Merge branch 'develop' into ci/try-numpy-2.0

.github/workflows/main.yml

@@ -56,12 +56,16 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install dependencies (python)
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip wheel build
+
+      - name: Build package
         run: |
-          python -m pip install --upgrade pip wheel build
-          pip install -r requirements.txt
-          pip install -r requirements-test.txt
-          pip install codecov
+          python -m build
+          python -m pip install .[test]
+
+      - name: Show libraries
+        run: python -m pip freeze
 
       - name: Install numpy, scipy nightlies
         if: matrix.python-version == '3.11' && matrix.os != 'windows-latest'
@@ -75,22 +79,6 @@ jobs:
           pylint -v cmdstanpy test
           mypy cmdstanpy
 
-      - name: Build wheel
-        run: python -m build
-
-      - name: Install wheel (Linux, macOS)
-        if: matrix.os != 'windows-latest'
-        run: pip install dist/*.whl
-
-      - name: Install wheel (Windows)
-        if: matrix.os == 'windows-latest'
-        run: |
-          $whl = Get-ChildItem -Path dist -Filter *.whl | Select-Object -First 1
-          pip install "$whl"
-
-      - name: Show libraries
-        run: python -m pip freeze
-
       - name: CmdStan installation cacheing
         id: cache-cmdstan
         if: ${{ !startswith(needs.get-cmdstan-version.outputs.version, 'git:') }}
@@ -123,13 +111,8 @@ jobs:
           cd run_tests
           pytest -v ../test --cov=../cmdstanpy
 
-      - name: Run model with requirements-optional.txt
-        run: |
-          cd run_tests
-          python -m pip install -r ../requirements-optional.txt
-          python ../test/example_script.py
-
       - name: Submit codecov
         run: |
+          pip install codecov
           cd run_tests
           codecov

.github/workflows/release.yml

@@ -32,9 +32,8 @@ jobs:
 
       - name: Install dependencies (python)
         run: |
-          python -m pip install --upgrade pip wheel twine codecov "sphinx>5,<6" nbsphinx ipython ipykernel "pydata-sphinx-theme<0.9" requests sphinx-copybutton xarray matplotlib
-          pip install -r requirements.txt
-          pip install -e .
+          python -m pip install --upgrade pip wheel build twine requests
+          pip install -e .[doc,test]
 
       - name: Install CmdStan
         run: |
@@ -80,7 +79,7 @@ jobs:
           git push -f origin master
 
       - name: Build wheel
-        run: python setup.py sdist bdist_wheel
+        run: python -m build
 
       - name: Install bdist_wheel
         run: pip install dist/*.whl

.pre-commit-config.yaml

@@ -23,7 +23,6 @@ repos:
     rev: v1.5.0
     hooks:
       - id: mypy
-        # Copied from setup.cfg
         exclude: ^test/
         additional_dependencies: [ numpy >= 1.22]
   # local uses the user-installed pylint, this allows dependency checking

MANIFEST.in

@@ -1,6 +1,4 @@
 # This file is used to include extra files in source distributions.
-# (Source distributions are generated by running `python setup.py sdist`.)
 
-include requirements*.txt
 include LICENSE.md
 include cmdstanpy/py.typed

cmdstanpy/__init__.py

@@ -22,7 +22,7 @@ def _cleanup_tmpdir() -> None:
 
 
 from ._version import __version__  # noqa
-from .compilation import compile_stan_file
+from .compilation import compile_stan_file, format_stan_file
 from .install_cmdstan import rebuild_cmdstan
 from .model import CmdStanModel
 from .stanfit import (
@@ -50,6 +50,7 @@ def _cleanup_tmpdir() -> None:
     'set_make_env',
     'install_cmdstan',
     'compile_stan_file',
+    'format_stan_file',
     'CmdStanMCMC',
     'CmdStanMLE',
     'CmdStanGQ',

cmdstanpy/compilation.py

@@ -9,11 +9,17 @@
 import shutil
 import subprocess
 from copy import copy
+from datetime import datetime
 from pathlib import Path
 from typing import Any, Dict, Iterable, List, Optional, Union
 
 from cmdstanpy.utils import get_logger
-from cmdstanpy.utils.cmdstan import EXTENSION, cmdstan_path
+from cmdstanpy.utils.cmdstan import (
+    EXTENSION,
+    cmdstan_path,
+    cmdstan_version,
+    cmdstan_version_before,
+)
 from cmdstanpy.utils.command import do_command
 from cmdstanpy.utils.filesystem import SanitizedOrTmpFilePath
 
