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

Author: mitzimorris

.pylintrc

@@ -60,8 +60,7 @@ confidence=
 # --enable=similarities". If you want to run only the classes checker, but have
 # no Warning level messages displayed, use "--disable=all --enable=classes
 # --disable=W".
-disable=bad-continuation,
-    consider-using-in,
+disable=consider-using-in,
     cyclic-import,
     fixme,
     import-outside-toplevel,
@@ -267,13 +266,6 @@ max-line-length=100
 # Maximum number of lines in a module.
 max-module-lines=5000
 
-# List of optional constructs for which whitespace checking is disabled. `dict-
-# separator` is used to allow tabulation in dicts, etc.: {1  : 1,\n222: 2}.
-# `trailing-comma` allows a space between comma and closing bracket: (a, ).
-# `empty-line` allows space-only lines.
-no-space-check=trailing-comma,
-               dict-separator
-
 # Allow the body of a class to be on the same line as the declaration if body
 # contains single statement.
 single-line-class-stmt=no

cmdstanpy/model.py

@@ -1150,7 +1150,7 @@ def sample(
                 sys.stdout.write('\n')
                 get_logger().info('CmdStan done processing.')
 
-            get_logger().debug('runset\n%s', runset.__repr__())
+            get_logger().debug('runset\n%s', repr(runset))
 
             # hack needed to parse CSV files if model has no params
             # needed if exe is supplied without stan file
@@ -1176,14 +1176,21 @@ def sample(
                 )
 
             errors = runset.get_err_msgs()
-            if errors or not runset._check_retcodes():
+            if not runset._check_retcodes():
                 msg = (
                     f'Error during sampling:\n{errors}\n'
                     + f'Command and output files:\n{repr(runset)}\n'
                     + 'Consider re-running with show_console=True if the above'
                     + ' output is unclear!'
                 )
                 raise RuntimeError(msg)
+            if errors:
+                msg = (
+                    f'Non-fatal error during sampling:\n{errors}\n'
+                    + 'Consider re-running with show_console=True if the above'
+                    + ' output is unclear!'
+                )
+                get_logger().warning(msg)
 
             mcmc = CmdStanMCMC(runset)
         return mcmc
@@ -1525,7 +1532,6 @@ def variational(
         vb = CmdStanVB(runset)
         return vb
 
-    # pylint: disable=no-self-use
     def _run_cmdstan(
         self,
         runset: RunSet,

cmdstanpy/stanfit/runset.py

@@ -6,6 +6,7 @@
 import os
 import re
 import shutil
+import tempfile
 from datetime import datetime
 from time import time
 from typing import List, Optional
@@ -50,7 +51,10 @@ def __init__(
         if args.output_dir is not None:
             self._output_dir = args.output_dir
         else:
-            self._output_dir = _TMPDIR
+            # make a per-run subdirectory of our master temp directory
+            self._output_dir = tempfile.mkdtemp(
+                prefix=args.model_name, dir=_TMPDIR
+            )
 
         # output files prefix: ``<model_name>-<YYYYMMDDHHMM>_<chain_id>``
         self._base_outfile = (

cmdstanpy/utils.py

@@ -132,7 +132,6 @@ def get_latest_cmdstan(cmdstan_dir: str) -> Optional[str]:
     # unmunge as needed
     mmp = latest.split('.')
     if int(mmp[2]) < 0:
-        print("here")
         rc_num = str(int(mmp[2]) + 100)
         mmp[2] = "0-rc" + rc_num
         latest = '.'.join(mmp)

docsrc/installation.rst

@@ -173,7 +173,8 @@ The CmdStanPy commands ``cmdstan_path`` and ``set_cmdstan_path``
 get and set this environment variable:
 
 .. code-block:: python
-
+    
+    import os
     from cmdstanpy import cmdstan_path, set_cmdstan_path
 
     oldpath = cmdstan_path()

test/__init__.py

@@ -24,7 +24,6 @@ def assertRaisesRegexNested(self, exc, msg):
             exn_string += "\n" + str(exception)
         self.assertRegex(exn_string, msg)
 
