Merge branch 'Cantera:main' into main

.gitmodules

@@ -13,3 +13,6 @@
 [submodule "ext/yaml-cpp"]
 	path = ext/yaml-cpp
 	url = https://github.com/jbeder/yaml-cpp.git
+[submodule "ext/HighFive"]
+	path = ext/HighFive
+	url = https://github.com/BlueBrain/HighFive.git

AUTHORS

@@ -31,6 +31,7 @@ Yuanjie Jiang
 Benjamin Kee (@lionkey)
 Gandhali Kogekar (@gkogekar)
 Daniel Korff (@korffdm), Colorado School of Mines
+Corey R. Randall (@c-randall), Colorado School of Mines
 Jon Kristofer
 Samesh Lakothia (@sameshl)
 Kyle Linevitch, Jr. (@KyleLinevitchJr)
@@ -63,3 +64,4 @@ Armin Wehrfritz (@awehrfritz)
 Richard West (@rwest), Northeastern University
 Chao Xu (@12Chao), Northeastern University
 Thorsten Zirwes (@g3bk47), Karlsruhe Institute of Technology
+Su Sun (@ssun30), Northeastern University

CONTRIBUTING.md

@@ -102,8 +102,8 @@
 
 * Style generally follows PEP8 (https://www.python.org/dev/peps/pep-0008/)
 * Code in `.py` and `.pyx` files needs to be written to work with Python 3
-* The minimum Python version that Cantera supports is Python 3.7, so code should only
-  use features added in Python 3.7 or earlier
+* The minimum Python version that Cantera supports is Python 3.8, so code should only
+  use features added in Python 3.8 or earlier
 * Indicate the version added for new functions and classes with an annotation like
   `.. versionadded:: X.Y` where `X.Y` is the next Cantera version. Significant changes
   in behavior should be indicated with `.. versionchanged:: X.Y`.

SConstruct

@@ -65,7 +65,7 @@ Additional command options:
 # and simplest option that will reliably trigger an error in Python 2
 # and provide actionable feedback for users.
 f"""
-Cantera must be built using Python 3.7 or higher. You can invoke SCons by executing
+Cantera must be built using Python 3.8 or higher. You can invoke SCons by executing
     python3 `which scons`
 followed by any desired options.
 """
@@ -167,11 +167,25 @@ logger.info(
 windows_options = [
     Option(
         "msvc_version",
-        """Version of Visual Studio to use. The default is the newest
-           installed version. Specify '14.1' ('14.1x') Visual Studio 2017, '14.2'
-           ('14.2x') for Visual Studio 2019, or '14.3' ('14.3x') for
-           Visual Studio 2022. For version numbers in parentheses,
-           'x' is a placeholder for a minor version number. Windows MSVC only.""",
+        """Version of Visual Studio to use. The default is the newest installed version.
+        Note that since multiple MSVC toolsets can be installed for a single version of
+        Visual Studio, you probably want to use ``msvc_toolset_version`` unless you
+        specifically installed multiple versions of Visual Studio. Windows MSVC only.
+        """,
+        ""),
+    Option(
+        "msvc_toolset_version",
+        """Version of the MSVC toolset to use. The default is the default version for
+        the given ``msvc_version``. Note that the toolset selected here must be
+        installed in the MSVC version selected by ``msvc_version``. The default
+        toolsets associated with various Visual Studio versions are:
+
+        * '14.1' ('14.1x'): Visual Studio 2017
+        * '14.2' ('14.2x'): Visual Studio 2019
+        * '14.3' ('14.3x'): Visual Studio 2022.
+
+        For version numbers in parentheses, 'x' is a placeholder for a minor version
+        number. Windows MSVC only.""",
         ""),
     EnumOption(
         "target_arch",
@@ -342,6 +356,34 @@ config_options = [
            must include the shared version of the library, for example,
            'libfmt.so'.""",
         "default", ("default", "y", "n")),
+    EnumOption(
+        "hdf_support",
+        """Select whether to support HDF5 container files natively ('y'), disable HDF5
+           support ('n'), or to decide automatically based on the system configuration
+           ('default'). Native HDF5 support uses the HDF5 library as well as the
+           header-only HighFive C++ wrapper (see option 'system_highfive'). Specifying
+           'hdf_include' or 'hdf_libdir' changes the default to 'y'.""",
+        "default", ("default", "y", "n")),
+    PathOption(
+        "hdf_include",
+        """The directory where the HDF5 header files are installed. This should be the
+           directory that contains files 'H5Version.h' and 'H5Public.h', amongst others.
+           Not needed if the headers are installed in a standard location, for example,
+           '/usr/include'.""",
+        "", PathVariable.PathAccept),
+    PathOption(
+        "hdf_libdir",
+        """The directory where the HDF5 libraries are installed. Not needed if the
+           libraries are installed in a standard location, for example, '/usr/lib'.""",
+        "", PathVariable.PathAccept),
+    EnumOption(
+        "system_highfive",
+        """Select whether to use HighFive from a system installation ('y'), from a
+           Git submodule ('n'), or to decide automatically ('default'). If HighFive
+           is not installed directly into a system include directory, for example, it
+           is installed in '/opt/include/HighFive', then you will need to add
+           '/opt/include/HighFive' to 'extra_inc_dirs'.""",
+        "default", ("default", "y", "n")),
     EnumOption(
         "system_yamlcpp",
         """Select whether to use the yaml-cpp library from a system installation
@@ -428,7 +470,7 @@ config_options = [
         """Environment variables to propagate through to SCons. Either the
            string 'all' or a comma separated list of variable names, for example,
            'LD_LIBRARY_PATH,HOME'.""",
-        "PATH,LD_LIBRARY_PATH,DYLD_LIBRARY_PATH,PYTHONPATH"),
+        "PATH,LD_LIBRARY_PATH,DYLD_LIBRARY_PATH,PYTHONPATH,USERPROFILE"),
     BoolOption(
         "use_pch",
         "Use a precompiled-header to speed up compilation",
@@ -722,7 +764,7 @@ if os.name == "nt":
     if "64 bit" not in sys.version:
         config["target_arch"].default = "x86"
 
