fixed errors in code and unit tests; pinned unit test order

Author: mitzimorris

cmdstanpy/model.py

@@ -1320,9 +1320,8 @@ def _run_cmdstan(
                 fd_out.write(stdout)
                 if show_console:
                     lines = stdout.split('\n')
-                    print(f' ****** lines to process: {len(lines)}')
                     for line in lines:
-                        print('chain {}: {}'.format(idx + 1, stdout))
+                        print('chain {}: {}'.format(idx + 1, line))
 
             fd_out.close()
         except OSError as e:

requirements-test.txt

@@ -2,6 +2,7 @@ flake8
 pylint
 pytest
 pytest-cov
+pytest-order
 mypy
 testfixtures
 tqdm

test/test_generate_quantities.py

@@ -470,7 +470,7 @@ def test_show_console(self):
                 mcmc_sample=bern_fit,
                 show_console=True,
             )
-            console = sys_stdout.getvalue()
+        console = sys_stdout.getvalue()
         self.assertTrue('chain 1: method = generate' in console)
         self.assertTrue('chain 2: method = generate' in console)
         self.assertTrue('chain 3: method = generate' in console)

test/test_optimize.py

@@ -603,7 +603,7 @@ def test_show_console(self):
                 data=jdata,
                 show_console=True,
             )
-            console = sys_stdout.getvalue()
+        console = sys_stdout.getvalue()
         self.assertTrue('chain 1: method = optimize' in console)
 
 

test/test_sample.py

@@ -578,7 +578,7 @@ def test_show_console(self, stanfile='bernoulli.stan'):
                 iter_sampling=100,
                 show_console=True,
             )
-            console = sys_stdout.getvalue()
+        console = sys_stdout.getvalue()
         self.assertTrue('chain 1: method = sample' in console)
         self.assertTrue('chain 2: method = sample' in console)
 
@@ -592,7 +592,7 @@ def test_show_progress(self, stanfile='bernoulli.stan'):
             bern_model.sample(
                 data=jdata, chains=2, parallel_chains=2, show_progress=True
             )
-            console = sys_stderr.getvalue()
+        console = sys_stderr.getvalue()
         self.assertTrue('chain 1' in console)
         self.assertTrue('chain 2' in console)
         self.assertTrue('Sampling completed' in console)

test/test_variational.py

@@ -246,7 +246,8 @@ def test_variational_eta_fail(self):
     def test_single_row_csv(self):
         stan = os.path.join(DATAFILES_PATH, 'matrix_var.stan')
         model = CmdStanModel(stan_file=stan)
-        vb_fit = model.variational()
+        # testing data parsing, allow non-convergence
+        vb_fit = model.variational(require_converged=False, seed=12345)
         self.assertTrue(isinstance(vb_fit.stan_variable('theta'), float))
         z_as_ndarray = vb_fit.stan_variable(var="z")
         self.assertEqual(z_as_ndarray.shape, (4, 3))
@@ -261,11 +262,14 @@ def test_show_console(self):
 
         sys_stdout = io.StringIO()
         with contextlib.redirect_stdout(sys_stdout):
+            # testing data parsing, allow non-convergence
             bern_model.variational(
                 data=jdata,
                 show_console=True,
+                require_converged=False,
+                seed=12345,
             )
-            console = sys_stdout.getvalue()
+        console = sys_stdout.getvalue()
         self.assertTrue('chain 1: method = variational' in console)