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.

This adds transactionality and with e.g. NEO[1] allows to distribute
objects to nodes into cluster.

We hook into ZODB two-phase commit process as a separate data manager,
and synchronize changes to memory, to changes to object only at that
time.

Alternative would be to get notified on every page change, and mark
appropriate object as dirty right at that moment.

But I wanted to stay close to filesystem design (we don't get
notification for every file change from kernel) - that's why it is done
the first way.

[1] http://www.neoppod.org/

Exposes BigFile - this way users can define BigFile backend in Python.

Also exposed are BigFile handles, and VMA objects which are results of
mmaping.

We'll use py.test for unit-testing of Python part.

This thing allows to get aliasable RAM from OS kernel and to manage it.
Currently we get memory from a tmpfs mount, and hugetlbfs should also
work, but is TODO because hugetlbfs in the kernel needs to be improved.

We need aliasing because we'll need to be able to memory map the same
page into several places in address space, e.g. for taking two slices
overlapping slice of the same array at different times.

Comes with test programs that show we aliasing does not work for
anonymous memory.

This will be the core of virtual memory subsystem. For now we just
define a structure to describe pages of memory and add utility to
allocate address space from OS.

We hook into SIGSEGV and handle read/write pagefaults this way.

In this patch there goes stub code that only detects faults and
determines (in arch specific way) whether fault was for read or write
and there is a TODO to pass that information to higher level.

It also comes with tests to detect we still crash if we access something
incorrectly, so people could have coredumps and investigate them.

For BigFiles we'll needs to maintain `{} offset-in-file -> void *` mapping. A
hash or a binary tree could be used there, but since we know files are
most of the time accessed sequentially and locally in pages-batches, we
can also organize the mapping in batches of keys.

Specifically offset bits are so divided into parts, that every part
addresses 1 entry in a table of hardware-page in size. To get to the actual
value, the system lookups first table by first part of offset, then from
first table and next part from address - second table, etc.

To clients this looks like a dictionary with get/set/del & clear methods,
but lookups are O(1) time always, and in contrast to hashes values are
stored with locality (= adjacent lookups almost always access the same tables).

We'll be testing C code in a similiar-to-python way - keep test_*.c
files nearby and compile/executing them as needed.

Tests are run several times in several ways - as plainly compiled and
also with additional error checkers:

 - AddressSanitizer
 - ThreadSanitizer
 - and similiar checkers from Valgrind

Like C bzero / memset & memcopy - but work on python buffers. We
leverage NumPy for doing actual work, and this way NumPy becomes a
depenency.

Having NumPy as a dependency is ok - we'll for sure need it later as we
are trying to build out-of-core ndarrays.

Like taking an exact integer log2, upcasting pointers for C-style
inheritance done in a Plan9 way, and wrappers to functions which should
never fail.

Modelled by ones used in Linux kernel.

It is an early project decision to use gnu99 & Plan9 C extensions, to
simplify C code.

So far we only build stub wendelin/bigfile/_bigfile.so .

Makefile is introduced because there will be targets which are easier to
handle at make level. For end users no make knowledge is required -
usual `python setup.py build|install|...` work, redirecting to make
where necessary.

As was promised (e870781d "Top-level in-tree import redirector")
setup.py contains install-time hooks to handle in-tree wendelin.py and
install it as a module namespace.

For sdist, we just use `git ls-files` info if we are in a checkout.