Add flake8 for test dir

.travis.yml

@@ -26,6 +26,7 @@ script:
   - mkdir new_dir
   - cd new_dir
   - flake8 --extend-ignore=E127,E201,E202,E203,E231,E252,E266,E402,E999,F401,F841,W503,W605 --max-line-length=80 ../cmdstanpy
+  - flake8 --extend-ignore=E127,E201,E202,E203,E231,E252,E266,E402,E999,F841,W503,W605 --max-line-length=80 ../test
   - pytest -v ../test
   - python -m pip install -r ../requirements-optional.txt
   - python ../test/example_script.py

test/example_script.py

@@ -3,9 +3,9 @@
 import sys
 
 # explicit import to test if it is installed
-import tqdm
+import tqdm # noqa
 
-from cmdstanpy import CmdStanModel, cmdstan_path, set_make_env
+from cmdstanpy import CmdStanModel, cmdstan_path
 
 
 def run_bernoulli_fit():

test/test_cmdstan_args.py

@@ -1,8 +1,6 @@
 import os
 import unittest
 
-from cmdstanpy import TMPDIR
-
 from cmdstanpy.cmdstan_args import (
     Method,
     SamplerArgs,
@@ -30,7 +28,6 @@ def test_args_algorithm_init_alpha(self):
         args.validate()
         cmd = args.compose(None, cmd=['output'])
 
-
         self.assertIn('init_alpha=0.0002', ' '.join(cmd))
         args = OptimizeArgs(init_alpha=-1.0)
         self.assertRaises(ValueError, lambda: args.validate())
@@ -155,12 +152,14 @@ def test_adapt(self):
         args = SamplerArgs(adapt_engaged=False)
         args.validate(chains=4)
         cmd = args.compose(1, cmd=[])
-        self.assertIn('method=sample algorithm=hmc adapt engaged=0', ' '.join(cmd))
+        self.assertIn('method=sample algorithm=hmc adapt engaged=0',
+                      ' '.join(cmd))
 
         args = SamplerArgs(adapt_engaged=True)
         args.validate(chains=4)
         cmd = args.compose(1, cmd=[])
-        self.assertIn('method=sample algorithm=hmc adapt engaged=1', ' '.join(cmd))
+        self.assertIn('method=sample algorithm=hmc adapt engaged=1',
+                      ' '.join(cmd))
 
         args = SamplerArgs()
         args.validate(chains=4)
@@ -172,22 +171,26 @@ def test_metric(self):
         args = SamplerArgs(metric='dense_e')
         args.validate(chains=4)
         cmd = args.compose(1, cmd=[])
-        self.assertIn('method=sample algorithm=hmc metric=dense_e', ' '.join(cmd))
+        self.assertIn('method=sample algorithm=hmc metric=dense_e',
+                      ' '.join(cmd))
 
         args = SamplerArgs(metric='dense')
         args.validate(chains=4)
         cmd = args.compose(1, cmd=[])
-        self.assertIn('method=sample algorithm=hmc metric=dense_e', ' '.join(cmd))
+        self.assertIn('method=sample algorithm=hmc metric=dense_e',
+                      ' '.join(cmd))
 
         args = SamplerArgs(metric='diag_e')
         args.validate(chains=4)
         cmd = args.compose(1, cmd=[])
-        self.assertIn('method=sample algorithm=hmc metric=diag_e', ' '.join(cmd))
+        self.assertIn('method=sample algorithm=hmc metric=diag_e',
+                      ' '.join(cmd))
 
         args = SamplerArgs(metric='diag')
         args.validate(chains=4)
         cmd = args.compose(1, cmd=[])
-        self.assertIn('method=sample algorithm=hmc metric=diag_e', ' '.join(cmd))
+        self.assertIn('method=sample algorithm=hmc metric=diag_e',
+                      ' '.join(cmd))
 
         args = SamplerArgs()
         args.validate(chains=4)
@@ -511,6 +514,7 @@ def test_args_fitted_params(self):
         self.assertIn('method=generate_quantities', ' '.join(cmd))
         self.assertIn('fitted_params={}'.format(csv_files[0]), ' '.join(cmd))
 
+
 class VariationalTest(unittest.TestCase):
     def test_args_variational(self):
         args = VariationalArgs()

test/test_cxx_installation.py

@@ -1,11 +1,6 @@
-import argparse
-import os
 import unittest
-from unittest import mock
 import platform
-import shutil
 
