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How to use test_single_run method in Molotov
Best Python code snippet using molotov_python
workflow_test.py
Source:workflow_test.py 
...14class Base(object):15 """Base class to test the full workflow16 """17 @pytest.mark.workflowtest18 def test_single_run(self, extension, bilby=False):19 """Test the full workflow for a single result file case20 Parameters21 ----------22 result_file: str23 path to result file you wish to run with24 """25 opts, inputs = make_argparse(outdir=self.tmpdir, 26 gw=False, extension=extension, bilby=bilby)27 func = functions(opts)28 PlotGeneration(inputs)29 WebpageGeneration(inputs)30 func["MetaFile"](inputs)31 func["FinishingTouches"](inputs)32 plots = sorted(glob.glob("{}/plots/*.png".format(self.tmpdir)))33 files = sorted(glob.glob("{}/html/*.html".format(self.tmpdir)))34 assert all(i == j for i, j in zip(plots, get_list_of_plots(outdir=self.tmpdir, gw=False)))35 assert all(i in plots for i in get_list_of_plots(outdir=self.tmpdir, gw=False))36 assert all(i in get_list_of_plots(outdir=self.tmpdir, gw=False) for i in plots)37 assert all(i == j for i, j in zip(files, get_list_of_files(outdir=self.tmpdir, gw=False)))38 assert all(i in files for i in get_list_of_files(outdir=self.tmpdir, gw=False))39 assert all(i in get_list_of_files(outdir=self.tmpdir, gw=False) for i in files)40 self.check_samples(extension, bilby=bilby)41 def check_samples(self, extension, bilby=False):42 """Check that the samples in the result file are consistent with the43 inputs44 """45 from pesummary.core.file.read import read46 initial_samples = read_result_file(extension=extension, bilby=bilby, outdir=self.tmpdir)47 data = read("{}/samples/posterior_samples.h5".format(self.tmpdir))48 samples = data.samples_dict49 label = data.labels[0]50 for param in initial_samples.keys():51 for i, j in zip(initial_samples[param], samples[label][param]):52 assert np.round(i, 8) == np.round(j, 8)53 54class GWBase(Base):55 """Base class to test the full workflow including gw specific options56 """57 @pytest.mark.workflowtest58 def test_single_run(self, extension, bilby=False, lalinference=False):59 """Test the full workflow for a single result file case60 Parameters61 ----------62 result_file: str63 path to result file you wish to run with64 """65 opts, inputs = make_argparse(outdir=self.tmpdir, 66 gw=True, extension=extension, bilby=bilby, lalinference=lalinference)67 print(opts)68 func = functions(opts)69 PlotGeneration(inputs, gw=True)70 WebpageGeneration(inputs, gw=True)71 func["MetaFile"](inputs)72 func["FinishingTouches"](inputs)73 plots = sorted(glob.glob("{}/plots/*.png".format(self.tmpdir)))74 files = sorted(glob.glob("{}/html/*.html".format(self.tmpdir)))75 assert all(i == j for i, j in zip(plots, get_list_of_plots(outdir=self.tmpdir, gw=True)))76 assert all(i in plots for i in get_list_of_plots(outdir=self.tmpdir, gw=True))77 assert all(i in get_list_of_plots(outdir=self.tmpdir, gw=True) for i in plots)78 for i, j in zip(files, get_list_of_files(outdir=self.tmpdir, gw=True)):79 print(i, j)80 assert all(i == j for i, j in zip(files, get_list_of_files(outdir=self.tmpdir, gw=True)))81 assert all(i in files for i in get_list_of_files(outdir=self.tmpdir, gw=True))82 assert all(i in get_list_of_files(outdir=self.tmpdir, gw=True) for i in files)83 self.check_samples(extension, bilby=bilby, lalinference=lalinference)84 def check_samples(self, extension, bilby=False, lalinference=False):85 """Check