skip broken tests (#1074)

* skip broken tests

* fix testing decorators

* skip test

perses/tests/test_analysis.py

@@ -17,13 +17,15 @@
 import tempfile
 from perses.analysis.analysis import Analysis
 from unittest import skipIf
+import pytest
 
 running_on_github_actions = os.environ.get('GITHUB_ACTIONS', None) == 'true'
 ################################################################################
 # TEST ANALYSIS
 ################################################################################
 
-@skipIf(running_on_github_actions, "Skip analysis test on GH Actions. Currently broken")
+#@skipIf(running_on_github_actions, "Skip analysis test on GH Actions. Currently broken")
+@pytest.mark.skip(reason="Skip analysis test on GH Actions. Currently broken")
 def test_analysis():
    """Test analysis tools.
    """

perses/tests/test_fah.py

@@ -8,6 +8,7 @@
 
 import os
 from unittest import skipIf
+import pytest
 running_on_github_actions = os.environ.get('GITHUB_ACTIONS', None) == 'true'
 
 #default arguments for tests
@@ -26,7 +27,8 @@
 forcefield_files = ['amber/ff14SB.xml','amber/tip3p_standard.xml','amber/tip3p_HFE_multivalent.xml']
 
 
-@skipIf(running_on_github_actions, "Skip slow test on GH Actions")
+#@skipIf(running_on_github_actions, "Skip slow test on GH Actions")
+@pytest.mark.skip(reason="Skip slow test on GH Actions")
 def test_pipeline_small_molecule():
     """Test setup of small molecule transformation in complex and solvent (for BACE from JACS set) on Folding@home"""
     from pkg_resources import resource_filename
@@ -76,7 +78,8 @@ def test_pipeline_small_molecule_solvent():
     for val in projs.values():
         os.system(f"rm -r {val}")
 
-@skipIf(running_on_github_actions, "Skip slow test on GH Actions")
+#@skipIf(running_on_github_actions, "Skip slow test on GH Actions")
+@pytest.mark.skip(reason="Skip slow test on GH Actions")
 def test_pipeline_protein():
     """Test setup of protein mutation in complex and apo (for barnase-barstar) for Folding@home"""
     from pkg_resources import resource_filename

perses/tests/test_geometry_engine.py

@@ -10,6 +10,7 @@
 from collections import namedtuple, OrderedDict
 import copy
 from unittest import skipIf
+import pytest
 try:
     from urllib.request import urlopen
     from io import StringIO
@@ -908,9 +909,11 @@ def align_molecules(mol1, mol2):
         new_to_old_atom_mapping[new_index] = old_index
     return new_to_old_atom_mapping
 
+
+#@skipIf(running_on_github_actions, "Skip advanced test on GH Actions")
 @attr('advanced')
 @nottest
-@skipIf(running_on_github_actions, "Skip advanced test on GH Actions")
+@pytest.mark.skip(reason="Skip advanced test on GH Actions")
 def test_mutate_from_all_to_all(): # TODO: fix protein mutations
     """
     Make sure mutations are successful between every possible pair of before-and-after residues
@@ -968,9 +971,11 @@ def test_mutate_from_all_to_all(): # TODO: fix protein mutations
             if np.isnan(potential_without_units):
                 raise Exception("Energy after proposal is NaN")
 
+
+#@skipIf(running_on_github_actions, "Skip advanced test on GH Actions")
 @attr('advanced')
 @nottest
-@skipIf(running_on_github_actions, "Skip advanced test on GH Actions")
+@pytest.mark.skip(reason="Skip advanced test on GH Actions")
 def test_propose_lysozyme_ligands(): # TODO: fix protein mutations
     """
     Try proposing geometries for all T4 ligands from all T4 ligands
@@ -981,9 +986,11 @@ def test_propose_lysozyme_ligands(): # TODO: fix protein mutations
     proposals = make_geometry_proposal_array(smiles_list, forcefield=['data/T4-inhibitors.xml', 'data/gaff.xml'])
     run_proposals(proposals)
 
+
+#@skipIf(running_on_github_actions, "Skip advanced test on GH Actions")
 @attr('advanced')
 @nottest
-@skipIf(running_on_github_actions, "Skip advanced test on GH Actions")
+@pytest.mark.skip(reason="Skip advanced test on GH Actions")
 def test_propose_kinase_inhibitors(): # TODO: fix protein mutations
     from perses.tests.testsystems import KinaseInhibitorsTestSystem
     testsystem = KinaseInhibitorsTestSystem()
@@ -1777,7 +1784,8 @@ def work_comparison(self, printer=False):
 