-from cmdstanpy import TMPDIR
 from cmdstanpy import install_cxx_toolchain
 
 
@@ -37,7 +32,8 @@ def test_install_not_windows(self):
 
         with self.assertRaisesRegex(
             NotImplementedError,
-            r'Download for the C\+\+ toolchain on the current platform has not been implemented:\s*\S+',
+            r'Download for the C\+\+ toolchain on the current platform has not '
+            'been implemented:\s*\S+',
         ):
             install_cxx_toolchain.main()
 

test/test_generate_quantities.py

@@ -1,16 +1,8 @@
 import os
 import unittest
 
-from cmdstanpy.cmdstan_args import Method, SamplerArgs, CmdStanArgs
-from cmdstanpy.utils import EXTENSION
+from cmdstanpy.cmdstan_args import Method
 from cmdstanpy.model import CmdStanModel
-from cmdstanpy.stanfit import RunSet
-from contextlib import contextmanager
-import logging
-from multiprocessing import cpu_count
-import numpy as np
-import sys
-from testfixtures import LogCapture
 
 here = os.path.dirname(os.path.abspath(__file__))
 datafiles_path = os.path.join(here, 'data')
@@ -62,15 +54,14 @@ def test_gen_quantities_csv_files(self):
                              bern_gqs.mcmc_sample.shape[1] +
                              bern_gqs.generated_quantities_pd.shape[1])
 
-
-
     def test_gen_quantities_csv_files_bad(self):
         stan = os.path.join(datafiles_path, 'bernoulli_ppc.stan')
         model = CmdStanModel(stan_file=stan)
         jdata = os.path.join(datafiles_path, 'bernoulli.data.json')
 
         # synthesize list of filenames
-        goodfiles_path = os.path.join(datafiles_path, 'runset-bad', 'bad-draws-bern')
+        goodfiles_path = os.path.join(datafiles_path, 'runset-bad',
+                                      'bad-draws-bern')
         csv_files = []
         for i in range(4):
             csv_files.append('{}-{}.csv'.format(goodfiles_path, i+1))
@@ -81,7 +72,6 @@ def test_gen_quantities_csv_files_bad(self):
                 mcmc_sample=csv_files
                 )
 
-
     def test_gen_quanties_mcmc_sample(self):
         stan = os.path.join(datafiles_path, 'bernoulli.stan')
         bern_model = CmdStanModel(stan_file=stan)
@@ -123,7 +113,8 @@ def test_gen_quanties_mcmc_sample(self):
             'y_rep.10',
         ]
         self.assertEqual(bern_gqs.column_names, tuple(column_names))
-        self.assertEqual(bern_fit.get_drawset().shape, bern_gqs.mcmc_sample.shape)
+        self.assertEqual(bern_fit.get_drawset().shape,
+                         bern_gqs.mcmc_sample.shape)
         self.assertEqual(bern_gqs.sample_plus_quantities.shape[1],
                              bern_gqs.mcmc_sample.shape[1] +
                              bern_gqs.generated_quantities_pd.shape[1])
@@ -144,6 +135,5 @@ def test_sample_plus_quantities_dedup(self):
                              bern_gqs.mcmc_sample.shape[1])
 
 
-
 if __name__ == '__main__':
     unittest.main()

test/test_model.py

@@ -2,15 +2,11 @@
 import pytest
 import unittest
 
-from cmdstanpy.cmdstan_args import Method, SamplerArgs, CmdStanArgs
 from cmdstanpy.utils import EXTENSION
 from cmdstanpy.model import CmdStanModel
-from contextlib import contextmanager
 
 from cmdstanpy.utils import cmdstan_path
 
-import sys
-
 here = os.path.dirname(os.path.abspath(__file__))
 datafiles_path = os.path.join(here, 'data')
 
@@ -47,7 +43,7 @@ def show_cmdstan_version(self):
     def test_model_good(self):
         stan = os.path.join(datafiles_path, 'bernoulli.stan')
         exe = os.path.join(datafiles_path, 'bernoulli' + EXTENSION)
-        
+
         # compile on instantiation
         model = CmdStanModel(stan_file=stan)
         self.assertEqual(stan, model.stan_file)
@@ -94,7 +90,6 @@ def test_model_bad(self):
         with self.assertRaises(Exception):
             model = CmdStanModel(stan_file=stan)
 
-
     def test_repr(self):
         stan = os.path.join(datafiles_path, 'bernoulli.stan')
         model = CmdStanModel(stan_file=stan)
@@ -153,6 +148,5 @@ def test_model_compile_includes(self):
         self.assertTrue(model3.exe_file.endswith(exe.replace('\\', '/')))
 
