tox: v↑ everything

- 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.

setup.py

@@ -273,8 +273,8 @@ setup(
         Programming Language :: Python :: 2
         Programming Language :: Python :: 2.7
         Programming Language :: Python :: 3
-        Programming Language :: Python :: 3.4
         Programming Language :: Python :: 3.5
+        Programming Language :: Python :: 3.6
         Programming Language :: Python :: Implementation :: CPython
         Topic :: Software Development :: Libraries :: Python Modules
         Framework :: ZODB\

tox.ini

 # wendelin.core | tox setup
 [tox]
-envlist = py27-ZODB3-{zblk0,zblk1}-{fs,zeo,neo}-{numpy110,numpy111}, {py27,py34,py35}-ZODB4-{zblk0,zblk1}-{fs,zeo}-{numpy110,numpy111}
+envlist = py27-{ZODB3,ZODB4,ZODB5}-{zblk0,zblk1}-{fs,zeo,neo}-{numpy113,numpy114}, {py35,py36}-{ZODB4,ZODB5}-{zblk0,zblk1}-{fs,zeo}-{numpy113,numpy114}
 # (NOTE ZODB3 does not work on python3)
-# (NOTE NEO does not work on ZODB4)
+# (NOTE NEO does not work on python3 at all)
+# (XXX ZODB5-*-neo are currently failing)
 
 [testenv]
 deps    =
@@ -20,7 +21,11 @@ deps    =
     ZODB4:  ZODB >=4.0, <5.0dev
     ZODB4:  ZEO  >=4.0, <5.0dev
 
-    neo:    neoppod >= 1.6.2
+    # latest current ZODB 5
+    ZODB5:  ZODB >=5.0,	<6.0dev
+    ZODB5:  ZEO	 >=5.0, <6.0dev
+
+    neo:    neoppod >= 1.9
     # neo.tests also imports MySQLdb unconditionally
     neo:    mysqlclient
 
@@ -28,8 +33,8 @@ deps    =
     # zeo: ZEO is already required by ZODB, but for testing utilities from ZEO we also need:
     zeo:    zope.testing
 
-    numpy110: numpy >=1.10.4, <1.11.0
-    numpy19: numpy >=1.11.0, <1.12.0
+    numpy114: numpy >=1.14.0, <1.15.0
+    numpy113: numpy >=1.13.0, <1.14.0
 
 setenv =
     fs:  WENDELIN_CORE_TEST_DB=<fs>

[Kirill Smelkov]

@jm, FYI, I've tried to run Wendelin.core tests with all ZODB versions, and while it works with ZODB{3,4}-ZEO, ZODB{3,4}-NEO and ZODB5-ZEO5, for ZODB5-NEO it stably breaks:

$ (venv) kirr@deco:~/src/wendelin/r/try/wendelin.core-0.12$ tox
...
  py27-ZODB3-zblk0-fs-numpy113: commands succeeded
  py27-ZODB3-zblk0-fs-numpy114: commands succeeded
  py27-ZODB3-zblk0-zeo-numpy113: commands succeeded
  py27-ZODB3-zblk0-zeo-numpy114: commands succeeded
  py27-ZODB3-zblk0-neo-numpy113: commands succeeded
  py27-ZODB3-zblk0-neo-numpy114: commands succeeded
  py27-ZODB3-zblk1-fs-numpy113: commands succeeded
  py27-ZODB3-zblk1-fs-numpy114: commands succeeded
  py27-ZODB3-zblk1-zeo-numpy113: commands succeeded
  py27-ZODB3-zblk1-zeo-numpy114: commands succeeded
  py27-ZODB3-zblk1-neo-numpy113: commands succeeded
  py27-ZODB3-zblk1-neo-numpy114: commands succeeded
  py27-ZODB4-zblk0-fs-numpy113: commands succeeded
  py27-ZODB4-zblk0-fs-numpy114: commands succeeded
  py27-ZODB4-zblk0-zeo-numpy113: commands succeeded
  py27-ZODB4-zblk0-zeo-numpy114: commands succeeded
  py27-ZODB4-zblk0-neo-numpy113: commands succeeded
  py27-ZODB4-zblk0-neo-numpy114: commands succeeded
  py27-ZODB4-zblk1-fs-numpy113: commands succeeded
  py27-ZODB4-zblk1-fs-numpy114: commands succeeded
  py27-ZODB4-zblk1-zeo-numpy113: commands succeeded
  py27-ZODB4-zblk1-zeo-numpy114: commands succeeded
  py27-ZODB4-zblk1-neo-numpy113: commands succeeded
  py27-ZODB4-zblk1-neo-numpy114: commands succeeded
  py27-ZODB5-zblk0-fs-numpy113: commands succeeded
  py27-ZODB5-zblk0-fs-numpy114: commands succeeded
  py27-ZODB5-zblk0-zeo-numpy113: commands succeeded
  py27-ZODB5-zblk0-zeo-numpy114: commands succeeded
ERROR:   py27-ZODB5-zblk0-neo-numpy113: commands failed
ERROR:   py27-ZODB5-zblk0-neo-numpy114: commands failed
  py27-ZODB5-zblk1-fs-numpy113: commands succeeded
  py27-ZODB5-zblk1-fs-numpy114: commands succeeded
  py27-ZODB5-zblk1-zeo-numpy113: commands succeeded
  py27-ZODB5-zblk1-zeo-numpy114: commands succeeded
ERROR:   py27-ZODB5-zblk1-neo-numpy113: commands failed
ERROR:   py27-ZODB5-zblk1-neo-numpy114: commands failed
  py35-ZODB4-zblk0-fs-numpy113: commands succeeded
  py35-ZODB4-zblk0-fs-numpy114: commands succeeded
  py35-ZODB4-zblk0-zeo-numpy113: commands succeeded
  py35-ZODB4-zblk0-zeo-numpy114: commands succeeded
  py35-ZODB4-zblk1-fs-numpy113: commands succeeded
  py35-ZODB4-zblk1-fs-numpy114: commands succeeded
  py35-ZODB4-zblk1-zeo-numpy113: commands succeeded
  py35-ZODB4-zblk1-zeo-numpy114: commands succeeded
  py35-ZODB5-zblk0-fs-numpy113: commands succeeded
  py35-ZODB5-zblk0-fs-numpy114: commands succeeded
  py35-ZODB5-zblk0-zeo-numpy113: commands succeeded
  py35-ZODB5-zblk0-zeo-numpy114: commands succeeded
  py35-ZODB5-zblk1-fs-numpy113: commands succeeded
  py35-ZODB5-zblk1-fs-numpy114: commands succeeded
  py35-ZODB5-zblk1-zeo-numpy113: commands succeeded
  py35-ZODB5-zblk1-zeo-numpy114: commands succeeded
  py36-ZODB4-zblk0-fs-numpy113: commands succeeded
  py36-ZODB4-zblk0-fs-numpy114: commands succeeded
  py36-ZODB4-zblk0-zeo-numpy113: commands succeeded
  py36-ZODB4-zblk0-zeo-numpy114: commands succeeded
  py36-ZODB4-zblk1-fs-numpy113: commands succeeded
  py36-ZODB4-zblk1-fs-numpy114: commands succeeded
  py36-ZODB4-zblk1-zeo-numpy113: commands succeeded
  py36-ZODB4-zblk1-zeo-numpy114: commands succeeded
  py36-ZODB5-zblk0-fs-numpy113: commands succeeded
  py36-ZODB5-zblk0-fs-numpy114: commands succeeded
  py36-ZODB5-zblk0-zeo-numpy113: commands succeeded
  py36-ZODB5-zblk0-zeo-numpy114: commands succeeded
  py36-ZODB5-zblk1-fs-numpy113: commands succeeded
  py36-ZODB5-zblk1-fs-numpy114: commands succeeded
  py36-ZODB5-zblk1-zeo-numpy113: commands succeeded
  py36-ZODB5-zblk1-zeo-numpy114: commands succeeded