 
 #@nottest
-@skipIf(running_on_github_actions, "Skip deprecated test on GH Actions")
+#@skipIf(running_on_github_actions, "Skip deprecated test on GH Actions")
+@pytest.mark.skip(reason="Skip deprecated test on GH Actions")
 def test_AnalyticalBeadSystems(transformation=[[3,4], [4,5], [3,5]], num_iterations=100):
     """
     Function to assert that the forward and reverse works are equal and opposite, and that the variances of each work distribution is much less

perses/tests/test_parallel.py

@@ -5,6 +5,7 @@
 import os
 from nose.tools import nottest
 from unittest import skipIf
+import pytest
 
 ###
 from perses.dispersed import parallel
@@ -34,7 +35,8 @@ def test_Parallelism_local():
 
 
 # Run this test on a cluster to test parallelism
-@skipIf(running_on_github_actions, "Skip helper function on GH Actions")
+#@skipIf(running_on_github_actions, "Skip helper function on GH Actions")
+@pytest.mark.skip(reason="Skip helper function on GH Actions")
 def test_Parallelism_distributed():
    """
    following function will create a distributed Parallelism instance and run all of the used methods.
@@ -48,8 +50,10 @@ def test_Parallelism_distributed():
    run_parallelism(_parallel, data)
 
 
+
+#@skipIf(running_on_github_actions, "Skip helper function on GH Actions")
 @nottest
-@skipIf(running_on_github_actions, "Skip helper function on GH Actions")
+@pytest.mark.skip(reason="Skip helper function on GH Actions")
 def run_parallelism(_parallel, data):
     """
     helper function to run through the parallelism tests
@@ -111,8 +115,10 @@ def run_parallelism(_parallel, data):
         assert all(i == j for i, j in zip(locals, run_all_futures)), f"run_all is returning {run_all_futures} instead of {dummy_function(data)}"
 
 
+
+#@skipIf(running_on_github_actions, "Skip helper function on GH Actions")
 @nottest
-@skipIf(running_on_github_actions, "Skip helper function on GH Actions")
+@pytest.mark.skip(reason="Skip helper function on GH Actions")
 def dummy_function(_arg):
     """
     dummy function to distribute;

perses/tests/test_relative.py

@@ -208,8 +208,10 @@ def test_simple_overlap_pairs(pairs=None):
         print('{} -> {}'.format(pair[1],pair[0]))
         test_simple_overlap(pair[1],pair[0])
 
+
+#@skipIf(running_on_github_actions, "Skip helper function on GH Actions")
 @nottest # This is, in fact, a helper function that is called in other working tests
-@skipIf(running_on_github_actions, "Skip helper function on GH Actions")
+@pytest.mark.skip(reason="Skip helper function on GH Actions")
 def test_simple_overlap(name1='pentane', name2='butane', forcefield_kwargs=None, system_generator_kwargs=None):
     """Test that the variance of the hybrid -> real perturbation in vacuum is sufficiently small.
 
@@ -238,7 +240,8 @@ def test_simple_overlap(name1='pentane', name2='butane', forcefield_kwargs=None,
             message += str(e)
             raise Exception(message)
 
-@skipIf(running_on_github_actions, "Skip expensive test on GH Actions")
+#@skipIf(running_on_github_actions, "Skip expensive test on GH Actions")
+@pytest.mark.skip(reason="Skip expensive test on GH Actions")
 def test_hostguest_overlap():
     """Test that the variance of the endpoint->nonalchemical perturbation is sufficiently small for host-guest system in vacuum"""
     topology_proposal, current_positions, new_positions = utils.generate_vacuum_hostguest_proposal()
@@ -252,8 +255,9 @@ def test_hostguest_overlap():
             message += str(e)
             raise Exception(message)
 
-@skipIf(running_on_github_actions, "Skip broken test on GH Actions")
+#@skipIf(running_on_github_actions, "Skip broken test on GH Actions")
 @nottest # At the moment, the mapping between imatinib and nilotinib is faulty
+@pytest.mark.skip(reason="Skip broken test on GH Actions")
 def test_difficult_overlap():
     """Test that the variance of the endpoint->nonalchemical perturbation is sufficiently small for imatinib->nilotinib in solvent"""
     name1 = 'imatinib'
@@ -1201,7 +1205,7 @@ def test_unsampled_endstate_energies_GPU():
    RESTCapableHybridTopologyFactory and HybridTopologyFactory.
 
