============================= test session starts ============================== platform linux -- Python 3.7.3, pytest-3.6.2, py-1.7.0, pluggy-0.6.0 rootdir: /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/EupsBuildDir/Linux64/sims_catalogs-2.13.0.sims/sims_catalogs-2.13.0.sims, inifile: plugins: flake8-1.0.1, xdist-1.20.1, forked-0.2, session2file-0.1.9, cov-2.5.1, remotedata-0.3.1, openfiles-0.3.2, doctestplus-0.3.0, arraydiff-0.3 gw0 I / gw1 I / gw2 I / gw3 I / gw4 I / gw5 I / gw6 I / gw7 I / gw8 I / gw9 I / gw10 I / gw11 I gw0 [119] / gw1 [119] / gw2 [119] / gw3 [119] / gw4 [119] / gw5 [119] / gw6 [119] / gw7 [119] / gw8 [119] / gw9 [119] / gw10 [119] / gw11 [119] scheduling tests via LoadScheduling .....................................................F..FFFFF.F...............F......F.FFFF..F...........F............. =================================== FAILURES =================================== ___________________ CompoundCatalogTest.testCompoundCatalog ____________________ [gw1] linux -- Python 3.7.3 /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/bin/python3.7 self = def testCompoundCatalog(self): """ Test that a CompoundInstanceCatalog produces the expected output """ fileName = os.path.join(self.scratch_dir, 'simplest_compound_catalog.txt') compoundCat = CompoundInstanceCatalog([Cat1, Cat2, Cat3], [table1DB1, table1DB2, table2DB1]) > compoundCat.write_catalog(fileName) tests/testCompoundInstanceCatalog.py:271: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ python/lsst/sims/catalogs/definitions/CompoundInstanceCatalog.py:242: in write_catalog write_mode=write_mode) python/lsst/sims/catalogs/definitions/CompoundInstanceCatalog.py:319: in _write_compound local_recarray.dtype = new_dtype_list[ix] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = rec.array([(-4.48318279, -84.34274658, 0, 21.42031646, 134.83444279), ( 0.31354632, 24.55387403, 1, 15.8...','id','mag','table1DB1_raJ2000'], 'formats':[' raise exctype(value) E ValueError: When changing to a smaller dtype, its size must be a divisor of the size of original dtype ../../../../../../python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/core/records.py:487: ValueError ______________________ CompoundCatalogTest.testConstraint ______________________ [gw1] linux -- Python 3.7.3 /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/bin/python3.7 self = def testConstraint(self): """ Test that CompoundInstanceCatalog handles constraint properly """ fileName = os.path.join(self.scratch_dir, 'compound_constraint_test_cat.txt') compoundCat = CompoundInstanceCatalog([Cat1, Cat2, Cat3], [table1DB1, table1DB2, table2DB1], constraint='mag>20.0') > compoundCat.write_catalog(fileName) tests/testCompoundInstanceCatalog.py:464: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ python/lsst/sims/catalogs/definitions/CompoundInstanceCatalog.py:242: in write_catalog write_mode=write_mode) python/lsst/sims/catalogs/definitions/CompoundInstanceCatalog.py:319: in _write_compound local_recarray.dtype = new_dtype_list[ix] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = rec.array([(-4.48318279, -84.34274658, 0, 21.42031646, 134.83444279), ( 1.37429901, 1.54272441, 3, 23.9...','id','mag','table1DB1_raJ2000'], 'formats':[' raise exctype(value) E ValueError: When changing to a smaller dtype, its size must be a divisor of the size of original dtype ../../../../../../python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/core/records.py:487: ValueError _________ CompoundCatalogTest.testDefaultCustomCompoundCatalogDBObject _________ [gw3] linux -- Python 3.7.3 /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/bin/python3.7 self = def testDefaultCustomCompoundCatalogDBObject(self): """ Test that CompoundInstanceCatalog can properly parse multiple CompoundCatalogDBobjects """ fileName = os.path.join(self.scratch_dir, 'simplest_compound_catalog.txt') # negativeDecComopound_table2 should not come into play, since the # multiple queries are directed at table1 compoundCat = CompoundInstanceCatalog([Cat1, Cat2, Cat3], [table1DB1, table1DB2, table2DB1], compoundDBclass=[negativeDecCompound_table2, negativeRaCompound]) > compoundCat.write_catalog(fileName) tests/testCompoundInstanceCatalog.py:683: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ python/lsst/sims/catalogs/definitions/CompoundInstanceCatalog.py:242: in write_catalog write_mode=write_mode) python/lsst/sims/catalogs/definitions/CompoundInstanceCatalog.py:319: in _write_compound local_recarray.dtype = new_dtype_list[ix] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = rec.array([(21.42031646, -84.34274658, -4.48318279, -134.83444279, 0), (15.84139965, 24.55387403, 0.3135...,'dmag','table1DB1_raJ2000','id'], 'formats':[' raise exctype(value) E ValueError: When changing to a smaller dtype, its size must be a divisor of the size of original dtype ../../../../../../python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/core/records.py:487: ValueError ___________ CompoundCatalogTest.testObservationMetaDataAndConstraint ___________ [gw9] linux -- Python 3.7.3 /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/bin/python3.7 self = def testObservationMetaDataAndConstraint(self): """ Test that CompoundInstanceCatalog handles ObservationMetaData and a constraint properly """ fileName = os.path.join(self.scratch_dir, 'compound_obs_metadata_test_cat.txt') obs = ObservationMetaData(pointingRA = 180.0, pointingDec = 0.0, boundType = 'box', boundLength = (80.0, 25.0), mjd=53850.0) compoundCat = CompoundInstanceCatalog([Cat1, Cat2, Cat3], [table1DB1, table1DB2, table2DB1], obs_metadata=obs, constraint='mag>20.0') > compoundCat.write_catalog(fileName) tests/testCompoundInstanceCatalog.py:541: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ python/lsst/sims/catalogs/definitions/CompoundInstanceCatalog.py:242: in write_catalog write_mode=write_mode) python/lsst/sims/catalogs/definitions/CompoundInstanceCatalog.py:319: in _write_compound local_recarray.dtype = new_dtype_list[ix] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = rec.array([(23.98554189, 1.54272441, 3, 1.37429901, 215.51705431), (23.4922341 , 7.08160354, 19, -2.4...,'id','dmag','table1DB1_raJ2000'], 'formats':[' raise exctype(value) E ValueError: When changing to a smaller dtype, its size must be a divisor of the size of original dtype ../../../../../../python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/core/records.py:487: ValueError __________ CompoundCatalogTest.testCustomCompoundCatalogDBObjectList ___________ [gw11] linux -- Python 3.7.3 /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/bin/python3.7 self = def testCustomCompoundCatalogDBObjectList(self): """ Test that CompoundInstanceCatalog behaves properly when there are two sets of multiple queries, one to table1, one to table2 """ fileName = os.path.join(self.scratch_dir, 'simplest_compound_catalog.txt') compoundCat = CompoundInstanceCatalog([Cat1, Cat2, Cat3, Cat4], [table1DB1, table1DB2, table2DB1, table2DB2], compoundDBclass=[negativeRaCompound, negativeDecCompound_table2]) > compoundCat.write_catalog(fileName) tests/testCompoundInstanceCatalog.py:735: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ python/lsst/sims/catalogs/definitions/CompoundInstanceCatalog.py:242: in write_catalog write_mode=write_mode) python/lsst/sims/catalogs/definitions/CompoundInstanceCatalog.py:319: in _write_compound local_recarray.dtype = new_dtype_list[ix] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = rec.array([(21.42031646, -84.34274658, -4.48318279, 0, -134.83444279), (15.84139965, 24.55387403, 0.3135...,'dmag','id','table1DB1_raJ2000'], 'formats':[' raise exctype(value) E ValueError: When changing to a smaller dtype, its size must be a divisor of the size of original dtype ../../../../../../python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/core/records.py:487: ValueError _________________ CompoundCatalogTest.testObservationMetaData __________________ [gw3] linux -- Python 3.7.3 /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/bin/python3.7 self = def testObservationMetaData(self): """ Test that CompoundInstanceCatalog handles ObservationMetaData properly """ fileName = os.path.join(self.scratch_dir, 'compound_obs_metadata_test_cat.txt') obs = ObservationMetaData(pointingRA = 180.0, pointingDec = 0.0, boundType = 'box', boundLength = (80.0, 25.0), mjd=53850.0) compoundCat = CompoundInstanceCatalog([Cat1, Cat2, Cat3], [table1DB1, table1DB2, table2DB1], obs_metadata=obs) > compoundCat.write_catalog(fileName) tests/testCompoundInstanceCatalog.py:380: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ python/lsst/sims/catalogs/definitions/CompoundInstanceCatalog.py:242: in write_catalog write_mode=write_mode) python/lsst/sims/catalogs/definitions/CompoundInstanceCatalog.py:319: in _write_compound local_recarray.dtype = new_dtype_list[ix] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = rec.array([(23.98554189, 1.54272441, 1.37429901, 215.51705431, 3), (23.4922341 , 7.08160354, -2.49757...,'dmag','table1DB1_raJ2000','id'], 'formats':[' raise exctype(value) E ValueError: When changing to a smaller dtype, its size must be a divisor of the size of original dtype ../../../../../../python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/core/records.py:487: ValueError ___________________ CompoundCatalogTest.testSharedVariables ____________________ [gw11] linux -- Python 3.7.3 /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/bin/python3.7 self = def testSharedVariables(self): """ Test that, if I set a transformations dict in the CompoundInstanceCatalog, that gets propagated to all of the InstanceCatalogs inside it. """ fileName = os.path.join(self.scratch_dir, 'transformed_compound_catalog.txt') class TransformedCompoundCatalog(CompoundInstanceCatalog): transformations = {'raObs': np.degrees, 'decObs': np.degrees} compoundCat = TransformedCompoundCatalog([Cat1, Cat2, Cat3], [table1DB1, table1DB2, table2DB1]) > compoundCat.write_catalog(fileName) tests/testCompoundInstanceCatalog.