Backported bug fixes for 3.2 branch

.github/workflows/linters.yml

@@ -59,6 +59,7 @@ jobs:
           echo "test/data/*.inp -diff" >> .gitattributes
           echo "test/data/*.xml -diff" >> .gitattributes
           echo "test/data/*.cti -diff" >> .gitattributes
+          echo "test/data/*.dat -diff" >> .gitattributes
           echo "test_problems/**/*blessed* -diff" >> .gitattributes
 
           git config --global core.autocrlf false

.github/workflows/main.yml

@@ -30,7 +30,8 @@ jobs:
     name: >
       ${{ matrix.os }} with Python ${{ matrix.python-version }},
       Numpy ${{ matrix.numpy || 'latest' }}, Cython ${{ matrix.cython || 'latest' }},
-      SCons ${{ matrix.scons || 'latest' }}
+      SCons ${{ matrix.scons || 'latest' }},
+      setuptools ${{ matrix.setuptools || 'latest' }}
     runs-on: ${{ matrix.os }}
     timeout-minutes: 60
     strategy:
@@ -41,6 +42,7 @@ jobs:
         numpy: ['']
         cython: ['!=3.1.2'] # Specifier can be dropped after 3.1.3 or 3.2.0 is released
         scons: ['']
+        setuptools: ['']
         include:
           # Keep some test cases with NumPy 1.x until we drop support
         - python-version: '3.12'
@@ -53,6 +55,7 @@ jobs:
           os: 'ubuntu-22.04'
           cython: "==0.29.31" # minimum supported version
           scons: '==4.0.1' # minimum supported version
+          setuptools: "==75.7.0" # latest version that leaves package name uppercase
         - python-version: '3.11'
           os: 'ubuntu-22.04'
           cython: "==3.0.8" # System version for Ubuntu 24.04
@@ -697,7 +700,7 @@ jobs:
         # See https://unix.stackexchange.com/a/392973 for an explanation of the -exec part.
         # Skip 1D_packed_bed.py due to difficulty installing scikits.odes.
         # Increase figure limit to handle flame_speed_convergence_analysis.py.
-        # Skip examples for Python releases where pandas/pyarrow or CoolProp are not available
+        # Skip examples for Python releases where pandas/pyarrow or CoolProp are not available.
         run: |
           echo "Running on `cat /proc/cpuinfo | grep 'model name' | head -n 1 | cut -d ':' -f 2`"
           ln -s libcantera_shared.so build/lib/libcantera_shared.so.3
@@ -722,9 +725,10 @@ jobs:
           find samples/python -type f -iname "*.py" \
           -exec sh -c 'for n; do echo "$n" | tee -a results.txt && python3 "$n" >> results.txt || exit 1; done' sh {} +
         env:
-          # The pyparsing ignore setting is due to a new warning introduced in Matplotlib==3.6.0
-          # Ignore NasaPoly2 warnings from n-hexane-NUIG-2015.yaml
-          PYTHONWARNINGS: "error,ignore:warn_name_set_on_empty_Forward::pyparsing,ignore:datetime.datetime.utcfromtimestamp:DeprecationWarning:,ignore:NasaPoly2:UserWarning:"
+          # Fail on warnings attributed to direct example usage while ignoring
+          # transitive dependency warnings.
+          # Ignore known Cantera NasaPoly2 warnings from n-hexane-NUIG-2015.yaml.
+          PYTHONWARNINGS: "ignore,error:::__main__,ignore:NasaPoly2:UserWarning:"
           MPLBACKEND: Agg
       - name: Save the results file for inspection
         uses: actions/upload-artifact@v5
@@ -1256,8 +1260,8 @@ jobs:
       # MATLAB requires a specific library name: libcantera_shared.so.X
       # Recreating all symlinks to replicate status after build process
       run: |
-        ln -s libcantera_shared.so libcantera_shared.so.3.2.0
-        ln -s libcantera_shared.so.3.2.0 libcantera_shared.so.3
+        ln -s libcantera_shared.so libcantera_shared.so.3.2.1
+        ln -s libcantera_shared.so.3.2.1 libcantera_shared.so.3
       if: runner.os == 'Linux'
     - name: Download the Cantera shared library (macOS)
       uses: actions/download-artifact@v5
@@ -1270,8 +1274,8 @@ jobs:
       # MATLAB requires a specific library name: libcantera_shared.X.Y.Z.dylib
       # Recreating all symlinks to replicate status after build process
       run: |
-        ln -s libcantera_shared.dylib libcantera_shared.3.2.0.dylib
-        ln -s libcantera_shared.3.2.0.dylib libcantera_shared.3.dylib
+        ln -s libcantera_shared.dylib libcantera_shared.3.2.1.dylib
+        ln -s libcantera_shared.3.2.1.dylib libcantera_shared.3.dylib
       if: runner.os == 'macOS'
     - name: Download the Cantera shared library (Windows)
       uses: actions/download-artifact@v5

