bigfile/tests/test_filezodb.py ........W: testdb: teardown: <Connection at 7f8fe2b43b90> left not closed by test code; opened by:
  ...
  File "/home/kirr/src/wendelin/wendelin.core/bigfile/tests/test_filezodb.py", line 754, in test_bigfile_zblk1_zdata_reuse
    _test_bigfile_zblk1_zdata_reuse()
  File "/home/kirr/src/wendelin/wendelin.core/bigfile/tests/test_filezodb.py", line 759, in _test_bigfile_zblk1_zdata_reuse
    root = dbopen()
  File "/home/kirr/src/wendelin/wendelin.core/bigfile/tests/test_filezodb.py", line 47, in dbopen
    return testdb.dbopen()
  File "/home/kirr/src/wendelin/wendelin.core/lib/testing.py", line 188, in dbopen
    self.connv.append( (weakref.ref(conn), ''.join(traceback.format_stack())) )

lib/tests/test_zodb.py .W: testdb: teardown: <Connection at 7f8fe26f13d0> left not closed by test code; opened by:
  ...
  File "/home/kirr/src/wendelin/wendelin.core/lib/tests/test_zodb.py", line 49, in test_deactivate_btree
    root = dbopen()
  File "/home/kirr/src/wendelin/wendelin.core/lib/tests/test_zodb.py", line 30, in dbopen
    return testdb.dbopen()
  File "/home/kirr/src/wendelin/wendelin.core/lib/testing.py", line 188, in dbopen
    self.connv.append( (weakref.ref(conn), ''.join(traceback.format_stack())) )

If a test forgets to explicitly close ZODB connection it was using, this
connection stays alive in transaction synchronizers (it is a weakset),
and continues to be used on e.g. transaction.commit() when all
synchronizers are invoked. This could lead to crashes like below when
underlying ZODB storage was closed by test module teardown and testing
moved on to another test module:

    $ WENDELIN_CORE_TEST_DB="<neo>" py.test  bigfile/tests/test_filezodb.py::test_bigfile_zblk1_zdata_reuse lib/tests/test_zodb.py
    ======= test session starts ========
    platform linux2 -- Python 2.7.14+, pytest-3.5.0, py-1.5.3, pluggy-0.6.0
    rootdir: /home/kirr/src/wendelin/wendelin.core, inifile:
    collected 2 items

    bigfile/tests/test_filezodb.py .                                     [ 50%]
    lib/tests/test_zodb.py F                                             [100%]

    ______ test_deactivate_btree _______

        def test_deactivate_btree():
            root = dbopen()
            # init btree with many leaf nodes
            leafv = []
            root['btree'] = B = IOBTree()
            for i in range(10000):
                B[i] = xi = XInt(i)
                leafv.append(xi)
    >       transaction.commit()

    lib/tests/test_zodb.py:56:
    _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
    ../venv/z5/local/lib/python2.7/site-packages/transaction/_manager.py:131: in commit
        return self.get().commit()
    ../venv/z5/local/lib/python2.7/site-packages/transaction/_transaction.py:316: in commit
        self._synchronizers.map(lambda s: s.afterCompletion(self))
    ../venv/z5/local/lib/python2.7/site-packages/transaction/weakset.py:62: in map
        f(elt)
    ../venv/z5/local/lib/python2.7/site-packages/transaction/_transaction.py:316: in <lambda>
        self._synchronizers.map(lambda s: s.afterCompletion(self))
    ../venv/z5/local/lib/python2.7/site-packages/ZODB/Connection.py:757: in afterCompletion
        self.newTransaction(transaction, False)
    ../venv/z5/local/lib/python2.7/site-packages/ZODB/Connection.py:737: in newTransaction
        invalidated = self._storage.poll_invalidations()
    ../venv/z5/local/lib/python2.7/site-packages/ZODB/mvccadapter.py:131: in poll_invalidations
        self._start = p64(u64(self._storage.lastTransaction()) + 1)
    _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

    self = <neo.client.Storage.Storage object at 0x7ffa1be8d410>

        def lastTransaction(self):
            # Used in ZODB unit tests
    >       return self.app.last_tid
    E       AttributeError: 'NoneType' object has no attribute 'last_tid'

    ../../neo/src/lab.nexedi.com/kirr/neo/neo/client/Storage.py:181: AttributeError

where NEO's Storage.app is None because the storage was closed.