that the samples in the result file are consistent with the86 inputs87 """88 from pesummary.core.file.read import read89 initial_samples = read_result_file(90 extension=extension, bilby=bilby, lalinference=lalinference,91 outdir=self.tmpdir92 )93 data = read("{}/samples/posterior_samples.h5".format(self.tmpdir))94 samples = data.samples_dict95 label = data.labels[0]96 for param in initial_samples.keys():97 for i, j in zip(initial_samples[param], samples[label][param]):98 assert np.round(i, 8) == np.round(j, 8)99class TestCoreDat(Base):100 """Test the full workflow with a core dat file101 """102 def setup(self):103 """Setup the TestCoreDat class104 """105 self.tmpdir = tempfile.TemporaryDirectory(prefix=".", dir=".").name106 if not os.path.isdir(self.tmpdir):107 os.mkdir(self.tmpdir)108 def teardown(self):109 """Remove the files and directories created from this class110 """111 if os.path.isdir(self.tmpdir):112 shutil.rmtree(self.tmpdir)113 @pytest.mark.workflowtest114 def test_single_run(self):115 """Test the full workflow with a core dat result file116 """117 extension = "dat"118 super(TestCoreDat, self).test_single_run(extension)119class TestCoreJson(Base):120 """Test the full workflow with a core json file121 """122 def setup(self):123 """Setup the TestCoreJson class124 """125 self.tmpdir = tempfile.TemporaryDirectory(prefix=".", dir=".").name126 if not os.path.isdir(self.tmpdir):127 os.mkdir(self.tmpdir)128 def teardown(self):129 """Remove the files and directories created from this class130 """131 if os.path.isdir(self.tmpdir):132 shutil.rmtree(self.tmpdir)133 @pytest.mark.workflowtest134 def test_single_run(self):135 """Test the full workflow with a core json result file136 """137 extension = "json"138 super(TestCoreJson, self).test_single_run(extension)139class TestCoreHDF5(Base):140 """Test the full workflow with a core hdf5 file141 """142 def setup(self):143 """Setup the TestCoreHDF5 class144 """145 self.tmpdir = tempfile.TemporaryDirectory(prefix=".", dir=".").name146 if not os.path.isdir(self.tmpdir):147 os.mkdir(self.tmpdir)148 def teardown(self):149 """Remove the files and directories created from this class150 """151 if os.path.isdir(self.tmpdir):152 shutil.rmtree(self.tmpdir)153 @pytest.mark.workflowtest154 def test_single_run(self):155 """Test the full workflow with a core hdf5 result file156 """157 extension = "h5"158 super(TestCoreHDF5, self).test_single_run(extension)159class TestCoreBilbyJson(Base):160 """Test the full workflow with a core json bilby file161 """162 def setup(self):163 """Setup the TestCoreBilby class164 """165 self.tmpdir = tempfile.TemporaryDirectory(prefix=".", dir=".").name166 if not os.path.isdir(self.tmpdir):167 os.mkdir(self.tmpdir)168 def teardown(self):169 """Remove the files and directories created from this class170 """171 if os.path.isdir(self.tmpdir):172 shutil.rmtree(self.tmpdir)173 if os.path.isdir("{}_pesummary".format(self.tmpdir)):174 shutil.rmtree("{}_pesummary".format(self.tmpdir))175 @pytest.mark.workflowtest176 def test_single_run(self):177 """Test the full workflow with a core bilby result file178 """179 extension = "json"180 super(TestCoreBilbyJson, self).test_single_run(extension, bilby=True)181 @pytest.mark.workflowtest182 def test_double_run(self):183 """Test the full workflow for 2 lalinference result files184 """185 opts, inputs = make_argparse(outdir=self.tmpdir, 186 gw=False, extension="json", bilby=True, number=2)187 func = functions(opts)188 PlotGeneration(inputs)189 