README.rst

@@ -91,7 +91,7 @@ possible.
 Development Site
 ================
 
-The current development version is 3.3.0a1. The current stable version is
+The current development version is 4.0.0a1. The current stable version is
 3.2.0. The `latest Cantera source code <https://github.com/Cantera/cantera>`_,
 the `issue tracker <https://github.com/Cantera/cantera/issues>`_ for bugs and
 enhancement requests, `downloads of Cantera releases and binary installers

SConstruct

@@ -158,7 +158,7 @@ logger.info(
     f"SCons {SCons.__version__} is using the following Python interpreter:\n"
     f"    {sys.executable} (Python {python_version})", print_level=False)
 
-cantera_version = "3.2.0"
+cantera_version = "3.2.1b1"
 # For use where pre-release tags are not permitted (MSI, sonames)
 cantera_pure_version = re.match(r'(\d+\.\d+\.\d+)', cantera_version).group(0)
 cantera_short_version = re.match(r'(\d+\.\d+)', cantera_version).group(0)
@@ -1000,7 +1000,10 @@ def get_processor_name():
     elif platform.system() == "Darwin":
         os.environ['PATH'] = os.environ['PATH'] + os.pathsep + '/usr/sbin'
         command ="sysctl -n machdep.cpu.brand_string"
-        return subprocess.check_output(command, shell=True).decode().strip()
+        try:
+            return subprocess.check_output(command, shell=True).decode().strip()
+        except subprocess.CalledProcessError:
+            return "<unknown processor>"
     elif platform.system() == "Linux":
         command = "lscpu || cat /proc/cpuinfo"
         all_info = subprocess.check_output(command, shell=True).decode().strip()

doc/doxygen/Doxyfile.in

@@ -48,7 +48,7 @@ PROJECT_NAME           = Cantera
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 3.2.0
+PROJECT_NUMBER         = 3.2.1b1
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

doc/doxygen/versions.md

@@ -9,8 +9,8 @@
 | Version | Status | Release Date |
 |---------|--------|--------------|
 | [dev/latest](https://cantera.org/dev/cxx/index.html) | unstable | -- |
-| [v3.2.0](https://cantera.org/stable/cxx/index.html) | stable |*November 2025* |
-| [v3.1.0](https://cantera.org/3.1/cxx/index.html) | stable |*December 2024* |
+| [v3.2.0](https://cantera.org/3.2/cxx/index.html) | stable |*November 2025* |
+| [v3.1.0](https://cantera.org/3.1/cxx/index.html) | legacy |*December 2024* |
 | [v3.0.0](https://cantera.org/3.0/doxygen/html/index.html) | legacy | *August 2023* |
 | [v2.6.0](https://cantera.org/2.6/doxygen/html/modules.html) | archived | *May 2022* |
 | [v2.5.1](https://cantera.org/2.5/doxygen/html/modules.html) | archived | *February 2021* |

doc/sphinx/reference/onedim/governing-equations.md

@@ -11,7 +11,7 @@ in Section 7.2 of {cite:t}`kee2017` and are implemented by class {ct}`Flow1D`.
 
