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Address tests that are flaky with pytest-xdist #512

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glatterf42 opened this issue Jan 15, 2024 · 2 comments · Fixed by #543
Closed

Address tests that are flaky with pytest-xdist #512

glatterf42 opened this issue Jan 15, 2024 · 2 comments · Fixed by #543
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bug ci Continuous integration
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3.10

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@glatterf42
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As mentioned in #510, pytest-xdist allows us to run tests on multiple tasks simultaneously, decreasing our run time. However, some tests show flaky behaviour since they attempt to read/write from processes they don't belong to. iiasa/message_ix#765 (comment) mentions a method with which to resolve this flakiness and successfully implements it on several tests in that repo. We should add the same/similar fixes here and then revert the mitigation added in #510.
@glatterf42 glatterf42 added bug ci Continuous integration labels Jan 15, 2024
@glatterf42 glatterf42 added this to the 3.9 milestone Jan 15, 2024
@glatterf42
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Possibly related to #467.

@glatterf42
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glatterf42 commented Mar 12, 2024 •
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Here's a list of flaky tests I recorded since 11.01.2024:

  • test_py_transport

    FAILED ixmp/tests/test_tutorials.py::test_py_transport - nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
# launch the ix modeling platform using the default back end
mp = ixmp.Platform()

# The following lines have the same effect:
# mp = ixmp.Platform(name='local')  # Default local database
# mp = ixmp.Platform(name='default')  # Default database -> 'local'
------------------


---------------------------------------------------------------------------
Exception                                 Traceback (most recent call last)
File Platform.java:110, in at.ac.iiasa.ixmp.Platform.<init>()

File Platform.java:163, in at.ac.iiasa.ixmp.Platform.initPlatform()

File DbDAO.java:238, in at.ac.iiasa.ixmp.database.DbDAO.create()

File DbDAO.java:318, in at.ac.iiasa.ixmp.database.DbDAO.updateSchemaIfNecessary()

File Flyway.java:910, in org.flywaydb.core.Flyway.migrate()

File Flyway.java:1238, in org.flywaydb.core.Flyway.execute()

File Flyway.java:910, in org.flywaydb.core.Flyway$1.execute()

File Flyway.java:918, in org.flywaydb.core.Flyway$1.execute()

File Flyway.java:78, in org.flywaydb.core.Flyway.access$100()

File Flyway.java:1037, in org.flywaydb.core.Flyway.doValidate()

Exception: Java Exception

The above exception was the direct cause of the following exception:

org.flywaydb.core.api.FlywayException     Traceback (most recent call last)
File ~/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/ixmp/backend/jdbc.py:297, in JDBCBackend.__init__(self, jvmargs, **kwargs)
    296 try:
--> 297     self.jobj = java.Platform("Python", properties)
    298 except java.NoClassDefFoundError as e:  # pragma: no cover

org.flywaydb.core.api.FlywayException: org.flywaydb.core.api.FlywayException: Validate failed: Detected failed migration to version 1 (hsql base version)

During handling of the above exception, another exception occurred:

RuntimeError                              Traceback (most recent call last)
Cell In[2], line 2
      1 # launch the ix modeling platform using the default back end
----> 2 mp = ixmp.Platform()
      4 # The following lines have the same effect:
      5 # mp = ixmp.Platform(name='local')  # Default local database
      6 # mp = ixmp.Platform(name='default')  # Default database -> 'local'

File ~/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/ixmp/core/platform.py:94, in Platform.__init__(self, name, backend, **backend_args)
     88     raise ValueError(
     89         f"backend class {repr(backend_class_name)} not among "
     90         + str(sorted(BACKENDS.keys()))
     91     )
     93 # Instantiate the backend
---> 94 self._backend = backend_class(**kwargs)

File ~/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/ixmp/backend/jdbc.py:320, in JDBCBackend.__init__(self, jvmargs, **kwargs)
    318     else:
    319         _raise_jexception(e)
--> 320     raise RuntimeError(f"{msg}\n(Java: {jclass})")
    322 # Set the log level
    323 self.set_log_level(log_level)

RuntimeError: when initializing database:
(Java: org.flywaydb.core.api.FlywayException)
On: macos-latest-py3.8, macos-latest-py3.10