-    # pylint: disable=no-self-use
     @contextlib.contextmanager
     def without_import(self, library, module):
         with unittest.mock.patch.dict('sys.modules', {library: None}):
@@ -33,7 +32,6 @@ def without_import(self, library, module):
         reload(module)
 
     # recipe from https://stackoverflow.com/a/34333710
-    # pylint: disable=no-self-use
     @contextlib.contextmanager
     def modified_environ(self, *remove, **update):
         """

test/data/linear_regression.data.json

@@ -0,0 +1,207 @@
+{
+    "x": [
+        -0.7138385321976433,
+        0.4935568322412949,
+        -1.3814289386914758,
+        -1.3083830490780055,
+        0.8594237856855641,
+        -0.5828201693491124,
+        0.41472726513726604,
+        -1.3096088915626156,
+        1.7488214394544888,
+        -0.05582078688738188,
+        -1.3353224485998705,
+        -1.7564315946342453,
+        0.48308013370199504,
+        0.5172253170304838,
+        -0.6719992453398311,
+        1.2602689891739454,
+        1.412043997788473,
+        0.20641523053812474,
+        0.5201078975322044,
+        1.5723251985671267,
+        1.3189655696099178,
+        -0.9111971580521261,
+        0.6393467227482712,
+        0.4650415534005901,
+        -0.5452984948053263,
+        -1.5130216352610142,
+        -0.22862960142670605,
+        0.6160324741955371,
+        -0.6031016074719313,
+        0.40594275421437453,
+        0.38508886717718016,
+        -1.0837724674547375,
+        2.3915682063493477,
+        -0.07839179990381143,
+        0.35656973307438666,
+        -0.2766314484210899,
+        0.7302456204684461,
+        0.08565219038050095,
+        1.445060390202212,
+        -0.21089429382395108,
+        -0.004354007671109179,
+        1.4964952578881543,
+        -1.2377789502217904,
+        1.1630189497108676,
+        0.1868059860973441,
+        1.0013767320556666,
+        0.17712191472558358,
+        2.2449838737047405,
+        0.5723783157495013,
+        -0.5866656693806949,
+        0.5553141820829578,
+        -1.0832025825922065,
+        0.021397186668024173,
+        1.0990490407588707,
+        -0.47857707758054946,
+        -1.0028128626128172,
+        -0.6541883777415636,
+        -2.157420733621822,
+        1.6494513567711457,
+        0.5326574665837476,
+        -1.2488626570176349,
+        1.8640634506194615,
+        -2.0015397292660646,
+        -1.165907209784441,
+        1.243275871223251,
+        1.2777634989564302,
+        -0.2540735659288359,
+        -0.7115336394378458,
+        2.5123445378647937,
+        -2.3620686383068192,
+        0.704711924978527,
+        0.20486730052438465,
+        -1.1481828167175874,
+        -0.5024671222986463,
+        1.1909459096186445,
+        -1.807532371463237,
+        1.5452345378964871,
+        0.9386793566797123,
+        0.06108017364184471,
+        0.44078590430668,
+        1.5390990507903806,
+        -0.14982494315528966,
+        0.008041862641953225,
+        -1.059362371600711,
+        -0.6458557072831949,
+        0.12174558659406327,
+        1.6343750745549894,
+        -0.006893657965902042,
+        -1.980063711207591,
+        -0.17769336879869058,
+        -0.04671777679973899,
+        1.4532456591905836,
+        -1.4029866194860872,
+        -1.5024900502317675,
+        1.4402148888890611,
+        -1.0727333689589642,
+        -0.6228552056768534,
+        0.3715735241216498,
+        -0.0371718458010515,
+        0.5704601721659295
+    ],
+    "y": [
+        0.6272150230712336,
+        0.9805824577664779,
+        0.3422690552470167,
+        -0.05146489851488395,
+        0.9046913839133488,
+        0.6925433494574392,
+        0.8699413738367437,
+        0.640327008582535,
+        0.39187605728779296,
+        0.21904955777565455,
+        0.3614380235604899,
+        -0.25588465129027244,
+        0.291608586376539,
+        -0.12437104481728656,
+        0.39699986298775203,
+        1.091844069641923,
+        1.0625362033977446,
+        1.1487142324952053,
+        0.6499370411907814,
+        0.7847133816156049,
+        0.949209681430482,
+        0.15135972083512655,
+        0.6742472860252764,
+        0.5405321316929282,
+        0.7549499219120746,
+        0.16511085413710583,
+        -0.02498036164663142,
+        0.6153043951506284,
+        0.6000720457920419,
+        1.3480303063520085,
+        0.3158006969256599,
+        0.3637296025891455,
+        1.1594053723296478,
+        0.5970385913046845,
+        0.5946450550774676,
+        0.8203529738679207,
+        1.3062075618596822,
+        0.9328024321713398,
+        0.7743457946449005,
+        0.3251962426760894,
+        0.6054087282349804,
+        0.7934998350966271,
+        0.8831208411206976,
+        0.7894760893728714,
+        0.8976865289354727,
+        0.44217549478023965,
+        0.38284855187218103,
+        1.095780907185152,
+        0.6549679342197391,
+        0.23387184425362467,
+        0.6049693148613544,
+        0.4028784177001803,
+        0.6250343428214425,
+        0.567319927379435,
+        0.5189952397494277,
+        0.4671091755131367,
+        0.748868640987746,
+        0.29251932173366013,
+        0.8245978901245103,
+        0.673071240496385,
+        0.775559253840947,
+        0.9595878211742477,
+        0.05153108078358959,
+        0.6958343543502022,
+        1.2920074084872448,
+        0.936543215882786,
+        -0.17826337795252567,
+        0.7061739968427398,
+        1.4127238083350044,
+        0.4014500370341516,
+        0.792652667869967,
+        0.3352243339909373,
+        0.4509809274388745,
+        0.6568885296125428,
+        0.6184394273698025,
+        0.18864416763201924,
+        1.0875801300709682,
+        0.9177333084623992,
+        0.5919873026862967,
+        0.9297749171130603,
+        0.814520099852734,
+        0.8465674480525497,
+        0.028620564426356743,
+        0.2639034807770741,
+        0.9495620232603935,
+        0.4000550997372736,
+        0.7506260736682799,
+        0.8257633294514362,
+        0.1294350823440999,
+        0.9276942903866539,
+        0.8068646299718158,
+        0.7626459434600884,
+        0.4057250786938288,
+        0.6216165062482524,
+        0.9989570513537478,
+        0.12153467332478934,
+        0.9175681261236525,
+        0.5831590468381432,
+        0.6800265152948471,
+        1.0027971008115968
+    ],
+    "N": 100
+}