WebpageGeneration(inputs)190 func["MetaFile"](inputs)191 func["FinishingTouches"](inputs)192 plots = sorted(glob.glob("{}/plots/*.png".format(self.tmpdir)))193 files = sorted(glob.glob("{}/html/*.html".format(self.tmpdir)))194 assert all(i == j for i, j in zip(plots, get_list_of_plots(outdir=self.tmpdir, 195 gw=False, number=2)))196 assert all(i in plots for i in get_list_of_plots(outdir=self.tmpdir, gw=False, number=2))197 assert all(i in get_list_of_plots(outdir=self.tmpdir, gw=False, number=2) for i in plots)198 assert all(i == j for i, j in zip(files, get_list_of_files(outdir=self.tmpdir, 199 gw=False, number=2)))200 assert all(i in files for i in get_list_of_files(outdir=self.tmpdir, gw=False, number=2))201 assert all(i in get_list_of_files(outdir=self.tmpdir, gw=False, number=2) for i in files)202 @pytest.mark.workflowtest203 def test_existing_run(self):204 """Test the fill workflow for when you add to an existing webpage205 """206 opts, inputs = make_argparse(outdir=self.tmpdir, 207 gw=False, extension="json", bilby=True)208 func = functions(opts)209 PlotGeneration(inputs)210 WebpageGeneration(inputs)211 func["MetaFile"](inputs)212 func["FinishingTouches"](inputs)213 opts, inputs = make_argparse(outdir=self.tmpdir, 214 gw=False, extension="json", bilby=True, existing=True)215 func = functions(opts)216 PlotGeneration(inputs)217 WebpageGeneration(inputs)218 func["MetaFile"](inputs)219 func["FinishingTouches"](inputs)220 plots = sorted(glob.glob("{}/plots/*.png".format(self.tmpdir)))221 files = sorted(glob.glob("{}/html/*.html".format(self.tmpdir)))222 assert all(i == j for i, j in zip(plots, get_list_of_plots(outdir=self.tmpdir, 223 gw=False, number=2)))224 assert all(i in plots for i in get_list_of_plots(outdir=self.tmpdir, gw=False, number=2))225 assert all(i in get_list_of_plots(outdir=self.tmpdir, gw=False, number=2) for i in plots)226 assert all(i == j for i, j in zip(files, get_list_of_files(outdir=self.tmpdir, 227 gw=False, number=2)))228 assert all(i in files for i in get_list_of_files(outdir=self.tmpdir, gw=False, number=2))229 assert all(i in get_list_of_files(outdir=self.tmpdir, gw=False, number=2) for i in files)230 @pytest.mark.workflowtest231 def test_pesummary_input(self):232 """Test the full workflow for a pesummary input file233 """234 opts, inputs = make_argparse(outdir=self.tmpdir, 235 gw=False, extension="json", bilby=True, number=2)236 func = functions(opts)237 PlotGeneration(inputs)238 WebpageGeneration(inputs)239 func["MetaFile"](inputs)240 func["FinishingTouches"](inputs)241 plots = sorted(glob.glob("{}/plots/*.png".format(self.tmpdir)))242 files = sorted(glob.glob("{}/html/*.html".format(self.tmpdir)))243 from pesummary.core.cli.command_line import command_line244 parser = command_line()245 default_args = ["--webdir", "{}_pesummary".format(self.tmpdir),246 "--samples", "{}/samples/posterior_samples.h5".format(self.tmpdir),247 "--disable_expert"]248 opts = parser.parse_args(default_args)249 func = functions(opts)250 inputs = func["input"](opts)251 PlotGeneration(inputs)252 WebpageGeneration(inputs)253 func["MetaFile"](inputs)254 func["FinishingTouches"](inputs)255 plots_pesummary = sorted(glob.glob("{}_pesummary/plots/*.png".format(self.tmpdir)))256 files_pesummary = sorted(glob.glob("{}_pesummary/html/*.html".format(self.tmpdir)))257 assert all(i.split("/")[-1] == j.split("/")[-1] for i, j in zip(258 plots, plots_pesummary))259 assert all(i.split("/")[-1] == j.split("/")[-1] for i, j in zip(260 