@@ -476,3 +482,98 @@ def compile_stan_file(
                 f"Failed to compile Stan model '{src}'. " f"Console:\n{console}"
             )
         return str(exe_target)
+
+
+def format_stan_file(
+    stan_file: Union[str, os.PathLike],
+    *,
+    overwrite_file: bool = False,
+    canonicalize: Union[bool, str, Iterable[str]] = False,
+    max_line_length: int = 78,
+    backup: bool = True,
+    stanc_options: Optional[Dict[str, Any]] = None,
+) -> None:
+    """
+    Run stanc's auto-formatter on the model code. Either saves directly
+    back to the file or prints for inspection
+
+    :param stan_file: Path to Stan program file.
+    :param overwrite_file: If True, save the updated code to disk, rather
+        than printing it. By default False
+    :param canonicalize: Whether or not the compiler should 'canonicalize'
+        the Stan model, removing things like deprecated syntax. Default is
+        False. If True, all canonicalizations are run. If it is a list of
+        strings, those options are passed to stanc (new in Stan 2.29)
+    :param max_line_length: Set the wrapping point for the formatter. The
+        default value is 78, which wraps most lines by the 80th character.
+    :param backup: If True, create a stanfile.bak backup before
+        writing to the file. Only disable this if you're sure you have other
+        copies of the file or are using a version control system like Git.
+    :param stanc_options: Additional options to pass to the stanc compiler.
+    """
+    stan_file = Path(stan_file).resolve()
+
+    if not stan_file.exists():
+        raise ValueError(f'File does not exist: {stan_file}')
+
+    try:
+        cmd = (
+            [os.path.join(cmdstan_path(), 'bin', 'stanc' + EXTENSION)]
+            # handle include-paths, allow-undefined etc
+            + CompilerOptions(stanc_options=stanc_options).compose_stanc(None)
+            + [str(stan_file)]
+        )
+
+        if canonicalize:
+            if cmdstan_version_before(2, 29):
+                if isinstance(canonicalize, bool):
+                    cmd.append('--print-canonical')
+                else:
+                    raise ValueError(
+                        "Invalid arguments passed for current CmdStan"
+                        + " version({})\n".format(
+                            cmdstan_version() or "Unknown"
+                        )
+                        + "--canonicalize requires 2.29 or higher"
+                    )
+            else:
+                if isinstance(canonicalize, str):
+                    cmd.append('--canonicalize=' + canonicalize)
+                elif isinstance(canonicalize, Iterable):
+                    cmd.append('--canonicalize=' + ','.join(canonicalize))
+                else:
+                    cmd.append('--print-canonical')
+
+        # before 2.29, having both --print-canonical
+        # and --auto-format printed twice
+        if not (cmdstan_version_before(2, 29) and canonicalize):
+            cmd.append('--auto-format')
+
+        if not cmdstan_version_before(2, 29):
+            cmd.append(f'--max-line-length={max_line_length}')
+        elif max_line_length != 78:
+            raise ValueError(
+                "Invalid arguments passed for current CmdStan version"
+                + " ({})\n".format(cmdstan_version() or "Unknown")
+                + "--max-line-length requires 2.29 or higher"
+            )
+
+        out = subprocess.run(cmd, capture_output=True, text=True, check=True)
+        if out.stderr:
+            get_logger().warning(out.stderr)
+        result = out.stdout
+        if overwrite_file:
+            if result:
+                if backup:
+                    shutil.copyfile(
+                        stan_file,
+                        str(stan_file)
+                        + '.bak-'
+                        + datetime.now().strftime("%Y%m%d%H%M%S"),
+                    )
+                stan_file.write_text(result)
+        else:
+            print(result)
+
+    except (ValueError, RuntimeError) as e:
+        raise RuntimeError("Stanc formatting failed") from e

cmdstanpy/model.py

@@ -10,7 +10,6 @@
 import threading
 from collections import OrderedDict
 from concurrent.futures import ThreadPoolExecutor
-from datetime import datetime
 from io import StringIO
 from multiprocessing import cpu_count
 from typing import (
@@ -57,9 +56,7 @@
     from_csv,
 )
 from cmdstanpy.utils import (
-    EXTENSION,
     cmdstan_path,
-    cmdstan_version,
     cmdstan_version_before,
     do_command,
     get_logger,
@@ -320,6 +317,7 @@ def src_info(self) -> Dict[str, Any]:
             return {}
         return compilation.src_info(str(self.stan_file), self._compiler_options)
 
