cmdstanpy 1.2.2__tar.gz → 1.2.4__tar.gz

{cmdstanpy-1.2.2/cmdstanpy.egg-info → cmdstanpy-1.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cmdstanpy
-Version: 1.2.2
+Version: 1.2.4
 Summary: Python interface to CmdStan
 Author: Stan Dev Team
 License: BSD-3-Clause

cmdstanpy-1.2.4/cmdstanpy/_version.py

@@ -0,0 +1,3 @@
+"""PyPi Version"""
+
+__version__ = '1.2.4'

{cmdstanpy-1.2.2 → cmdstanpy-1.2.4}/cmdstanpy/install_cmdstan.py

@@ -523,6 +523,8 @@ def retrieve_version(version: str, progress: bool = True) -> None:
         first = tar.next()
         if first is not None:
             top_dir = first.name
+        else:
+            top_dir = ''
         cmdstan_dir = f'cmdstan-{version}'
         if top_dir != cmdstan_dir:
             raise CmdStanInstallError(

{cmdstanpy-1.2.2 → cmdstanpy-1.2.4}/cmdstanpy/install_cxx_toolchain.py

@@ -235,8 +235,10 @@ def get_toolchain_name() -> str:
     return ''
 
 
+# TODO(2.0): drop 3.5 support
 def get_url(version: str) -> str:
     """Return URL for toolchain."""
+    url = ''
     if platform.system() == 'Windows':
         if version == '4.0':
             # pylint: disable=line-too-long
@@ -277,6 +279,8 @@ def run_rtools_install(args: Dict[str, Any]) -> None:
 
     if 'verbose' in args:
         verbose = args['verbose']
+    else:
+        verbose = False
 
     install_dir = args['dir']
     if install_dir is None:

{cmdstanpy-1.2.2 → cmdstanpy-1.2.4}/cmdstanpy/stanfit/pathfinder.py

@@ -214,8 +214,10 @@ class CmdStanPathfinder:
         """
         return (  # type: ignore
             self._metadata.cmdstan_config.get("num_paths", 4) > 1
-            and self._metadata.cmdstan_config.get('psis_resample', 1) == 1
-            and self._metadata.cmdstan_config.get('calculate_lp', 1) == 1
+            and self._metadata.cmdstan_config.get('psis_resample', 1)
+            in (1, 'true')
+            and self._metadata.cmdstan_config.get('calculate_lp', 1)
+            in (1, 'true')
         )
 
     def save_csvfiles(self, dir: Optional[str] = None) -> None:

{cmdstanpy-1.2.2 → cmdstanpy-1.2.4}/cmdstanpy/stanfit/runset.py

@@ -61,18 +61,26 @@ class RunSet:
         self._base_outfile = (
             f'{args.model_name}-{datetime.now().strftime(time_fmt)}'
         )
-        # per-process console messages
+        # per-process outputs
         self._stdout_files = [''] * self._num_procs
+        self._profile_files = [''] * self._num_procs  # optional
         if one_process_per_chain:
             for i in range(chains):
                 self._stdout_files[i] = self.file_path("-stdout.txt", id=i)
+                if args.save_profile:
+                    self._profile_files[i] = self.file_path(
+                        ".csv", extra="-profile", id=chain_ids[i]
+                    )
         else:
             self._stdout_files[0] = self.file_path("-stdout.txt")
+            if args.save_profile:
+                self._profile_files[0] = self.file_path(
+                    ".csv", extra="-profile"
+                )
 
         # per-chain output files
         self._csv_files: List[str] = [''] * chains
         self._diagnostic_files = [''] * chains  # optional
-        self._profile_files = [''] * chains  # optional
 
         if chains == 1:
             self._csv_files[0] = self.file_path(".csv")
@@ -80,10 +88,6 @@ class RunSet:
                 self._diagnostic_files[0] = self.file_path(
                     ".csv", extra="-diagnostic"
                 )
-            if args.save_profile:
-                self._profile_files[0] = self.file_path(
-                    ".csv", extra="-profile"
-                )
         else:
             for i in range(chains):
                 self._csv_files[i] = self.file_path(".csv", id=chain_ids[i])
@@ -91,10 +95,6 @@ class RunSet:
                     self._diagnostic_files[i] = self.file_path(
                         ".csv", extra="-diagnostic", id=chain_ids[i]
                     )
-                if args.save_profile:
-                    self._profile_files[i] = self.file_path(
-                        ".csv", extra="-profile", id=chain_ids[i]
-                    )
 
     def __repr__(self) -> str:
         repr = 'RunSet: chains={}, chain_ids={}, num_processes={}'.format(

