Merge branch 'develop' of https://github.com/stan-dev/cmdstanpy into develop

Author: mitzimorris

cmdstanpy/install_cmdstan.py

@@ -163,7 +163,7 @@ def validate_dir(install_dir):
     if not os.path.exists(install_dir):
         try:
             os.makedirs(install_dir)
-        except OSError as e:
+        except (IOError, OSError, PermissionError) as e:
             raise ValueError(
                 'Cannot create directory: {}'.format(install_dir)
             ) from e
@@ -176,7 +176,7 @@ def validate_dir(install_dir):
             with open('tmp_test_w', 'w'):
                 pass
             os.remove('tmp_test_w')  # cleanup
-        except OSError as e:
+        except (IOError, OSError, PermissionError) as e:
             raise ValueError(
                 'Cannot write files to directory {}'.format(install_dir)
             ) from e

cmdstanpy/install_cxx_toolchain.py

@@ -211,7 +211,7 @@ def validate_dir(install_dir):
     if not os.path.exists(install_dir):
         try:
             os.makedirs(install_dir)
-        except OSError as e:
+        except (IOError, OSError, PermissionError) as e:
             raise ValueError(
                 'Cannot create directory: {}'.format(install_dir)
             ) from e

cmdstanpy/stanfit.py

@@ -235,7 +235,7 @@ def save_csvfiles(self, dir: str = None) -> None:
             with open(test_path, 'w'):
                 pass
             os.remove(test_path)  # cleanup
-        except OSError:
+        except (IOError, OSError, PermissionError):
             raise Exception('cannot save to path: {}'.format(dir))
 
         for i in range(self.chains):

test/test_runset.py

@@ -3,6 +3,7 @@
 import os
 import unittest
 
+from cmdstanpy import _TMPDIR
 from cmdstanpy.cmdstan_args import SamplerArgs, CmdStanArgs
 from cmdstanpy.utils import EXTENSION
 from cmdstanpy.stanfit import RunSet
@@ -95,6 +96,34 @@ def test_commands(self):
         self.assertIn('id=1', runset._cmds[0])
         self.assertIn('id=4', runset._cmds[3])
 
+    def test_save_diagnostics(self):
+        exe = os.path.join(DATAFILES_PATH, 'bernoulli' + EXTENSION)
+        jdata = os.path.join(DATAFILES_PATH, 'bernoulli.data.json')
+        sampler_args = SamplerArgs()
+        chain_ids = [1, 2, 3, 4]
+        cmdstan_args = CmdStanArgs(
+            model_name='bernoulli',
+            model_exe=exe,
+            chain_ids=chain_ids,
+            data=jdata,
+            method_args=sampler_args,
+            save_diagnostics=True,
+        )
+        runset = RunSet(args=cmdstan_args)
+        self.assertIn(_TMPDIR, runset.diagnostic_files[0])
+
+        cmdstan_args = CmdStanArgs(
+            model_name='bernoulli',
+            model_exe=exe,
+            chain_ids=chain_ids,
+            data=jdata,
+            method_args=sampler_args,
+            save_diagnostics=True,
+            output_dir=os.path.abspath('.'),
+        )
+        runset = RunSet(args=cmdstan_args)
+        self.assertIn(os.path.abspath('.'), runset.diagnostic_files[0])
+
     def test_chain_ids(self):
         exe = os.path.join(DATAFILES_PATH, 'bernoulli' + EXTENSION)
         jdata = os.path.join(DATAFILES_PATH, 'bernoulli.data.json')

test/test_sample.py

@@ -5,11 +5,14 @@
 import logging
 import shutil
 from multiprocessing import cpu_count
+import tempfile
+import stat
 import unittest
 from time import time
 from testfixtures import LogCapture
 import pytest
 
