Merge pull request #764 from stan-dev/bugfix/textual_true_false

Scan string true and false in scan_config

Author: WardBrian

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()

docsrc/changes.rst

@@ -7,6 +7,12 @@ What's New
 
 For full changes, see the `Releases page <https://github.com/stan-dev/cmdstanpy/releases>`_ on GitHub.
 
+CmdStanPy 1.2.4
+---------------
+
+- Fixed a bug in `from_csv` which prevented reading files created by CmdStan 2.35.0+
+
+Reminder: The next non-bugfix release of CmdStanPy will be version 2.0, which will remove all existing deprecations.
 
 CmdStanPy 1.2.3
 ---------------

test/test_sample.py

@@ -2030,6 +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