Add pypi package

.github/workflows/main.yml

@@ -344,7 +344,7 @@ jobs:
           architecture: x64
       - name: Install Python dependencies
         run: |
-          python -m pip install -U pip 'setuptools>=47.0.0,<48'
+          python -m pip install -U pip 'setuptools>=43.0.0'
           python -m pip install scons pypiwin32 numpy ruamel.yaml cython h5py pandas pytest pytest-github-actions-annotate-failures
       - name: Restore Boost cache
         uses: actions/cache@v2

SConstruct

@@ -88,7 +88,8 @@ if os.name not in ["nt", "posix"]:
     sys.exit(1)
 
 valid_commands = ("build", "clean", "install", "uninstall",
-                  "help", "msi", "samples", "sphinx", "doxygen", "dump")
+                  "help", "msi", "samples", "sphinx", "doxygen", "dump",
+                  "sdist")
 
 for command in COMMAND_LINE_TARGETS:
     if command not in valid_commands and not command.startswith('test'):
@@ -106,8 +107,12 @@ if "clean" in COMMAND_LINE_TARGETS:
     remove_directory("include/cantera/ext")
     remove_file("interfaces/cython/cantera/_cantera.cpp")
     remove_file("interfaces/cython/cantera/_cantera.h")
-    remove_file("interfaces/cython/setup.py")
-    remove_file("interfaces/python_minimal/setup.py")
+    remove_file("interfaces/cython/setup.cfg")
+    remove_file("interfaces/cython/LICENSE.txt")
+    remove_file("interfaces/cython/README.rst")
+    remove_file("interfaces/python_minimal/setup.cfg")
+    remove_file("interfaces/python_minimal/LICENSE.txt")
+    remove_file("interfaces/python_minimal/README.rst")
     remove_file("config.log")
     remove_directory("doc/sphinx/matlab/examples")
     remove_file("doc/sphinx/matlab/examples.rst")
@@ -239,6 +244,10 @@ config_options = [
            Cython) are installed. Note: 'y' is a synonym for 'full' and 'n'
            is a synonym for 'none'.""",
         "default", ("full", "minimal", "none", "n", "y", "default")),
+    BoolOption(
+        "python_sdist",
+        """Setting this option to True builds the Python sdist.""",
+        False),
     PathOption(
         "python_cmd",
         """Cantera needs to know where to find the Python interpreter. If
@@ -817,6 +826,8 @@ if 'doxygen' in COMMAND_LINE_TARGETS:
     env['doxygen_docs'] = True
 if 'sphinx' in COMMAND_LINE_TARGETS:
     env['sphinx_docs'] = True
+if "sdist" in COMMAND_LINE_TARGETS:
+    env["python_sdist"] = True
 
 for arg in ARGUMENTS:
     if arg not in config:
@@ -1349,7 +1360,7 @@ if env['VERBOSE']:
 env['python_cmd_esc'] = quoted(env['python_cmd'])
 
 # Python Package Settings
-python_min_version = parse_version('3.5')
+python_min_version = parse_version("3.6")
 # The string is used to set python_requires in setup.py.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
@@ -1868,6 +1879,10 @@ if env['matlab_toolbox'] == 'y':
 if env['doxygen_docs'] or env['sphinx_docs']:
     SConscript('doc/SConscript')
 
+if env["python_sdist"]:
+    VariantDir("build/python_sdist", "interfaces/python_sdist", duplicate=1)
+    SConscript("interfaces/python_sdist/SConscript", variant_dir="build/python_sdist")
+
 # Sample programs (also used from test_problems/SConscript)
 VariantDir('build/samples', 'samples', duplicate=0)
 sampledir_excludes = ['\\.o$', '^~$', '\\.in', 'SConscript']
@@ -1896,12 +1911,10 @@ def postBuildMessage(target, source, env):
     print("- To run the test suite, type 'scons test'.")
     print("- To list available tests, type 'scons test-help'.")
     if env['googletest'] == 'none':
-        print("  WARNING: You set the 'googletest' to 'none' and all it's tests will be skipped.")
+        print("  WARNING: You set the 'googletest' to 'none' and all its tests will be skipped.")
+    print("- To install, type 'scons install'.")
     if os.name == 'nt':
-        print("- To install, type 'scons install'.")
         print("- To create a Windows MSI installer, type 'scons msi'.")
-    else:
-        print("- To install, type 'scons install'.")
     print("*******************************************************")
 
