Stan 2.33: Move IO munging to external package, refactors

.github/workflows/main.yml

@@ -15,6 +15,11 @@ on:
         required: false
         default: ''
 
+# only run one copy per PR
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
 jobs:
   get-cmdstan-version:
     # get the latest cmdstan version to use as part of the cache key
@@ -27,7 +32,8 @@ jobs:
             if [[ "${{ github.event.inputs.cmdstan-version }}" != "" ]]; then
               echo "version=${{ github.event.inputs.cmdstan-version }}" >> $GITHUB_OUTPUT
             else
-                python -c 'import requests;print("version="+requests.get("https://api.github.com/repos/stan-dev/cmdstan/releases/latest").json()["tag_name"][1:])' >> $GITHUB_OUTPUT
+              echo "version=git:develop" >> $GITHUB_OUTPUT
+              # python -c 'import requests;print("version="+requests.get("https://api.github.com/repos/stan-dev/cmdstan/releases/latest").json()["tag_name"][1:])' >> $GITHUB_OUTPUT
             fi
     outputs:
       version: ${{ steps.check-cmdstan.outputs.version }}
@@ -39,7 +45,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.7.1 - 3.7.16", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:

.pre-commit-config.yaml

@@ -12,15 +12,15 @@ repos:
       - id: isort
   # https://github.com/python/black#version-control-integration
   - repo: https://github.com/psf/black
-    rev: 22.10.0
+    rev: 23.7.0
     hooks:
       - id: black
   - repo: https://github.com/pycqa/flake8
     rev: 3.9.2
     hooks:
       - id: flake8
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.982
+    rev: v1.5.0
     hooks:
       - id: mypy
         # Copied from setup.cfg

cmdstanpy/compiler_opts.py

@@ -275,8 +275,12 @@ def add_include_path(self, path: str) -> None:
         elif path not in self._stanc_options['include-paths']:
             self._stanc_options['include-paths'].append(path)
 
-    def compose_stanc(self) -> List[str]:
+    def compose_stanc(self, filename_in_msg: Optional[str]) -> List[str]:
         opts = []
+
+        if filename_in_msg is not None:
+            opts.append(f'--filename-in-msg={filename_in_msg}')
+
         if self._stanc_options is not None and len(self._stanc_options) > 0:
             for key, val in self._stanc_options.items():
                 if key == 'include-paths':
@@ -295,11 +299,19 @@ def compose_stanc(self) -> List[str]:
                     opts.append(f'--{key}')
         return opts
 
-    def compose(self) -> List[str]:
-        """Format makefile options as list of strings."""
+    def compose(self, filename_in_msg: Optional[str] = None) -> List[str]:
+        """
+        Format makefile options as list of strings.
+
+        Parameters
+        ----------
+        filename_in_msg : str, optional
+            filename to be displayed in stanc3 error messages
+            (if different from actual filename on disk), by default None
+        """
         opts = [
             'STANCFLAGS+=' + flag.replace(" ", "\\ ")
-            for flag in self.compose_stanc()
+            for flag in self.compose_stanc(filename_in_msg)
         ]
         if self._cpp_options is not None and len(self._cpp_options) > 0:
             for key, val in self._cpp_options.items():

cmdstanpy/install_cxx_toolchain.py

@@ -7,7 +7,7 @@
     Linux: Not implemented
 Optional command line arguments:
    -v, --version : version, defaults to latest
-   -d, --dir : install directory, defaults to '~/.cmdstan(py)
+   -d, --dir : install directory, defaults to '~/.cmdstan
    -s (--silent) : install with /VERYSILENT instead of /SILENT for RTools
    -m --no-make : don't install mingw32-make (Windows RTools 4.0 only)
    --progress : flag, when specified show progress bar for RTools download
@@ -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:
@@ -333,7 +333,7 @@ def parse_cmdline_args() -> Dict[str, Any]:
     parser = argparse.ArgumentParser()
     parser.add_argument('--version', '-v', help="version, defaults to latest")
     parser.add_argument(
-        '--dir', '-d', help="install directory, defaults to '~/.cmdstan(py)"
+        '--dir', '-d', help="install directory, defaults to '~/.cmdstan"
     )
     parser.add_argument(
         '--silent',

cmdstanpy/model.py

@@ -22,6 +22,7 @@
     Dict,
     Iterable,
     List,
+    Literal,
     Mapping,
     Optional,
     TypeVar,
@@ -117,8 +118,7 @@ def __init__(
         model_name: Optional[str] = None,
         stan_file: OptionalPath = None,
         exe_file: OptionalPath = None,
-        # TODO should be Literal['force'] not str
-        compile: Union[bool, str] = True,
+        compile: Union[bool, Literal['force']] = True,
         stanc_options: Optional[Dict[str, Any]] = None,
         cpp_options: Optional[Dict[str, Any]] = None,
         user_header: OptionalPath = None,
@@ -300,7 +300,7 @@ def src_info(self) -> Dict[str, Any]:
         cmd = (
             [os.path.join(cmdstan_path(), 'bin', 'stanc' + EXTENSION)]
             # handle include-paths, allow-undefined etc
-            + self._compiler_options.compose_stanc()
+            + self._compiler_options.compose_stanc(None)
             + ['--info', str(self.stan_file)]
         )
         proc = subprocess.run(cmd, capture_output=True, text=True, check=False)
@@ -343,7 +343,7 @@ def format(
             cmd = (
                 [os.path.join(cmdstan_path(), 'bin', 'stanc' + EXTENSION)]
                 # handle include-paths, allow-undefined etc
-                + self._compiler_options.compose_stanc()
+                + self._compiler_options.compose_stanc(None)
                 + [str(self.stan_file)]
             )
 
@@ -528,7 +528,7 @@ def compile(
             )
             cmd = [make]
             if self._compiler_options is not None:
-                cmd.extend(self._compiler_options.compose())
+                cmd.extend(self._compiler_options.compose(self._stan_file))
             cmd.append(Path(exe_file).as_posix())
 
             sout = io.StringIO()
@@ -996,10 +996,7 @@ def sample(
             fixed_param = self._fixed_param
 
         if chains is None:
-            if fixed_param:
-                chains = 1
-            else:
-                chains = 4
+            chains = 4
         if chains < 1:
             raise ValueError(
                 'Chains must be a positive integer value, found {}.'.format(
@@ -1090,8 +1087,7 @@ def sample(
             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 fixed_param or (chains == 1):
+            if chains == 1:
                 force_one_process_per_chain = True
 
             if (
@@ -1195,19 +1191,6 @@ def sample(
                     sampler_args.fixed_param = True
                     runset._args.method_args = sampler_args
 
-            # if there was an exe-file only initialization,
-            # this could happen, so throw a nice error
-            if (
-                sampler_args.fixed_param
-                and not one_process_per_chain
-                and chains > 1
-            ):
-                raise RuntimeError(
-                    "Cannot use single-process multichain parallelism"
-                    " with algorithm fixed_param.\nTry setting argument"
-                    " force_one_process_per_chain to True"
-                )
-
             errors = runset.get_err_msgs()
             if not runset._check_retcodes():
                 msg = (