files, files_pesummary))261class TestCoreBilbyHDF5(Base):262 """Test the full workflow with a core hdf5 bilby file263 """264 def setup(self):265 """Setup the TestCoreBilby class266 """267 self.tmpdir = tempfile.TemporaryDirectory(prefix=".", dir=".").name268 if not os.path.isdir(self.tmpdir):269 os.mkdir(self.tmpdir)270 def teardown(self):271 """Remove the files and directories created from this class272 """273 if os.path.isdir(self.tmpdir):274 shutil.rmtree(self.tmpdir)275 @pytest.mark.workflowtest276 def test_single_run(self):277 """Test the full workflow with a core bilby result file278 """279 extension = "h5"280 super(TestCoreBilbyHDF5, self).test_single_run(extension, bilby=True)281class TestGWDat(GWBase):282 """Test the full workflow with a gw dat file283 """284 def setup(self):285 """Setup the TestCoreDat class286 """287 self.tmpdir = tempfile.TemporaryDirectory(prefix=".", dir=".").name288 if not os.path.isdir(self.tmpdir):289 os.mkdir(self.tmpdir)290 def teardown(self):291 """Remove the files and directories created from this class292 """293 if os.path.isdir(self.tmpdir):294 shutil.rmtree(self.tmpdir)295 @pytest.mark.workflowtest296 def test_single_run(self):297 """Test the full workflow with a gw dat result file298 """299 extension = "dat"300 super(TestGWDat, self).test_single_run(extension)301class TestGWJson(GWBase):302 """Test the full workflow with a json dat file303 """304 def setup(self):305 """Setup the TestGWJson class306 """307 self.tmpdir = tempfile.TemporaryDirectory(prefix=".", dir=".").name308 if not os.path.isdir(self.tmpdir):309 os.mkdir(self.tmpdir)310 def teardown(self):311 """Remove the files and directories created from this class312 """313 if os.path.isdir(self.tmpdir):314 shutil.rmtree(self.tmpdir)315 @pytest.mark.workflowtest316 def test_single_run(self):317 """Test the full workflow with a gw json result file318 """319 extension = "json"320 super(TestGWJson, self).test_single_run(extension)321class TestGWBilbyJson(GWBase):322 """Test the full workflow with a gw bilby json file323 """324 def setup(self):325 """Setup the TestGWJson class326 """327 self.tmpdir = tempfile.TemporaryDirectory(prefix=".", dir=".").name328 if not os.path.isdir(self.tmpdir):329 os.mkdir(self.tmpdir)330 def teardown(self):331 """Remove the files and directories created from this class332 """333 if os.path.isdir(self.tmpdir):334 shutil.rmtree(self.tmpdir)335 @pytest.mark.workflowtest336 def test_single_run(self):337 """Test the full workflow with a gw bilby json result file338 """339 extension = "json"340 super(TestGWBilbyJson, self).test_single_run(extension, bilby=True)341class TestGWBilbyHDF5(GWBase):342 """Test the full workflow with a gw bilby HDF5 file343 """344 def setup(self):345 """Setup the TestGWJson class346 """347 self.tmpdir = tempfile.TemporaryDirectory(prefix=".", dir=".").name348 if not os.path.isdir(self.tmpdir):349 os.mkdir(self.tmpdir)350 def teardown(self):351 """Remove the files and directories created from this class352 """353 if os.path.isdir(self.tmpdir):354 shutil.rmtree(self.tmpdir)355 @pytest.mark.workflowtest356 def test_single_run(self):357 """Test the full workflow with a gw bilby HDF5 result file358 """359 extension = "h5"360 super(TestGWBilbyHDF5, self).test_single_run(extension, bilby=True)361class TestGWLALInference(GWBase):362 """Test the full workflow with a lalinference file363 """364 def setup(self):365 """Setup the TestGWJson class366 """367 self.tmpdir = tempfile.TemporaryDirectory(prefix=".", dir=".").name368 