{cmdstanpy-1.2.2 → cmdstanpy-1.2.4}/cmdstanpy/utils/stancsv.py

@@ -52,7 +52,7 @@ def check_sampler_csv(
             )
         )
     if save_warmup:
-        if not ('save_warmup' in meta and meta['save_warmup'] == 1):
+        if not ('save_warmup' in meta and meta['save_warmup'] in (1, 'true')):
             raise ValueError(
                 'bad Stan CSV file {}, '
                 'config error, expected save_warmup = 1'.format(path)
@@ -116,6 +116,7 @@ def scan_optimize_csv(path: str, save_iters: bool = False) -> Dict[str, Any]:
                 all_iters[i, :] = [float(x) for x in xs]
             if i == iters - 1:
                 mle: np.ndarray = np.array(xs, dtype=float)
+    # pylint: disable=possibly-used-before-assignment
     dict['mle'] = mle
     if save_iters:
         dict['all_iters'] = all_iters
@@ -192,7 +193,12 @@ def scan_config(fd: TextIO, config_dict: Dict[str, Any], lineno: int) -> int:
                     try:
                         val = float(raw_val)
                     except ValueError:
-                        val = raw_val
+                        if raw_val == "true":
+                            val = 1
+                        elif raw_val == "false":
+                            val = 0
+                        else:
+                            val = raw_val
                 config_dict[key_val[0].strip()] = val
         cur_pos = fd.tell()
         line = fd.readline().strip()

{cmdstanpy-1.2.2 → cmdstanpy-1.2.4/cmdstanpy.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cmdstanpy
-Version: 1.2.2
+Version: 1.2.4
 Summary: Python interface to CmdStan
 Author: Stan Dev Team
 License: BSD-3-Clause

{cmdstanpy-1.2.2 → cmdstanpy-1.2.4}/test/test_optimize.py

@@ -262,12 +262,13 @@ def test_variables_3d() -> None:
     )
     vars_iters = multidim_mle_iters.stan_variables(inc_iterations=True)
     assert len(vars_iters) == len(multidim_mle_iters.metadata.stan_vars)
+    assert 'frac_60' in vars_iters
+    n_iter = vars_iters['frac_60'].shape[0]
+    assert n_iter > 1
     assert 'y_rep' in vars_iters
-    assert vars_iters['y_rep'].shape == (8, 5, 4, 3)
+    assert vars_iters['y_rep'].shape == (n_iter, 5, 4, 3)
     assert 'beta' in vars_iters
-    assert vars_iters['beta'].shape == (8, 2)
-    assert 'frac_60' in vars_iters
-    assert vars_iters['frac_60'].shape == (8,)
+    assert vars_iters['beta'].shape == (n_iter, 2)
 
 
 def test_optimize_good() -> None:

{cmdstanpy-1.2.2 → cmdstanpy-1.2.4}/test/test_sample.py

@@ -1748,33 +1748,36 @@ def test_save_latent_dynamics() -> None:
 
 def test_save_profile() -> None:
     stan = os.path.join(DATAFILES_PATH, 'profile_likelihood.stan')
-    profile_model = CmdStanModel(stan_file=stan)
+    profile_model = CmdStanModel(
+        stan_file=stan, cpp_options={"STAN_THREADS": '1'}, force_compile=True
+    )
+
     profile_fit = profile_model.sample(
         chains=2,
         parallel_chains=2,
+        force_one_process_per_chain=True,
         seed=12345,
         iter_warmup=100,
         iter_sampling=200,
         save_profile=True,
     )
-    for i in range(profile_fit.runset.chains):
-        profile_file = profile_fit.runset.profile_files[i]
+    assert len(profile_fit.runset.profile_files) == 2
+    for profile_file in profile_fit.runset.profile_files:
         assert os.path.exists(profile_file)
 
     profile_fit = profile_model.sample(
         chains=2,
         parallel_chains=2,
+        force_one_process_per_chain=False,
         seed=12345,
+        iter_warmup=100,
         iter_sampling=200,
-        save_latent_dynamics=True,
         save_profile=True,
     )
 
