In PEP517 mode setup.py is sourced - not executed - and the build fails
with ImportError like this:

    Preparing wheel metadata ... error
    ERROR: Command errored out with exit status 1:
     command: /home/kirr/src/wendelin/venv/z-dev/bin/python2 /home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/pip/_vendor/pep517/_in_process.py prepare_metadata_for_build_wheel /tmp/tmp2F3aEs
         cwd: /home/kirr/src/wendelin/wendelin.core
    Complete output (53 lines):
    running dist_info
    creating /tmp/pip-modern-metadata-sPiqUt/wendelin.core.egg-info
    writing requirements to /tmp/pip-modern-metadata-sPiqUt/wendelin.core.egg-info/requires.txt
    writing /tmp/pip-modern-metadata-sPiqUt/wendelin.core.egg-info/PKG-INFO
    writing top-level names to /tmp/pip-modern-metadata-sPiqUt/wendelin.core.egg-info/top_level.txt
    writing dependency_links to /tmp/pip-modern-metadata-sPiqUt/wendelin.core.egg-info/dependency_links.txt
    writing entry points to /tmp/pip-modern-metadata-sPiqUt/wendelin.core.egg-info/entry_points.txt
    writing manifest file '/tmp/pip-modern-metadata-sPiqUt/wendelin.core.egg-info/SOURCES.txt'
    package init file '__init__.py' not found (or not a regular file)
    Traceback (most recent call last):
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/pip/_vendor/pep517/_in_process.py", line 257, in <module>
        main()
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/pip/_vendor/pep517/_in_process.py", line 240, in main
        json_out['return_val'] = hook(**hook_input['kwargs'])
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/pip/_vendor/pep517/_in_process.py", line 110, in prepare_metadata_for_build_wheel
        return hook(metadata_directory, config_settings)
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/setuptools/build_meta.py", line 155, in prepare_metadata_for_build_wheel
        self.run_setup()
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/setuptools/build_meta.py", line 234, in run_setup
        self).run_setup(setup_script=setup_script)
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/setuptools/build_meta.py", line 141, in run_setup
        exec(compile(code, __file__, 'exec'), locals())
      File "setup.py", line 374, in <module>
        """.splitlines()]
      File "/home/kirr/src/tools/go/pygolang/golang/pyx/build.py", line 118, in setup
        setuptools_dso.setup(**kw)
      File "/home/kirr/src/tools/py/pypa/setuptools_dso/src/setuptools_dso/__init__.py", line 37, in setup
        _setup(**kws)
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/setuptools/__init__.py", line 145, in setup
        return distutils.core.setup(**attrs)
      File "/usr/lib/python2.7/distutils/core.py", line 151, in setup
        dist.run_commands()
      File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands
        self.run_command(cmd)
      File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
        cmd_obj.run()
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/setuptools/command/dist_info.py", line 31, in run
        egg_info.run()
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/setuptools/command/egg_info.py", line 296, in run
        self.find_sources()
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/setuptools/command/egg_info.py", line 303, in find_sources
        mm.run()
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/setuptools/command/egg_info.py", line 534, in run
        self.add_defaults()
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/setuptools/command/egg_info.py", line 574, in add_defaults
        rcfiles = list(walk_revctrl())
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/setuptools/command/sdist.py", line 20, in walk_revctrl
        for item in ep.load()(dirname):
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2434, in load
        return self.resolve()
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2444, in resolve
        raise ImportError(str(exc))
    ImportError: 'module' object has no attribute 'git_lsfiles'

See comments added to register_as_entrypoint for explanation of what
happens.

Wendelin.core will soon switch to PEP517 mode (by adding pyproject.toml)
to build-require Cython, Pygolang and friends.

This is needed so that e.g. a Python class implemented in C or Cython
(cdef class) could inherit from PyBigFile.

Don't put _bigfile.h into separate include/ directory, and keep it along
main .c file, similarly to how pygolang is organized.

For tests this makes sure that if one test fails, it won't make following
tests fail just because the next test will fail trying to lock test database.

For regular code (demo_zbigarray.py) this is also a good thing to do -
to always close the database irregardless of whether an exception was
raised before program reached end of main.

Pygolang becomes regular - not test only - dependency. Being regular
dependency is currently required only by demo_zbigarray.py, but it will
be also used in upcoming wcfs, so adding pygolang into wendelin.core
dependencies aligns with the plan.

dbclose now uses defer almost everywhere - there are still few places in
tests, where one test function is opening/closing test database multiple
times - those were not (yet ?) converted.

Let's keep on test coverage for last 2 stable Python releases.

