It's been a while since last ZODB3 3.10.7 release in 2016 and the last
commit in upstream ZODB3 repository (3.10 branch) is from 2017. The
world switched since then to ZODB4 and to ZODB5 after that.

We were still requiring ZODB3, because ZODB3 3.11 egg was just a
dependency on newer ZODB, ZEO, BTrees and persistent; and this way we
could be supporting all ZODB3.10.x and  ZODB4 and ZODB5 via ZODB3.11.

However upcoming Wendelin.core 2, for its proper working, needs MVCC
semantic as implemented in ZODB5. This forces us, even for ZODB4, to
backport non-trivial bits from ZODB5 (see [1]). Maintaining ZODB3
support at this point becomes non-practical, because, to our knowledge,
there is no wendelin.core user that plans to continue using ZODB3
without switching to at least ZODB4 in the near future.

So goodbye ZODB3. Even though ZODB still stays with us, it gives a
feeling similar to [2], because in 2014, when I was myself learning
ZODB, it was through ZODB3 - still at the time when all ZODB bits were
living together in one place.

[1] ZODB!1
[2] https://lists.osuosl.org/pipermail/darcs-users/2008-September/014095.html

DB.close() does `del self.storage`.

https://github.com/zopefoundation/ZODB/blob/5.6.0-14-g0eae10cd0/src/ZODB/DB.py#L646

This way if DB was closed, but some conn(s) were not, it will crash in
teardown as e.g. below:

    _____________ ERROR at teardown of test_bigfile_zblk1_zdata_reuse ______________

        def teardown_module():
    >       testdb.teardown()

    bigfile/tests/test_filezodb.py:58:
    _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

    self = <wendelin.lib.testing.TestDB_ZEO object at 0x7fb9c0216350>

        def teardown(self):
            # close connections that test code forgot to close
            for connref, tb in self.connv:
                conn = connref()
                if conn is None:
                    continue
                if not conn.opened:
                    continue    # still alive, but closed
                print("W: testdb: teardown: %s left not closed by test code"
                      "; opened by:\n%s" % (conn, tb), file=sys.stderr)

                db = conn.db()
    >           stor = db.storage
    E           AttributeError: 'DB' object has no attribute 'storage'

    lib/testing.py:217: AttributeError

The fix is simple - don't use db.storage at all, because it is not actually used in that code.

Since ZBigFile keeps references to fileh objects that are created
through it it forms a file <=> fileh cycle that is not collected without
cyclic GC:

https://lab.nexedi.com/nexedi/wendelin.core/blob/v0.13-52-ga702d41/bigfile/file_zodb.py#L497
https://lab.nexedi.com/nexedi/wendelin.core/blob/v0.13-52-ga702d41/bigfile/file_zodb.py#L566-571

We did not noticed this leak until now because it is small, but with
upcoming wendelin.core 2 it is important to release a fileh, because
there is WCFS connection associated with fileh, and if fileh is not
released, that connection also stays alive, keeping on-WCFS resources
still being used, and preventing WCFS from being unmounted cleanly.

-> Add cyclic GC support to PyBigFile / PyBigFileH

NOTE: we still don't allow PyVMA <=> PyBigFileH cycles to be collected,
because fileh_close called from fileh.__del__ asserts that there are no
live mappings left. See added comments for details. There is no
known practical need to use such cycles, so this should be ok.

See also other patches on cyclic GC topic:

- 450ad804 (bigarray: ArrayRef support for BigArray)  // adds cyclic GC support for PyVMA
- d97641d2 (bigfile/py: Properly untrack PyVMA from GC before dealloc)

/proposed-for-review-on nexedi/wendelin.core!12

The logic in pyvma_traverse and pyvma_clear needs to be synchronized
with PyVMA deallocation. In the next patche we'll be amending this
logic, and it will help a reader to keep all those functions together.

For the reference: PyVMA support for cyclic GC was introduced in
450ad804 (bigarray: ArrayRef support for BigArray). See also d97641d2
(bigfile/py: Properly untrack PyVMA from GC before dealloc).

/proposed-for-review-on nexedi/wendelin.core!12

Otherwise when /bin/sh is dash it fails with

    t/tfault-run: 35: test: on_pagefault: unexpected operator

Otherwise, if previous test.fault failed, tfault-run fails to start, e.g.