if not os.path.isdir(self.tmpdir):369 os.mkdir(self.tmpdir)370 def teardown(self):371 """Remove the files and directories created from this class372 """373 if os.path.isdir(self.tmpdir):374 shutil.rmtree(self.tmpdir)375 if os.path.isdir("{}_pesummary".format(self.tmpdir)):376 shutil.rmtree("{}_pesummary".format(self.tmpdir))377 @pytest.mark.workflowtest378 def test_single_run(self):379 """Test the full workflow with a lalinference result file380 """381 extension = "hdf5"382 super(TestGWLALInference, self).test_single_run(extension, lalinference=True)383 @pytest.mark.workflowtest384 def test_double_run(self):385 """Test the full workflow for 2 lalinference result files386 """387 opts, inputs = make_argparse(outdir=self.tmpdir, 388 gw=True, extension="hdf5", lalinference=True, number=2)389 func = functions(opts)390 PlotGeneration(inputs, gw=True)391 WebpageGeneration(inputs, gw=True)392 func["MetaFile"](inputs)393 func["FinishingTouches"](inputs)394 plots = sorted(glob.glob("{}/plots/*.png".format(self.tmpdir)))395 files = sorted(glob.glob("{}/html/*.html".format(self.tmpdir)))396 assert all(i == j for i, j in zip(plots, get_list_of_plots(outdir=self.tmpdir, ...
simulator_test.py
Source:simulator_test.py
...37 plt.legend(loc="upper right")38 plt.xlabel('staff num')39 plt.ylabel('y axis')4041def test_single_run(simulator, round):42 (average_staff_used, average_time_waited) = simulator.run(round)43 print(average_staff_used)44 print(average_time_waited)4546def test_staff_num(simulator, round):47 total_staff_used_list = []48 total_time_waited_list = []49 staff_num_list = [i for i in range(1, GROUP_SIZE + 1)]5051 for staff_num in range(1, GROUP_SIZE + 1):52 print("this is time %d" % staff_num)53 simulator.set_staff_num(staff_num)54 (average_staff_used, average_time_waited) = simulator.run(round)55 total_staff_used_list.append(average_staff_used)56 total_time_waited_list.append(average_time_waited)5758 return total_staff_used_list, total_time_waited_list5960def test_influence_of_distance(simulator, round, range_start, range_end):61 rec_total_staff_used_list = []62 rec_total_time_waited_list = []63 rec_staff_num_list = []64 for distance in range(range_start, range_end):65 simulator.set_distance(distance)66 print("\n\n\n\n\nthis is distance %d\n\n\n\n\n" % distance)67 (total_staff_used_list, total_time_waited_list) = test_staff_num(simulator, round)68 rec_total_staff_used_list.append(total_staff_used_list)69 rec_total_time_waited_list.append(total_time_waited_list)70 rec_staff_num_list.append([i for i in range(1, GROUP_SIZE + 1)])7172 draw_graph_staff_num(rec_staff_num_list, rec_total_staff_used_list)73 draw_graph_time_waited(rec_staff_num_list, rec_total_time_waited_list)74 plt.show()757677if __name__ == '__main__':78 test_round = 1000079 simulator = Simulator(FAILURE_RATE, GROUP_SIZE, GROUP_NUM, STAFF_NUM, GROUP_INTERVAL, MACHINE_INTERVAL, SPEED, FIX_TIME, X_DIVIDE)80 # test_influence_of_distance(simulator, test_round, 0, 1)81 time_start = time.time()82 test_single_run(simulator, test_round)83 time_end = time.time()84 print("time for this run is:")85 print(time_end - time_start)8687 # (total_staff_used_list, total_time_waited_list) = test_staff_num(simulator, test_round)88 # draw_graph_time_waited([[i for i in range(1, GROUP_SIZE + 1)]], [total_time_waited_list])89 # plt.show()909192 # result_staff = []93 # result_waited_time = []94 # staff_num_list = []95 # for i in range(1, GROUP_SIZE + 1):96 # simulator.set_staff_num(i)
...
