cmdstanpy 1.2.3__tar.gz → 1.2.5__tar.gz

{cmdstanpy-1.2.3/cmdstanpy.egg-info → cmdstanpy-1.2.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cmdstanpy
-Version: 1.2.3
+Version: 1.2.5
 Summary: Python interface to CmdStan
 Author: Stan Dev Team
 License: BSD-3-Clause

cmdstanpy-1.2.5/cmdstanpy/_version.py

@@ -0,0 +1,3 @@
+"""PyPi Version"""
+
+__version__ = '1.2.5'

{cmdstanpy-1.2.3 → cmdstanpy-1.2.5}/cmdstanpy/model.py

@@ -205,9 +205,9 @@ class CmdStanModel:
                 self._compiler_options.add_include_path(path)
 
             # try to detect models w/out parameters, needed for sampler
-            if not cmdstan_version_before(
-                2, 27
-            ):  # unknown end of version range
+            if (not cmdstan_version_before(2, 27)) and cmdstan_version_before(
+                2, 36
+            ):
                 try:
                     model_info = self.src_info()
                     if 'parameters' in model_info:

{cmdstanpy-1.2.3 → cmdstanpy-1.2.5}/cmdstanpy/stanfit/mcmc.py

@@ -412,7 +412,7 @@ class CmdStanMCMC:
                     self._step_size[chain] = float(step_size.strip())
                     if self._metadata.cmdstan_config['metric'] != 'unit_e':
                         line = fd.readline().strip()  # metric type
-                        line = fd.readline().lstrip(' #\t')
+                        line = fd.readline().lstrip(' #\t').rstrip()
                         num_unconstrained_params = len(line.split(','))
                         if chain == 0:  # can't allocate w/o num params
                             if self.metric_type == 'diag_e':
@@ -429,18 +429,21 @@ class CmdStanMCMC:
                                     ),
                                     dtype=float,
                                 )
-                        if self.metric_type == 'diag_e':
-                            xs = line.split(',')
-                            self._metric[chain, :] = [float(x) for x in xs]
-                        else:
-                            xs = line.split(',')
-                            self._metric[chain, 0, :] = [float(x) for x in xs]
-                            for i in range(1, num_unconstrained_params):
-                                line = fd.readline().lstrip(' #\t').strip()
+                        if line:
+                            if self.metric_type == 'diag_e':
                                 xs = line.split(',')
-                                self._metric[chain, i, :] = [
+                                self._metric[chain, :] = [float(x) for x in xs]
+                            else:
+                                xs = line.strip().split(',')
+                                self._metric[chain, 0, :] = [
                                     float(x) for x in xs
                                 ]
+                                for i in range(1, num_unconstrained_params):
+                                    line = fd.readline().lstrip(' #\t').rstrip()
+                                    xs = line.split(',')
+                                    self._metric[chain, i, :] = [
+                                        float(x) for x in xs
+                                    ]
                     else:  # unit_e changed in 2.34 to have an extra line
                         pos = fd.tell()
                         line = fd.readline().strip()

{cmdstanpy-1.2.3 → cmdstanpy-1.2.5}/cmdstanpy/utils/stancsv.py

@@ -193,7 +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-1.2.3 → cmdstanpy-1.2.5/cmdstanpy.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cmdstanpy
-Version: 1.2.3
+Version: 1.2.5
 Summary: Python interface to CmdStan
 Author: Stan Dev Team
 License: BSD-3-Clause

{cmdstanpy-1.2.3 → cmdstanpy-1.2.5}/test/test_model.py

@@ -95,10 +95,13 @@ def test_exe_only() -> None:
     assert not model2._fixed_param
 
 
-def test_fixed_param() -> None:
+def test_legacy_fixed_param() -> None:
     stan = os.path.join(DATAFILES_PATH, 'datagen_poisson_glm.stan')
     model = CmdStanModel(stan_file=stan)
-    assert model._fixed_param
+    if cmdstan_version_before(2, 36):
+        assert model._fixed_param
+    else:
+        assert not model._fixed_param
 
 
 def test_model_pedantic(caplog: pytest.LogCaptureFixture) -> None:

{cmdstanpy-1.2.3 → cmdstanpy-1.2.5}/test/test_sample.py

@@ -642,13 +642,18 @@ def test_fixed_param_good() -> None:
     assert datagen_fit.step_size is None
 