----

To avoid such kind of failures make sure TestDB.teardown() always closes
all ZODB connections that were ever opened via TestDB.dbopen().

Add a warning about such force-closing with information about corresponding
connection and code place that created it, so that it is easy to
understand which test needs a fix.

/suggested-by @jm

- 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.

Since 7fc4ec66 (tests: Allow to test with ZEO & NEO ZODB storages) we
can run the tests with either FileStorage, ZEO or NEO. But ZEO test
adapter started to fail with ZEO5:

	self = <wendelin.lib.testing.TestDB_ZEO object at 0x7f1feb5091d0>

	    def setup(self):
	        port  = self.zeo_forker.get_port()
	        zconf = self.zeo_forker.ZEOConfig(('', port))
	        self.addr, self.adminaddr, self.pid, self.path = \
	>               self.zeo_forker.start_zeo_server(zeo_conf=zconf, port=port)
	E       ValueError: need more than 2 values to unpack

This is because in ZEO5 forker.start_zeo_server() was reworked to return only
addr and stop closure instead of returning all details and relying on caller to
implement stop itself.

Adapt the test to detect ZEO5 and use new calling convention.

With ZConfig==3.2.0 (released 2017-06-22) ZEO started to get file names
as unicode, which eventually breaks on assert in ZODB3.FileStorage code:

    Traceback (most recent call last):
      File "/home/kirr/src/wendelin/r/work/venv/local/lib/python2.7/site-packages/ZEO/tests/zeoserver.py", line 215, in <module>
        main()
      File "/home/kirr/src/wendelin/r/work/venv/local/lib/python2.7/site-packages/ZEO/tests/zeoserver.py", line 188, in main
        server = ZEO.runzeo.create_server({"1": storage}, zo)
      File "/home/kirr/src/wendelin/r/work/venv/local/lib/python2.7/site-packages/ZEO/runzeo.py", line 366, in create_server
        auth_realm = options.auth_realm,
      File "/home/kirr/src/wendelin/r/work/venv/local/lib/python2.7/site-packages/ZEO/StorageServer.py", line 890, in __init__
        self._setup_invq(name, storage)
      File "/home/kirr/src/wendelin/r/work/venv/local/lib/python2.7/site-packages/ZEO/StorageServer.py", line 928, in _setup_invq
        self.invq[name] = list(lastInvalidations(self.invq_bound))
      File "/home/kirr/src/wendelin/r/work/venv/local/lib/python2.7/site-packages/ZODB/FileStorage/FileStorage.py", line 1238, in lastInvalidations
        for trans in FileIterator(self._file_name, pos=pos)]
      File "/home/kirr/src/wendelin/r/work/venv/local/lib/python2.7/site-packages/ZODB/FileStorage/FileStorage.py", line 1640, in __init__
        assert isinstance(filename, str), `filename`
    AssertionError: u'/home/kirr/src/wendelin/r/work/wendelin.core/Data.fs'

-> So for ZODB3 pin ZConfig to ZConfig <3.2.0 which is known to work with ZODB3.

ArrayRef is a reference to NumPy array.

The reference is represented by root array object and instructions how to
create original array as some view of the root.

Such reference could be useful in situations where one needs to pass arrays
between processes and instead of copying array data, leverage the fact that
top-level array, for example ZBigArray, is already persisted separately, and
only send small amount of information referencing data in question.

Use `ArrayRef(array)` to create reference to an ndarray.

Use `.deref()` to convert ArrayRef to pointed array object.

NOTE

don't send ArrayRef unconditionally - for example when array object is
small regular ndarray with also regular, but big, root ndarray, sending
ArrayRef will send whole data for root object, not for small leaf.

Sending ArrayRef only makes sense when root object is known to be already
persisted by other means, for example something like below in ZODB context:

```python
  aref = ArrayRef(a)
  if isinstance(aref.root, Persistent):
      send aref
  else:
      send a 
```

Please see individual patches for more details.

/reviewed-on nexedi/wendelin.core!6