Not sure it is not my fault, but it is better you have a look too. Example of one failure:

py27-ZODB5-zblk1-neo-numpy113 create: /home/kirr/src/wendelin/r/try/wendelin.core-0.12/.tox/py27-ZODB5-zblk1-neo-numpy113
py27-ZODB5-zblk1-neo-numpy113 installdeps: pytest, ZODB >=5.0,  <6.0dev, ZEO     >=5.0, <6.0dev, neoppod >= 1.9, mysqlclient, numpy >=1.13.0, <1.14.0
py27-ZODB5-zblk1-neo-numpy113 inst: /home/kirr/src/wendelin/r/try/wendelin.core-0.12/.tox/dist/wendelin.core-0.12.zip
py27-ZODB5-zblk1-neo-numpy113 installed: attrs==17.4.0,BTrees==4.4.1,funcsigs==1.0.2,futures==3.2.0,more-itertools==4.1.0,mysqlclient==1.3.12,neoppod==1.9,numpy==1.13.3,persistent==4.2.4.2,pkg-resources==0.0.0,pluggy==0.6.0,psutil==5.4.5,py==1.5.3,pytest==3.5.0,python-dateutil==2.7.2,six==1.11.0,transaction==2.2.1,trollius==2.2,wendelin.core==0.12,zc.lockfile==1.2.1,ZConfig==3.2.0,zdaemon==4.2.0,ZEO==5.2.0,ZODB==5.4.0,ZODB3==3.11.0,zodbpickle==1.0,zope.interface==4.4.3
py27-ZODB5-zblk1-neo-numpy113 runtests: PYTHONHASHSEED='2650620925'
py27-ZODB5-zblk1-neo-numpy113 runtests: commands[0] | /home/kirr/src/wendelin/r/try/wendelin.core-0.12/.tox/py27-ZODB5-zblk1-neo-numpy113/bin/python setup.py test
running test
/home/kirr/src/wendelin/r/try/wendelin.core-0.12/.tox/py27-ZODB5-zblk1-neo-numpy113/bin/python setup.py ll_build_ext --inplace
running ll_build_ext
copying build/lib.linux-x86_64-2.7/wendelin/bigfile/_bigfile.so -> bigfile
/home/kirr/src/wendelin/r/try/wendelin.core-0.12/.tox/py27-ZODB5-zblk1-neo-numpy113/bin/python -m pytest --ignore=3rdparty --ignore=build --ignore=t
========================================================================================== 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/r/try/wendelin.core-0.12, inifile:
collected 37 items                                                                                                                                                                                      

bigarray/tests/test_arrayzodb.py FF.....                                                                                                                                                          [ 18%]
bigarray/tests/test_basic.py ..........                                                                                                                                                           [ 45%]
bigfile/tests/test_basic.py .....                                                                                                                                                                 [ 59%]
bigfile/tests/test_filefile.py .                                                                                                                                                                  [ 62%]
bigfile/tests/test_filezodb.py FF...FFF                                                                                                                                                           [ 83%]
bigfile/tests/test_thread.py ....                                                                                                                                                                 [ 94%]
lib/tests/test_calc.py .                                                                                                                                                                          [ 97%]
lib/tests/test_zodb.py F                                                                                                                                                                          [100%]

=============================================================================================== FAILURES ================================================================================================
____________________________________________________________________________________________ test_zbigarray _____________________________________________________________________________________________

    def test_zbigarray():
        root = testdb.dbopen()
        root['zarray'] = ZBigArray((16*1024*1024,), uint8)
        transaction.commit()
    
        dbclose(root)
        del root
    
    
        root = testdb.dbopen()
        A = root['zarray']
    
        assert isinstance(A, ZBigArray)
>       assert A.shape  == (16*1024*1024,)

bigarray/tests/test_arrayzodb.py:58: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/ZODB/Connection.py:791: in setstate
    p, serial = self._storage.load(oid)
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/ZODB/mvccadapter.py:143: in load
    r = self._storage.loadBefore(oid, self._start)
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/client/Storage.py:119: in loadBefore
    return self.app.load(oid, None, tid)
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/client/app.py:363: in load
    data, tid, next_tid, _ = self._loadFromStorage(oid, tid, before_tid)
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/client/app.py:395: in _loadFromStorage
    askStorage)
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/client/app.py:285: in _askStorageForRead
    cell_list = pt.getCellList(object_id, True)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <neo.lib.pt.MTPartitionTable object at 0x7f6db4bbd750>, offset = '\x00\x00\x00\x00\x00\x00\x00\x01', readable = True

    def getCellList(self, offset, readable=False):
        if readable:
>           return filter(Cell.isReadable, self.partition_list[offset])
E           TypeError: list indices must be integers, not binary