-    opts.AddVariables(*config.to_scons(("msvc_version", "target_arch")))
+    opts.AddVariables(*config.to_scons(("msvc_version", "msvc_toolset_version", "target_arch")))
 
     windows_compiler_env = Environment()
     opts.Update(windows_compiler_env)
@@ -731,7 +773,7 @@ if os.name == "nt":
     if which("g++") and not which("cl.exe"):
         config["toolchain"].default = "mingw"
 
-    if windows_compiler_env["msvc_version"]:
+    if windows_compiler_env["msvc_version"] or windows_compiler_env["msvc_toolset_version"]:
         config["toolchain"].default = "msvc"
 
     opts.AddVariables(*config.to_scons("toolchain"))
@@ -741,9 +783,15 @@ if os.name == "nt":
         toolchain = ["default"]
         if windows_compiler_env["msvc_version"]:
             extraEnvArgs["MSVC_VERSION"] = windows_compiler_env["msvc_version"]
+        if windows_compiler_env["msvc_toolset_version"]:
+            extraEnvArgs["MSVC_TOOLSET_VERSION"] = windows_compiler_env["msvc_toolset_version"]
         msvc_version = (windows_compiler_env["msvc_version"] or
-                        windows_compiler_env["MSVC_VERSION"])
-        logger.info(f"Compiling with MSVC {msvc_version}", print_level=False)
+                        windows_compiler_env.get("MSVC_VERSION"))
+        logger.info(f"Compiling with MSVC version {msvc_version}", print_level=False)
+        msvc_toolset = (windows_compiler_env["msvc_toolset_version"] or
+                        windows_compiler_env.get("MSVC_TOOLSET_VERSION") or
+                        f"{msvc_version} (default)")
+        logger.info(f"Compiling with MSVC toolset {msvc_toolset}", print_level=False)
 
     elif windows_compiler_env["toolchain"] == "mingw":
         toolchain = ["mingw", "f90"]
@@ -1442,7 +1490,7 @@ if env['system_sundials'] == 'y':
     if sundials_ver < parse_version("3.0") or sundials_ver >= parse_version("7.0"):
         logger.error(f"Sundials version {env['sundials_version']!r} is not supported.")
         sys.exit(1)
-    elif sundials_ver > parse_version("6.2"):
+    elif sundials_ver > parse_version("6.4.1"):
         logger.warning(f"Sundials version {env['sundials_version']!r} has not been tested.")
 
     logger.info(f"Using system installation of Sundials version {sundials_version!r}.")
@@ -1477,6 +1525,76 @@ else: # env['system_sundials'] == 'n'
     env['sundials_version'] = '5.3'
     env['has_sundials_lapack'] = int(env['use_lapack'])
 