 finish_build = env.Command('finish_build', [], postBuildMessage)

ext/SConscript

@@ -1,11 +1,13 @@
+from pathlib import Path
 from buildutils import *
 
 Import('env', 'build', 'install', 'libraryTargets')
 localenv = env.Clone()
 copyenv = localenv.Clone() # no CPPPATH addition, to avoid circular dependencies
 
-license_files = [('Cantera', '#License.txt'),
-                 ('Libexecstream', 'libexecstream/doc/license.txt')]
+license_files = {"Cantera": File("#License.txt"),
+                 "Libexecstream": File("#ext/libexecstream/doc/license.txt")}
+
 
 def prep_default(env):
     localenv = env.Clone()
@@ -42,40 +44,54 @@ for subdir, extensions, prepFunction in libs:
     objects = localenv.SharedObject(multi_glob(localenv, subdir, *extensions))
     libraryTargets.extend(objects)
 
+ext_copies = []
+
 if not env['system_fmt']:
-    license_files.append(('fmtlib', 'fmt/LICENSE.rst'))
+    license_files["fmtlib"] = File("#ext/fmt/LICENSE.rst")
     localenv = prep_default(env)
     localenv.Prepend(CPPPATH=Dir('#ext/fmt/include'))
     libraryTargets.extend(
         localenv.SharedObject(multi_glob(localenv, 'fmt/src', 'cc')))
     for name in ('format.h', 'ostream.h', 'printf.h', 'core.h', 'format-inl.h'):
-        build(copyenv.Command("#include/cantera/ext/fmt/" + name,
-                              "#ext/fmt/include/fmt/" + name,
-                              Copy('$TARGET', '$SOURCE')))
+        ext_copies.extend(
+            copyenv.Command("#include/cantera/ext/fmt/" + name,
+                            "#ext/fmt/include/fmt/" + name,
+                            Copy("$TARGET", "$SOURCE"))
+        )
 
 if env['system_sundials'] == 'n':
     localenv = prep_default(env)
     localenv.Prepend(CPPPATH=[Dir('#include/cantera/ext'),
                               Dir('#ext/sundials/src/sundials')])
-    license_files.append(('Sundials', 'sundials/LICENSE'))
+    license_files["Sundials"] = File("#ext/sundials/LICENSE")
 
     # Generate sundials_config.h
     sundials_configh = {}
     if env['OS'] != 'Windows':
         sundials_configh['SUNDIALS_USE_GENERIC_MATH'] = 1
     if env['use_lapack']:
         sundials_configh['SUNDIALS_BLAS_LAPACK'] = 1
-    localenv.AlwaysBuild(env.Command('#include/cantera/ext/sundials/sundials_config.h',
-                                     'sundials_config.h.in',
-                                     ConfigBuilder(sundials_configh)))
+    sundials_configh_build = env.Command("#build/ext/sundials_config.h.build",
+                                         "sundials_config.h.in",
+                                         ConfigBuilder(sundials_configh))
+    # This separate copy operation, which SCons will skip if sundials_config.h.build is
+    # unmodified, prevents unnecessary re-copies of files in the #include directory
+    localenv.AlwaysBuild(sundials_configh_build)
+    ext_copies.extend(
+        localenv.Command("#include/cantera/ext/sundials/sundials_config.h",
+                         "#build/ext/sundials_config.h.build",
+                         Copy("$TARGET", "$SOURCE"))
+    )
 