.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/lib/pt.py:143: TypeError
----------------------------------------------------------------------------------------- Captured stdout setup -----------------------------------------------------------------------------------------
Using temp directory '/tmp/neo_tests/1523886487.708884'.
Using temp directory /tmp/neo_nmGBMT
------------------------------------------------------------------------------------------- Captured log call -------------------------------------------------------------------------------------------
Connection.py              809 ERROR    Couldn't load state for wendelin.bigarray.array_zodb.ZBigArray 0x01
Traceback (most recent call last):
  File "/home/kirr/src/wendelin/r/try/wendelin.core-0.12/.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/ZODB/Connection.py", line 791, in setstate
    p, serial = self._storage.load(oid)
  File "/home/kirr/src/wendelin/r/try/wendelin.core-0.12/.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/ZODB/mvccadapter.py", line 143, in load
    r = self._storage.loadBefore(oid, self._start)
  File "/home/kirr/src/wendelin/r/try/wendelin.core-0.12/.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/client/Storage.py", line 119, in loadBefore
    return self.app.load(oid, None, tid)
  File "/home/kirr/src/wendelin/r/try/wendelin.core-0.12/.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/client/app.py", line 363, in load
    data, tid, next_tid, _ = self._loadFromStorage(oid, tid, before_tid)
  File "/home/kirr/src/wendelin/r/try/wendelin.core-0.12/.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/client/app.py", line 395, in _loadFromStorage
    askStorage)
  File "/home/kirr/src/wendelin/r/try/wendelin.core-0.12/.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/client/app.py", line 285, in _askStorageForRead
    cell_list = pt.getCellList(object_id, True)
  File "/home/kirr/src/wendelin/r/try/wendelin.core-0.12/.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/lib/pt.py", line 143, in getCellList
    return filter(Cell.isReadable, self.partition_list[offset])
TypeError: list indices must be integers, not binary
_________________________________________________________________________________________ test_zbigarray_order __________________________________________________________________________________________

    def test_zbigarray_order():
        # make sure order is properly saved/restored to/from DB
        root = testdb.dbopen()
        root['carray'] = ZBigArray((16*1024*1024,), uint8)
        root['farray'] = ZBigArray((16*1024*1024,), uint8, order='F')
        transaction.commit()
    
        dbclose(root)
        del root
    
        root = testdb.dbopen()
        C = root['carray']
        F = root['farray']
    
        assert isinstance(C, ZBigArray)
>       assert C.shape  == (16*1024*1024,)

bigarray/tests/test_arrayzodb.py:213: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/ZODB/Connection.py:791: in setstate
    p, serial = self._storage.load(oid)
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/ZODB/mvccadapter.py:143: in load
    r = self._storage.loadBefore(oid, self._start)
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/client/Storage.py:119: in loadBefore
    return self.app.load(oid, None, tid)
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/client/app.py:363: in load
    data, tid, next_tid, _ = self._loadFromStorage(oid, tid, before_tid)
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/client/app.py:395: in _loadFromStorage
    askStorage)
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/client/app.py:285: in _askStorageForRead
    cell_list = pt.getCellList(object_id, True)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <neo.lib.pt.MTPartitionTable object at 0x7f6da3a7ab10>, offset = '\x00\x00\x00\x00\x00\x00\x00e', readable = True

    def getCellList(self, offset, readable=False):
        if readable:
>           return filter(Cell.isReadable, self.partition_list[offset])
E           TypeError: list indices must be integers, not binary

