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

Author: mitzimorris

.pylintrc

@@ -76,7 +76,7 @@ disable=bad-continuation,
     consider-using-with,
     consider-using-dict-items,
     unspecified-encoding,
-    consider-using-f-string
+    consider-using-f-string,
 
 # Enable the message, report, category or checker with the given id(s). You can
 # either give multiple identifier separated by comma (,) or put this option

README.md

@@ -7,6 +7,8 @@ CmdStanPy is a lightweight pure-Python interface to CmdStan which provides acces
 
 CmdStanPy is distributed via PyPi: https://pypi.org/project/cmdstanpy/
 
+or Conda Forge: https://anaconda.org/conda-forge/cmdstanpy
+
 ### Goals
 
 - Clean interface to Stan services so that CmdStanPy can keep up with Stan releases.

cmdstanpy/__init__.py

@@ -22,7 +22,6 @@
 _CMDSTAN_SAMPLING = 1000
 _CMDSTAN_THIN = 1
 _CMDSTAN_REFRESH = 100
-_DOT_CMDSTANPY = '.cmdstanpy'
 _DOT_CMDSTAN = '.cmdstan'
 
 

cmdstanpy/_version.py

@@ -1,3 +1,3 @@
 """PyPi Version"""
 
-__version__ = '0.9.77'
+__version__ = '1.0.0rc1'

cmdstanpy/cmdstan_args.py

@@ -1,7 +1,6 @@
 """
 CmdStan arguments
 """
-import logging
 import os
 from enum import Enum, auto
 from time import time
@@ -721,7 +720,6 @@ def __init__(
         save_latent_dynamics: bool = False,
         save_profile: bool = False,
         refresh: Optional[int] = None,
-        logger: Optional[logging.Logger] = None,
     ) -> None:
         """Initialize object."""
         self.model_name = model_name
@@ -745,11 +743,6 @@ def __init__(
         elif isinstance(method_args, VariationalArgs):
             self.method = Method.VARIATIONAL
         self.method_args.validate(len(chain_ids) if chain_ids else None)
-        if logger is not None:
-            get_logger().warning(
-                "Parameter 'logger' is deprecated."
-                " Control logging behavior via logging.getLogger('cmdstanpy')"
-            )
         self.validate()
 
     def validate(self) -> None:

cmdstanpy/compiler_opts.py

@@ -2,7 +2,6 @@
 Makefile options for stanc and C++ compilers
 """
 
-import logging
 import os
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Union
@@ -57,17 +56,11 @@ def __init__(
         stanc_options: Optional[Dict[str, Any]] = None,
         cpp_options: Optional[Dict[str, Any]] = None,
         user_header: Optional[str] = None,
-        logger: Optional[logging.Logger] = None,
     ) -> None:
         """Initialize object."""
         self._stanc_options = stanc_options if stanc_options is not None else {}
         self._cpp_options = cpp_options if cpp_options is not None else {}
         self._user_header = user_header if user_header is not None else ''
-        if logger is not None:
-            get_logger().warning(
-                "Parameter 'logger' is deprecated."
-                " Control logging behavior via logging.getLogger('cmdstanpy')"
-            )
 
     def __repr__(self) -> str:
         return 'stanc_options={}, cpp_options={}'.format(

cmdstanpy/install_cmdstan.py

@@ -30,11 +30,10 @@
 
 from tqdm.auto import tqdm
 
-from cmdstanpy import _DOT_CMDSTAN, _DOT_CMDSTANPY
+from cmdstanpy import _DOT_CMDSTAN
 from cmdstanpy.utils import (
     cmdstan_path,
     do_command,
-    get_logger,
     pushd,
     validate_dir,
     wrap_url_progress_hook,
@@ -465,15 +464,6 @@ def main(args: Dict[str, Any]) -> None:
         )
 
     cmdstan_dir = os.path.expanduser(os.path.join('~', _DOT_CMDSTAN))
-    if not os.path.exists(cmdstan_dir):
-        cmdstanpy_dir = os.path.expanduser(os.path.join('~', _DOT_CMDSTANPY))
-        if os.path.exists(cmdstanpy_dir):
-            cmdstan_dir = cmdstanpy_dir
-            get_logger().warning(
-                "Using ~/.cmdstanpy is deprecated and"
-                " will not be automatically detected in version 1.0!\n"
-                " Please rename to ~/.cmdstan"
-            )
 