 *Continuity*:
 
-$$  \pxpy{u}{z} + 2 \rho V = 0  $$
+$$  \pxpy{(\rho u)}{z} + 2 \rho V = 0  $$
 
 *Radial momentum*:
 

doc/sphinx/reference/releasenotes/v3.2.md

@@ -1,3 +1,30 @@
+# Cantera 3.2.1
+
+*Unreleased*
+
+This is a maintenance release which fixes issues identified since the release
+of Cantera 3.2.0.
+
+- Resolve some issues with Python type hinting related to `TypeForm` [#2064](https://github.com/Cantera/cantera/pull/2064)
+- Fix net surface mass flux calculation in `FlowReactor` [#2069](https://github.com/Cantera/cantera/pull/2069)
+- Fix handling of multi-site surface species in `MoleReactor` surfaces [#2093](https://github.com/Cantera/cantera/pull/2093)
+- Fix reservoir synchronization in `surf_pfr_chain.py` [#2069](https://github.com/Cantera/cantera/pull/2069)
+- Fix garbage collection error with `Mixture` objects [#2091](https://github.com/Cantera/cantera/pull/2091)
+- Add workaround for older versions of `typing_extensions` [#2056](https://github.com/Cantera/cantera/pull/2056)
+- Handle wheel renaming from specific setuptools versions [#2055](https://github.com/Cantera/cantera/pull/2055)
+- Fix documentation for 1D flame continuity equation [#2058](https://github.com/Cantera/cantera/pull/2058)
+- Fix species slicing error with Numpy 2.4.0 development version [#2063](https://github.com/Cantera/cantera/pull/2063)
+- Add workaround for Cython coverage reporting with Python 3.12+ [#2070](https://github.com/Cantera/cantera/pull/2070)
+- Fix stubtest allow list for Python type hinting [#2070]
+https://github.com/Cantera/cantera/pull/2070- Correct the "basis" parameter description for mole fraction basis [#2079](https://github.com/Cantera/cantera/pull/2079)
+- Fix swapped items returned by `Kinetics::getDerivativeSettings` [#2069](https://github.com/Cantera/cantera/pull/2069)
+- Ensure `PlasmaPhase` EEDF array is initialized [#2068](https://github.com/Cantera/cantera/pull/2068)
+- Add workaround for running macOS `sysctl` command via SCons in sandboxed environments  [#2086](https://github.com/Cantera/cantera/pull/2086)
+- Fix slowdowns in sandboxed environments due to repeated `locale` calls [#2086](https://github.com/Cantera/cantera/pull/2086)
+- Fix errors related to handling of derived Jacobian types in Python [#2069](https://github.com/Cantera/cantera/pull/2069)
+- Fix segfault when calling `ReactorNet.get_state` on networks containing `FlowReactor [#2098](https://github.com/Cantera/cantera/pull/2098)
+- Handle some non-standard formatting in CK-format input files related to surface species site occupancy, extended elemental composition, and whitespace in thermo entries [#2089](https://github.com/Cantera/cantera/pull/2089)
+
 # Cantera 3.2.0
 
 Published on November 17, 2025 | [Full release on GitHub](https://github.com/Cantera/cantera/releases/tag/v3.2.0)

interfaces/cython/.mypyignore

@@ -10,7 +10,7 @@ cantera._types.*
 # cantera\.((_|\w)+\.)+__(?!init__$)[a-zA-Z0-9_]*__
 
 # Exclude specific dunder methods
-cantera\.((_|\w)+\.)+__(.*cython|test|pyx_capi|mutable_keys|readonly_keys)__
+cantera\.((_|\w)+\.)+__(.*cython|test|pyx_capi|mutable_keys|readonly_keys|conditional_annotations)__
 
 # Current output of stubtest --generate-allowlist
 cantera.Arrhenius.__init__

interfaces/cython/SConscript

@@ -1,9 +1,10 @@
 """Cython-based Python Module"""
 import re
 from pathlib import Path
+from packaging.specifiers import SpecifierSet
 from packaging.version import parse as parse_version
 