.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/lib/pt.py:143: TypeError
------------------------------------------------------------------------------------------- Captured log call -------------------------------------------------------------------------------------------
Connection.py              809 ERROR    Couldn't load state for wendelin.bigarray.array_zodb.ZBigArray 0x65
Traceback (most recent call last):
  File "/home/kirr/src/wendelin/r/try/wendelin.core-0.12/.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/ZODB/Connection.py", line 791, in setstate
    p, serial = self._storage.load(oid)
  File "/home/kirr/src/wendelin/r/try/wendelin.core-0.12/.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/ZODB/mvccadapter.py", line 143, in load
    r = self._storage.loadBefore(oid, self._start)
  File "/home/kirr/src/wendelin/r/try/wendelin.core-0.12/.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/client/Storage.py", line 119, in loadBefore
    return self.app.load(oid, None, tid)
  File "/home/kirr/src/wendelin/r/try/wendelin.core-0.12/.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/client/app.py", line 363, in load
    data, tid, next_tid, _ = self._loadFromStorage(oid, tid, before_tid)
  File "/home/kirr/src/wendelin/r/try/wendelin.core-0.12/.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/client/app.py", line 395, in _loadFromStorage
    askStorage)
  File "/home/kirr/src/wendelin/r/try/wendelin.core-0.12/.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/client/app.py", line 285, in _askStorageForRead
    cell_list = pt.getCellList(object_id, True)
  File "/home/kirr/src/wendelin/r/try/wendelin.core-0.12/.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/lib/pt.py", line 143, in getCellList
    return filter(Cell.isReadable, self.partition_list[offset])
TypeError: list indices must be integers, not binary
__________________________________________________________________________________________ test_livepersistent __________________________________________________________________________________________

    def test_livepersistent():
        root = dbopen()
>       transaction.commit()    # set root._p_jar

bigfile/tests/test_filezodb.py:79: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/_manager.py:131: in commit
    return self.get().commit()
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/_transaction.py:316: in commit
    self._synchronizers.map(lambda s: s.afterCompletion(self))
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/weakset.py:62: in map
    f(elt)
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/_transaction.py:316: in <lambda>
    self._synchronizers.map(lambda s: s.afterCompletion(self))
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/ZODB/Connection.py:757: in afterCompletion
    self.newTransaction(transaction, False)
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/ZODB/Connection.py:737: in newTransaction
    invalidated = self._storage.poll_invalidations()
.tox/py27-ZODB5-zblk1-neo-numpy113/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 0x7f6da3a7a090>

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

.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/client/Storage.py:181: AttributeError
----------------------------------------------------------------------------------------- Captured stdout setup -----------------------------------------------------------------------------------------
Using temp directory /tmp/neo_smOdwv
_________________________________________________________________________________________ test_bigfile_filezodb _________________________________________________________________________________________

    def test_bigfile_filezodb():
        root = dbopen()
        root['zfile'] = f = ZBigFile(blksize)
>       transaction.commit()

bigfile/tests/test_filezodb.py:219: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/_manager.py:131: in commit
    return self.get().commit()
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/_transaction.py:316: in commit
    self._synchronizers.map(lambda s: s.afterCompletion(self))
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/weakset.py:62: in map
    f(elt)
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/_transaction.py:316: in <lambda>
    self._synchronizers.map(lambda s: s.afterCompletion(self))
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/ZODB/Connection.py:757: in afterCompletion
    self.newTransaction(transaction, False)
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/ZODB/Connection.py:737: in newTransaction
    invalidated = self._storage.poll_invalidations()
.tox/py27-ZODB5-zblk1-neo-numpy113/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 0x7f6da3a7a090>

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

.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/client/Storage.py:181: AttributeError
____________________________________________________________________________________ test_bigfile_filezodb_fileh_gc _____________________________________________________________________________________

    def test_bigfile_filezodb_fileh_gc():
        root1= dbopen()
        conn1= root1._p_jar
        db   = conn1.db()
        root1['zfile4'] = f1 = ZBigFile(blksize)
>       transaction.commit()

bigfile/tests/test_filezodb.py:685: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/_manager.py:131: in commit
    return self.get().commit()
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/_transaction.py:316: in commit
    self._synchronizers.map(lambda s: s.afterCompletion(self))
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/weakset.py:62: in map
    f(elt)
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/_transaction.py:316: in <lambda>
    self._synchronizers.map(lambda s: s.afterCompletion(self))
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/ZODB/Connection.py:757: in afterCompletion
    self.newTransaction(transaction, False)
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/ZODB/Connection.py:737: in newTransaction
    invalidated = self._storage.poll_invalidations()
.tox/py27-ZODB5-zblk1-neo-numpy113/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 0x7f6da3a7a090>