    >>> test.fault
    $ make test.fault # MAKEFLAGS=-j1
    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
    mkdir: cannot create directory ‘t/tfault-run.faultr’: File exists
    Makefile:186: recipe for target 'faultr.tfault' failed
    make: *** [faultr.tfault] Error 1
    rm bigfile/tests/tfault.t
    error   test.fault      0.433s  # 1t 1e 0f 0s

Nxdtest[1] is tox-like tool to run tests under Nexedi testing
infrastructure. See [2] for details.

[1] https://lab.nexedi.com/nexedi/nxdtest
[2] nexedi/slapos!839

We need the following patch of mine:

   http://git.ozlabs.org/?p=ccan;a=commitdiff;h=b97c7f0841f5173a07a2571f2c99f944d8405a90

It is hard for people to understand current wording, so let's expand
zconn_at description to additionally explain what it is providing with
second set of words, which, hopefully, lowers potential ambiguity a bit.

/reported-by @jwolf083

Pygolang egg provides "golang" python package, not "pygolang".
Bug introduced in 5c8340d2 (*: Use defer for dbclose & friends).

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.

Wendelin.core 2 will need to spawn WCFS filesystem server that accesses
the same ZODB database as the program that spawns it. The database
argument passed to WCFS is passed in the form of URL[1,2].  Even though
zodburi provides way to convert an URL into ZODB storage instance, there
is currently no way for reverse operation - to convert ZODB storage
instance into URL to access it(*). So we have to build it by our own.

Provide zstor_2zurl stub that currently works for FileStorage only.
ZEO and NEO support is TODO.

In the future we might want to move this functionality into
zodbtools/py.

[1] https://lab.nexedi.com/nexedi/zodbtools/blob/a2e4dd23/zodbtools/help.py#L27-53
[2] https://lab.nexedi.com/kirr/neo/blob/3d909114/go/zodb/zodbtools/help.go#L25-51

(*) contrary to ZODB/go where this functionality is provided out of the box:
    https://godoc.org/lab.nexedi.com/kirr/neo/go/zodb#IStorage

Wendelin.core 2 will need to hook into when client ZODB.Connection
changes its database view and readjust WCFS-level client connection
accordingly.

ZODB.Connection can change its view on either connection reopen, or even
without reopen on start of new transaction.

This patch implements ZODB.Connection.onResyncCallback for ZODB5 only.

ZODB4 and ZODB3 support is TODO.

For wendelin.core v2 we need a way to know at which particular database
state application-level ZODB connection is viewing the database. Knowing
that state, WCFS client library will interact with WCFS filesystem server
and, in simple terms, request the server to provide data as of that
particular database state.

Contrary to ZODB/go[1] ZODB/py does not provide the functionality to
obtain DB state of connection view, so we have to build it ourselves.
Let us call the function that for a client ZODB connection returns
database state corresponding to its database view as zconn_at.

It is relatively easy to implement zconn_at for ZODB5, since ZODB5
adopted MVCC uniformly and this patch does just that. However even with
ZODB5 currently all released ZODB5 versions have race in
Connection.open() vs invalidations[2], and so the first ZODB5 release
with which zconn_at implemented here will work reliable should be
upcoming ZODB 5.5.2

It is TODO to implement zconn_at for ZODB4 and ZODB3, which organize
things differently.

Please note what would happen if zconn_at gives, even a bit, incorrect
answer: wcfs client will ask wcfs server to provide array data as of
different database state compared to current on-client ZODB connection.
This will result in that data accessed via ZBigArray will _not_
correspond to all other data accessed via regular ZODB mechanism.
It is, in other words, would be a data corruptions.

[1] https://godoc.org/lab.nexedi.com/kirr/neo/go/zodb#Connection
[2] https://github.com/zopefoundation/ZODB/issues/290

This will be needed in the following patches to know how to inject
zconn_at or zconn resync functionality into particular ZODB version.

- mention in comments that _ZBigFileH not only proxies changes from
  virtmem -> ZODB, but also the other way: virtmem <- ZODB.
- refresh comments, fix typo.