Starting from Python 3.7 the place to keep exception state was changed:
https://github.com/python/cpython/commit/ae3087c638

NOTE ZEO4 does not wok with Python3.7, because ZEO4 uses "async" for a
variable and that breaks because starting from Python3.7 "async" became
a keyword.

After the fix wendelin.core tests pass under all python2.7, python3.6
and python3.7.

So that it can be available to everyone and in particular B & friends to
be available from introduced importable golang.testing package. The move
itself:

	kirr/pygolang@9bf03d9c

While moving the code was restructured / improved a bit and py.bench
interface reworked to mimic `go test -bench` in defaults.

- start testing NEO with ZODB4 and ZODB5. ZODB4-*-NEO works while
  ZODB5-*-NEO currently fails [1].
- update NumPy to latest releases.
- update Python 3 to latest releases.

Relicense to GPLv3+ with wide exception for all Free Software / Open Source projects + Business options.

Nexedi stack is licensed under Free Software licenses with various exceptions
that cover three business cases:

- Free Software
- Proprietary Software
- Rebranding

As long as one intends to develop Free Software based on Nexedi stack, no
license cost is involved. Developing proprietary software based on Nexedi stack
may require a proprietary exception license. Rebranding Nexedi stack is
prohibited unless rebranding license is acquired.

Through this licensing approach, Nexedi expects to encourage Free Software
development without restrictions and at the same time create a framework for
proprietary software to contribute to the long term sustainability of the
Nexedi stack.

Please see https://www.nexedi.com/licensing for details, rationale and options.

This updates and fixes 487e5226 (setup: specify setuptools location
explicitly when calling make.) to use @kazuhiko original idea to
propagate only setuptools location. The reason is - when propagating
whole sys.path things break under tox tests:

---- 8< ----
========================================================================== test session starts ===========================================================================
platform linux2 -- Python 2.7.12, pytest-2.9.2, py-1.4.31, pluggy-0.3.1
rootdir: /home/kirr/src/wendelin/release/wendelin.core, inifile:
collected 33 items

bigarray/tests/test_arrayzodb.py .......
bigarray/tests/test_basic.py ........
bigfile/tests/test_basic.py ....
bigfile/tests/test_filefile.py .
bigfile/tests/test_filezodb.py ........
bigfile/tests/test_thread.py ....
lib/tests/test_calc.py .

======================================================================= 33 passed in 14.14 seconds =======================================================================
x86_64-linux-gnu-gcc -pthread -g -Wall -D_GNU_SOURCE -std=gnu99 -fplan9-extensions -Wno-declaration-after-statement -Wno-error=declaration-after-statement  -Iinclude -I3rdparty/ccan -I3rdparty/include   bigfile/tests/tfault.c lib/bug.c lib/utils.c 3rdparty/ccan/ccan/tap/tap.c  -o bigfile/tests/tfault.t
t/tfault-run bigfile/tests/tfault.t faultr on_pagefault
ok 1 - !pagefault_init()
Fatal Python error: Py_Initialize: Unable to get the locale encoding
  File ".../wendelin.core/.tox/py27-ZODB3-zblk0-fs-numpy110/lib/python2.7/encodings/__init__.py", line 123
    raise CodecRegistryError,\
                            ^
SyntaxError: invalid syntax

Current thread 0x00007f9b80024780 (most recent call first):
t/tfault-run: line 28: 21521 Аварийный останов         (core dumped) gdb -q -batch $tfault core > core.info
E: can't gdb(core)
Makefile:189: ошибка выполнения рецепта для цели «faultr.tfault»
make: *** [faultr.tfault] Ошибка 1
rm bigfile/tests/test_virtmem.t bigfile/tests/test_ram.t bigfile/tests/tfault.t bigfile/tests/test_pagemap.t
error: Failed to execute `make test`
ERROR: InvocationError: '.../wendelin.core/.tox/py27-ZODB3-zblk0-fs-numpy110/bin/python setup.py test'
________________________________________________________________________________ summary _________________________________________________________________________________
ERROR:   py27-ZODB3-zblk0-fs-numpy110: commands failed
---- 8< ----

What happens here is:

- gdb is used in automated tests
- gdb is linked with libpython3.5
- tox is currently running tests with python27
- setup.py sets PYTHONPATH to whole path from python27
- gdb, upon starting, initializes python runtime, which tries to load
  py27 modules under py35 -> oops.

So propagating only setuptools location practically solves the issue for
now, but still there is potential risk that in future, there will be
other modules put in the same location as setuptools (location is parent
dir of a module/package) which python tries to load on startup and which
might be incompatible between 2 & 3.