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

.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/client/Storage.py:181: AttributeError
___________________________________________________________________________________ test_bigfile_filezodb_fmt_change ____________________________________________________________________________________

    def test_bigfile_filezodb_fmt_change():
        root = dbopen()
        root['zfile5'] = f = ZBigFile(blksize)
>       transaction.commit()

bigfile/tests/test_filezodb.py:714: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/_manager.py:131: in commit
    return self.get().commit()
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/_transaction.py:316: in commit
    self._synchronizers.map(lambda s: s.afterCompletion(self))
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/weakset.py:62: in map
    f(elt)
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/_transaction.py:316: in <lambda>
    self._synchronizers.map(lambda s: s.afterCompletion(self))
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/ZODB/Connection.py:757: in afterCompletion
    self.newTransaction(transaction, False)
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/ZODB/Connection.py:737: in newTransaction
    invalidated = self._storage.poll_invalidations()
.tox/py27-ZODB5-zblk1-neo-numpy113/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 0x7f6da3a7a090>

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

.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/client/Storage.py:181: AttributeError
____________________________________________________________________________________ test_bigfile_zblk1_zdata_reuse _____________________________________________________________________________________

    def test_bigfile_zblk1_zdata_reuse():
        # set ZBlk_fmt_write to ZBlk1 for this test
        fmt_write_save = file_zodb.ZBlk_fmt_write
        file_zodb.ZBlk_fmt_write = 'ZBlk1'
        try:
>           _test_bigfile_zblk1_zdata_reuse()

bigfile/tests/test_filezodb.py:754: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
bigfile/tests/test_filezodb.py:761: in _test_bigfile_zblk1_zdata_reuse
    transaction.commit()
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/_manager.py:131: in commit
    return self.get().commit()
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/_transaction.py:316: in commit
    self._synchronizers.map(lambda s: s.afterCompletion(self))
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/weakset.py:62: in map
    f(elt)
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/_transaction.py:316: in <lambda>
    self._synchronizers.map(lambda s: s.afterCompletion(self))
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/ZODB/Connection.py:757: in afterCompletion
    self.newTransaction(transaction, False)
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/ZODB/Connection.py:737: in newTransaction
    invalidated = self._storage.poll_invalidations()
.tox/py27-ZODB5-zblk1-neo-numpy113/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 0x7f6da3a7a090>

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

.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/client/Storage.py:181: AttributeError
----------------------------------------------------------------------------------------- Captured log teardown -----------------------------------------------------------------------------------------
master.py                  100 CRITICAL connection to primary master node closed
master.py                  100 CRITICAL connection to primary master node closed
master.py                  100 CRITICAL connection to primary master node closed
master.py                  100 CRITICAL connection to primary master node closed
master.py                  100 CRITICAL connection to primary master node closed
_________________________________________________________________________________________ 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: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/_manager.py:131: in commit
    return self.get().commit()
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/_transaction.py:316: in commit
    self._synchronizers.map(lambda s: s.afterCompletion(self))
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/weakset.py:62: in map
    f(elt)
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/transaction/_transaction.py:316: in <lambda>
    self._synchronizers.map(lambda s: s.afterCompletion(self))
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/ZODB/Connection.py:757: in afterCompletion
    self.newTransaction(transaction, False)
.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/ZODB/Connection.py:737: in newTransaction
    invalidated = self._storage.poll_invalidations()
.tox/py27-ZODB5-zblk1-neo-numpy113/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 0x7f6da3a7a090>

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

.tox/py27-ZODB5-zblk1-neo-numpy113/lib/python2.7/site-packages/neo/client/Storage.py:181: AttributeError
----------------------------------------------------------------------------------------- Captured stdout setup -----------------------------------------------------------------------------------------
Using temp directory /tmp/neo_lEdoc3
----------------------------------------------------------------------------------------- Captured log teardown -----------------------------------------------------------------------------------------
master.py                  100 CRITICAL connection to primary master node closed
================================================================================= 8 failed, 29 passed in 23.31 seconds ==================================================================================
Exception AttributeError: "'NoneType' object has no attribute 'close'" in <bound method NEOCluster.__del__ of <neo.tests.functional.NEOCluster object at 0x7f6da5086090>> ignored
Exception TypeError: 'expected string or buffer' in <bound method NEOCluster.__del__ of <neo.tests.functional.NEOCluster object at 0x7f6da39caf50>> ignored
Exception TypeError: 'expected string or buffer' in <bound method NEOCluster.__del__ of <neo.tests.functional.NEOCluster object at 0x7f6da4e9d2d0>> ignored
Makefile:174: ошибка выполнения рецепта для цели «test.py»
make: *** [test.py] Ошибка 1
error: Failed to execute `make test`
ERROR: InvocationError: '/home/kirr/src/wendelin/r/try/wendelin.core-0.12/.tox/py27-ZODB5-zblk1-neo-numpy113/bin/python setup.py test'

