Merge branch 'develop' into feature/tuple-io

Author: WardBrian

cmdstanpy/cmdstan_args.py

@@ -55,6 +55,7 @@ def __init__(
         adapt_metric_window: Optional[int] = None,
         adapt_step_size: Optional[int] = None,
         fixed_param: bool = False,
+        num_chains: int = 1,
     ) -> None:
         """Initialize object."""
         self.iter_warmup = iter_warmup
@@ -73,6 +74,7 @@ def __init__(
         self.adapt_step_size = adapt_step_size
         self.fixed_param = fixed_param
         self.diagnostic_file = None
+        self.num_chains = num_chains
 
     def validate(self, chains: Optional[int]) -> None:
         """
@@ -316,6 +318,10 @@ def validate(self, chains: Optional[int]) -> None:
                     'Argument "adapt_step_size" must be a non-negative integer,'
                     'found {}'.format(self.adapt_step_size)
                 )
+        if self.num_chains < 1 or not isinstance(
+            self.num_chains, (int, np.integer)
+        ):
+            raise ValueError("num_chains must be positive")
 
         if self.fixed_param and (
             self.max_treedepth is not None
@@ -378,6 +384,8 @@ def compose(self, idx: int, cmd: List[str]) -> List[str]:
             cmd.append('window={}'.format(self.adapt_metric_window))
         if self.adapt_step_size is not None:
             cmd.append('term_buffer={}'.format(self.adapt_step_size))
+        if self.num_chains > 1:
+            cmd.append('num_chains={}'.format(self.num_chains))
 
         return cmd
 
@@ -921,8 +929,12 @@ def validate(self) -> None:
                         )
                     )
             elif isinstance(self.inits, str):
-                if not os.path.exists(self.inits):
-                    raise ValueError('no such file {}'.format(self.inits))
+                if not (
+                    isinstance(self.method_args, SamplerArgs)
+                    and self.method_args.num_chains > 1
+                ):
+                    if not os.path.exists(self.inits):
+                        raise ValueError('no such file {}'.format(self.inits))
             elif isinstance(self.inits, list):
                 if self.chain_ids is None:
                     raise ValueError(
@@ -948,7 +960,6 @@ def compose_command(
         *,
         diagnostic_file: Optional[str] = None,
         profile_file: Optional[str] = None,
-        num_chains: Optional[int] = None,
     ) -> List[str]:
         """
         Compose CmdStan command for non-default arguments.
@@ -992,6 +1003,4 @@ def compose_command(
         if self.sig_figs is not None:
             cmd.append('sig_figs={}'.format(self.sig_figs))
         cmd = self.method_args.compose(idx, cmd)
-        if num_chains:
-            cmd.append('num_chains={}'.format(num_chains))
         return cmd

cmdstanpy/model.py

@@ -59,7 +59,6 @@
 )
 from cmdstanpy.utils import (
     EXTENSION,
-    MaybeDictToFilePath,
     SanitizedOrTmpFilePath,
     cmdstan_path,
     cmdstan_version,
@@ -68,6 +67,7 @@
     get_logger,
     returncode_msg,
 )
+from cmdstanpy.utils.filesystem import temp_inits, temp_single_json
 
 from . import progress as progbar
 
@@ -573,7 +573,7 @@ def optimize(
         self,
         data: Union[Mapping[str, Any], str, os.PathLike, None] = None,
         seed: Optional[int] = None,
-        inits: Union[Dict[str, float], float, str, os.PathLike, None] = None,
+        inits: Union[Mapping[str, Any], float, str, os.PathLike, None] = None,
         output_dir: OptionalPath = None,
         sig_figs: Optional[int] = None,
         save_profile: bool = False,
@@ -722,7 +722,9 @@ def optimize(
                 "in CmdStan 2.32 and above."
             )
 
