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

Author: mitzimorris

.github/ISSUE_TEMPLATE.md

@@ -10,4 +10,5 @@ Describe the issue as clearly as possible.
 Provide any additional information here.
 
 #### Current Version:
-
+Please include the output of `cmdstanpy.show_versions()`, or
+at least the cmdstan and cmdstanpy versions used.

.github/workflows/main.yml

@@ -96,14 +96,14 @@ jobs:
         run: |
           install_cmdstan -h
           install_cxx_toolchain -h
-          python -m cmdstanpy.install_cmdstan --version ${{ needs.get-cmdstan-version.outputs.version }}
+          python -c "import cmdstanpy; cmdstanpy.install_cmdstan(version='${{ needs.get-cmdstan-version.outputs.version }}', cores=2)"
 
       - name: Install CmdStan (Windows)
         if: matrix.os == 'windows-latest'
         run: |
           install_cmdstan -h
           install_cxx_toolchain -h
-          python -m cmdstanpy.install_cmdstan --compiler --version ${{ needs.get-cmdstan-version.outputs.version }}
+          python -m cmdstanpy.install_cmdstan --compiler --version ${{ needs.get-cmdstan-version.outputs.version }} --cores 2
 
       - name: Run tests
         run: |

.github/workflows/release.yml

@@ -32,7 +32,7 @@ jobs:
 
       - name: Install dependencies (python)
         run: |
-          python -m pip install --upgrade pip wheel twine codecov sphinx nbsphinx ipython ipykernel pydata-sphinx-theme requests sphinx-copybutton matplotlib
+          python -m pip install --upgrade pip wheel twine codecov "sphinx>4,<5" nbsphinx ipython ipykernel "pydata-sphinx-theme<0.9" requests sphinx-copybutton xarray matplotlib
           pip install -r requirements.txt
           pip install -e .
 

cmdstanpy/__init__.py

@@ -6,18 +6,6 @@
 import shutil
 import tempfile
 
-_STANSUMMARY_STATS = [
-    'Mean',
-    'MCSE',
-    'StdDev',
-    '5%',
-    '50%',
-    '95%',
-    'N_Eff',
-    'N_Eff/s',
-    'R_hat',
-]
-
 _TMPDIR = tempfile.mkdtemp()
 _CMDSTAN_WARMUP = 1000
 _CMDSTAN_SAMPLING = 1000
@@ -38,20 +26,20 @@ def _cleanup_tmpdir() -> None:
 
 from ._version import __version__  # noqa
 from .install_cmdstan import rebuild_cmdstan
-from .model import CmdStanModel  # noqa
-from .stanfit import (  # noqa
+from .model import CmdStanModel
+from .stanfit import (
     CmdStanGQ,
     CmdStanMCMC,
     CmdStanMLE,
     CmdStanVB,
     InferenceMetadata,
     from_csv,
 )
-from .utils import set_cmdstan_path  # noqa
 from .utils import (
     cmdstan_path,
     cmdstan_version,
     install_cmdstan,
+    set_cmdstan_path,
     set_make_env,
     show_versions,
     write_stan_json,

cmdstanpy/_version.py

@@ -1,3 +1,3 @@
 """PyPi Version"""
 
-__version__ = '1.0.1'
+__version__ = '1.0.4'

cmdstanpy/cmdstan_args.py

@@ -830,7 +830,7 @@ def validate(self) -> None:
                     '0 and 2**32-1, found {}.'.format(self.seed)
                 )
             if isinstance(self.seed, int):
-                if self.seed < 0 or self.seed > 2**32 - 1:
+                if self.seed < 0 or self.seed > 2 ** 32 - 1:
                     raise ValueError(
                         'Argument "seed" must be an integer between '
                         '0 and 2**32-1, found {}.'.format(self.seed)
@@ -849,7 +849,7 @@ def validate(self) -> None:
                         )
                     )
                 for seed in self.seed:
-                    if seed < 0 or seed > 2**32 - 1:
+                    if seed < 0 or seed > 2 ** 32 - 1:
                         raise ValueError(
                             'Argument "seed" must be an integer value'
                             ' between 0 and 2**32-1,'

cmdstanpy/install_cmdstan.py

@@ -7,11 +7,14 @@
 example model ``bernoulli.stan``.
 