     # Copy sundials header files into common include directory
     for subdir in ('sundials', 'nvector', 'cvodes', 'ida', 'sunmatrix',
                    'sunlinsol', 'sunnonlinsol'):
         for header in multi_glob(env, 'sundials/include/'+subdir, 'h'):
-            build(copyenv.Command('#include/cantera/ext/%s/%s' % (subdir, header.name),
-                                  '#ext/sundials/include/%s/%s' % (subdir, header.name),
-                                  Copy('$TARGET', '$SOURCE')))
+            ext_copies.extend(
+                copyenv.Command(f"#include/cantera/ext/{subdir}/{header.name}",
+                                f"#ext/sundials/include/{subdir}/{header.name}",
+                                Copy("$TARGET", "$SOURCE"))
+            )
 
     # Compile Sundials source files. Skip files related to the Sundials Fortran
     # interface, which start with 'fsun'.
@@ -93,14 +109,18 @@ if env['system_sundials'] == 'n':
 if not env['system_yamlcpp']:
     localenv = prep_default(env)
     localenv.Prepend(CPPPATH=Dir('#include/cantera/ext'))
-    license_files.append(('YAML-CPP', 'yaml-cpp/LICENSE'))
+    license_files["YAML-CPP"] = File("#ext/yaml-cpp/LICENSE")
 
     # Copy header files into common include directory
     for subdir in ('', 'contrib', 'node', 'node/detail'):
         for header in multi_glob(env, 'yaml-cpp/include/yaml-cpp/'+subdir, 'h'):
-            h = build(localenv.Command('#include/cantera/ext/yaml-cpp/{}/{}'.format(subdir, header.name),
-                                       '#ext/yaml-cpp/include/yaml-cpp/{}/{}'.format(subdir, header.name),
-                                       Copy('$TARGET', '$SOURCE')))
+            ext_copies.extend(
+                localenv.Command(
+                    f"#include/cantera/ext/yaml-cpp/{subdir}/{header.name}",
+                    f"#ext/yaml-cpp/include/yaml-cpp/{subdir}/{header.name}",
+                    Copy("$TARGET", "$SOURCE")
+                )
+            )
 
     # Compile yaml-cpp source files
     for subdir in ('', 'contrib'):
@@ -109,10 +129,11 @@ if not env['system_yamlcpp']:
 
 
 if not env['system_eigen']:
-    license_files.append(('Eigen', 'eigen/COPYING.MPL2'))
+    license_files["Eigen"] = File("#ext/eigen/COPYING.MPL2")
     h = build(copyenv.Command('#include/cantera/ext/Eigen', '#ext/eigen/Eigen',
                               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':
@@ -123,28 +144,35 @@ if env['googletest'] == 'submodule':
     gmock = build(localenv.Library('../lib/gmock',
                                    source=['googletest/googlemock/src/gmock-all.cc']))
 
-# Create license file containing licenses for Cantera and all included packages
+env["ext_include_copies_target"] = build(ext_copies)
+
+
 def generate_license(target, source, env):
-    stars = '*'*50 + '\n' + '*'*50 + '\n'
-    tpl = stars + 'The following license applies to {}\n' + stars + '\n{}\n'
+    target = Path(target[0].abspath)
+    stars = "*" * 50 + "\n" + "*" * 50 + "\n"
+    tpl = stars + "The following license applies to {}\n" + stars + "\n{}\n"
 
     license = []
-    for (package,_),filename in zip(license_files, source):
-        license.append(tpl.format(package, open(filename.path).read().strip()))
+    for package, license_file in env["license_files"].items():
+        license_file = Path(license_file.abspath)
+        license.append(tpl.format(package, license_file.read_text().strip()))
+    license = "\n".join(license)
+    if target.suffix == ".rtf":
+        license = license.replace("\\", "\\\\").replace("{", "\\{").replace("}", "\\}")
+        license = license.replace("\n", " \\par\n")
+        license = (r"{\rtf1\ansi{\fonttbl\f0\fswiss Arial;}\f0\pard\fs16 "
+                   + license + "}")
 