-        with MaybeDictToFilePath(data, inits) as (_data, _inits):
+        with temp_single_json(data) as _data, temp_inits(
+            inits, allow_multiple=False
+        ) as _inits:
             args = CmdStanArgs(
                 self._name,
                 self._exe_file,
@@ -766,7 +768,14 @@ def sample(
         threads_per_chain: Optional[int] = None,
         seed: Union[int, List[int], None] = None,
         chain_ids: Union[int, List[int], None] = None,
-        inits: Union[Dict[str, float], float, str, List[str], None] = None,
+        inits: Union[
+            Mapping[str, Any],
+            float,
+            str,
+            List[str],
+            List[Mapping[str, Any]],
+            None,
+        ] = None,
         iter_warmup: Optional[int] = None,
         iter_sampling: Optional[int] = None,
         save_warmup: bool = False,
@@ -1003,6 +1012,69 @@ def sample(
                     chains
                 )
             )
+
+        if parallel_chains is None:
+            parallel_chains = max(min(cpu_count(), chains), 1)
+        elif parallel_chains > chains:
+            get_logger().info(
+                'Requested %u parallel_chains but only %u required, '
+                'will run all chains in parallel.',
+                parallel_chains,
+                chains,
+            )
+            parallel_chains = chains
+        elif parallel_chains < 1:
+            raise ValueError(
+                'Argument parallel_chains must be a positive integer, '
+                'found {}.'.format(parallel_chains)
+            )
+        if threads_per_chain is None:
+            threads_per_chain = 1
+        if threads_per_chain < 1:
+            raise ValueError(
+                'Argument threads_per_chain must be a positive integer, '
+                'found {}.'.format(threads_per_chain)
+            )
+
+        parallel_procs = parallel_chains
+        num_threads = threads_per_chain
+        one_process_per_chain = True
+        info_dict = self.exe_info()
+        stan_threads = info_dict.get('STAN_THREADS', 'false').lower()
+        # run multi-chain sampler unless algo is fixed_param or 1 chain
+        if chains == 1:
+            force_one_process_per_chain = True
+
+        if (
+            force_one_process_per_chain is None
+            and not cmdstan_version_before(2, 28, info_dict)
+            and stan_threads == 'true'
+        ):
+            one_process_per_chain = False
+            num_threads = parallel_chains * num_threads
+            parallel_procs = 1
+        if force_one_process_per_chain is False:
+            if not cmdstan_version_before(2, 28, info_dict):
+                one_process_per_chain = False
+                num_threads = parallel_chains * num_threads
+                parallel_procs = 1
+                if stan_threads == 'false':
+                    get_logger().warning(
+                        'Stan program not compiled for threading, '
+                        'process will run chains sequentially. '
+                        'For multi-chain parallelization, recompile '
+                        'the model with argument '
+                        '"cpp_options={\'STAN_THREADS\':\'TRUE\'}.'
+                    )
+            else:
+                get_logger().warning(
+                    'Installed version of CmdStan cannot multi-process '
+                    'chains, will run %d processes. '
+                    'Run "install_cmdstan" to upgrade to latest version.',
+                    chains,
+                )
+        os.environ['STAN_NUM_THREADS'] = str(num_threads)
+
         if chain_ids is None:
             chain_ids = [i + 1 for i in range(chains)]
         else:
@@ -1014,6 +1086,13 @@ def sample(
                     )
                 chain_ids = [i + chain_ids for i in range(chains)]
             else:
+                if not one_process_per_chain:
+                    for i, j in zip(chain_ids, chain_ids[1:]):
+                        if i != j - 1:
+                            raise ValueError(
+                                'chain_ids must be sequential list of integers,'
+                                ' found {}.'.format(chain_ids)
+                            )
                 if not len(chain_ids) == chains:
                     raise ValueError(
                         'Chain_ids must correspond to number of chains'
@@ -1029,6 +1108,7 @@ def sample(
                         )
 
         sampler_args = SamplerArgs(
+            num_chains=1 if one_process_per_chain else chains,
             iter_warmup=iter_warmup,
             iter_sampling=iter_sampling,
             save_warmup=save_warmup,
@@ -1043,14 +1123,25 @@ def sample(
             adapt_step_size=adapt_step_size,
             fixed_param=fixed_param,
         )
-        with MaybeDictToFilePath(data, inits) as (_data, _inits):
+
+        with temp_single_json(data) as _data, temp_inits(
+            inits, id=chain_ids[0]
+        ) as _inits:
+            cmdstan_inits: Union[str, List[str], int, float, None]
+            if one_process_per_chain and isinstance(inits, list):  # legacy
+                cmdstan_inits = [
+                    f"{_inits[:-5]}_{i}.json" for i in chain_ids  # type: ignore
+                ]
+            else:
+                cmdstan_inits = _inits
+
             args = CmdStanArgs(
                 self._name,
                 self._exe_file,
                 chain_ids=chain_ids,
                 data=_data,
                 seed=seed,
-                inits=_inits,
+                inits=cmdstan_inits,
                 output_dir=output_dir,
                 sig_figs=sig_figs,
                 save_latent_dynamics=save_latent_dynamics,
@@ -1059,67 +1150,6 @@ def sample(
                 refresh=refresh,
             )
 