-    for i in range(profile_fit.runset.chains):
-        profile_file = profile_fit.runset.profile_files[i]
+    assert len(profile_fit.runset.profile_files) == 1
+    for profile_file in profile_fit.runset.profile_files:
         assert os.path.exists(profile_file)
-        diagnostics_file = profile_fit.runset.diagnostic_files[i]
-        assert os.path.exists(diagnostics_file)
 
 
 def test_xarray_draws() -> None:
@@ -2027,6 +2030,26 @@ def test_tuple_data_in() -> None:
     data_model.sample(data, chains=1, iter_warmup=1, iter_sampling=1)
 
 
+def test_csv_roundtrip():
+    stan = os.path.join(DATAFILES_PATH, 'matrix_var.stan')
+    model = CmdStanModel(stan_file=stan)
+    fit = model.sample(
+        iter_sampling=10, iter_warmup=9, chains=2, save_warmup=True
+    )
+    z = fit.stan_variable(var="z")
+    assert z.shape == (20, 4, 3)
+    z_with_warmup = fit.stan_variable(var="z", inc_warmup=True)
+    assert z_with_warmup.shape == (38, 4, 3)
+
+    # mostly just asserting that from_csv always succeeds
+    # in parsing latest cmdstan headers
+    fit_from_csv = from_csv(fit.runset.csv_files)
+    z_from_csv = fit_from_csv.stan_variable(var="z")
+    assert z_from_csv.shape == (20, 4, 3)
+    z_with_warmup_from_csv = fit.stan_variable(var="z", inc_warmup=True)
+    assert z_with_warmup_from_csv.shape == (38, 4, 3)
+
+
 @pytest.mark.order(before="test_no_xarray")
 def test_serialization(stanfile='bernoulli.stan'):
     # This test must before any test that uses the `without_import` context

{cmdstanpy-1.2.2 → cmdstanpy-1.2.4}/test/test_variational.py

@@ -15,6 +15,7 @@ import pytest
 from cmdstanpy.cmdstan_args import CmdStanArgs, VariationalArgs
 from cmdstanpy.model import CmdStanModel
 from cmdstanpy.stanfit import CmdStanVB, RunSet, from_csv
+from cmdstanpy.utils.cmdstan import cmdstan_version_before
 
 HERE = os.path.dirname(os.path.abspath(__file__))
 DATAFILES_PATH = os.path.join(HERE, 'data')
@@ -150,12 +151,12 @@ def test_variational_good() -> None:
         'mu[2]',
     )
     # fixed seed, id=1 by default will give known output values
-    assert variational.eta == 100
+    assert variational.eta == 10
     np.testing.assert_almost_equal(
-        variational.variational_params_dict['mu[1]'], 311.545, decimal=2
+        variational.variational_params_dict['mu[1]'], 302.142, decimal=2
     )
     np.testing.assert_almost_equal(
-        variational.variational_params_dict['mu[2]'], 532.801, decimal=2
+        variational.variational_params_dict['mu[2]'], 361.005, decimal=2
     )
     np.testing.assert_almost_equal(
         variational.variational_params_np[0],
@@ -177,7 +178,11 @@ def test_variational_eta_small() -> None:
         DATAFILES_PATH, 'variational', 'eta_should_be_small.stan'
     )
     model = CmdStanModel(stan_file=stan)
-    variational = model.variational(algorithm='meanfield', seed=12345)
+    if cmdstan_version_before(2, 35):
+        seed = 12345
+    else:
+        seed = 1234
+    variational = model.variational(algorithm='meanfield', seed=seed)
     assert variational.column_names == (
         'lp__',
         'log_p__',

cmdstanpy-1.2.2/cmdstanpy/_version.py

@@ -1,3 +0,0 @@
-"""PyPi Version"""
-
-__version__ = '1.2.2'