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I added a _PyCoreConfig structure to Python 3.7 which contains almost all parameters used to configure Python. Problems: _PyCoreConfig uses bytes and Unicode strings (char* and wchar_t*) whereas it is also used to setup the memory allocator and (filesystem, locale and stdio) encodings.
I propose to add a new _PyPreConfig which is the "strict minimum" configuration to setup encodings and the memory allocator. In practice, it also contains parameters which directly or indirectly impacts the allocator and encodings. For example, isolated impacts use_environment which impacts the allocator (PYTHONMALLOC environment variable). Another example: dev_mode=1 sets the allocator to "debug".
The command line arguments are now parsed twice. _PyPreConfig only parses a few parameters like -E, -I and -X. A temporary _PyPreCmdline is used to store command line arguments like -X options.
I moved structures closer to where they are used. "Global" _PyMain structure has been removed. _PyCmdline now lives way shorter than previously and is moved from main.c to coreconfig.c. The idea is to better control when and how memory is allocated.
In term of API, we get something like:
 _PyCoreConfig config = _PyCoreConfig_INIT;
 config.preconfig.stdio_encoding = "iso8859-1";
 config.preconfig.stdio_errors = "replace";
 config.user_site_directory = 0;
 ...
 _PyInitError err = _Py_InitializeFromConfig(&config);
 if (_Py_INIT_FAILED(err)) {
 _Py_ExitInitError(err);
 }
 ...
 Py_Finalize();
 return 0;
"config.preconfig.stdio_errors" syntax isn't great, but it's simpler to implement than duplicating all _PyPreConfig fields into _PyCoreConfig.

PR 12087 is a WIP change which implements everything as a single commit.
I'm not 100% sure yet that it's best approach for Python initialization, but I'm sure that it solves real interdependencies issues between _PyCoreConfig parameters. IHMO have a "pre-initialization" step to setup the memory allocator and the encodings is a better design.

New changeset f684d83d86e1990784816d4b243d724e6ab8304f by Victor Stinner in branch 'master':
bpo-36142: Exclude coreconfig.h from Py_LIMITED_API (GH-12111)
https://github.com/python/cpython/commit/f684d83d86e1990784816d4b243d724e6ab8304f

TODO: check if _Py_ClearFileSystemEncoding() uses the right memory allocator. _Py_SetFileSystemEncoding() doesn't change temporarily the memory allocator.

New changeset dfe884759d1f4441c889695f8985bc9feb9f37eb by Victor Stinner in branch 'master':
bpo-36142: Rework error reporting in pymain_main() (GH-12113)
https://github.com/python/cpython/commit/dfe884759d1f4441c889695f8985bc9feb9f37eb

New changeset 95e2cbf32f8156c239b27dae558ba058d0f2d496 by Victor Stinner in branch 'master':
bpo-36142: Move command line parsing to coreconfig.c (GH-12123)
https://github.com/python/cpython/commit/95e2cbf32f8156c239b27dae558ba058d0f2d496

New changeset 91b9ecf82c3287b45f39158c5134a87414ff26bc by Victor Stinner in branch 'master':
bpo-36142: Add preconfig.c (GH-12128)
https://github.com/python/cpython/commit/91b9ecf82c3287b45f39158c5134a87414ff26bc

New changeset 62be763348d16ba90f96667aa0240503261393f0 by Victor Stinner in branch 'master':
bpo-36142: Remove _PyMain structure (GH-12120)
https://github.com/python/cpython/commit/62be763348d16ba90f96667aa0240503261393f0

Agreed - I think the biggest thing we learned from the pre-implementation in Python 3.7 is that the "Let's move as much config as we can to Python C API data types" fell down in a couple of areas:
1. The embedding application is likely to speak char* and/or wchar_* natively, not PyObject*, and this applies even for CPython's own current `Py_Main` implementation.
2. There's some core system libc interaction scaffolding that we need in place first, giving 3 phases, not two:
- initialise anything needed to read configuration settings from the environment and command line (i.e. memory allocators, interface encodings)
- initialise the things needed to execute builtin and frozen Python modules (core data types, random hash seed, etc)
- initialise the things needed to execute external Python modules (sys.path, etc)
I'll update PEP 432 so it at least mentions some of the lessons learned, and points to the current internal configuration API definitions in the CPython source tree.