/cc @Tyagov, @klaus

[Julien Muchembled]

Can you test the 'zodb5' branch of NEO ?

[Kirill Smelkov]

@jm thanks for feedback. With zodb5 branch it looks better, but there is still 1 failure:

(z5) kirr@deco:~/src/wendelin/wendelin.core$ pip list
Package         Version            Location                                      
--------------- ------------------ ----------------------------------------------
attrs           17.4.0             
bcc             0.3.0.post11686367 
BTrees          4.4.1              
funcsigs        1.0.2              
futures         3.2.0              
more-itertools  4.1.0              
mysqlclient     1.3.12             
neoppod         1.9                /home/kirr/src/neo/src/lab.nexedi.com/kirr/neo
numpy           1.14.2             
persistent      4.2.4.2            
pip             10.0.0             
pkg-resources   0.0.0              
pluggy          0.6.0              
psutil          5.4.5              
py              1.5.3              
pytest          3.5.0              
python-dateutil 2.7.2              
setuptools      39.0.1             
six             1.11.0             
transaction     2.2.1              
trollius        2.2                
wendelin.core   0.12               /home/kirr/src/wendelin/wendelin.core         
wheel           0.31.0             
zc.lockfile     1.2.1              
ZConfig         3.2.0              
zdaemon         4.2.0              
ZEO             5.2.0              
ZODB            5.4.0              
ZODB3           3.11.0             
zodbpickle      1.0                
zope.interface  4.4.3              
zope.testing    4.6.2              

(z5) kirr@deco:~/src/wendelin/wendelin.core$ WENDELIN_CORE_TEST_DB="<neo>" make test.py
python setup.py ll_build_ext --inplace
running ll_build_ext
copying build/lib.linux-x86_64-2.7/wendelin/bigfile/_bigfile.so -> bigfile
python -m pytest --ignore=3rdparty --ignore=build --ignore=t
================================================== 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 37 items                                                                                                      

bigarray/tests/test_arrayzodb.py .......                                                                          [ 18%]
bigarray/tests/test_basic.py ..........                                                                           [ 45%]
bigfile/tests/test_basic.py .....                                                                                 [ 59%]
bigfile/tests/test_filefile.py .                                                                                  [ 62%]
bigfile/tests/test_filezodb.py ........                                                                           [ 83%]
bigfile/tests/test_thread.py ....                                                                                 [ 94%]
lib/tests/test_calc.py .                                                                                          [ 97%]
lib/tests/test_zodb.py F                                                                                          [100%]

======================================================= FAILURES ========================================================
_________________________________________________ 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 0x7fc221bdd290>

    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
------------------------------------------------- Captured stdout setup -------------------------------------------------
Using temp directory /tmp/neo_wp4xUo
------------------------------------------------- Captured log teardown -------------------------------------------------
master.py                  100 CRITICAL connection to primary master node closed
========================================= 1 failed, 36 passed in 46.65 seconds ==========================================
Exception TypeError: 'expected string or buffer' in <bound method NEOCluster.__del__ of <neo.tests.functional.NEOCluster object at 0x7fc222b9b350>> ignored
Exception TypeError: 'expected string or buffer' in <bound method NEOCluster.__del__ of <neo.tests.functional.NEOCluster object at 0x7fc221bdd410>> ignored
Exception TypeError: 'expected string or buffer' in <bound method NEOCluster.__del__ of <neo.tests.functional.NEOCluster object at 0x7fc221be7490>> ignored
Makefile:173: ошибка выполнения рецепта для цели «test.py»
make: *** [test.py] Ошибка 1

[Julien Muchembled]

self.app should not be None: it seems that Storage.close was called unexpectedly. Can you add a breakpoint and get the traceback to see why it's called ?

