buildout: Fix CI

/reviewed-on https://github.com/zopefoundation/ZODB/pull/346
/reviewed-by @d-maurer

Commit 75c703fc (Security fix documentation dependencies (#342)) changed
requirements for pygments from

    # pygments 2.6 stops the support for python2
    pygments<2.6

to

    # Silence dependabot claiming a security issue in older versions:
    pygments >= 2.7.4

However this broke CI for python2, as sphinx now fails to install:

    Collecting Sphinx
      Using cached Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB)
    ERROR: Could not find a version that satisfies the requirement pygments>=2.7.4 (from -r doc/requirements.txt (line 3)) (from versions: 0.5, 0.5.1, 0.6, 0.7, 0.7.1, 0.8, 0.8.1, 0.9, 0.10, 0.11, 0.11.1, 1.0, 1.1, 1.1.1, 1.2, 1.2.1, 1.2.2, 1.3, 1.3.1, 1.4, 1.5, 1.6rc1, 1.6, 2.0rc1, 2.0, 2.0.1, 2.0.2, 2.1, 2.1.1, 2.1.2, 2.1.3, 2.2.0, 2.3.0, 2.3.1, 2.4.0, 2.4.1, 2.4.2, 2.5.1, 2.5.2)
    ERROR: No matching distribution found for pygments>=2.7.4 (from -r doc/requirements.txt (line 3))
    The command "if [[ $TRAVIS_PYTHON_VERSION != pypy3* ]]; then pip install --upgrade --requirement doc/requirements.txt; fi" exited with 1.

(see e.g. https://travis-ci.com/github/zopefoundation/ZODB/jobs/499836548)

Try to fix that by bringing back requirement for `pygments < 2.6` on
python2.

It is not only py2 as build on py3 is also affected, e.g.

https://travis-ci.com/github/zopefoundation/ZODB/jobs/499826281

And even though Sphinx is going to be ready for newer docutils,
sphinx_rtd_theme requires docutils<0.17 for now:

https://github.com/readthedocs/sphinx_rtd_theme/blob/2026bb61ddf85a672141127b162d6f9181603725/setup.py#L119-L122

Else it is failing as:

    Got j1m.sphinxautozconfig 0.1.0.
    Getting distribution for 'sphinx_rtd_theme'.
    Got sphinx-rtd-theme 0.5.2.
    Version and requirements information containing docutils:
      Base installation request: 'Sphinx', 'docutils', 'ZODB', 'sphinxcontrib_zopeext', 'j1m.sphinxautozconfig', 'sphinx_rtd_theme'
      Requirement of sphinx_rtd_theme: docutils<0.17
      Requirement of j1m.sphinxautozconfig: docutils
      Requirement of Sphinx: docutils<0.17,>=0.12
    While:
      Installing sphinx.
    Error: There is a version conflict.
    We already have: docutils 0.17.1
    but sphinx-rtd-theme 0.5.2 requires 'docutils<0.17'.

(see e.g. https://travis-ci.com/github/zopefoundation/ZODB/jobs/499760337)

Suggested by @d-maurer.

Fix tiny issue with a remaining colon that was probably not deleted during updates of the README.

According to dependabot Pygment versions < 2.7.4 are vulnerable.
Updating to this version even though it should not be a problem with our static documentation.

Commit fc4c86e6 (Fix unbound local error when using the fsoids.py script
(#295)) wanted to refer to "issue 285", but put it as "issue 268" into
visible text.

* fsrefs: Optimize IO  (take 2)

Access objects in the order of their position in file instead of in the order
of their OID. This should give dramatical speedup when data are on HDD.

For example @perrinjerome reports that on a 73Go database it takes
almost 8h to run fsrefs (where on the same database, fstest takes 15
minutes) [1,2]. After the patch fsrefs took ~80 minutes to run on the same
database. In other words this is ~ 6x improvement.