 Optional command line arguments:
+   -i, --interactive: flag, when specified ignore other arguments and
+                      ask user for settings on STDIN
    -v, --version <release> : version, defaults to latest release version
    -d, --dir <path> : install directory, defaults to '$HOME/.cmdstan
    --overwrite: flag, when specified re-installs existing version
    --progress: flag, when specified show progress bar for CmdStan download
    --verbose: flag, when specified prints output from CmdStan build process
+   --cores: int, number of cores to use when building, defaults to 1
    -c, --compiler : flag, add C++ compiler to path (Windows only)
 """
 import argparse

cmdstanpy/install_cxx_toolchain.py

@@ -27,7 +27,7 @@
 from cmdstanpy.utils import pushd, validate_dir, wrap_url_progress_hook
 
 EXTENSION = '.exe' if platform.system() == 'Windows' else ''
-IS_64BITS = sys.maxsize > 2**32
+IS_64BITS = sys.maxsize > 2 ** 32
 
 
 def usage() -> None:

cmdstanpy/stanfit/__init__.py

@@ -12,7 +12,8 @@
 )
 from cmdstanpy.utils import check_sampler_csv, get_logger, scan_config
 
-from .mcmc import CmdStanGQ, CmdStanMCMC
+from .gq import CmdStanGQ
+from .mcmc import CmdStanMCMC
 from .metadata import InferenceMetadata
 from .mle import CmdStanMLE
 from .runset import RunSet
@@ -29,7 +30,8 @@
 
 
 def from_csv(
-    path: Union[str, List[str], None] = None, method: Optional[str] = None
+    path: Union[str, List[str], os.PathLike, None] = None,
+    method: Optional[str] = None,
 ) -> Union[CmdStanMCMC, CmdStanMLE, CmdStanVB, None]:
     """
     Instantiate a CmdStan object from a the Stan CSV files from a CmdStan run.
@@ -61,22 +63,22 @@ def from_csv(
     csvfiles = []
     if isinstance(path, list):
         csvfiles = path
-    elif isinstance(path, str):
-        if '*' in path:
-            splits = os.path.split(path)
-            if splits[0] is not None:
-                if not (os.path.exists(splits[0]) and os.path.isdir(splits[0])):
-                    raise ValueError(
-                        'Invalid path specification, {} '
-                        ' unknown directory: {}'.format(path, splits[0])
-                    )
-            csvfiles = glob.glob(path)
-        elif os.path.exists(path) and os.path.isdir(path):
+    elif isinstance(path, str) and '*' in path:
+        splits = os.path.split(path)
+        if splits[0] is not None:
+            if not (os.path.exists(splits[0]) and os.path.isdir(splits[0])):
+                raise ValueError(
+                    'Invalid path specification, {} '
+                    ' unknown directory: {}'.format(path, splits[0])
+                )
+        csvfiles = glob.glob(path)
+    elif isinstance(path, (str, os.PathLike)):
+        if os.path.exists(path) and os.path.isdir(path):
             for file in os.listdir(path):
-                if file.endswith(".csv"):
+                if os.path.splitext(file)[1] == ".csv":
                     csvfiles.append(os.path.join(path, file))
         elif os.path.exists(path):
-            csvfiles.append(path)
+            csvfiles.append(str(path))
         else:
             raise ValueError('Invalid path specification: {}'.format(path))
     else:
@@ -85,7 +87,7 @@ def from_csv(
     if len(csvfiles) == 0:
         raise ValueError('No CSV files found in directory {}'.format(path))
     for file in csvfiles:
-        if not (os.path.exists(file) and file.endswith('.csv')):
+        if not (os.path.exists(file) and os.path.splitext(file)[1] == ".csv"):
             raise ValueError(
                 'Bad CSV file path spec,'
                 ' includes non-csv file: {}'.format(file)