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ python/lsst/sims/catalogs/definitions/CompoundInstanceCatalog.py:242: in write_catalog write_mode=write_mode) python/lsst/sims/catalogs/definitions/CompoundInstanceCatalog.py:319: in _write_compound local_recarray.dtype = new_dtype_list[ix] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = rec.array([(21.42031646, -84.34274658, -4.48318279, 0, 134.83444279), (15.84139965, 24.55387403, 0.31354...,'dmag','id','table1DB1_raJ2000'], 'formats':[' raise exctype(value) E ValueError: When changing to a smaller dtype, its size must be a divisor of the size of original dtype ../../../../../../python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/core/records.py:487: ValueError ____________ CompoundCatalogTest.testCustomCompoundCatalogDBObject _____________ [gw10] linux -- Python 3.7.3 /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/bin/python3.7 self = def testCustomCompoundCatalogDBObject(self): """ Test that CompoundInstanceCatalog behaves properly when passed a custom CompoundCatalogDBObject """ fileName = os.path.join(self.scratch_dir, 'simplest_compound_catalog.txt') compoundCat = CompoundInstanceCatalog([Cat1, Cat2, Cat3], [table1DB1, table1DB2, table2DB1], compoundDBclass=negativeRaCompound) > compoundCat.write_catalog(fileName) tests/testCompoundInstanceCatalog.py:630: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ python/lsst/sims/catalogs/definitions/CompoundInstanceCatalog.py:242: in write_catalog write_mode=write_mode) python/lsst/sims/catalogs/definitions/CompoundInstanceCatalog.py:319: in _write_compound local_recarray.dtype = new_dtype_list[ix] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = rec.array([(-4.48318279, -134.83444279, -84.34274658, 21.42031646, 0), ( 0.31354632, -342.25715031, 24.55...,'table1DB1_decJ2000','mag','id'], 'formats':[' raise exctype(value) E ValueError: When changing to a smaller dtype, its size must be a divisor of the size of original dtype ../../../../../../python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/core/records.py:487: ValueError ______________ CompoundInstanceCatalogTestCase.test_compound_cat _______________ [gw0] linux -- Python 3.7.3 /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/bin/python3.7 self = def test_compound_cat(self): """ Test that a CompoundInstanceCatalog made up of InstanceCatalog classes that each filter on a different condition gives the correct outputs. """ class FilteringCatClass1(InstanceCatalog): column_outputs = ['id', 'ip1t'] cannot_be_null = ['ip1t'] @cached def get_ip1t(self): base = self.column_by_name('ip1') output = [] for bb in base: if bb%2 == 0: output.append(bb) else: output.append(None) return np.array(output) class FilteringCatClass2(InstanceCatalog): column_outputs = ['id', 'ip2t'] cannot_be_null = ['ip2t'] @cached def get_ip2t(self): base = self.column_by_name('ip2') ii = self.column_by_name('id') return np.where(ii < 4, base, None) class FilteringCatClass3(InstanceCatalog): column_outputs = ['id', 'ip3t'] cannot_be_null = ['ip3t'] @cached def get_ip3t(self): base = self.column_by_name('ip3') ii = self.column_by_name('id') return np.where(ii > 5, base, None) class DbClass(CatalogDBObject): host = None port = None database = self.db_name driver = 'sqlite' tableid = 'test' objid = 'silliness' idColKey = 'id' class DbClass1(DbClass): objid = 'silliness1' class DbClass2(DbClass): objid = 'silliness2' class DbClass3(DbClass): objid = 'silliness3' cat = CompoundInstanceCatalog([FilteringCatClass1, FilteringCatClass2, FilteringCatClass3], [DbClass1, DbClass2, DbClass3]) cat_name = os.path.join(self.scratch_dir, "compound_filter_output.txt") if os.path.exists(cat_name): os.unlink(cat_name) cat.write_catalog(cat_name) with open(cat_name, 'r') as input_file: input_lines = input_file.readlines() > self.assertEqual(len(input_lines), 14) E AssertionError: 29 != 14 tests/testFilteringCatalogs.py:731: AssertionError ________________ InstanceCatalogCannotBeNullTest.testCanBeNull _________________ [gw2] linux -- Python 3.7.3 /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/bin/python3.7 self = def setUp(self): self.scratch_dir = tempfile.mkdtemp(dir=ROOT, prefix='scratchSpace-') # Force the class to understand where the DB is meant to be myCannotBeNullDBObject.database = os.path.join(self.scratch_dir, 'cannotBeNullTest.db') > self.baselineOutput = createCannotBeNullTestDB(dir=self.scratch_dir) tests/testInstanceCatalog.py:345: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ filename = None, add_nans = True dir = '/home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/EupsBuildDir/Linux64/sims_catalogs-2.13.0.sims/sims_catalogs-2.13.0.sims/tests/scratchSpace-7y0y5w5d' def createCannotBeNullTestDB(filename=None, add_nans=True, dir=None): """ Create a database to test the 'cannot_be_null' functionality in InstanceCatalog This method will return the contents of the database as a recarray for baseline comparison in the unit tests. If the filename is not specified, it will be written in to directory "dir" if not none, else it will be written to the current directory """ if filename is None: dbName = 'cannotBeNullTest.db' if dir is not None: dbName = os.path.join(dir, dbName) else: dbName = filename rng = np.random.RandomState(32) dtype = np.dtype([('id', int), ('n1', np.float64), ('n2', np.float64), ('n3', np.float64), ('n4', (str_type, 40)), ('n5', (str_type, 40))]) output = None if os.path.exists(dbName): os.unlink(dbName) conn = sqlite3.connect(dbName) c = conn.cursor() try: c.execute('''CREATE TABLE testTable (id int, n1 float, n2 float, n3 float, n4 text, n5 text)''') conn.commit() except: raise RuntimeError("Error creating database.") for ii in range(100): values = rng.random_sample(3) for i in range(len(values)): draw = rng.random_sample(1) if draw[0] < 0.5 and add_nans: values[i] = None draw = rng.random_sample(1) if draw[0] < 0.5: w1 = 'None' else: w1 = 'word' draw = rng.random_sample(1) if draw[0] < 0.5: w2 = str('None') else: w2 = str('word') if output is None: output = np.array([(ii, values[0], values[1], values[2], w1, w2)], dtype=dtype) else: size = output.size > output.resize(size+1) E ValueError: cannot resize an array that references or is referenced E by another array in this way. E Use the np.resize function or refcheck=False tests/testInstanceCatalog.py:88: ValueError ______ CompoundInstanceCatalogTestCase.test_compound_cat_compound_column _______ [gw8] linux -- Python 3.7.3 /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/bin/python3.7 self = def test_compound_cat_compound_column(self): """ Test filtering a CompoundInstanceCatalog on a compound column """ class FilteringCatClass4(InstanceCatalog): column_outputs = ['id', 'a', 'b'] cannot_be_null = ['a'] @compound('a', 'b') def get_alphabet(self): a = self.column_by_name('ip1') a = a*a b = self.column_by_name('ip2') b = b*0.25 return np.array([np.where(a % 2 == 0, a, None), b]) class FilteringCatClass5(InstanceCatalog): column_outputs = ['id', 'a', 'b', 'filter'] cannot_be_null = ['b', 'filter'] @compound('a', 'b') def get_alphabet(self): ii = self.column_by_name('ip1') return np.array([self.column_by_name('ip2')**3, np.where(ii % 2 == 1, ii, None)]) @cached def get_filter(self): ii = self.column_by_name('ip1') return np.where(ii % 3 != 0, ii, None) class DbClass(CatalogDBObject): host = None port = None database = self.db_name driver = 'sqlite' tableid = 'test' idColKey = 'id' class DbClass4(DbClass): objid = 'silliness4' class DbClass5(DbClass): objid = 'silliness5' cat_name = os.path.join(self.scratch_dir, "compound_cat_compound_filter_cat.txt") if os.path.exists(cat_name): os.unlink(cat_name) cat = CompoundInstanceCatalog([FilteringCatClass4, FilteringCatClass5], [DbClass4, DbClass5]) cat.write_catalog(cat_name) # now make sure that the catalog contains the expected data with open(cat_name, 'r') as input_file: input_lines = input_file.readlines() self.assertEqual(len(input_lines), 9) # 8 data lines and a header first_cat_lines = ['1, 4, 0.75\n', '3, 16, 1.25\n', '5, 36, 1.75\n', '7, 64, 2.25\n', '9, 100, 2.75\n'] second_cat_lines = ['0, 8, 1, 1\n', '4, 216, 5, 5\n', '6, 512, 7, 7\n'] for i_line, line in enumerate(input_lines): if i_line is 0: continue elif i_line < 6: > self.assertEqual(line, first_cat_lines[i_line-1]) E AssertionError: '3, 4, 0.25\n' != '1, 4, 0.75\n' E - 3, 4, 0.25 E ? ^ ^ E + 1, 4, 0.75 E ? ^ ^ tests/testFilteringCatalogs.py:824: AssertionError _________ InstanceCatalogCannotBeNullTest.testCannotBeNull_pre_screen __________ [gw0] linux -- Python 3.7.3 /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/bin/python3.7 self = def setUp(self): self.scratch_dir = tempfile.mkdtemp(dir=ROOT, prefix='scratchSpace-') # Force the class to understand where the DB is meant to be myCannotBeNullDBObject.database = os.path.join(self.scratch_dir, 'cannotBeNullTest.db') > self.baselineOutput = createCannotBeNullTestDB(dir=self.scratch_dir) tests/testInstanceCatalog.py:345: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ filename = None, add_nans = True dir = '/home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/EupsBuildDir/Linux64/sims_catalogs-2.13.0.sims/sims_catalogs-2.13.0.sims/tests/scratchSpace-a99_8gsz' def createCannotBeNullTestDB(filename=None, add_nans=True, dir=None): """ Create a database to test the 'cannot_be_null' functionality in InstanceCatalog This method will return the contents of the database as a recarray for baseline comparison in the unit tests. If the filename is not specified, it will be written in to directory "dir" if not none, else it will be written to the current directory """ if filename is None: dbName = 'cannotBeNullTest.db' if dir is not None: dbName = os.path.join(dir, dbName) else: dbName = filename rng = np.random.RandomState(32) dtype = np.dtype([('id', int), ('n1', np.float64), ('n2', np.float64), ('n3', np.float64), ('n4', (str_type, 40)), ('n5', (str_type, 40))]) output = None if os.path.exists(dbName): os.unlink(dbName) conn = sqlite3.connect(dbName) c = conn.cursor() try: c.execute('''CREATE TABLE testTable (id int, n1 float, n2 float, n3 float, n4 text, n5 text)''') conn.commit() except: raise RuntimeError("Error creating database.") for ii in range(100): values = rng.random_sample(3) for i in range(len(values)): draw = rng.random_sample(1) if draw[0] < 0.5 and add_nans: values[i] = None draw = rng.random_sample(1) if draw[0] < 0.5: w1 = 'None' else: w1 = 'word' draw = rng.random_sample(1) if draw[0] < 0.5: w2 = str('None') else: w2 = str('word') if output is None: output = np.array([(ii, values[0], values[1], values[2], w1, w2)], dtype=dtype) else: size = output.size > output.resize(size+1) E ValueError: cannot resize an array that references or is referenced E by another array in this way. E Use the np.resize function or refcheck=False tests/testInstanceCatalog.py:88: ValueError __________________ InstanceCatalogMetaDataTest.testArgValues ___________________ [gw10] linux -- Python 3.7.3 /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/bin/python3.7 self = def testArgValues(self): """ Test that columns added using the contructor ags return the correct value """ with lsst.utils.tests.getTempFilePath(".db") as dbName: > baselineData = createCannotBeNullTestDB(filename=dbName, add_nans=False) tests/testInstanceCatalog.py:296: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ filename = '/home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/EupsBuildDir/Linux64/sims_catalogs-2.13.0.sims/sims_catalogs-2.13.0.sims/tests/.tests/testInstanceCatalog_testArgValues-oosu6g72.db' add_nans = False, dir = None def createCannotBeNullTestDB(filename=None, add_nans=True, dir=None): """ Create a database to test the 'cannot_be_null' functionality in InstanceCatalog This method will return the contents of the database as a recarray for baseline comparison in the unit tests. If the filename is not specified, it will be written in to directory "dir" if not none, else it will be written to the current directory """ if filename is None: dbName = 'cannotBeNullTest.db' if dir is not None: dbName = os.path.join(dir, dbName) else: dbName = filename rng = np.random.RandomState(32) dtype = np.dtype([('id', int), ('n1', np.float64), ('n2', np.float64), ('n3', np.float64), ('n4', (str_type, 40)), ('n5', (str_type, 40))]) output = None if os.path.exists(dbName): os.unlink(dbName) conn = sqlite3.connect(dbName) c = conn.cursor() try: c.execute('''CREATE TABLE testTable (id int, n1 float, n2 float, n3 float, n4 text, n5 text)''') conn.commit() except: raise RuntimeError("Error creating database.") for ii in range(100): values = rng.random_sample(3) for i in range(len(values)): draw = rng.random_sample(1) if draw[0] < 0.5 and add_nans: values[i] = None draw = rng.random_sample(1) if draw[0] < 0.5: w1 = 'None' else: w1 = 'word' draw = rng.random_sample(1) if draw[0] < 0.5: w2 = str('None') else: w2 = str('word') if output is None: output = np.array([(ii, values[0], values[1], values[2], w1, w2)], dtype=dtype) else: size = output.size > output.resize(size+1) E ValueError: cannot resize an array that references or is referenced E by another array in this way. E Use the np.resize function or refcheck=False tests/testInstanceCatalog.py:88: ValueError _______________ InstanceCatalogCannotBeNullTest.testCannotBeNull _______________ [gw2] linux -- Python 3.7.3 /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/bin/python3.7 self = def setUp(self): self.scratch_dir = tempfile.mkdtemp(dir=ROOT, prefix='scratchSpace-') # Force the class to understand where the DB is meant to be myCannotBeNullDBObject.database = os.path.join(self.scratch_dir, 'cannotBeNullTest.db') > self.baselineOutput = createCannotBeNullTestDB(dir=self.scratch_dir) tests/testInstanceCatalog.py:345: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ filename = None, add_nans = True dir = '/home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/EupsBuildDir/Linux64/sims_catalogs-2.13.0.sims/sims_catalogs-2.13.0.sims/tests/scratchSpace-9h9w01sy' def createCannotBeNullTestDB(filename=None, add_nans=True, dir=None): """ Create a database to test the 'cannot_be_null' functionality in InstanceCatalog This method will return the contents of the database as a recarray for baseline comparison in the unit tests. If the filename is not specified, it will be written in to directory "dir" if not none, else it will be written to the current directory """ if filename is None: dbName = 'cannotBeNullTest.db' if dir is not None: dbName = os.path.join(dir, dbName) else: dbName = filename rng = np.random.RandomState(32) dtype = np.dtype([('id', int), ('n1', np.float64), ('n2', np.float64), ('n3', np.float64), ('n4', (str_type, 40)), ('n5', (str_type, 40))]) output = None if os.path.exists(dbName): os.unlink(dbName) conn = sqlite3.connect(dbName) c = conn.cursor() try: c.execute('''CREATE TABLE testTable (id int, n1 float, n2 float, n3 float, n4 text, n5 text)''') conn.commit() except: raise RuntimeError("Error creating database.") for ii in range(100): values = rng.random_sample(3) for i in range(len(values)): draw = rng.random_sample(1) if draw[0] < 0.5 and add_nans: values[i] = None draw = rng.random_sample(1) if draw[0] < 0.5: w1 = 'None' else: w1 = 'word' draw = rng.random_sample(1) if draw[0] < 0.5: w2 = str('None') else: w2 = str('word') if output is None: output = np.array([(ii, values[0], values[1], values[2], w1, w2)], dtype=dtype) else: size = output.size > output.resize(size+1) E ValueError: cannot resize an array that references or is referenced E by another array in this way. E Use the np.resize function or refcheck=False tests/testInstanceCatalog.py:88: ValueError _____________ InstanceCatalogMetaDataTest.testAllCalculatedColumns _____________ [gw8] linux -- Python 3.7.3 /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/bin/python3.7 self = def testAllCalculatedColumns(self): """ Unit test to make sure that _actually_calculated_columns contains all of the dependent columns """ class otherCartoonValueCatalog(InstanceCatalog): column_outputs = ['n1', 'n2', 'difference'] def get_difference(self): n1 = self.column_by_name('n1') n3 = self.column_by_name('n3') return n1-n3 with lsst.utils.tests.getTempFilePath(".db") as dbName: > createCannotBeNullTestDB(filename=dbName, add_nans=False) tests/testInstanceCatalog.py:330: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ filename = '/home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/EupsBuildDir/Linux64/sims_catalogs-2.13.0.sims/sims_catalogs-2.13.0.sims/tests/.tests/testInstanceCatalog_testAllCalculatedColumns-9pbh8x8_.db' add_nans = False, dir = None def createCannotBeNullTestDB(filename=None, add_nans=True, dir=None): """ Create a database to test the 'cannot_be_null' functionality in InstanceCatalog This method will return the contents of the database as a recarray for baseline comparison in the unit tests. If the filename is not specified, it will be written in to directory "dir" if not none, else it will be written to the current directory """ if filename is None: dbName = 'cannotBeNullTest.db' if dir is not None: dbName = os.path.join(dir, dbName) else: dbName = filename rng = np.random.RandomState(32) dtype = np.dtype([('id', int), ('n1', np.float64), ('n2', np.float64), ('n3', np.float64), ('n4', (str_type, 40)), ('n5', (str_type, 40))]) output = None if os.path.exists(dbName): os.unlink(dbName) conn = sqlite3.connect(dbName) c = conn.cursor() try: c.execute('''CREATE TABLE testTable (id int, n1 float, n2 float, n3 float, n4 text, n5 text)''') conn.commit() except: raise RuntimeError("Error creating database.") for ii in range(100): values = rng.random_sample(3) for i in range(len(values)): draw = rng.random_sample(1) if draw[0] < 0.5 and add_nans: values[i] = None draw = rng.random_sample(1) if draw[0] < 0.5: w1 = 'None' else: w1 = 'word' draw = rng.random_sample(1) if draw[0] < 0.5: w2 = str('None') else: w2 = str('word') if output is None: output = np.array([(ii, values[0], values[1], values[2], w1, w2)], dtype=dtype) else: size = output.size > output.resize(size+1) E ValueError: cannot resize an array that references or is referenced E by another array in this way. E Use the np.resize function or refcheck=False tests/testInstanceCatalog.py:88: ValueError generated xml file: /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/EupsBuildDir/Linux64/sims_catalogs-2.13.0.sims/sims_catalogs-2.13.0.sims/tests/.tests/pytest-sims_catalogs.xml ----------- coverage: platform linux, python 3.7.3-final-0 ----------- Name Stmts Miss Branch BrPart Cover ---------------------------------------------------------------------------------------------------- python/lsst/__init__.py 2 0 0 0 100% python/lsst/sims/__init__.py 2 0 0 0 100% python/lsst/sims/catalogs/__init__.py 2 0 0 0 100% python/lsst/sims/catalogs/db/CompoundCatalogDBObject.py 151 16 102 12 88% python/lsst/sims/catalogs/db/__init__.py 3 0 0 0 100% python/lsst/sims/catalogs/db/dbConnection.py 467 92 233 40 77% python/lsst/sims/catalogs/db/utils.py 94 21 46 8 74% python/lsst/sims/catalogs/decorators/__init__.py 1 0 0 0 100% python/lsst/sims/catalogs/decorators/decorators.py 39 1 10 2 94% python/lsst/sims/catalogs/definitions/CompoundInstanceCatalog.py 151 14 107 17 88% python/lsst/sims/catalogs/definitions/InstanceCatalog.py 337 44 203 24 84% python/lsst/sims/catalogs/definitions/ParallelCatalogWriter.py 48 8 24 3 85% python/lsst/sims/catalogs/definitions/__init__.py 3 0 0 0 100% python/lsst/sims/catalogs/utils/__init__.py 1 0 0 0 100% python/lsst/sims/catalogs/utils/testUtils.py 159 34 28 5 73% tests/testCatalogDBObject.py 812 13 182 8 98% tests/testCatalogs.py 467 11 92 16 95% tests/testColumnOrigins.py 198 6 12 5 95% tests/testCompoundCatalogDBObject.py 414 9 86 13 96% tests/testCompoundInstanceCatalog.py 468 287 140 8 33% tests/testConnectionCache.py 83 3 10 4 92% tests/testConnectionPassing.py 118 6 28 10 89% tests/testDBObject.py 310 16 64 10 93% tests/testFileDBObject.py 53 2 12 3 92% tests/testFilteringCatalogs.py 544 35 174 31 89% tests/testInstanceCatalog.py 310 135 106 14 50% tests/testMethodRegistry.py 52 2 10 1 95% tests/testParallelCatalogWriter.py 174 5 42 8 94% ---------------------------------------------------------------------------------------------------- TOTAL 5463 760 1711 242 82% Coverage HTML written to dir tests/.tests/pytest-sims_catalogs.xml-htmlcov Coverage XML written to file tests/.tests/pytest-sims_catalogs.xml-cov-sims_catalogs.xml =============================== warnings summary =============================== tests/testCatalogDBObject.py::CatalogDBObjectTestCase::testDbObj /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:374: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly args = inspect.formatargspec(*spec) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:384: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly spec[2], None, spec[4]) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:405: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly formatvalue=lambda x: '=' + x) tests/testCatalogDBObject.py::CatalogDBObjectTestCase::testArbitraryChunkIterator_passConnection /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:374: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly args = inspect.formatargspec(*spec) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:384: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly spec[2], None, spec[4]) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:405: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly formatvalue=lambda x: '=' + x) tests/testCatalogDBObject.py::CatalogDBObjectTestCase::testArbitraryChunkIterator /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:374: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly args = inspect.formatargspec(*spec) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:384: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly spec[2], None, spec[4]) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:405: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly formatvalue=lambda x: '=' + x) tests/testCatalogDBObject.py::CatalogDBObjectTestCase::testArbitraryQuery /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:374: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly args = inspect.formatargspec(*spec) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:384: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly spec[2], None, spec[4]) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:405: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly formatvalue=lambda x: '=' + x) tests/testCatalogDBObject.py::CatalogDBObjectTestCase::testNonsenseArbitraryConstraints_passConnection /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:374: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly args = inspect.formatargspec(*spec) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:384: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly spec[2], None, spec[4]) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:405: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly formatvalue=lambda x: '=' + x) tests/testCatalogDBObject.py::CatalogDBObjectTestCase::testClassVariables /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:374: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly args = inspect.formatargspec(*spec) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:384: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly spec[2], None, spec[4]) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:405: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly formatvalue=lambda x: '=' + x) tests/testCatalogDBObject.py::CatalogDBObjectTestCase::testChunking /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:374: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly args = inspect.formatargspec(*spec) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:384: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly spec[2], None, spec[4]) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:405: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly formatvalue=lambda x: '=' + x) tests/testCatalogDBObject.py::CatalogDBObjectTestCase::testNonsenseArbitraryConstraints /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:374: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly args = inspect.formatargspec(*spec) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:384: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly spec[2], None, spec[4]) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:405: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly formatvalue=lambda x: '=' + x) tests/testCatalogDBObject.py::CatalogDBObjectTestCase::testArbitraryQuery_passConnection /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:374: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly args = inspect.formatargspec(*spec) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:384: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly spec[2], None, spec[4]) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:405: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly formatvalue=lambda x: '=' + x) tests/testCatalogDBObject.py::CatalogDBObjectTestCase::testNonsenseBoxConstraints_passConnection /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:374: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly args = inspect.formatargspec(*spec) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:384: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly spec[2], None, spec[4]) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:405: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly formatvalue=lambda x: '=' + x) tests/testCatalogDBObject.py::CatalogDBObjectTestCase::testNonsenseBoxConstraints /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:374: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly args = inspect.formatargspec(*spec) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:384: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly spec[2], None, spec[4]) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:405: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly formatvalue=lambda x: '=' + x) tests/testCatalogDBObject.py::CatalogDBObjectTestCase::testNonsenseCircularConstraints /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:374: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly args = inspect.formatargspec(*spec) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:384: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly spec[2], None, spec[4]) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/Linux64/sqlalchemy/1.2.2+2/lib/python/SQLAlchemy-1.2.2-py3.7-linux-x86_64.egg/sqlalchemy/util/langhelpers.py:405: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly formatvalue=lambda x: '=' + x) tests/testCatalogDBObject.py::fileDBObjectTestCase::testChunking /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCatalogDBObject.py::fileDBObjectTestCase::testNonsenseSelectOnlySomeColumns /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCatalogDBObject.py::fileDBObjectTestCase::testDatabaseName /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCatalogDBObject.py::fileDBObjectTestCase::testNonsenseArbitraryConstraints /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCatalogDBObject.py::fileDBObjectTestCase::testNonsenseBoxConstraints /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCatalogDBObject.py::fileDBObjectTestCase::testNonsenseCircularConstraints /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCompoundCatalogDBObject.py::CompoundCatalogDBObjectTestCase::testChunks /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCompoundCatalogDBObject.py::CompoundWithObsMetaData::testObsMetadataAndConstraint /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCompoundCatalogDBObject.py::CompoundWithObsMetaData::testConstraint /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCatalogs.py::InstanceCatalogTestCase::test_iter_catalog /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCatalogs.py::InstanceCatalogTestCase::test_transformation /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCompoundCatalogDBObject.py::CompoundCatalogDBObjectTestCase::testTableRestriction /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCompoundCatalogDBObject.py::CompoundCatalogDBObjectTestCase::testCompoundCatalogDBObject_method /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCatalogs.py::boundingBoxTest::testCircBounds /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCompoundInstanceCatalog.py::CompoundCatalogTest::testCompoundCatalog /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCatalogs.py::boundingBoxTest::test_very_positive_RA /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCompoundInstanceCatalog.py::CompoundCatalogTest::testDefaultCustomCompoundCatalogDBObject /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCompoundInstanceCatalog.py::CompoundCatalogTest::testCustomCompoundCatalogDBObjectList /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCompoundInstanceCatalog.py::CompoundCatalogTest::testObservationMetaDataAndConstraint /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCompoundCatalogDBObject.py::CompoundWithObsMetaData::testObsMetaData /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testFileDBObject.py::FileDBObjectTestCase::test_ingest /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testFilteringCatalogs.py::InstanceCatalogTestCase::test_adding_filter /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCatalogs.py::boundingBoxTest::testBoxBounds /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCompoundInstanceCatalog.py::CompoundCatalogTest::testCustomCompoundCatalogDBObject /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCatalogs.py::InstanceCatalogTestCase::testStarLike /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testConnectionPassing.py::ConnectionPassingTest::test_passing /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testFilteringCatalogs.py::CompoundInstanceCatalogTestCase::test_compound_cat /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testFilteringCatalogs.py::CompoundInstanceCatalogTestCase::test_compound_cat_compound_column /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) tests/testCompoundCatalogDBObject.py::CompoundCatalogDBObjectTestCase::testExceptions /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/EupsBuildDir/Linux64/sims_catalogs-2.13.0.sims/sims_catalogs-2.13.0.sims/python/lsst/sims/catalogs/db/dbConnection.py:540: UserWarning: duplicate object identifier dummy specified. This will override previous definition on line 218 of /home/tanguita/lsst/stack/miniconda3-4.5.12-1172c30/EupsBuildDir/Linux64/sims_catalogs-2.13.0.sims/sims_catalogs-2.13.0.sims/tests/testCompoundCatalogDBObject.py (srcline, srcfile)) tests/testFilteringCatalogs.py::InstanceCatalogTestCase::test_compound_column /home/tanguita/lsst/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead 'a.item() instead', DeprecationWarning, stacklevel=1) -- Docs: http://doc.pytest.org/en/latest/warnings.html ============= 15 failed, 104 passed, 67 warnings in 39.09 seconds ==============