+    # TODO(2.0) remove
     def format(
         self,
         overwrite_file: bool = False,
@@ -329,6 +327,8 @@ def format(
         backup: bool = True,
     ) -> None:
         """
+        Deprecated: Use :func:`cmdstanpy.format_stan_file()` instead.
+
         Run stanc's auto-formatter on the model code. Either saves directly
         back to the file or prints for inspection
 
@@ -345,72 +345,24 @@ def format(
             writing to the file. Only disable this if you're sure you have other
             copies of the file or are using a version control system like Git.
         """
-        if self.stan_file is None or not os.path.isfile(self.stan_file):
-            raise ValueError("No Stan file found for this module")
-        try:
-            cmd = (
-                [os.path.join(cmdstan_path(), 'bin', 'stanc' + EXTENSION)]
-                # handle include-paths, allow-undefined etc
-                + self._compiler_options.compose_stanc(None)
-                + [str(self.stan_file)]
-            )
 
-            if canonicalize:
-                if cmdstan_version_before(2, 29):
-                    if isinstance(canonicalize, bool):
-                        cmd.append('--print-canonical')
-                    else:
-                        raise ValueError(
-                            "Invalid arguments passed for current CmdStan"
-                            + " version({})\n".format(
-                                cmdstan_version() or "Unknown"
-                            )
-                            + "--canonicalize requires 2.29 or higher"
-                        )
-                else:
-                    if isinstance(canonicalize, str):
-                        cmd.append('--canonicalize=' + canonicalize)
-                    elif isinstance(canonicalize, Iterable):
-                        cmd.append('--canonicalize=' + ','.join(canonicalize))
-                    else:
-                        cmd.append('--print-canonical')
-
-            # before 2.29, having both --print-canonical
-            # and --auto-format printed twice
-            if not (cmdstan_version_before(2, 29) and canonicalize):
-                cmd.append('--auto-format')
-
-            if not cmdstan_version_before(2, 29):
-                cmd.append(f'--max-line-length={max_line_length}')
-            elif max_line_length != 78:
-                raise ValueError(
-                    "Invalid arguments passed for current CmdStan version"
-                    + " ({})\n".format(cmdstan_version() or "Unknown")
-                    + "--max-line-length requires 2.29 or higher"
-                )
+        get_logger().warning(
+            "CmdStanModel.format() is deprecated and will be "
+            "removed in the next major version.\n"
+            "Use cmdstanpy.format_stan_file() instead."
+        )
 
-            out = subprocess.run(
-                cmd, capture_output=True, text=True, check=True
-            )
-            if out.stderr:
-                get_logger().warning(out.stderr)
-            result = out.stdout
-            if overwrite_file:
-                if result:
-                    if backup:
-                        shutil.copyfile(
-                            self.stan_file,
-                            str(self.stan_file)
-                            + '.bak-'
-                            + datetime.now().strftime("%Y%m%d%H%M%S"),
-                        )
-                    with open(self.stan_file, 'w') as file_handle:
-                        file_handle.write(result)
-            else:
-                print(result)
+        if self.stan_file is None:
+            raise ValueError("No Stan file found for this module")
 
-        except (ValueError, RuntimeError) as e:
-            raise RuntimeError("Stanc formatting failed") from e
+        compilation.format_stan_file(
+            self.stan_file,
+            overwrite_file=overwrite_file,
+            max_line_length=max_line_length,
+            canonicalize=canonicalize,
+            backup=backup,
+            stanc_options=self.stanc_options,
+        )
 
     @property
     def stanc_options(self) -> Dict[str, Union[bool, int, str]]:

docsrc/api.rst

@@ -84,6 +84,17 @@ CmdStanGQ
 Functions
 *********
 
+compile_stan_model
+=============
+
+.. autofunction:: cmdstanpy.compile_stan_model
+
+
+format_stan_model
+=============
+
+.. autofunction:: cmdstanpy.format_stan_model
+
 show_versions
 =============
 

docsrc/env.yml

@@ -5,18 +5,12 @@ channels:
 dependencies:
   - python=3.9
   - ipykernel
-  - ipython
-  - ipywidgets
-  - numpy>=1.15
+  - numpy
   - pandas
   - xarray
-  - sphinx>5,<6
-  - nbsphinx
-  - pydata-sphinx-theme>0.7,<0.9
-  - sphinx-copybutton
   - matplotlib-base
   - pip
   - cmdstan
   - tqdm
   - pip:
-      - -e ../
+      - -e ../.[docs]