PEP 432 tweaked: https://github.com/python/peps/pull/904/files 

New changeset cad1f747da47849ab5d8b0b881f7a0b94564d290 by Victor Stinner in branch 'master':
bpo-36142: Add _PyPreConfig structure (GH-12172)
https://github.com/python/cpython/commit/cad1f747da47849ab5d8b0b881f7a0b94564d290

New changeset 6dcb54228e7520abd058897440c26e323f62afcd by Victor Stinner in branch 'master':
bpo-36142: Add _PyPreConfig_ReadFromArgv() (GH-12173)
https://github.com/python/cpython/commit/6dcb54228e7520abd058897440c26e323f62afcd

New changeset 5a02e0d1c8a526fc4e80a2fb8b4a9d5bc64c7d82 by Victor Stinner in branch 'master':
bpo-36142: Add _PyPreConfig.utf8_mode (GH-12174)
https://github.com/python/cpython/commit/5a02e0d1c8a526fc4e80a2fb8b4a9d5bc64c7d82

New changeset b35be4b3334fbc471a39abbeb68110867b72e3e5 by Victor Stinner in branch 'master':
bpo-36142: Add _PyPreConfig.allocator (GH-12181)
https://github.com/python/cpython/commit/b35be4b3334fbc471a39abbeb68110867b72e3e5

New changeset a9df651eb4c18a07ec309df190419613e95cba7b by Victor Stinner in branch 'master':
bpo-36142: Add _PyMem_GetDebugAllocatorsName() (GH-12185)
https://github.com/python/cpython/commit/a9df651eb4c18a07ec309df190419613e95cba7b

New changeset 7d2ef3ef5042356aaeaf832ad4204b7dad2e1b8c by Victor Stinner in branch 'master':
bpo-36142: _PyPreConfig_Write() sets the allocator (GH-12186)
https://github.com/python/cpython/commit/7d2ef3ef5042356aaeaf832ad4204b7dad2e1b8c

New changeset c656e25667c9acc0d13e5bb16d3df2938d0f614b by Victor Stinner in branch 'master':
bpo-36142: Add _PyPreConfig_SetAllocator() (GH-12187)
https://github.com/python/cpython/commit/c656e25667c9acc0d13e5bb16d3df2938d0f614b

New changeset 4fffd380a4070aff39b7fd443d90e60746c1b623 by Victor Stinner in branch 'master':
bpo-36142: _PyPreConfig_Read() sets LC_CTYPE (GH-12188)
https://github.com/python/cpython/commit/4fffd380a4070aff39b7fd443d90e60746c1b623

Description of this long serie of changes.
I modified Py_Main() and _Py_InitializeCore() to clearly separate "pre-configuration" from "configuration" steps. The pre-configuration now decodes temporarily the command line arguments and uses its own command line parser to get -E, -I and -X options (-X is needed for -X utf8). The pre-configuration is designed to be as small as possible, it configures:
* memory allocators
* LC_CTYPE locale and set the UTF-8 mode
The _PyPreConfig structure has 8 fields:
* allocator
* coerce_c_locale
* coerce_c_locale_warn
* dev_mode
* isolated
* (Windows only) legacy_windows_fs_encoding
* use_environment
* utf8_mode
I had to include fields which have an impact on other fields. Examples:
* dev_mode=1 sets allocator to "default";
* isolated=1 sets use_environment to 0;
* legacy_windows_fs_encoding=& sets utf8_mode to 0.
_PyCoreConfig_Read() is now only called after the memory allocator and the locale (LC_CTYPE locale and UTF-8 mode) are properly configured.
I removed the last side effects of _PyCoreConfig_Read(): it no longer modify the locale. Same for the new _PyPreConfig_Read(): zero size effect.
The new _PyPreConfig_Write() and _PyCoreConfig_Write() are now responsible to write the new configurations.
There are functions to read the configuration from command line arguments:
* _PyPreConfig_ReadFromArgv()
* _PyCoreConfig_ReadFromArgv()
These functions expect a _PyArgv structure which accepts bytes (wchar*) or Unicode (wchar_t*).
I moved coreconfig.h from Include/ to Include/cpython/ to be more explicit that it's excluded from the stable API and that it's CPython specific.
I moved all config functions to a new Include/internal/pycore_coreconfig.h. Functions are internal to allow us to modify us anytime until a proper clean public API is designed on top of it.
If _PyPreConfig.allocator is set, _PyPreConfig_Write() re-allocate the configuration with the new memory allocator. This tiny thing avoids the new to force a specific memory allocator in many functions. I was able to remove the following code:
 PyMemAllocatorEx old_alloc;
 _PyMem_SetDefaultAllocator(PYMEM_DOMAIN_RAW, &old_alloc);
 ...
 PyMem_SetAllocator(PYMEM_DOMAIN_RAW, &old_alloc);
Calling Py_Main() after Py_Initialize() is still supported. In this case, it no longer checks the memory allocators name because _PyMem_GetAllocatorsName() returns "pymalloc_debug" (or "malloc_debug" if pymalloc is disabled) after _PyMem_SetupAllocators("debug") is called: names are diffrent.

I created bpo-36202: "Calling Py_DecodeLocale() before _PyPreConfig_Write() can produce mojibake".

Ok, the _PyPreConfig structure is now available and used internally. The API can likely be enhanced, but I prefer to open new follow-up issues like bpo-36202, since this issue has already a long list of changes :-) I close this issue.
Nick: thanks for updating the PEP 432 ;-

New changeset 25d13f37aa6743282d0b8b4df687ff89999964b2 by Victor Stinner in branch 'master':
bpo-36142: PYTHONMALLOC overrides PYTHONDEV (GH-12191)
https://github.com/python/cpython/commit/25d13f37aa6743282d0b8b4df687ff89999964b2