-    license = '\n'.join(license)
-    if target[0].path.endswith('.rtf'):
-        license = license.replace('\\', '\\\\').replace('{', '\\{').replace('}', '\\}')
-        license = license.replace('\n', ' \\par\n')
-        license = r'{\rtf1\ansi{\fonttbl\f0\fswiss Arial;}\f0\pard\fs16 ' + license + '}'
+    target.write_text(license)
 
-    open(target[0].path, 'w').write(license)
 
-license = build(localenv.Command('LICENSE.txt', [x[1] for x in license_files],
+localenv["license_files"] = license_files
+license = build(localenv.Command("LICENSE.txt", license_files.values(),
                                  generate_license))
+env["license_target"] = license
 install('$inst_docdir', license)
 
 if env['OS'] == 'Windows':
     # RTF version is required for Windows installer
-    build(localenv.Command('LICENSE.rtf', [x[1] for x in license_files],
+    build(localenv.Command("LICENSE.rtf", license_files.values(),
                            generate_license))

include/cantera/base/global.h

@@ -113,6 +113,7 @@ std::string gitCommit();
  * @returns a string containing the name of the base directory where %Cantera is
  *     installed. If the environmental variable CANTERA_ROOT is defined, this
  *     function will return its value, preferentially.
+ * @deprecated Unused within Cantera. To be removed after Cantera 2.6
  *
  * @ingroup inputfiles
  */

interfaces/cython/.gitignore

@@ -2,10 +2,8 @@ cantera/*.cpp
 cantera/*.c
 cantera/data
 cantera/test/data
-setup.py
-scripts/ctml_writer.py
-scripts/ctml_writer
-scripts/ck2cti.py
-scripts/ck2cti
 Cantera.egg-info
 dist
+setup.cfg
+LICENSE.txt
+README.rst

interfaces/cython/SConscript

@@ -4,6 +4,7 @@ from os.path import join as pjoin
 from os.path import normpath
 from pathlib import Path
 from pkg_resources import parse_version
+import json
 from buildutils import *
 
 Import('env', 'build', 'install')
@@ -32,36 +33,55 @@ testFiles = localenv.RecursiveInstall('#interfaces/cython/cantera/test/data',
 build(testFiles)
 
 # Get information needed to build the Python module
-script = '\n'.join(("from distutils.sysconfig import *",
-                    "import numpy",
-                    "print(get_config_var('EXT_SUFFIX') or get_config_var('SO'))",
-                    "print(get_config_var('INCLUDEPY'))",
-                    "print(get_config_var('LDLIBRARY'))",
-                    "print(get_config_var('prefix'))",
-                    "print(get_python_version())",
-                    "print(numpy.get_include())"))
-info = get_command_output(localenv["python_cmd"], "-c", script)
-module_ext, inc, pylib, prefix, py_version, numpy_include = info.splitlines()[-6:]
+script = """\
+from sysconfig import *
+import numpy
+import json
+vars = get_config_vars()
+vars["plat"] = get_platform()
+vars["numpy_include"] = numpy.get_include()
+print(json.dumps(vars))
+"""
+info = json.loads(get_command_output(localenv["python_cmd"], "-c", script))
+module_ext = info["EXT_SUFFIX"]
+inc = info["INCLUDEPY"]
+pylib = info.get("LDLIBRARY")
+prefix = info["prefix"]
+py_version_short = parse_version(info["py_version_short"])
+py_version_full = parse_version(info["py_version"])
+numpy_include = info["numpy_include"]
 localenv.Prepend(CPPPATH=[Dir('#include'), inc, numpy_include])
 localenv.Prepend(LIBS=localenv['cantera_libs'])
 