 
-
 if __name__ == '__main__':
     unittest.main()

test/test_optimize.py

@@ -3,16 +3,10 @@
 import unittest
 import json
 
-from cmdstanpy.cmdstan_args import Method, OptimizeArgs, CmdStanArgs
+from cmdstanpy.cmdstan_args import OptimizeArgs, CmdStanArgs
 from cmdstanpy.utils import EXTENSION
 from cmdstanpy.model import CmdStanModel
 from cmdstanpy.stanfit import RunSet, CmdStanMLE
-from contextlib import contextmanager
-import logging
-from multiprocessing import cpu_count
-import numpy as np
-import sys
-from testfixtures import LogCapture
 
 here = os.path.dirname(os.path.abspath(__file__))
 datafiles_path = os.path.join(here, 'data')
@@ -54,7 +48,6 @@ def test_set_mle_attrs(self):
         self.assertEqual(mle.column_names,('lp__', 'x', 'y'))
         self.assertAlmostEqual(mle.optimized_params_dict['x'], 1, places=3)
         self.assertAlmostEqual(mle.optimized_params_dict['y'], 1, places=3)
-
 
 
 class OptimizeTest(unittest.TestCase):
@@ -112,7 +105,6 @@ def test_optimize_good_dict(self):
         self.assertAlmostEqual(mle.optimized_params_np[0], -5, places=2)
         self.assertAlmostEqual(mle.optimized_params_np[1], 0.2, places=3)
 
-
     def test_optimize_rosenbrock(self):
         stan = os.path.join(datafiles_path, 'optimize', 'rosenbrock.stan')
         rose_model = CmdStanModel(stan_file=stan)
@@ -127,12 +119,13 @@ def test_optimize_rosenbrock(self):
         self.assertAlmostEqual(mle.optimized_params_dict['x'], 1, places=3)
         self.assertAlmostEqual(mle.optimized_params_dict['y'], 1, places=3)
 
-
     def test_optimize_bad(self):
-        stan = os.path.join(datafiles_path, 'optimize', 'exponential_boundary.stan')
+        stan = os.path.join(datafiles_path, 'optimize',
+                            'exponential_boundary.stan')
         exp_bound_model = CmdStanModel(stan_file=stan)
         no_data = {}
-        with self.assertRaisesRegex(Exception, 'Error during optimizing, error code 70'):
+        with self.assertRaisesRegex(Exception,
+                                    'Error during optimizing, error code 70'):
             exp_bound_model.optimize(
                 data=no_data,
                 seed=1239812093,

test/test_sample.py

@@ -16,6 +16,7 @@
 goodfiles_path = os.path.join(datafiles_path, 'runset-good')
 badfiles_path = os.path.join(datafiles_path, 'runset-bad')
 
+
 class SampleTest(unittest.TestCase):
 
     @pytest.fixture(scope="class", autouse=True)
@@ -129,9 +130,6 @@ def test_init_types(self):
                 inits=-1
             )
 
-
-
-
     def test_bernoulli_bad(self):
         stan = os.path.join(datafiles_path, 'bernoulli.stan')
         bern_model = CmdStanModel(stan_file=stan)
@@ -189,7 +187,7 @@ def test_fixed_param_good(self):
             self.assertTrue(os.path.exists(txt_file))
 
         self.assertEqual(datagen_fit.runset.chains, 1)
-                             
+
         column_names = [
             'lp__',
             'accept_stat__',
@@ -288,7 +286,9 @@ def test_bernoulli_file_with_space(self):
         self.test_bernoulli_good('bernoulli with space in name.stan')
 
     def test_bernoulli_path_with_space(self):
-        self.test_bernoulli_good('path with space/bernoulli_path_with_space.stan')
+        self.test_bernoulli_good('path with space/'
+                                 'bernoulli_path_with_space.stan')
+
 
 class CmdStanMCMCTest(unittest.TestCase):
     def test_validate_good_run(self):

test/test_utils.py

@@ -2,7 +2,6 @@
 import os
 import unittest
 import platform
-import tempfile
 import shutil
 import string
 import random
@@ -11,7 +10,6 @@
 
 from cmdstanpy import TMPDIR
 from cmdstanpy.utils import (
-    EXTENSION,
     cmdstan_path,
     set_cmdstan_path,
     validate_cmdstan_path,
@@ -150,7 +148,6 @@ def test_jsondump(self):
             self.assertEqual(json.load(fp), dict_zero_matrix)
 
 
-
 class ReadStanCsvTest(unittest.TestCase):
     def test_check_sampler_csv_1(self):
         csv_good = os.path.join(datafiles_path, 'bernoulli_output_1.csv')
@@ -380,7 +377,7 @@ def test_roundtrip_metric(self):
         os.remove(dfile_tmp)
 
     def test_parse_rdump_value(self):
-        s1 = 'structure(c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16),.Dim=c(2,8))'
+        s1 = 'structure(c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16),.Dim=c(2,8))'
         v_s1 = parse_rdump_value(s1)
         self.assertEqual(v_s1.shape, (2, 8))
         self.assertEqual(v_s1[1, 0], 2)
@@ -390,7 +387,7 @@ def test_parse_rdump_value(self):
         v_s2 = parse_rdump_value(s2)
         self.assertEqual(v_s2.shape, (1, 16))
 
-        s3 = 'structure(c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16),.Dim = c(8, 2))'
+        s3 = 'structure(c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16),.Dim=c(8,2))'
         v_s3 = parse_rdump_value(s3)
         self.assertEqual(v_s3.shape, (8, 2))
         self.assertEqual(v_s3[1, 0], 2)