-from buildutils import (get_command_output, which, multi_glob,
+from buildutils import (get_command_output, which, multi_glob, logger,
                         get_pip_install_location, setup_python_env)
 
 Import('env', 'build', 'install')
@@ -26,6 +27,7 @@ if localenv["example_data"]:
 install(localenv.RecursiveInstall, "$inst_sampledir/python", "#samples/python")
 
 setup_python_env(localenv)
+logger.info(f"Using setuptools version {localenv['setuptools_version']}")
 # Python module shouldn't explicitly link to Python library (added in other cases to
 # support Python-based extensions), except when using MinGW
 if localenv["toolchain"] != "mingw":
@@ -40,7 +42,11 @@ localenv.Depends(license, localenv["license_target"])
 directives = {"binding": True}
 if env["coverage"]:
     directives["linetrace"] = True
-    localenv.Append(CPPDEFINES={"CYTHON_TRACE": 1})
+    localenv.Append(CPPDEFINES={
+        "CYTHON_TRACE": 1,
+        # TODO: Remove after https://github.com/coveragepy/coveragepy/issues/1790 is resolved.
+        "CYTHON_USE_SYS_MONITORING": 0}
+    )
 
 # Build the Python module
 cython_obj = []
@@ -86,8 +92,10 @@ build_cmd = ("$python_cmd_esc -m pip wheel -v --no-build-isolation --no-deps "
 if parse_version(localenv["py_version_short"]) >= env["python_max_version"]:
     build_cmd += " --ignore-requires-python"
 
-# Setuptools 75.3.1 and later always lowercase the package name
-if localenv["setuptools_version"] >= parse_version("75.3.1"):
+# Newer setuptools versions always lowercase the package name
+spec1 = SpecifierSet(">=75.8.1")
+spec2 = SpecifierSet("~=75.3.1")  # change backported to this branch
+if localenv["setuptools_version"] in spec1 or localenv["setuptools_version"] in spec2:
     pkg_name = "cantera"
 else:
     pkg_name = "Cantera"

interfaces/cython/cantera/_onedim.pyx

@@ -1687,7 +1687,7 @@ cdef class Sim1D:
         :param compression:
             Compression level (0-9); optional (default=0; HDF only)
         :param basis:
-            Output mass (``Y``/``mass``) or mole (``Y``/``mass``) fractions;
+            Output mass (``Y``/``mass``) or mole (``X``/``mole``) fractions;
             if not specified (`None`), the native basis of the underlying `ThermoPhase`
             manager is used.
 

interfaces/cython/cantera/_types.py

@@ -7,6 +7,7 @@
     Any,
     Concatenate,
     Literal,
+    ParamSpec,
     TypeAlias,
     TypedDict,
     TypeGuard,
@@ -18,7 +19,13 @@
 import numpy as np
 from numpy.typing import ArrayLike as ArrayLike
 from numpy.typing import NDArray
-from typing_extensions import ParamSpec, TypeForm
+try:
+    # Requires typing_extensions >= 4.13, or possibly Python >= 3.15
+    from typing_extensions import TypeForm as TypeForm
+except ImportError:
+    # Wrong, but better than crashing with an ImportError at runtime
+    from typing_extensions import Type as TypeForm
+
 
 Array: TypeAlias = NDArray[np.float64]
 Index: TypeAlias = EllipsisType | int | slice | tuple[EllipsisType | int | slice, ...]
@@ -194,7 +201,7 @@ def __init__(self, d: int, e: int, /, *args: Any, **kwargs: Any) -> None:
     return lambda f: f
 
 
-def literal_type_guard(tag: str, literal: TypeForm[_T0]) -> TypeGuard[_T0]:  # type: ignore[valid-type]
+def literal_type_guard(tag: str, literal: TypeForm[_T0]) -> TypeGuard[_T0]:
     """Utility function for narrowing strings to specified literals.
 
     Typically used to check a string against the permissible keys of a