Reenable multithreading tests (#850)

* Disable threading support for JSONCollection on Windows. * Change all xfailed tests to conditional skips on Windows. * Enable xfail strict. * Don't try to modify locks when threading support doesn't exist. * Reset the filename whether or not we need to play with locks. * Remove debug prints. * Minor cleanup. * Address PR comments. * Fix typo in comment. * Setting filename also requires the lock. * Centralize ON_WINDOWS. * Update changelog. * No special behavior for cygwin. * Disable multithreading on Cygwin. Tests were failing. Co-authored-by: Bradley Dice <[email protected]>
glotzerlab · Nov 8, 2022 · e69e629 · e69e629
1 parent c6c0b48
commit e69e629
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diff --git a/changelog.txt b/changelog.txt
@@ -30,6 +30,7 @@ Changed
  - Rather than searching upwards until the root, ``load_config`` will only load configuration files in the specified directory, which is assumed to be a project directory, as well as the user's home directory (#711).
  - Changed the ``root`` parameter to ``path`` in the ``signac.get_project`` and ``signac.init_project`` functions and corresponding ``Project`` methods (#757, #758).
  - The prefix argument to ``$ signac view`` is now optional and can be provided with ``-p/--prefix`` (#653, #774).
+ - Tests are run with ``xfail_strict = True`` (#850).
  - Detection of an invalid config will raise an error rather than a debug log (#855).
 
 Removed

diff --git a/setup.cfg b/setup.cfg
@@ -35,6 +35,7 @@ omit =
 	*/signac/common/deprecation/*.py
 
 [tool:pytest]
+xfail_strict = True
 filterwarnings = 
 	error::FutureWarning:signac.*
 	error::DeprecationWarning:signac.*

diff --git a/signac/_synced_collections/backends/collection_json.py b/signac/_synced_collections/backends/collection_json.py
@@ -6,6 +6,7 @@
 import errno
 import json
 import os
+import sys
 import uuid
 from collections.abc import Mapping, Sequence
 from typing import Callable, FrozenSet
@@ -27,6 +28,9 @@
 from ..utils import AbstractTypeResolver, SyncedCollectionJSONEncoder
 from ..validators import json_format_validator, no_dot_in_key, require_string_key
 
+ON_WINDOWS = sys.platform.startswith("win32") or sys.platform.startswith("cygwin")
+
+
 """
 There are many classes defined in this file. Most of the definitions are
 trivial since logic is largely inherited, but the large number of classes
@@ -127,11 +131,13 @@ class JSONCollection(SyncedCollection):
 
     **Thread safety**
 
-    The :class:`JSONCollection` is thread-safe. To make these collections safe, the
-    ``write_concern`` flag is ignored in multithreaded execution, and the
-    write is **always** performed via a write to temporary file followed by a
+    The :class:`JSONCollection` is thread-safe on Unix-like systems (not
+    Windows, see the Warnings section). To make these collections safe, the
+    ``write_concern`` flag is ignored in multithreaded execution, and the write
+    is **always** performed via a write to temporary file followed by a
     replacement of the original file. The file replacement operation uses
-    :func:`os.replace`, which is guaranteed to be atomic by the Python standard.
+    :func:`os.replace`, which is guaranteed to be atomic by the Python
+    standard.
 
     Parameters
     ----------
@@ -145,10 +151,17 @@ class JSONCollection(SyncedCollection):
     \*\*kwargs :
         Keyword arguments forwarded to parent constructors.
 
+    Warnings
+    --------
+    This class is _not_ thread safe on Windows. It relies on ``os.replace`` for
+    atomic file writes, and that method can fail in multithreaded situations if
+    open handles exist to the destination file within the same process on a
+    different thread. See https://bugs.python.org/issue46003 for more
+    information.
     """
 
     _backend = __name__  # type: ignore
-    _supports_threading = True
+    _supports_threading = not ON_WINDOWS
     _validators: Sequence_t[Callable] = (require_string_key, json_format_validator)
 
     def __init__(self, filename=None, write_concern=False, *args, **kwargs):
@@ -200,9 +213,21 @@ def _save_to_resource(self):
 