+from cmdstanpy import _TMPDIR
 from cmdstanpy.cmdstan_args import Method, SamplerArgs, CmdStanArgs
 from cmdstanpy.utils import EXTENSION
 from cmdstanpy.stanfit import RunSet, CmdStanMCMC
@@ -76,6 +79,36 @@ def test_bernoulli_good(self, stanfile='bernoulli.stan'):
         self.assertEqual(bern_fit.stepsize.shape, (2,))
         self.assertEqual(bern_fit.metric.shape, (2, 1))
 
+        bern_fit = bern_model.sample(
+            data=jdata,
+            chains=2,
+            parallel_chains=2,
+            seed=12345,
+            iter_warmup=1000,
+            iter_sampling=100,
+            metric='dense_e',
+        )
+        self.assertIn('CmdStanMCMC: model=bernoulli', bern_fit.__repr__())
+        self.assertIn('method=sample', bern_fit.__repr__())
+
+        self.assertEqual(bern_fit.runset._args.method, Method.SAMPLE)
+
+        for i in range(bern_fit.runset.chains):
+            csv_file = bern_fit.runset.csv_files[i]
+            stdout_file = bern_fit.runset.stdout_files[i]
+            self.assertTrue(os.path.exists(csv_file))
+            self.assertTrue(os.path.exists(stdout_file))
+
+        self.assertEqual(bern_fit.runset.chains, 2)
+        self.assertEqual(bern_fit.num_draws, 100)
+        self.assertEqual(bern_fit.column_names, tuple(BERNOULLI_COLS))
+
+        bern_sample = bern_fit.sample
+        self.assertEqual(bern_sample.shape, (100, 2, len(BERNOULLI_COLS)))
+        self.assertEqual(bern_fit.metric_type, 'dense_e')
+        self.assertEqual(bern_fit.stepsize.shape, (2,))
+        self.assertEqual(bern_fit.metric.shape, (2, 1, 1))
+
         bern_fit = bern_model.sample(
             data=jdata,
             chains=2,
@@ -510,9 +543,9 @@ def test_validate_big_run(self):
         self.assertEqual((2000, 3), mo_phis.shape)
         phi2095 = fit.get_drawset(params=['phi.2095'])
         self.assertEqual((2000, 1), phi2095.shape)
-        with self.assertRaises(Exception):
+        with self.assertRaisesRegex(ValueError, 'unknown parameter: phi.2096'):
             fit.get_drawset(params=['phi.2096'])
-        with self.assertRaises(Exception):
+        with self.assertRaisesRegex(ValueError, 'unknown parameter: ph'):
             fit.get_drawset(params=['ph'])
 
     # pylint: disable=no-self-use
@@ -575,7 +608,9 @@ def test_save_csv(self):
         for i in range(bern_fit.runset.chains):
             csv_file = bern_fit.runset.csv_files[i]
             self.assertTrue(os.path.exists(csv_file))
-        with self.assertRaisesRegex(Exception, 'file exists'):
+        with self.assertRaisesRegex(
+            ValueError, 'file exists, not overwriting: '
+        ):
             bern_fit.save_csvfiles(dir=DATAFILES_PATH)
 
         tmp2_dir = os.path.join(HERE, 'tmp2')
@@ -611,6 +646,15 @@ def test_save_csv(self):
             if os.path.exists(bern_fit.runset.stderr_files[i]):
                 os.remove(bern_fit.runset.stderr_files[i])
 
+        with self.assertRaisesRegex(ValueError, 'cannot access csv file'):
+            bern_fit.save_csvfiles(dir=DATAFILES_PATH)
+
+        if platform.system() != "Windows":
+            with self.assertRaisesRegex(Exception, 'cannot save to path: '):
+                dir = tempfile.mkdtemp(dir=_TMPDIR)
+                os.chmod(dir, stat.S_IRUSR | stat.S_IRGRP | stat.S_IROTH)
+                bern_fit.save_csvfiles(dir=dir)
+
     def test_diagnose_divergences(self):
         exe = os.path.join(DATAFILES_PATH, 'bernoulli' + EXTENSION)
         sampler_args = SamplerArgs()