diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 26ab547..a871ed3 100644 --- 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/github-action@v2.2.3 diff --git a/setup.py b/setup.py index df4f7e2..abb24b8 100644 --- 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 index c7c080c..479e1e7 100644 --- 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 index ed5152f..e1aa0f7 100644 --- 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 index ceae57e..0aded42 100644 --- 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 index 05a833b..3f61caa 100644 --- 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):