  • test_py_transport_scenario

    FAILED ixmp/tests/test_tutorials.py::test_py_transport_scenario - nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
# launch the ix modeling platform using the default local database
mp = ixmp.Platform()
------------------


---------------------------------------------------------------------------
Exception                                 Traceback (most recent call last)
File Platform.java:110, in at.ac.iiasa.ixmp.Platform.<init>()

File Platform.java:163, in at.ac.iiasa.ixmp.Platform.initPlatform()

File DbDAO.java:238, in at.ac.iiasa.ixmp.database.DbDAO.create()

File DbDAO.java:318, in at.ac.iiasa.ixmp.database.DbDAO.updateSchemaIfNecessary()

File Flyway.java:910, in org.flywaydb.core.Flyway.migrate()

File Flyway.java:1238, in org.flywaydb.core.Flyway.execute()

File Flyway.java:910, in org.flywaydb.core.Flyway$1.execute()

File Flyway.java:918, in org.flywaydb.core.Flyway$1.execute()

File Flyway.java:78, in org.flywaydb.core.Flyway.access$100()

File Flyway.java:1037, in org.flywaydb.core.Flyway.doValidate()

Exception: Java Exception

The above exception was the direct cause of the following exception:

org.flywaydb.core.api.FlywayException     Traceback (most recent call last)
File ~/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/ixmp/backend/jdbc.py:297, in JDBCBackend.__init__(self, jvmargs, **kwargs)
    296 try:
--> 297     self.jobj = java.Platform("Python", properties)
    298 except java.NoClassDefFoundError as e:  # pragma: no cover

org.flywaydb.core.api.FlywayException: org.flywaydb.core.api.FlywayException: Validate failed: Detected failed migration to version 1 (hsql base version)

During handling of the above exception, another exception occurred:

RuntimeError                              Traceback (most recent call last)
Cell In[2], line 2
      1 # launch the ix modeling platform using the default local database
----> 2 mp = ixmp.Platform()

File ~/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/ixmp/core/platform.py:94, in Platform.__init__(self, name, backend, **backend_args)
     88     raise ValueError(
     89         f"backend class {repr(backend_class_name)} not among "
     90         + str(sorted(BACKENDS.keys()))
     91     )
     93 # Instantiate the backend
---> 94 self._backend = backend_class(**kwargs)

File ~/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/ixmp/backend/jdbc.py:320, in JDBCBackend.__init__(self, jvmargs, **kwargs)
    318     else:
    319         _raise_jexception(e)
--> 320     raise RuntimeError(f"{msg}\n(Java: {jclass})")
    322 # Set the log level
    323 self.set_log_level(log_level)

RuntimeError: when initializing database:
(Java: org.flywaydb.core.api.FlywayException)
On: macos-latest-py3.8, macos-latest-py3.10

  • test_R_transport

    FAILED ixmp/tests/test_tutorials.py::test_R_transport - nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
# launch the ix modeling platform using a local HSQL database instance
mp <- ixmp$Platform()
------------------


when initializing database:
(Java: org.flywaydb.core.api.FlywayException)Traceback:

1. ixmp$Platform()
2. py_call_impl(callable, call_args$unnamed, call_args$named)
On: macos-latest-py3.8, macos-latest-py3.10

  • test_R_transport_scenario

    FAILED ixmp/tests/test_tutorials.py::test_R_transport_scenario - nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
# launch the ix modeling platform using the local default database
mp <- ixmp$Platform()
------------------


when initializing database:
(Java: org.flywaydb.core.api.FlywayException)Traceback:

1. ixmp$Platform()
2. py_call_impl(callable, call_args$unnamed, call_args$named)
On: macos-latest-py3.8, macos-latest-py3.10

  • test_del_ts

    FAILED ixmp/tests/backend/test_jdbc.py::test_del_ts - assert 8 == (1 + 8)
 +  where 8 = len(<WeakKeyDictionary at 0x120d52330>)
 +    where <WeakKeyDictionary at 0x120d52330> = <ixmp.backend.jdbc.JDBCBackend object at 0x14b0e3890>.jindex
 +      where <ixmp.backend.jdbc.JDBCBackend object at 0x14b0e3890> = <ixmp.core.platform.Platform object at 0x14b0e2bd0>._backend
On: macos-latest-py3.12