test_enrichr.py
Source:test_enrichr.py
...4from magine.enrichment.enrichr import Enrichr, clean_drug_dbs, clean_tf_names, \5 get_background_list, get_libraries, run_enrichment_for_project6from magine.tests.sample_experimental_data import exp_data7e = Enrichr()8def test_single_run():9 e.print_valid_libs()10 list_2 = ['CASP3', 'CASP6', 'FAS', 'FADD', 'CASP8', 'CFLAR', 'BFAR', 'BAD',11 'BID', 'PMAIP1', 'MCL1', 'BCL2', 'BCL2L1', 'BAX', 'BAK1',12 'DIABLO', 'CYCS', 'PARP1', 'APAF1', 'XIAP']13 df = e.run(list_2, 'GO_Biological_Process_2017')14 terms = df['term_name']15 ok_(len(terms) == 185)16def test_libaries():17 get_libraries()18def test_project():19 slimmed = exp_data.species.copy()20 slimmed = slimmed.loc[slimmed.source.isin(['label_free', 'silac'])]21 slimmed = slimmed.loc[slimmed.sample_id.isin(['Time_1', 'Time_2', ])]22 slimmed = ExperimentalData(slimmed)23 run_enrichment_for_project(slimmed, 'test',24 databases=['KEGG_2016'])25 slimmed = exp_data.species.copy()26 slimmed = slimmed.loc[slimmed.source.isin(['label_free'])]27 slimmed = slimmed.loc[slimmed.sample_id.isin(['Time_1', 'Time_2', ])]28 slimmed = ExperimentalData(slimmed)29 run_enrichment_for_project(slimmed, 'test',30 databases=['KEGG_2016'])31def test_get_gene_set_lib():32 get_background_list('Phosphatase_Substrates_from_DEPOD')33def test_clean_drug_dbs():34 list_2 = ['CASP3', 'CASP6', 'FAS', 'FADD', 'CASP8', 'CFLAR', 'BFAR', 'BAD',35 'BID', 'PMAIP1', 'MCL1', 'BCL2', 'BCL2L1', 'BAX', 'BAK1',36 'DIABLO', 'CYCS', 'PARP1', 'APAF1', 'XIAP']37 df = e.run(list_2, ['Drug_Perturbations_from_GEO_2014',38 'LINCS_L1000_Chem_Pert_up'39 ])40 df = clean_drug_dbs(df)41 ok_(len(df['term_name']) == 6243)42 ok_(len(df.sig['term_name']) == 249)43def test_multi_sample():44 lists = [['BAX', 'BCL2', 'CASP3'],45 ['CASP10', 'CASP8', 'BAK'],46 ['BIM', 'CASP3']]47 df2 = e.run_samples(lists, ['1', '2', '3'], save_name='enrichr_test')48 ok_(df2.shape == (111, 11))49def test_multi_sample_plotting():50 up = exp_data.genes.sig.up_by_sample51 out_dir = tempfile.mkdtemp()52 e.run_samples(up, ['1', '2', '3'],53 gene_set_lib=['Human_Phenotype_Ontology',54 'MGI_Mammalian_Phenotype_2017'],55 save_name='enrichr_test',56 exp_data=exp_data,57 create_html=True,58 pivot=True,59 out_dir=out_dir)60def test_set_of_dbs():61 lists = [['BAX', 'BCL2', 'CASP3'],62 ['CASP10', 'CASP8', 'BAK'],63 ['BIM', 'CASP3']]64 df2 = e.run_samples(lists, ['1', '2', '3'],65 gene_set_lib=['KEGG_2016', 'NCI-Nature_2016']66 )67 ok_(df2.shape == (128, 11))68def test_tf_names():69 df = e.run(['BAX', 'BCL2', 'MCL1'], ['ARCHS4_TFs_Coexp', 'ChEA_2016'])70 tfs = clean_tf_names(df)71 for i in tfs['term_name']:72 ok_('_' not in i)73if __name__ == '__main__':...
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