test/data/linear_regression.stan

@@ -0,0 +1,13 @@
+data {
+  int<lower=0> N;
+  vector[N] x;
+  vector[N] y;
+}
+parameters {
+  real alpha;
+  real beta;
+  real<lower=0> sigma;
+}
+model {
+  y ~ normal(alpha + beta * x, sigma);
+}

test/data/normal-rng.stan

@@ -0,0 +1,7 @@
+transformed data{
+  real x_;
+  x_ = std_normal_rng();
+}
+generated quantities{
+  real x = x_;
+}

test/test_compiler_opts.py

@@ -1,8 +1,8 @@
 """Compiler options tests"""
 
+import logging
 import os
 import unittest
-import logging
 
 from testfixtures import LogCapture
 
@@ -33,7 +33,7 @@ def test_opts_empty(self):
         opts = CompilerOptions()
         opts.validate()
         self.assertEqual(opts.compose(), [])
-        self.assertEqual(opts.__repr__(), 'stanc_options={}, cpp_options={}')
+        self.assertEqual(repr(opts), 'stanc_options={}, cpp_options={}')
 
         stanc_opts = {}
         opts = CompilerOptions(stanc_options=stanc_opts)
@@ -48,7 +48,7 @@ def test_opts_empty(self):
         opts = CompilerOptions(stanc_options=stanc_opts, cpp_options=cpp_opts)
         opts.validate()
         self.assertEqual(opts.compose(), [])
-        self.assertEqual(opts.__repr__(), 'stanc_options={}, cpp_options={}')
+        self.assertEqual(repr(opts), 'stanc_options={}, cpp_options={}')
 
     def test_opts_stanc(self):
         stanc_opts = {}