+# Fix the module extension for Windows from the sysconfig library.
+# See https://github.com/python/cpython/pull/22088 and
+# https://bugs.python.org/issue39825
+if (
+    py_version_full < parse_version("3.8.7")
+    and localenv["OS"] == "Windows"
+    and module_ext == ".pyd"
+):
+    module_ext = f".cp{info['py_version_nodot']}-{info['plat'].replace('-', '_')}.pyd"
+
 # Don't print deprecation warnings for internal Python changes.
 # Only applies to Python 3.8. The field that is deprecated in Python 3.8
 # and causes the warnings to appear will be removed in Python 3.9 so no
 # further warnings should be issued.
-if localenv['HAS_CLANG'] and parse_version(py_version) == parse_version('3.8'):
+if localenv["HAS_CLANG"] and py_version_short == parse_version("3.8"):
     localenv.Append(CXXFLAGS='-Wno-deprecated-declarations')
 
 if localenv['OS'] == 'Darwin':
     localenv.Append(LINKFLAGS='-undefined dynamic_lookup')
 elif localenv['OS'] == 'Windows':
     localenv.Append(LIBPATH=prefix+'/libs')
     if localenv['toolchain'] == 'mingw':
-        localenv.Append(LIBS='python{}'.format(py_version.replace('.','')))
+        localenv.Append(LIBS=f"python{info['py_version_nodot']}")
         if localenv['OS_BITS'] == 64:
             localenv.Append(CPPDEFINES='MS_WIN64')
-        # fix for http://bugs.python.org/issue11566
-        localenv.Append(CPPDEFINES={'_hypot':'hypot'})
+        # Fix for https://bugs.python.org/issue11566. Fixed in 3.7.3 and higher.
+        # See https://github.com/python/cpython/pull/11283
+        if py_version_full < parse_version("3.7.3"):
+            localenv.Append(CPPDEFINES={"_hypot": "hypot"})
 elif localenv['OS'] == 'Cygwin':
     # extract 'pythonX.Y' from 'libpythonX.Y.dll.a'
     localenv.Append(LIBS=pylib[3:-6])
@@ -73,16 +93,19 @@ ext = localenv.LoadableModule('#build/python/cantera/_cantera{}'.format(module_e
                             SHLIBPREFIX='', LIBSUFFIXES=[module_ext])
 localenv['py_extension'] = ext[0].name
 
-localenv.SubstFile('setup.py', 'setup.py.in')
+setup_cfg = localenv.SubstFile("setup.cfg", "setup.cfg.in")
+readme = localenv.Command("README.rst", "#README.rst", Copy("$TARGET", "$SOURCE"))
+license = localenv.Command("LICENSE.txt", "#build/ext/LICENSE.txt",
+                           Copy("$TARGET", "$SOURCE"))
+localenv.Depends(license, localenv["license_target"])
 build_cmd = ('cd interfaces/cython &&'
              ' $python_cmd_esc setup.py build --build-lib=../../build/python')
-mod = build(localenv.Command('#build/python/cantera/__init__.py', 'setup.py',
+mod = build(localenv.Command("#build/python/cantera/__init__.py", "setup.cfg",
                              build_cmd))
 env['python_module'] = mod
 env['python_extension'] = ext
 
-localenv.Depends(mod, ext)
-localenv.Depends(mod, dataFiles + testFiles)
+localenv.Depends(mod, [ext, dataFiles, testFiles, setup_cfg, readme, license])
 localenv.Depends(ext, localenv['cantera_staticlib'])
 
 for f in (multi_glob(localenv, 'cantera', 'py') +

interfaces/cython/cantera/test/__init__.py

@@ -15,5 +15,5 @@
 from .test_transport import *
 from .test_utils import *
 
-cantera.add_directory(Path(__file__) / "data")
+cantera.add_directory(Path(__file__).parent / "data")
 cantera.add_directory(Path(__file__).parents[1] / "examples" / "surface_chemistry")