Fsrefs has no tests. I tested it only lightly via generating a bit
corrupt database with deleted referred object(*), and it gives the same
output as unmodified fsrefs.

    oid 0x0 __main__.Object
    last updated: 1979-01-03 21:00:42.900001, tid=0x285cbacb70a3db3
    refers to invalid objects:
            oid 0x07 missing: '<unknown>'
            oid 0x07 object creation was undone: '<unknown>'

This "take 2" version is derived from https://github.com/zopefoundation/ZODB/pull/338
and only iterates objects in the order of their in-file position without
building complete references graph in-RAM, because that in-RAM graph would
consume ~12GB of memory.

Added pos2oid in-RAM index also consumes memory: for the 73GB database in
question fs._index takes ~700MB, while pos2oid takes ~2GB. In theory it could be less,
because we need only array of oid sorted by key(oid)=fs._index[oid]. However
array.array does not support sorting, and if we use plain list to keep just
[]oid, the memory consumption just for that list is ~5GB. Also because
list.sort(key=...) internally allocates memory for key array (and
list.sort(cmp=...) was removed from Python3), total memory consumption just to
produce list of []oid ordered by pos is ~10GB.
So without delving into C/Cython and/or manually sorting the array in Python (=
slow), using QQBTree seems to be the best out-of-the-box option for oid-by-pos index.

[1] zodbtools!19 (comment 129480)
[2] zodbtools!19 (comment 129551)

(*) test database generated via a bit modified gen_testdata.py from
zodbtools:

https://lab.nexedi.com/nexedi/zodbtools/blob/v0.0.0.dev8-28-g129afa6/zodbtools/test/gen_testdata.py

+

```diff
--- a/zodbtools/test/gen_testdata.py
+++ b/zodbtools/test/gen_testdata.py
@@ -229,7 +229,7 @@ def ext(subj): return {}
         # delete an object
         name = random.choice(list(root.keys()))
         obj = root[name]
-        root[name] = Object("%s%i*" % (name, i))
+#       root[name] = Object("%s%i*" % (name, i))
         # NOTE user/ext are kept empty on purpose - to also test this case
         commit(u"", u"predelete %s" % unpack64(obj._p_oid), {})
```

/cc @tim-one, @jeremyhylton, @jamadden
/reviewed-by @jamadden, @perrinjerome 
/reviewed-on https://github.com/zopefoundation/ZODB/pull/340

to trigger the new web hook.

Update badge URL for Travis

Committed via https://github.com/asottile/all-repos

Co-authored-by: ale-rt <alessandro.pisa@gmail.com>

To manually mark an object modified, `_p_changed` attribute must be set, no `_p_changed__`

setutools 50.0.0 does not seem compatible with the pypy3 used on travis.

Currently invalidate documentation is not clear whether it should be
called for every transaction and whether it should include full set of
objects created/modified by that transaction. Until now this was working
relatively well for the sole purpose of invalidating client ZEO cache,
because for that particular task it is relatively OK not to include just
created objects into invalidation messages, and even to completely skip
sending invalidation if transaction only create - not modify - objects.
Due to this fact the workings of the client cache was indifferent to the
ambiguity of the interface.

In 2016 skipping transactions with only created objects was reconsidered
as bug and fixed in ZEO5 because ZODB5 relies more heavily on MVCC
semantic and needs to be notified about every transaction committed to
storage to be able to properly update ZODB.Connection view:

https://github.com/zopefoundation/ZEO/commit/02943acd#diff-52fb76aaf08a1643cdb8fdaf69e37802L889-R834
https://github.com/zopefoundation/ZEO/commit/9613f09b

However just-created objects were not included into invalidation
messages until, hopefully, recently:

https://github.com/zopefoundation/ZEO/pull/160

As ZODB is started to be used more widely in areas where it was not
traditionally used before, the ambiguity in invalidate interface and the
lack of guarantees - for any storage - to be notified with full set of
information, creates at least the following problems:

- a ZODB client (not necessarily native ZODB/py client) can maintain
  raw cache for the storage. If such client tries to load an oid at
  database view when that object did not existed yet, gets "no object"
  reply and stores that information into raw cache, to properly invalidate
  the cache it needs an invalidation message from ZODB server that
  *includes* created object.

- tools like `zodb watch` [1,2,3] don't work properly (give incorrect output)
  if not all objects modified/created by a transaction are included into
  invalidation messages.