     @property
     def filename(self):
-        """str: The name of the associated JSON file on disk."""
+        """str: Get or set the name of the associated JSON file on disk."""
         return self._filename
 
+    @filename.setter
+    def filename(self, value):
+        # When setting the filename we must also remap the locks.
+        with self._thread_lock:
+            if type(self)._threading_support_is_active:
+                old_lock_id = self._lock_id
+
+            self._filename = value
+
+            if type(self)._threading_support_is_active:
+                type(self)._locks[self._lock_id] = type(self)._locks.pop(old_lock_id)
+
     @property
     def _lock_id(self):
         return self._filename
@@ -227,6 +252,7 @@ def _lock_id(self):
         "registry",
         # These keys are specific to the JSON backend.
         "_filename",
+        "filename",
         "_write_concern",
     )
 )

diff --git a/signac/contrib/job.py b/signac/contrib/job.py
@@ -123,18 +123,15 @@ def _save(self):
             job._initialize_lazy_properties()
 
         # Remove the temporary state point file if it was created. Have to do it
-        # here because we need to get the updated job state point filename.
+        # here so that we can get the updated job state point filename and set
+        # it to self.filename below.
         try:
             os.remove(job._statepoint_filename + "~")
         except OSError as error:
             if error.errno != errno.ENOENT:
                 raise
 
-        # Since all the jobs are equivalent, just grab the filename from the
-        # last one and init it. Also migrate the lock for multithreaded support.
-        old_lock_id = self._lock_id
-        self._filename = job._statepoint_filename
-        type(self)._locks[self._lock_id] = type(self)._locks.pop(old_lock_id)
+        self.filename = job._statepoint_filename
 
         if should_init:
             # Only initializing one job assumes that all changes in init are
@@ -164,7 +161,7 @@ def save(self, force=False):
         """
         try:
             # Open the file for writing only if it does not exist yet.
-            if force or not os.path.isfile(self._filename):
+            if force or not os.path.isfile(self.filename):
                 super()._save()
         except Exception as error:
             if not isinstance(error, OSError) or error.errno not in (
@@ -174,7 +171,7 @@ def save(self, force=False):
                 # Attempt to delete the file on error, to prevent corruption.
                 # OSErrors that are EEXIST or EACCES don't need to delete the file.
                 try:
-                    os.remove(self._filename)
+                    os.remove(self.filename)
                 except Exception:  # ignore all errors here
                     pass
                 raise

diff --git a/tests/test_synced_collections/synced_collection_test.py b/tests/test_synced_collections/synced_collection_test.py
@@ -451,13 +451,6 @@ class A:
             with pytest.raises(TypeError):
                 synced_collection[key] = testdata
 
-    @pytest.mark.xfail(
-        reason=(
-            "This test sometimes fails. This may indicate a race condition. "
-            "The test fails more consistently on Windows but also appears on "
-            "Linux in CI."
-        ),
-    )
     def test_multithreaded(self, synced_collection):
         """Test multithreaded runs of synced dicts."""
         if not type(synced_collection)._supports_threading:
@@ -770,13 +763,6 @@ def test_nested_list_with_dict(self, synced_collection):
         assert isinstance(child2, SyncedCollection)
         assert isinstance(child1, SyncedCollection)
 
-    @pytest.mark.xfail(
-        reason=(
-            "This test sometimes fails. This may indicate a race condition. "
-            "The test fails more consistently on Windows but also appears on "
-            "Linux in CI."
-        ),
-    )
     def test_multithreaded(self, synced_collection):
         """Test multithreaded runs of synced lists."""
         if not type(synced_collection)._supports_threading:

diff --git a/tests/test_synced_collections/test_json_buffered_collection.py b/tests/test_synced_collections/test_json_buffered_collection.py
@@ -4,6 +4,7 @@
 import itertools
 import json
 import os
+import sys
 import time
 from concurrent.futures import ThreadPoolExecutor
 
@@ -23,6 +24,8 @@
 )
 from signac._synced_collections.errors import BufferedError, MetadataError
 