Thus not setting PYTHONPATH at all - e.g. creating environments
virtualenv way - would be better, but buildout fundamentally works the
other way. We can not also use -c 'buildout sys.path hack' in $PYTHON
itself, as $PYTHON is used in general way inside Makefile.

So let the hack with setuptools location in PYTHONPATH stay there until
it practically works.

If wendelin.core is built under buildout and setuptools exists only in
buildout environment, 'python setup.py' called inside make will fail
without this change.

    Building 'wendelin.core'
    Running easy_install:
    "/path/to/python2.7" "-c" "import sys; sys.path[0:0] = ['/path/to/setuptools-19.6.2-py2.7.egg']; from setuptools.command.easy_install import main; main()"...
    path_list=['/path/to/setuptools-19.6.2-py2.7.egg']
    ...
    <<< setup.py: os.system('make %s PYTHON="%s"' % (target, sys.executable))
    ...
    make[1]: Leaving directory '/tmp/xxx/wendelin.core-0.6/3rdparty/ccan'
    /path/to/python2.7 setup.py ll_build_ext --inplace
    Traceback (most recent call last):
      File "setup.py", line 18, in <module>
        from setuptools import setup, Extension, Command, find_packages
    ImportError: No module named setuptools
    Makefile:40: recipe for target 'bigfile/_bigfile.so' failed
    make: *** [bigfile/_bigfile.so] Error 1
    error: Setup script exited with error: Failed to execute `make all`

[ @kirr: as a solution we are propagating whole python path via make.

  This should cover both setuptools case, and any other future potential
  "preloaded-by-buildout" egg. ]

/reviewed-on !1

@kazuhiko reports that wendelin.core build is currently broken on Python 3.5.
Indeed it was:

    In file included from bigfile/_bigfile.c:37:0:
    ./include/wendelin/compat_py2.h: In function ‘_PyThreadState_UncheckedGetx’:
    ./include/wendelin/compat_py2.h:66:28: warning: implicit declaration of function ‘_Py_atomic_load_relaxed’ [-Wimplicit-function-declaration]
         return (PyThreadState*)_Py_atomic_load_relaxed(&_PyThreadState_Current);
                                ^
    ./include/wendelin/compat_py2.h:66:53: error: ‘_PyThreadState_Current’ undeclared (first use in this function)
         return (PyThreadState*)_Py_atomic_load_relaxed(&_PyThreadState_Current);
                                                         ^
    ./include/wendelin/compat_py2.h:66:53: note: each undeclared identifier is reported only once for each function it appears in
    ./include/wendelin/compat_py2.h:67:1: warning: control reaches end of non-void function [-Wreturn-type]
     }
     ^

The story here is that in 3.5 they decided to remove direct access to
_PyThreadState_Current and atomic implementations - because that might
semantically conflict with other headers implementing atomics - and
provide only access by function.

Starting from Python 3.5.2rc1 the function to get current thread state
without asserting it is !NULL - _PyThreadState_UncheckedGet() - was added:

    https://github.com/python/cpython/commit/df858591

so for those python versions we can directly use it.

After the fix wendelin.core tox tests pass under all python2.7, python3.4 and python3.5.

More context here:

    https://bugs.python.org/issue26154
    https://bugs.python.org/issue25150

Fixes: #1

This continues c7750965 (changelog: Convert it to pretty rst) - without
.rst extension gitlab shows this file as plain text.

With the target being to show it on pypi project page.

Now we have at least some readme, so this way it is more convenient.

ZODB 3.10.4 was released almost 4 years ago, and contains significant
change how ghost objects coming from DB are initially setup.

As discussion in https://bitbucket.org/pypa/setuptools/issue/313
unveiled, setuptools do not have to carry setuptools.file_finders
entrypoint with it in order to support _other_ projects to use
.file_finders entry point.

In our case it means that is is normal that we have to make sure that
the group we are going to register entry-point into, exists.

Remove erroneous comments introduced in 11d130d1 (setup: Ensure
setuptools.file_finders entry-point group is registered).

py2-only syntax introduced in acf7e91d (setup/runcmd: Properly report
errors, if running command is missing):

      File "setup.py", line 168
        except Exception, e:
                        ^
    SyntaxError: invalid syntax

We currently use subprocess.check_output() for running external command
(git), and check_output() checks running command status code, as its
name promises:

    https://github.com/python/cpython/blob/2.7/Lib/subprocess.py#L569

and reports it appropriately to user:

    https://github.com/python/cpython/blob/2.7/Lib/subprocess.py#L411

but if the command is not found, it is just single

    error: [Errno 2] No such file or directory

which gets output to the log and it is not clear what command failed, or
evern if it is from runcmd() call.