+if env["hdf_include"]:
+    env["hdf_include"] = Path(env["hdf_include"]).as_posix()
+    env.Append(CPPPATH=[env["hdf_include"]])
+    env["hdf_support"] = "y"
+if env["hdf_libdir"]:
+    env["hdf_libdir"] = Path(env["hdf_libdir"]).as_posix()
+    env.Append(LIBPATH=[env["hdf_libdir"]])
+    env["hdf_support"] = "y"
+    if env["use_rpath_linkage"]:
+        env.Append(RPATH=env["hdf_libdir"])
+
+if env["hdf_support"] == "n":
+    env["use_hdf5"] = False
+else:
+    env["use_hdf5"] = conf.CheckLib("hdf5", autoadd=False)
+    if not env["use_hdf5"] and env["hdf_support"] == "y":
+        config_error("HDF5 support has been specified but libraries were not found.")
+
+if env["use_hdf5"] and env["system_highfive"] in ("n", "default"):
+    env["system_highfive"] = False
+    if not os.path.exists("ext/eigen/HighFive/include"):
+        if not os.path.exists(".git"):
+            config_error("HighFive is missing. Install HighFive in ext/HighFive.")
+
+        try:
+            code = subprocess.call(["git", "submodule", "update", "--init",
+                                    "--recursive", "ext/HighFive"])
+        except Exception:
+            code = -1
+        if code:
+            config_error("HighFive not found and submodule checkout failed.\n"
+                        "Try manually checking out the submodule with:\n\n"
+                        "    git submodule update --init --recursive ext/HighFive\n")
+
+    env["use_hdf5"] = conf.CheckLibWithHeader(
+        "hdf5", "../ext/HighFive/include/highfive/H5File.hpp",
+        language="C++", autoadd=False)
+
+    if env["use_hdf5"]:
+        logger.info("Using private installation of HighFive.")
+    elif env["hdf_support"] == "y":
+        config_error("HDF5 support has been specified but HighFive configuration failed.")
+    else:
+        logger.warning("HighFive is not configured correctly; skipping.")
+        env["use_hdf5"] = False
+
+elif env["use_hdf5"]:
+    env["system_highfive"] = True
+    env["use_hdf5"] = conf.CheckLibWithHeader(
+        "hdf5", "highfive/H5File.hpp", language="C++", autoadd=False)
+    if env["use_hdf5"]:
+        logger.info("Using system installation of HighFive.")
+    else:
+        config_error("Unable to locate system HighFive installation.")
+
+if env["use_hdf5"]:
+    hdf_version = textwrap.dedent("""\
+        #include <iostream>
+        #include "H5public.h"
+        int main(int argc, char** argv) {
+            std::cout << H5_VERS_MAJOR << "." << H5_VERS_MINOR << "." << H5_VERS_RELEASE;
+            return 0;
+        }
+    """)
+    retcode, hdf_version = conf.TryRun(hdf_version, ".cpp")
+    if retcode:
+        logger.info(f"Compiling against HDF5 version {hdf_version}")
+    else:
+        logger.warning("Failed to determine HDF5 version.")
+
 def set_fortran(pattern, value):
     # Set compiler / flags for all Fortran versions to be the same
     for version in ("FORTRAN", "F77", "F90", "F95", "F03", "F08"):
@@ -1558,7 +1676,7 @@ logger.debug("\n".join(debug_message), print_level=False)
 env['python_cmd_esc'] = quoted(env['python_cmd'])
 
 # Python Package Settings
-python_min_version = parse_version("3.7")
+python_min_version = parse_version("3.8")
 # The string is used to set python_requires in setup.cfg.in
 env['py_min_ver_str'] = str(python_min_version)
 # Note: cython_min_version is redefined below if the Python version is 3.8 or higher
@@ -2003,6 +2121,8 @@ cdefine('LAPACK_FTN_TRAILING_UNDERSCORE', 'lapack_ftn_trailing_underscore')
 cdefine('FTN_TRAILING_UNDERSCORE', 'lapack_ftn_trailing_underscore')
 cdefine('LAPACK_NAMES_LOWERCASE', 'lapack_names', 'lower')
 cdefine('CT_USE_LAPACK', 'use_lapack')
+cdefine("CT_USE_HDF5", "use_hdf5")
+cdefine("CT_USE_SYSTEM_HIGHFIVE", "system_highfive")
 cdefine("CT_USE_SYSTEM_EIGEN", "system_eigen")
 cdefine("CT_USE_SYSTEM_EIGEN_PREFIXED", "system_eigen_prefixed")
 cdefine('CT_USE_SYSTEM_FMT', 'system_fmt')
@@ -2092,6 +2212,9 @@ else:
 env["external_libs"] = []
 env["external_libs"].extend(env["sundials_libs"])
 
+if env["use_hdf5"]:
+    env["external_libs"].append("hdf5")
+
 if env["system_fmt"]:
     env["external_libs"].append("fmt")
 

ext/SConscript

@@ -125,6 +125,14 @@ if not env['system_eigen']:
     copyenv.Depends(copyenv['config_h_target'], h)
     ext_copies.extend(h)
 
+if not env["system_highfive"]:
+    localenv = prep_default(env)
+    license_files["HighFive"] = File("#ext/HighFive/LICENSE")
+    h = build(copyenv.Command('#include/cantera/ext/HighFive', '#ext/HighFive/include/highfive',
+                              Copy('$TARGET', '$SOURCE')))
+    copyenv.Depends(copyenv['config_h_target'], h)
+    ext_copies.extend(h)
+
 # Google Test: Used internally for Cantera unit tests.
 if env['googletest'] == 'submodule':
     localenv = prep_gtest(env)

include/cantera/base/AnyMap.h

@@ -12,6 +12,7 @@
 
 #include <unordered_map>
 #include <functional>
+#include <set>
 
 namespace boost
 {
@@ -447,6 +448,10 @@ class AnyMap : public AnyBase
     //! messages, for example
     std::string keys_str() const;
 
+    //! Return an unordered set of keys
+    //! @since  New in Cantera 3.0.
+    std::set<std::string> keys() const;
+
     //! Set a metadata value that applies to this AnyMap and its children.
     //! Mainly for internal use in reading or writing from files.
     void setMetadata(const std::string& key, const AnyValue& value);