make_mhc_model(mhc_class, "HLA-A*02:01")
-        yield (expect_binder, mhc_model, "SLYNTVATL")
+        expect_binder(mhc_model, "SLYNTVATL")
diff --git a/tests/test_netmhc_pan.py b/tests/test_netmhc_pan.py
@@ -36,10 +36,10 @@
 
 
 def test_netmhc_pan():
-    yield check_netmhc_pan, "netMHCpan", True  # required
+    check_netmhc_pan("netMHCpan", True)  # required
 
     for program_name in OPTIONAL_NETMHCPAN_PROGRAM_NAMES:
-        yield check_netmhc_pan, program_name, False  # optional
+        check_netmhc_pan(program_name, False)  # optional
 
 
 def check_netmhc_pan(program_name, fail_if_no_such_program=True):

diff --git a/tests/test_netmhc_stabpan.py b/tests/test_netmhc_stabpan.py
@@ -40,8 +40,7 @@
 def test_netmhc_stabpan_accuracy():    
     # Check that the netMHCstabpan program is working and returning th eexpected outputs.
     predictor = NetMHCstabpan(
-    alleles=[DEFAULT_ALLELE], program_name='netMHCstabpan'
-    )
+        alleles=[DEFAULT_ALLELE], program_name='netMHCstabpan')
 
     binding_predictions = predictor.predict_peptides(protein_sequences)
     stability_predictions = [p.score for p in binding_predictions]

diff --git a/tests/test_netmhcii_pan.py b/tests/test_netmhcii_pan.py
@@ -132,10 +132,10 @@ def test_netmhcii_pan_mouse():
 
 # follows similar model to test_netmhc_pan.py
 def test_netmhcii_pan():
-    yield check_netmhcii_pan, "netMHCIIpan", True  # required
+    check_netmhcii_pan("netMHCIIpan", True)  # required
 
     for program_name in OPTIONAL_NETMHCIIPAN_PROGRAM_NAMES:
-        yield check_netmhcii_pan, program_name, False  # optional
+        check_netmhcii_pan(program_name, False)  # optional
 
 # TODO: add more actual tests to this
 def check_netmhcii_pan(program_name, fail_if_no_such_program=True):