Redo our runcmd() manually, so that it always report erros with context
- what command it was trying to run. The error now becomes:

   RuntimeError: (['missing-command'],): [Errno 2] No such file or directory

/cc @Tyagov

If setuptools.file_finders group is not registered,
dist.get_entry_map('setuptools.file_finders') returns just {} not
connected to entry map, and further modifications of this dict go
nowhere (and thus, our git_lsfiles() is not hooked -> sdist fails to
produce correct source archive).

This is a workaround for setuptools 9.0 dropping
`setuptools.file_finders` entrypoint group registration:

    https://bitbucket.org/pypa/setuptools/commits/f191c8a1225bd58a5fb5aa9abb31b06dc710f0b9#Lsetup.pyF175
    https://bitbucket.org/pypa/setuptools/issue/313

issue reported back:

    https://bitbucket.org/pypa/setuptools/issue/313#comment-18430008

In 5755a6b3 (Basic setup.py / Makefile to build/install/sdist stuff +
bigfile.so skeleton) we overlooked one thing:

    when tailing from setup.py to make level, we forgot to setup the
    PYTHON env variable properly, and that leads to changing building
    with std python.

Look e.g.

    $ python3 setup.py build_ext -i
    running build_ext
    python setup.py ll_build_ext --inplace
    ^^^

which is obviously not correct.

Fix it.

The tox setup we have setup for testing with multiple interpreters
(7af2b2d7 "Tox setup to test things with py27 & py34 and several
versions of ZODB") did not caught this, because for every python and
environment versions tox initializes separate virtualenv, in which
.../bin/python is a link to chosen python, and this way both python and
my-selected-for-build-python are the same.

Cc: @Tyagov

In C99 declaration after statement is ok, and we explicitly compile with -std=gnu99.

Python >= 3.4 however adds -Werror=declaration-after-statement even for extension
modules irregardless of their compilation flags:

  https://bugs.python.org/issue21121

and the build fails this way:

    building 'wendelin.bigfile._bigfile' extension
    creating build/temp.linux-x86_64-3.4
    creating build/temp.linux-x86_64-3.4/bigfile
    creating build/temp.linux-x86_64-3.4/lib
    gcc -pthread -Wno-unused-result -Werror=declaration-after-statement -DNDEBUG -fmessage-length=0 -grecord-gcc-switches -O2 -Wall
-D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DOPENSSL_LOAD_CONF -fPIC -D_GNU_SOURCE
-I./include -I./3rdparty/ccan -I./3rdparty/include -I/usr/include/python3.4m -c bigfile/_bigfile.c -o build/temp.linux-x86_64-3.4/bigfile/_bigfile.o
-std=gnu99 -fplan9-extensions -fvisibility=hidden
    bigfile/_bigfile.c: In function ‘pyfile_new’:
    bigfile/_bigfile.c:679:5: error: ISO C90 forbids mixed declarations and code [-Werror=declaration-after-statement]
         static char *kw_list[] = {"blksize", NULL};
         ^
    cc1: some warnings being treated as errors
    error: command 'gcc' failed with exit status 1

Ensure we turn off this warning and error because we already rely on compiling in C99 mode.
Reported-and-tested-by: Ivan Tyagov <ivan@tyagov.com>

This shows how to first generate such arrays (in steps, as every
transaction change should fit in memory), and then gather data from
whole array using C/Fortran/etc code.

It shows how to compute mean via NumPy's ndarray.mean()

It also shows that e.g. ndarray.var() wants to create temporaries in
size of original ndarray and that would fail, because it does not fit
into RAM.

ndarray.var() should not need to create such temporaries in principle -
all it has to do is to first compute mean, and then compute

    sum (Xi - <X>)^2

in a loop.

<X> is scalar, Xi - is just access to original array.

~~~~

So this also show NumPy can be incrementally improved to avoid creating
such temporaries, and then it will work.

For this, a small wrapper over py.test is developed (to discover/collect
functions to benchmar, etc) and then it runs such functions several
times in a boxed enveronment.

Benchmarks should be named bench_*.py

I.e. something like numpy.memmap for numpy.ndarray and OS files. The whole
bigarray cannot be used as a drop-in replacement for numpy arrays, but BigArray
_slices_ are real ndarrays and can be used everywhere ndarray can be used,
including in C/Fortran code. Slice size is limited by mapping-size (=
address-space size) limit, i.e. to ~ max 127TB on Linux/amd64.

Changes to bigarray memory are changes to bigfile memory mapping and as such
can be discarded or saved back to bigfile using mapping (= BigFileH) dirty
discard/writeout interface.

For the same reason the whole amount of changes to memory is limited by amount
of physical RAM.