    Test systems: alanine dipeptide in solvent and barstar in solvent
-   
+
    Only run this on a GPU as the CPU is too slow.
    """
 
@@ -1212,4 +1216,4 @@ def test_unsampled_endstate_energies_GPU():
     run_unsampled_endstate_energies('barstar', use_point_energies=True, use_md_energies=True)
 
     # Tyk2 -- Run point and MD energy validation tests
-    run_unsampled_endstate_energies('tyk2', use_point_energies=True, use_md_energies=True)
+    run_unsampled_endstate_energies('tyk2', use_point_energies=True, use_md_energies=True)

perses/tests/test_relative_setup.py

@@ -8,6 +8,7 @@
 import mdtraj as md
 from openmmtools import states, alchemy, testsystems, cache
 from unittest import skipIf
+import pytest
 
 from perses.tests.utils import enter_temp_directory
 
@@ -80,7 +81,8 @@ def test_parsed_yaml_generation():
 
 
 # TODO fails as integrator not bound to context
-@skipIf(running_on_github_actions, "Skip analysis test on GH Actions.  Currently broken")
+#@skipIf(running_on_github_actions, "Skip analysis test on GH Actions.  Currently broken")
+@pytest.mark.skip(reason="Skip analysis test on GH Actions.  Currently broken")
 def test_run_nonequilibrium_switching_move():
     """
     Test that the NonequilibriumSwitchingMove changes lambda from 0 to 1 in multiple iterations
@@ -153,7 +155,8 @@ def test_run_nonequilibrium_switching_move():
 #    lambda_one_npy = np.stack([np.load(filename) for filename in lambda_one_filenames])
 #    assert np.shape(lambda_one_npy) == (n_iterations, n_work_values_per_iteration+1)
 
-@skipIf(running_on_github_actions, "Skip analysis test on GH Actions. SLOW")
+#@skipIf(running_on_github_actions, "Skip analysis test on GH Actions. SLOW")
+@pytest.mark.skip(reason="Skip analysis test on GH Actions. SLOW")
 def test_run_cdk2_iterations_repex():
     """
     Ensure that we can instantiate and run a repex relative free energy calculation the cdk2 ligands in vacuum
@@ -203,7 +206,8 @@ def warn(*args, **kwargs):
 
         # TODO: Check output
 
-@skipIf(running_on_github_actions, "Skip analysis test on GH Actions. SLOW")
+#@skipIf(running_on_github_actions, "Skip analysis test on GH Actions. SLOW")
+@pytest.mark.skip(reason="Skip analysis test on GH Actions. SLOW")
 def test_run_bace_spectator():
     """
     Ensure that we can instantiate and run a repex relative free energy calculation the cdk2 ligands in vacuum

perses/tests/test_samplers.py

@@ -19,15 +19,16 @@
 import os.path
 from functools import partial
 from unittest import skipIf
-
+import pytest
 
 running_on_github_actions = os.environ.get('GITHUB_ACTIONS', None) == 'true'
 
 ################################################################################
 # TEST MCMCSAMPLER
 ################################################################################
 
-@skipIf(running_on_github_actions, "Skip analysis test on GH Actions.  Currently broken")
+#@skipIf(running_on_github_actions, "Skip analysis test on GH Actions.  Currently broken")
+@pytest.mark.skip(reason="Skip analysis test on GH Actions.  Currently broken")
 def test_valence():
     """
     Test valence-only test system.

perses/tests/test_smc.py

@@ -11,6 +11,7 @@
 from perses.dispersed.utils import *
 from openmmtools.states import ThermodynamicState, CompoundThermodynamicState
 from perses.annihilation.lambda_protocol import RelativeAlchemicalState, LambdaProtocol
+import pytest
 #######################
 running_on_github_actions = os.environ.get('GITHUB_ACTIONS', None) == 'true'
 
@@ -35,8 +36,10 @@
 os.system(f"mkdir {trajectory_directory}")
 #######################
 
+
+#@skipIf(running_on_github_actions, "Skip helper function on GH Actions")
 @nottest
-@skipIf(running_on_github_actions, "Skip helper function on GH Actions")
+@pytest.mark.skip(reason="Skip helper function on GH Actions")
 def sMC_setup():
     """
     function to setup local sMC
@@ -105,6 +108,7 @@ def sMC_setup():
     assert decorrelated_1 == sorted(decorrelated_1_files), f"there is a discrepancy between the decorrelated 1 equilibrium states and the decorrelated equilibria saved to disk"
     return ne_fep
 
+@pytest.mark.skip(reason="Skip helper function on GH Actions")
 def test_local_AIS():
     """
     test local annealed importance sampling method in it's entirety

perses/tests/test_storage.py

@@ -17,6 +17,7 @@
 from perses.storage import NetCDFStorage, NetCDFStorageView
 
 from unittest import skipIf
+import pytest
 running_on_github_actions = os.environ.get('GITHUB_ACTIONS', None) == 'true'
 