- similarly to `zodb watch`, a monitoring tool, that would want to be
  notified of all created/modified objects, won't see full
  database-change picture, and so won't work properly without knowing
  which objects were created.

- wendelin.core 2 - which builds data from ZODB BTrees and data objects
  into virtual filesystem - needs to get invalidation messages with both
  modified and created objects to properly implement its own lazy
  invalidation and isolation protocol for file blocks in OS cache: when
  a block of file is accessed, all clients, that have this block mmaped,
  need to be notified and asked to remmap that block into particular
  revision of the file depending on a client's view of the filesystem and
  database [4,5].

  To compute to where a client needs to remmap the block, WCFS server
  (that in turn acts as ZODB client wrt ZEO/NEO server), needs to be able
  to see whether client's view of the filesystem is before object creation
  (and then ask that client to pin that block to hole), or after creation
  (and then ask the client to pin that block to corresponding revision).

  This computation needs ZODB server to send invalidation messages in
  full: with both modified and just created objects.

Also:

- the property that all objects - both modified and just created -
  are included into invalidation messages is required and can help to
  remove `next_serial` from `loadBefore` return in the future.
  This, in turn, can help to do 2x less SQL queries in loadBefore for
  NEO and RelStorage (and maybe other storages too):
  https://github.com/zopefoundation/ZODB/issues/318#issuecomment-657685745

Current state of storages with respect to new requirements:

- ZEO: does not skip transactions, but includes only modified - not
  created - objects. This is fixed by https://github.com/zopefoundation/ZEO/pull/160

- NEO: already implements the requirements in full

- RelStorage: already implements the requirements in full, if I
  understand correctly:

  https://github.com/zodb/relstorage/blob/3.1.2-1-gaf57d6c/src/relstorage/adapters/poller.py#L28-L145

While editing invalidate documentation, use the occasion to document
recently added property that invalidate(tid) is always called before
storage starts to report its lastTransaction() ≥ tid - see 4a6b0283
(mvccadapter: check if the last TID changed without invalidation).

/cc @jimfulton, @jamadden, @jmuchemb, @vpelletier, @arnaud-fontaine, @gidzit, @klawlf82, @jwolf083
/reviewed-on https://github.com/zopefoundation/ZODB/pull/319
/reviewed-by @dataflake
/reviewed-by @jmuchemb

[1] https://lab.nexedi.com/kirr/neo/blob/049cb9a0/go/zodb/zodbtools/watch.go
[2] kirr/neo@e0d59f5d
[3] kirr/neo@c41c2907

[4] https://lab.nexedi.com/kirr/wendelin.core/blob/1efb5876/wcfs/wcfs.go#L94-182
[5] https://lab.nexedi.com/kirr/wendelin.core/blob/1efb5876/wcfs/client/wcfs.h#L20-71

Fix requirements for sphinx on python2

For consistency, defined all versions constraints in version section.
Also don't mention python34 since ZODB no longer supports python3.4

Starting from 1.2.0 sphinxcontrib-websupport officially only supports python3.
Since 1.2.4 it depends on sphinxcontrib-serializinghtml which can not even be
imported on python2

It is pointless for lastTransaction() to block until it is allowed to
return the TID of a transaction that has just been committed, because
it may still not be the real last TID (e.g. for some storage
implementations, invalidations are received from a shared server
via the network). While invalidations are still being processed,
it's fine to return immediately with the previous last TID.

This was clarified in commit 4a6b0283
("mvccadapter: check if the last TID changed without invalidation").

See pull request #316

In the early days, before MVCC was introduced, ZODB used to raise
ReadConflictError on access to object that was simultaneously changed by
another client in concurrent transaction. However, as
doc/articles/ZODB-overview.rst says

	Since Zope 2.8 ZODB has implemented **Multi Version Concurrency Control**.
	This means no more ReadConflictErrors, each transaction is guaranteed to be
	able to load any object as it was when the transaction begun.

So today the only way to get a ReadConflictError should be

  1) at commit time for an object that was requested to stay unchanged
     via checkCurrentSerialInTransaction, and

  2) at plain access time, if a pack running simultaneously to current
     transaction, removes object revision that we try to load.