[Kirill Smelkov]

@jm, I of course could do it, but maybe it makes more sense just to reproduce the issue on your side? The command to run tests is:

$ WENDELIN_CORE_TEST_DB="<neo>" make test.py

and initial environment is easy to prepare with virtualenvand pip in 3 - 5 minutes.

Does the breakage reproduce on your side?

[Julien Muchembled]

Ouch no. Too heavy for me. Fortunately, it was easy to reduce testing.py and test_zodb to something of ~70 lines. I tested by running the beginning of test_deactivate_btree 2 times, with your whole setup/teardown code around each call. If I also add print self, self.app at the beginning of Storage.lastTransaction, we see:

Using temp directory '/tmp/neo_tests/1523904777.938541'.
Using temp directory /tmp/neo_x5jcmP
<neo.client.Storage.Storage object at 0x7f76134d8b90>
<neo.client.Storage.Storage object at 0x7f76134d8b90> <neo.client.app.Application object at 0x7f760cfe09d0>
<neo.client.Storage.Storage object at 0x7f76134d8b90> <neo.client.app.Application object at 0x7f760cfe09d0>
<neo.client.Storage.Storage object at 0x7f76134d8b90> <neo.client.app.Application object at 0x7f760cfe09d0>
<neo.client.Storage.Storage object at 0x7f76134d8b90> <neo.client.app.Application object at 0x7f760cfe09d0>
<neo.client.Storage.Storage object at 0x7f76134d8b90> <neo.client.app.Application object at 0x7f760cfe09d0>
Using temp directory /tmp/neo_jUi06h
<neo.client.Storage.Storage object at 0x7f760cfc82d0>
<neo.client.Storage.Storage object at 0x7f760cfc82d0> <neo.client.app.Application object at 0x7f760cfb9410>
<neo.client.Storage.Storage object at 0x7f760cfc82d0> <neo.client.app.Application object at 0x7f760cfb9410>
<neo.client.Storage.Storage object at 0x7f760cfc82d0> <neo.client.app.Application object at 0x7f760cfb9410>
<neo.client.Storage.Storage object at 0x7f760cfc82d0> <neo.client.app.Application object at 0x7f760cfb9410>
<neo.client.Storage.Storage object at 0x7f76134d8b90> None
Traceback (most recent call last):
...

Which means that it keeps using a Storage object of a previous test. Note also that before Review Connection/DB closure , we get the following traceback:

Traceback (most recent call last):
  File "../zodb5/bin/python", line 41, in <module>
    exec(compile(__file__f.read(), __file__, "exec"))
  File "test.py", line 69, in <module>
    test_deactivate_btree()
  File "test.py", line 63, in test_deactivate_btree
    transaction.commit()
  File "transaction/_manager.py", line 124, in commit
    return self.get().commit()
  File "transaction/_transaction.py", line 316, in commit
    self._synchronizers.map(lambda s: s.afterCompletion(self))
  File "transaction/weakset.py", line 62, in map
    f(elt)
  File "transaction/_transaction.py", line 316, in <lambda>
    self._synchronizers.map(lambda s: s.afterCompletion(self))
  File "ZODB/Connection.py", line 762, in afterCompletion
    self.newTransaction(transaction, False)
  File "ZODB/Connection.py", line 747, in newTransaction
    assert self._storage is None
AssertionError

About my question above, the storage is obviously closed by functional.NEOCluster itself. It's "luck" if it does not fail with other ZODB storages.

I already suspected something wrong in the way you use ZODB. I suggest to close the DB explicitly in teardown.

[Julien Muchembled]

If I also add print self, self.app at the beginning of Storage.lastTransaction

(... and a print stor in TestDB_Base.dbopen)

[Kirill Smelkov]

Too heavy?? Anyway, you are right that connections from previous test could be left there alive, and since transaction keeps weak references to them and invoke at synchronization points (e.g. at transaction.commit()) this could lead to situations when connection tries to use closed storage.

I've pushed up the following fixes: kirr/wendelin.core@5a5ed2c7, kirr/wendelin.core@01b995a4.