 
-def test_fixed_param_unspecified() -> None:
+def test_sample_no_params() -> None:
     stan = os.path.join(DATAFILES_PATH, 'datagen_poisson_glm.stan')
     datagen_model = CmdStanModel(stan_file=stan)
     datagen_fit = datagen_model.sample(iter_sampling=100, show_progress=False)
-    assert datagen_fit.step_size is None
     summary = datagen_fit.summary()
-    assert 'lp__' not in list(summary.index)
+
+    if cmdstan_version_before(2, 36):
+        assert 'lp__' not in list(summary.index)
+        assert datagen_fit.step_size is None
+    else:
+        assert 'lp__' in list(summary.index)
+        assert np.isnan(datagen_fit.step_size).all()
 
     exe_only = os.path.join(DATAFILES_PATH, 'exe_only')
     shutil.copyfile(datagen_model.exe_file, exe_only)
@@ -656,9 +661,14 @@ def test_fixed_param_unspecified() -> None:
     datagen2_model = CmdStanModel(exe_file=exe_only)
     datagen2_fit = datagen2_model.sample(iter_sampling=200, show_console=True)
     assert datagen2_fit.chains == 4
-    assert datagen2_fit.step_size is None
     summary = datagen2_fit.summary()
-    assert 'lp__' not in list(summary.index)
+
+    if cmdstan_version_before(2, 36):
+        assert datagen2_fit.step_size is None
+        assert 'lp__' not in list(summary.index)
+    else:
+        assert np.isnan(datagen2_fit.step_size).all()
+        assert 'lp__' in list(summary.index)
 
 
 def test_index_bounds_error() -> None:
@@ -823,7 +833,7 @@ def test_validate_good_run() -> None:
     assert 'Treedepth satisfactory for all transitions.' in diagnostics
     assert 'No divergent transitions found.' in diagnostics
     assert 'E-BFMI satisfactory' in diagnostics
-    assert 'Effective sample size satisfactory.' in diagnostics
+    assert 'effective sample size satisfactory' in diagnostics.lower()
 
 
 def test_validate_big_run() -> None:
@@ -986,6 +996,12 @@ def test_from_csv_fixed_param() -> None:
     assert fixed_param_sample.draws_pd().shape == (100, 88)
 
 
+def test_from_csv_no_param_hmc() -> None:
+    csv_path = os.path.join(DATAFILES_PATH, 'no_param_hmc_sample.csv')
+    no_parameters_sample = from_csv(path=csv_path)
+    assert no_parameters_sample.draws_pd().shape == (100, 93)
+
+
 def test_custom_metric() -> None:
     stan = os.path.join(DATAFILES_PATH, 'bernoulli.stan')
     jdata = os.path.join(DATAFILES_PATH, 'bernoulli.data.json')
@@ -1621,33 +1637,18 @@ def test_validate_sample_sig_figs(stanfile='bernoulli.stan'):
 
 
 def test_validate_summary_sig_figs() -> None:
-    # construct CmdStanMCMC from logistic model output, config
-    exe = os.path.join(DATAFILES_PATH, 'logistic' + EXTENSION)
-    rdata = os.path.join(DATAFILES_PATH, 'logistic.data.R')
-    sampler_args = SamplerArgs(iter_sampling=100)
-    cmdstan_args = CmdStanArgs(
-        model_name='logistic',
-        model_exe=exe,
-        chain_ids=[1, 2, 3, 4],
-        seed=12345,
-        data=rdata,
-        output_dir=DATAFILES_PATH,
-        sig_figs=17,
-        method_args=sampler_args,
+    # construct CmdStanMCMC from logistic model output
+    fit = from_csv(
+        [
+            os.path.join(DATAFILES_PATH, 'logistic_output_1.csv'),
+            os.path.join(DATAFILES_PATH, 'logistic_output_2.csv'),
+            os.path.join(DATAFILES_PATH, 'logistic_output_3.csv'),
+            os.path.join(DATAFILES_PATH, 'logistic_output_4.csv'),
+        ]
     )
-    runset = RunSet(args=cmdstan_args, chains=4)
-    runset._csv_files = [
-        os.path.join(DATAFILES_PATH, 'logistic_output_1.csv'),
-        os.path.join(DATAFILES_PATH, 'logistic_output_2.csv'),
-        os.path.join(DATAFILES_PATH, 'logistic_output_3.csv'),
-        os.path.join(DATAFILES_PATH, 'logistic_output_4.csv'),
-    ]
-    retcodes = runset._retcodes
-    for i in range(len(retcodes)):
-        runset._set_retcode(i, 0)
-    fit = CmdStanMCMC(runset)
 
     sum_default = fit.summary()
+
     beta1_default = format(sum_default.iloc[1, 0], '.18g')
     assert beta1_default.startswith('1.3')
 
@@ -2030,6 +2031,26 @@ 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-1.2.3 → cmdstanpy-1.2.5}/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-1.2.3/cmdstanpy/_version.py

@@ -1,3 +0,0 @@
-"""PyPi Version"""
-
-__version__ = '1.2.3'