The second point is a bit unfortunate, since when load discovers that
object was deleted or not yet created, it is logically more clean to
raise POSKeyError. However due to backward compatibility we still want
to raise ReadConflictError in this case - please see comments added to
MVCCAdapter for details.

Anyway, let's remove leftovers of handling regular read-conflicts from
pre-MVCC era:

Adjust docstring of ReadConflictError to explicitly describe that this
error can only happen at commit time for objects requested to be
current, or at plain access if pack is running simultaneously under
connection foot.

There were also leftover code, comment and test bits in Connection,
interfaces, testmvcc and testZODB, that are corrected/removed
correspondingly. testZODB actually had ReadConflictTests that was
completely deactivated: commit b0f992fd ("Removed the mvcc option..."; 2007)
moved read-conflict-on-access related tests out of ZODBTests, but did not
activated moved parts at all, because as that commit says when MVCC is
always on unconditionally, there is no on-access conflicts:

    Removed the mvcc option.  Everybody wants mvcc and removing us lets us
    simplify the code a little. (We'll be able to simplify more when we
    stop supporting versions.)

Today, if I try to manually activate that ReadConflictTests via

    @@ -637,6 +637,7 @@ def __init__(self, poisonedjar):
     def test_suite():
         return unittest.TestSuite((
             unittest.makeSuite(ZODBTests, 'check'),
    +        unittest.makeSuite(ReadConflictTests, 'check'),
             ))

     if __name__ == "__main__":

it fails in dumb way showing that this tests were unmaintained for ages:

    Error in test checkReadConflict (ZODB.tests.testZODB.ReadConflictTests)
    Traceback (most recent call last):
      File "/usr/lib/python2.7/unittest/case.py", line 320, in run
        self.setUp()
      File "/home/kirr/src/wendelin/z/ZODB/src/ZODB/tests/testZODB.py", line 451, in setUp
        ZODB.tests.utils.TestCase.setUp(self)
    AttributeError: 'module' object has no attribute 'utils'

Since today ZODB always uses MVCC and there is no way to get
ReadConflictError on concurrent plain read/write access, those tests
should be also gone together with old pre-MVCC way of handling
concurrency.

/cc @jimfulton
/reviewed-on https://github.com/zopefoundation/ZODB/pull/320
/reviewed-by @jamadden

Add a change note for #280

ConnectionPool and ConnectionPool.map both had docstrings and were used by third-party code. People should be warned about this potentially breaking change.

Since commit b5895a5c ("mvccadapter:
fix race with invalidations when starting a new transaction"),
a ZEO test fails as follows:

    File "src/ZEO/tests/drop_cache_rather_than_verify.txt", line 114, in drop_cache_rather_than_verify.txt
    Failed example:
        conn.root()[1].x
    Expected:
        6
    Got:
        1

Earlier in the test, the ZEO server is restarted and then another
client commits. When disconnected, the first client does not receive
invalidations anymore and the connection gets stuck in the past until
there's a new commit after it reconnected. It was possible to make the
test pass with the following patch:

--- a/src/ZEO/ClientStorage.py
+++ b/src/ZEO/ClientStorage.py
@@ -357,6 +357,7 @@ def notify_connected(self, conn, info):

         # invalidate our db cache
         if self._db is not None:
+            self._db.invalidate(self.lastTransaction(), ())
             self._db.invalidateCache()

         logger.info("%s %s to storage: %s",

Other implementations like NEO are probably affected the same way.

Rather than changing interfaces in a backward-incompatible way,
this commit revert to the original behaviour, and all the changes
that were done in existing tests are reverted.

However, the interfaces are clarified about the fact that storage
implementations must update at a precise moment the value that is
returned by lastTransaction(): just after invalidate() or
tpc_finish callback.

Fix inconsistent resolution order with zope.interface v5.

The j1m.sphinxautointerface dependency can be dropped, the functionality is now in https://pypi.org/project/sphinxcontrib-zopeext

Leave the direct definition of IBlobStorage in place, only expand the definition if necessary inside the __init__.