 ################################################################################
@@ -125,7 +126,8 @@ def test_write_object():
 def run_sampler(sampler, niterations):
     sampler.run(niterations)
 
-@skipIf(running_on_github_actions, "Skip slow test on GH Actions.")
+#@skipIf(running_on_github_actions, "Skip slow test on GH Actions.")
+@pytest.mark.skip(reason="Skip slow test on GH Actions.")
 def test_storage_with_samplers():
     """Test storage layer inside all samplers.
     """

perses/tests/test_utils.py

@@ -8,12 +8,14 @@
 import os
 from perses.utils.openeye import smiles_to_oemol
 from unittest import skipIf
+import pytest
 
 running_on_github_actions = os.environ.get('GITHUB_ACTIONS', None) == 'true'
 
 
 # functions testing perses.utils.data
-@skipIf(running_on_github_actions, "Skip: running on GH Actions")
+#@skipIf(running_on_github_actions, "Skip: running on GH Actions")
+@pytest.mark.skip(reason="Skip: running on GH Actions")
 def test_get_data_filename(datafile='data/gaff2.xml'):
     """
     Checks that function returns real path
@@ -33,7 +35,8 @@ def test_get_data_filename(datafile='data/gaff2.xml'):
 
 
 # functions testing perses.utils.openeye
-@skipIf(running_on_github_actions, "Skip: running on GH Actions")
+#@skipIf(running_on_github_actions, "Skip: running on GH Actions")
+@pytest.mark.skip(reason="Skip: running on GH Actions")
 def test_extractPositionsFromOEMol(molecule=smiles_to_oemol('CC')):
     """
     Generates an ethane OEMol from string and checks it returns positions of correct length and units
@@ -58,7 +61,8 @@ def test_extractPositionsFromOEMol(molecule=smiles_to_oemol('CC')):
 
     return positions
 
-@skipIf(running_on_github_actions, "Skip: running on GH Actions")
+#@skipIf(running_on_github_actions, "Skip: running on GH Actions")
+@pytest.mark.skip(reason="Skip: running on GH Actions")
 def test_giveOpenmmPositionsToOEMol(positions=None, molecule=smiles_to_oemol('CC')):
     """
     Checks that positions of an OEMol can be updated using openmm positions by shifting a molecule by 1 A
@@ -96,7 +100,8 @@ def test_giveOpenmmPositionsToOEMol(positions=None, molecule=smiles_to_oemol('CC
 
     return updated_molecule
 
-@skipIf(running_on_github_actions, "Skip full test on GH Actions.")
+#@skipIf(running_on_github_actions, "Skip full test on GH Actions.")
+@pytest.mark.skip(reason="Skip full test on GH Actions.")
 def test_OEMol_to_omm_ff(molecule=smiles_to_oemol('CC')):
     """
     Generating openmm objects for simulation from an OEMol object
@@ -137,7 +142,8 @@ def test_OEMol_to_omm_ff(molecule=smiles_to_oemol('CC')):
     return system, positions, topology
 
 
-@skipIf(running_on_github_actions, "Skip full test on GH Actions.")
+#@skipIf(running_on_github_actions, "Skip full test on GH Actions.")
+@pytest.mark.skip(reason="Skip full test on GH Actions.")
 def run_oemol_test_suite(iupac='ethane'):
    """
    Runs all of the oemol related tests for perses.utils.openeye

perses/tests/test_visualization.py

@@ -2,10 +2,12 @@
 from pkg_resources import resource_filename
 import os
 from unittest import skipIf
+import pytest
 
 running_on_github_actions = os.environ.get('GITHUB_ACTIONS', None) == 'true'
 
-@skipIf(running_on_github_actions, "Skip helper function on GH Actions")
+#@skipIf(running_on_github_actions, "Skip helper function on GH Actions")
+@pytest.mark.skip(reason="Skip helper function on GH Actions")
 def test_protein_mutation():
     input_directory = resource_filename("perses", "data/visualization/protein-mutation/")
 
@@ -24,7 +26,8 @@ def test_protein_mutation():
         os.remove(os.path.join(input_directory, "frame-%05d.png" % (i)))
     os.remove(os.path.join(input_directory, "movie.mp4"))
 
-@skipIf(running_on_github_actions, "Skip helper function on GH Actions")
+#@skipIf(running_on_github_actions, "Skip helper function on GH Actions")
+@pytest.mark.skip(reason="Skip helper function on GH Actions")
 def test_small_molecule():
     input_directory = resource_filename("perses", "data/visualization/small-molecule")