     install_dir = cmdstan_dir
     if args['dir']:

cmdstanpy/install_cxx_toolchain.py

@@ -23,9 +23,8 @@
 from time import sleep
 from typing import Any, Dict, List
 
-from cmdstanpy import _DOT_CMDSTAN, _DOT_CMDSTANPY
+from cmdstanpy import _DOT_CMDSTAN
 from cmdstanpy.utils import (
-    get_logger,
     pushd,
     validate_dir,
     wrap_url_progress_hook,
@@ -285,19 +284,7 @@ def main(args: Dict[str, Any]) -> None:
 
     install_dir = args['dir']
     if install_dir is None:
-        cmdstan_dir = os.path.expanduser(os.path.join('~', _DOT_CMDSTAN))
-        if not os.path.exists(cmdstan_dir):
-            cmdstanpy_dir = os.path.expanduser(
-                os.path.join('~', _DOT_CMDSTANPY)
-            )
-            if os.path.exists(cmdstanpy_dir):
-                cmdstan_dir = cmdstanpy_dir
-                get_logger().warning(
-                    "Using ~/.cmdstanpy is deprecated and"
-                    " will not be automatically detected in version 1.0!\n"
-                    " Please rename to ~/.cmdstan"
-                )
-        install_dir = cmdstan_dir
+        install_dir = os.path.expanduser(os.path.join('~', _DOT_CMDSTAN))
     validate_dir(install_dir)
     print('Install directory: {}'.format(install_dir))
 

cmdstanpy/model.py

@@ -1,7 +1,6 @@
 """CmdStanModel"""
 
 import io
-import logging
 import os
 import platform
 import re
@@ -91,7 +90,6 @@ def __init__(
         stanc_options: Optional[Dict[str, Any]] = None,
         cpp_options: Optional[Dict[str, Any]] = None,
         user_header: Optional[str] = None,
-        logger: Optional[logging.Logger] = None,
     ) -> None:
         """
         Initialize object given constructor args.
@@ -113,11 +111,6 @@ def __init__(
             cpp_options=cpp_options,
             user_header=user_header,
         )
-        if logger is not None:
-            get_logger().warning(
-                "Parameter 'logger' is deprecated."
-                " Control logging behavior via logging.getLogger('cmdstanpy')"
-            )
 
         if model_name is not None:
             if not model_name.strip():
@@ -1181,6 +1174,7 @@ def variational(
         :param iter: Maximum number of ADVI iterations.
 
         :param grad_samples: Number of MC draws for computing the gradient.
+            Default is 10.  If problems arise, try doubling current value.
 
         :param elbo_samples: Number of MC draws for estimate of ELBO.
 
@@ -1247,14 +1241,10 @@ def variational(
 
         # treat failure to converge as failure
         transcript_file = runset.stdout_files[dummy_chain_id]
-        valid = True
         pat = re.compile(r'The algorithm may not have converged.', re.M)
         with open(transcript_file, 'r') as transcript:
             contents = transcript.read()
-            errors = re.findall(pat, contents)
-            if len(errors) > 0:
-                valid = False
-        if not valid:
+        if len(re.findall(pat, contents)) > 0:
             if require_converged:
                 raise RuntimeError(
                     'The algorithm may not have converged.\n'
@@ -1268,12 +1258,25 @@ def variational(
                 'Proceeding because require_converged is set to False',
             )
         if not runset._check_retcodes():
-            msg = 'Error during variational inference:\n{}'.format(
-                runset.get_err_msgs()
-            )
-            msg = '{}Command and output files:\n{}'.format(
-                msg, runset.__repr__()
+            transcript_file = runset.stdout_files[dummy_chain_id]
+            with open(transcript_file, 'r') as transcript:
+                contents = transcript.read()
+            pat = re.compile(
+                r'stan::variational::normal_meanfield::calc_grad:', re.M
             )
+            if len(re.findall(pat, contents)) > 0:
+                if grad_samples is None:
+                    grad_samples = 10
+                msg = (
+                    'Variational algorithm gradient calculation failed. '
+                    'Double the value of argument "grad_samples", '
+                    'current value is {}.'.format(grad_samples)
+                )
+            else:
+                msg = (
+                    'Variational algorithm failed.\n '
+                    'Console output:\n{}'.format(contents)
+                )
             raise RuntimeError(msg)
         # pylint: disable=invalid-name
         vb = CmdStanVB(runset)