- Provide brief top-level overview + refresh loadblk/storeblk/release comments.
- Add `typedef struct bigfile_ops bigfile_ops` that we usually add for all structs.

It is valid to compare a Page and a VMA only if they belong to the same
fileh.

-> into vma_page_infilerange().

We will soon need to use this functionality from several places.

Start preparing vma early, not after the call to mem_valloc.
This codeflow will be more convenient when we add mmap-through-wcfs codepath.

We are soon going to use this functionality from several places.

The place to perform the mmap is changed slightly because vma_mmap_page
deduces prot from page->state and for that we have to finish preparing
page->state first.

Freed Page structs must be in PAGE_EMPTY state.

The code sequence of

        list_del(&page->lru);
        bzero(page, sizeof(*page)); /* just in case */
        free(page);

was open-coded several times.

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.

Provide package-level documentation that gives brief overview of what
this package does. Split internal notes into separate comment.

Starting from 5755a6b3 (Basic setup.py / Makefile to build/install/sdist
stuff + bigfile.so skeleton) and 35eb95c2 (bigfile: Python wrapper
around virtual memory subsystem) we were using Plan9 C extensions[1] for
simple inheritance. Those extensions are supported by GCC with
-fplan9-extensions option. However that option is supported only for C,
while for C++ it does not work at all with error produced by the compiler
on Plan9 syntax.

Soon we'll need to add another extension - written in C++ - to
wendelin.core . This extension will be providing client side of WCFS and
integrating that with virtmem. In that extension we'll need to use
_bigfile data structures - in particular we'll need to use PyBigFile and
extend it with another `cdef class` children written in Cython/C++.

This patch prepares for that: first stop using Plan9 C extensions in
_bigfile py module data structures and adapt the code correspondingly.
In the next patch we'll move those data structures into an .h file.

We don't drop -fplan9-extensions from setup.py, because Plan9-style
inheritance continues to be used internally by virtmem - e.g. in
ram_shmfs.c and friends.

A bit pity to drop that good stuff, but given that we'll need to use C++
for WCFS client for other good stuff provided by pygolang[2], it is a
reasonable compromise.

[1] http://9p.io/sys/doc/comp.html  "Extensions" section
[2] https://pypi.org/project/pygolang

It was from long-ago marked as "XXX move to common place".

I noticed this while working on WCFS: if file blocks topology change,
the invalidation process is not working correctly. It is also not
correct with respect to live cache pressure.

Add FIXME in the code and test for live cache pressure.

5a4562fc
48eb692f
d1a579b2
69c94fbc

For ZBlk0 this is trivial, but for ZBlk1 it may seem that we could avoid
changing ZBlk object itself and mark only pointed-to ZData object as
changed. However that would be not correct to do if we consider
invalidations.

Noticed while working on WCFS.

Add package-level documentation to

  - bigfile/file_zodb.py,
  - bigarray/array_zodb.py, and
  - lib/zodb.py

The most interesting read is file_zodb.py .

Slightly improve documenation for functions in a couple of places.

Improving documentation was long overdue and it is improved only slightly by this commit.

We already keep FileStorage test database on /tmp/ and NEO itself (via
neo.tests.functional.NEOCluster) also keeps test data on tmpfs. However
test database for ZEO was created in current directory and was wearing
out SSD unnecessarily.

FIXME zeo_forker currently does not provide API to keep all server files
in particular place. This way server conf and log are still emitted in
current directory, but at least we move data.fs away. Since conf and log
are uniquely named, e.g. server-<ΧΧΧ>.conf and tmpYYY.log, and it was
only that Data.fs was named non-uniquely, by moving Data.fs into unique
per-server place, this also helps with-ZEO tests to execute correctly in
parallel with `tox -p`.

Else it won't compile with C++. This needs my patch to CCAN to work.
Patch description and problem details are here:

http://git.ozlabs.org/?p=ccan;a=commitdiff;h=39b46a02b719

We are going to add C++ parts to wendelin.core soon.
Mark all current functionality with `extern "C"` as a preparatory step.

There was an XXX of whether fileh_open should be a BigFile method or
global function. However if it would be a global function it will need
to anyway accept file parameter to indicate which file is opened, and
that in turn suggests that it should be a file method. Remove XXX.