ZODB tries to avoid saving empty transactions to storage on
`transaction.commit()`. The way it works is: if no objects were changed
during ongoing transaction, ZODB.Connection does not join current
TransactionManager, and transaction.commit() performs two-phase commit
protocol only on joined DataManagers. In other words if no objects were
changed, no tpc_*() methods are called at all on ZODB.Connection at
transaction.commit() time.

This way application servers like Zope/ZServer/ERP5/... can have
something as

    try:
        # process incoming request
        transaction.commit()    # processed ok
    except:
        transaction.abort()
        # problem: log + reraise

in top-level code to process requests without creating many on-disk
transactions with empty data changes just because read-only requests
were served.

Everything is working as intended.

However at storage level, FileStorage currently also checks whether
transaction that is being committed also comes with empty data changes,
and _skips_ saving transaction into disk *at all* for such cases, even
if it has been explicitly told to commit the transaction via two-phase
commit protocol calls done at storage level.

This creates the situation, where contrary to promise in
ZODB/interfaces.py(*), after successful tpc_begin/tpc_vote/tpc_finish()
calls made at storage level, transaction is _not_ made permanent,
despite tid of "committed" transaction being returned to caller. In other
words FileStorage, when asked to commit a transaction, even if one with
empty data changes, reports "ok" and gives transaction ID to the caller,
without creating corresponding transaction record on disk.

This behaviour is

a) redundant to application-level avoidance to create empty transaction
   on storage described in the beginning, and

b) creates problems:

The first problem is that application that works at storage-level might
be interested in persisting transaction, even with empty changes to
data, just because it wants to save the metadata similarly to e.g.
`git commit --allow-empty`.

The other problem is that an application view and data in database
become inconsistent: an application is told that a transaction was
created with corresponding transaction ID, but if the storage is
actually inspected, e.g. by iteration, the transaction is not there.
This, in particular, can create problems if TID of committed transaction
is reported elsewhere and that second database client does not find the
transaction it was told should exist.

I hit this particular problem with wendelin.core. In wendelin.core,
there is custom virtual memory layer that keeps memory in sync with
data in ZODB. At commit time, the memory is inspected for being dirtied,
and if a page was changed, virtual memory layer joins current
transaction _and_ forces corresponding ZODB.Connection - via which it
will be saving data into ZODB objects - to join the transaction too,
because it would be too late to join ZODB.Connection after 2PC process
has begun(+). One of the format in which data are saved tries to
optimize disk space usage, and it actually might happen, that even if
data in RAM were dirtied, the data itself stayed the same and so nothing
should be saved into ZODB. However ZODB.Connection is already joined
into transaction and it is hard not to join it because joining a
DataManager when the 2PC is already ongoing does not work.

This used to work ok with wendelin.core 1, but with wendelin.core 2 -
where separate virtual filesystem is also connected to the database to
provide base layer for arrays mappings - this creates problem, because
when wcfs (the filesystem) is told to synchronize to view the database
@tid of committed transaction, it can wait forever waiting for that, or
later, transaction to appear on disk in the database, creating
application-level deadlock.

I agree that some more effort might be made at wendelin.core side to
avoid committing transactions with empty data at storage level.

However the most clean way to fix this problem in my view is to fix
FileStorage itself, because if at storage level it was asked to commit
something, it should not silently skip doing so and dropping even non-empty
metadata + returning ok and committed transaction ID to the caller.

As described in the beginning this should not create problems for
application-level ZODB users, while at storage-level the implementation
is now consistently matching interface and common sense.

----

(*) tpc_finish: Finish the transaction, making any transaction changes permanent.
    Changes must be made permanent at this point.
    ...

    https://github.com/zopefoundation/ZODB/blob/5.5.1-35-gb5895a5c2/src/ZODB/interfaces.py#L828-L831

(+) https://lab.nexedi.com/kirr/wendelin.core/blob/9ff5ed32/bigfile/file_zodb.py#L788-822

Update package links from pypi.python.org to pypi.org

Added newtdb link

Removed log.ini

Use python3 for coverage