-            if parallel_chains is None:
-                parallel_chains = max(min(cpu_count(), chains), 1)
-            elif parallel_chains > chains:
-                get_logger().info(
-                    'Requested %u parallel_chains but only %u required, '
-                    'will run all chains in parallel.',
-                    parallel_chains,
-                    chains,
-                )
-                parallel_chains = chains
-            elif parallel_chains < 1:
-                raise ValueError(
-                    'Argument parallel_chains must be a positive integer, '
-                    'found {}.'.format(parallel_chains)
-                )
-            if threads_per_chain is None:
-                threads_per_chain = 1
-            if threads_per_chain < 1:
-                raise ValueError(
-                    'Argument threads_per_chain must be a positive integer, '
-                    'found {}.'.format(threads_per_chain)
-                )
-
-            parallel_procs = parallel_chains
-            num_threads = threads_per_chain
-            one_process_per_chain = True
-            info_dict = self.exe_info()
-            stan_threads = info_dict.get('STAN_THREADS', 'false').lower()
-            if chains == 1:
-                force_one_process_per_chain = True
-
-            if (
-                force_one_process_per_chain is None
-                and not cmdstan_version_before(2, 28, info_dict)
-                and stan_threads == 'true'
-            ):
-                one_process_per_chain = False
-                num_threads = parallel_chains * num_threads
-                parallel_procs = 1
-            if force_one_process_per_chain is False:
-                if not cmdstan_version_before(2, 28, info_dict):
-                    one_process_per_chain = False
-                    num_threads = parallel_chains * num_threads
-                    parallel_procs = 1
-                    if stan_threads == 'false':
-                        get_logger().warning(
-                            'Stan program not compiled for threading, '
-                            'process will run chains sequentially. '
-                            'For multi-chain parallelization, recompile '
-                            'the model with argument '
-                            '"cpp_options={\'STAN_THREADS\':\'TRUE\'}.'
-                        )
-                else:
-                    get_logger().warning(
-                        'Installed version of CmdStan cannot multi-process '
-                        'chains, will run %d processes. '
-                        'Run "install_cmdstan" to upgrade to latest version.',
-                        chains,
-                    )
-            os.environ['STAN_NUM_THREADS'] = str(num_threads)
-
             if show_console:
                 show_progress = False
             else:
@@ -1359,7 +1389,7 @@ def generate_quantities(
             csv_files=fit_csv_files
         )
         generate_quantities_args.validate(chains)
-        with MaybeDictToFilePath(data, None) as (_data, _inits):
+        with temp_single_json(data) as _data:
             args = CmdStanArgs(
                 self._name,
                 self._exe_file,
@@ -1534,7 +1564,9 @@ def variational(
             output_samples=output_samples,
         )
 
-        with MaybeDictToFilePath(data, inits) as (_data, _inits):
+        with temp_single_json(data) as _data, temp_inits(
+            inits, allow_multiple=False
+        ) as _inits:
             args = CmdStanArgs(
                 self._name,
                 self._exe_file,
@@ -1641,7 +1673,9 @@ def log_prob(
                 "Method 'log_prob' not available for CmdStan versions "
                 "before 2.31"
             )
-        with MaybeDictToFilePath(data, params) as (_data, _params):
+        with temp_single_json(data) as _data, temp_single_json(
+            params
+        ) as _params:
             cmd = [
                 str(self.exe_file),
                 "log_prob",
@@ -1749,7 +1783,7 @@ def laplace_sample(
             cmdstan_mode.runset.csv_files[0], draws, jacobian
         )
 
-        with MaybeDictToFilePath(data) as (_data,):
+        with temp_single_json(data) as _data:
             args = CmdStanArgs(
                 self._name,
                 self._exe_file,

cmdstanpy/stanfit/runset.py

@@ -179,7 +179,6 @@ def cmd(self, idx: int) -> List[str]:
                 profile_file=self.file_path(".csv", extra="-profile")
                 if self._args.save_profile
                 else None,
-                num_chains=self._chains,
             )
 
     @property

cmdstanpy/utils/__init__.py

@@ -22,7 +22,6 @@
 from .command import do_command, returncode_msg
 from .data_munging import build_xarray_data, flatten_chains
 from .filesystem import (
-    MaybeDictToFilePath,
     SanitizedOrTmpFilePath,
     create_named_text_file,
     pushd,
@@ -112,7 +111,6 @@ def show_versions(output: bool = True) -> str:
 
 __all__ = [
     'EXTENSION',
-    'MaybeDictToFilePath',
     'SanitizedOrTmpFilePath',
     'build_xarray_data',
     'check_sampler_csv',