  • test_last_update[TimeSeries]

    FAILED ixmp/tests/core/test_timeseries.py::TestTimeSeries::test_last_update[TimeSeries] - assert datetime.timedelta(seconds=1, microseconds=390684) < datetime.timedelta(seconds=1)
 +  where datetime.timedelta(seconds=1, microseconds=390684) = abs((datetime.datetime(2024, 1, 12, 6, 36, 10, 712000) - datetime.datetime(2024, 1, 12, 6, 36, 12, 102684)))
 +    where datetime.datetime(2024, 1, 12, 6, 36, 12, 102684) = <built-in method now of type object at 0x109bc0ba8>()
 +      where <built-in method now of type object at 0x109bc0ba8> = datetime.now
 +  and   datetime.timedelta(seconds=1) = timedelta(seconds=1)
On: macos-latest-py3.12

  • test_export_timeseries_data

    FAILED ixmp/tests/core/test_platform.py::test_export_timeseries_data - AssertionError: DataFrame are different

DataFrame shape mismatch
[left]:  (2, 10)
[right]: (0, 10)
On: macos-latest-py3.8, macos-latest-py3.12

  • test_connect_message

    FAILED ixmp/tests/backend/test_jdbc.py::test_connect_message - assert "connected to database 'jdbc:hsqldb:mem://ixmptest' (user: ixmp)..." in ''
 +  where '' = CaptureResult(out='', err='').out
On: windows-latest-py3.9

  • test_del_ts

    FAILED ixmp/tests/backend/test_jdbc.py::test_del_ts - assert 8 == (1 + 8)
 +  where 8 = len(<WeakKeyDictionary at 0x1264df1a0>)
 +    where <WeakKeyDictionary at 0x1264df1a0> = <ixmp.backend.jdbc.JDBCBackend object at 0x151195730>.jindex
 +      where <ixmp.backend.jdbc.JDBCBackend object at 0x151195730> = <ixmp.core.platform.Platform object at 0x1511949e0>._backend
On: macos-latest-py3.12

  • test_close

    FAILED ixmp/tests/backend/test_jdbc.py::test_close - AssertionError: assert 'Database connection could not be closed or was already closed' in ''
 +  where '' = CaptureResult(out='', err='').out
On: windows-latest-py3.8

  • test_del_ts

    FAILED ixmp/tests/backend/test_jdbc.py::test_del_ts - AssertionError: ("<frame at 0x146cd3510, file '/Users/runner/work/ixmp/ixmp/ixmp/backend/jdbc.py', line 732, code check_out>
  <frame a..._>
  <frame at 0x1252f9e40, file '/Users/runner/work/ixmp/ixmp/ixmp/testing/data.py', line 220, code make_dantzig>", [])
assert 1 == (20 - 1)
 +  where 20 = getrefcount(<ixmp.core.scenario.Scenario object at 0x146b920f0>)
On: macos-latest-py3.12

  • test_platform_copy

    FAILED ixmp/tests/test_cli.py::test_platform_copy - AssertionError: Copy /tmp/pytest-of-runner/pytest-0/popen-gw0/test_platform_copy0/p2.script.new → /tmp/pytest-of-runner/pytest-0/popen-gw0/test_platform_copy0/p3.new
  Copy /tmp/pytest-of-runner/pytest-0/popen-gw0/test_platform_copy0/p2.properties.new → /tmp/pytest-of-runner/pytest-0/popen-gw0/test_platform_copy0/p3.new

assert (not True or 1 == 0)
 +  where 1 = <Result FileNotFoundError(2, 'No such file or directory')>.exit_code
On: ubuntu-latest-py3.12, macos-latest-py3.12

@glatterf42 glatterf42 mentioned this issue Mar 12, 2024
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2 tasks
@khaeru khaeru modified the milestones: 3.9, 3.10 Jun 4, 2024
@glatterf42 glatterf42 mentioned this issue Sep 11, 2024
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@glatterf42 glatterf42 linked a pull request Sep 11, 2024 that will close this issue
Make tests robust and independent #543
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