+ON_WINDOWS = sys.platform.startswith("win32") or sys.platform.startswith("cygwin")
+
 
 class BufferedJSONCollectionTest(JSONCollectionTest):
     def load(self, collection):
@@ -376,11 +379,11 @@ def multithreaded_buffering_test(self, op, tmpdir):
             # truly flushed correctly.
             assert self._collection_type.get_current_buffer_size() == 0
 
-    @pytest.mark.xfail(
+    @pytest.mark.skipif(
+        ON_WINDOWS,
         reason=(
-            "This test sometimes fails. This may indicate a race condition. "
-            "The test fails more consistently on Windows but also appears on "
-            "Linux in CI."
+            "The JSONCollection cannot be safely used in multithreaded settings "
+            "on Windows due to https://bugs.python.org/issue46003."
         ),
     )
     def test_multithreaded_buffering_setitem(self, tmpdir):
@@ -392,11 +395,11 @@ def setitem_dict(sd, data):
 
         self.multithreaded_buffering_test(setitem_dict, tmpdir)
 
-    @pytest.mark.xfail(
+    @pytest.mark.skipif(
+        ON_WINDOWS,
         reason=(
-            "This test sometimes fails. This may indicate a race condition. "
-            "The test fails more consistently on Windows but also appears on "
-            "Linux in CI."
+            "The JSONCollection cannot be safely used in multithreaded settings "
+            "on Windows due to https://bugs.python.org/issue46003."
         ),
     )
     def test_multithreaded_buffering_update(self, tmpdir):
@@ -407,11 +410,11 @@ def update_dict(sd, data):
 
         self.multithreaded_buffering_test(update_dict, tmpdir)
 
-    @pytest.mark.xfail(
+    @pytest.mark.skipif(
+        ON_WINDOWS,
         reason=(
-            "This test sometimes fails. This may indicate a race condition. "
-            "The test fails more consistently on Windows but also appears on "
-            "Linux in CI."
+            "The JSONCollection cannot be safely used in multithreaded settings "
+            "on Windows due to https://bugs.python.org/issue46003."
         ),
     )
     def test_multithreaded_buffering_reset(self, tmpdir):
@@ -422,11 +425,11 @@ def reset_dict(sd, data):
 
         self.multithreaded_buffering_test(reset_dict, tmpdir)
 
-    @pytest.mark.xfail(
+    @pytest.mark.skipif(
+        ON_WINDOWS,
         reason=(
-            "This test sometimes fails. This may indicate a race condition. "
-            "The test fails more consistently on Windows but also appears on "
-            "Linux in CI."
+            "The JSONCollection cannot be safely used in multithreaded settings "
+            "on Windows due to https://bugs.python.org/issue46003."
         ),
     )
     def test_multithreaded_buffering_clear(self, tmpdir):
@@ -474,11 +477,11 @@ def test_multithreaded_buffering_clear(self, tmpdir):
             # truly flushed correctly.
             assert self._collection_type.get_current_buffer_size() == 0
 
-    @pytest.mark.xfail(
+    @pytest.mark.skipif(
+        ON_WINDOWS,
         reason=(
-            "This test sometimes fails. This may indicate a race condition. "
-            "The test fails more consistently on Windows but also appears on "
-            "Linux in CI."
+            "The JSONCollection cannot be safely used in multithreaded settings "
+            "on Windows due to https://bugs.python.org/issue46003."
         ),
     )
     def test_multithreaded_buffering_load(self, tmpdir):
@@ -670,11 +673,11 @@ def multithreaded_buffering_test(self, op, requires_init, tmpdir):
             # truly flushed correctly.
             assert self._collection_type.get_current_buffer_size() == 0
 
-    @pytest.mark.xfail(
+    @pytest.mark.skipif(
+        ON_WINDOWS,
         reason=(
-            "This test sometimes fails. This may indicate a race condition. "
-            "The test fails more consistently on Windows but also appears on "
-            "Linux in CI."
+            "The JSONCollection cannot be safely used in multithreaded settings "
+            "on Windows due to https://bugs.python.org/issue46003."
         ),
     )
     def test_multithreaded_buffering_setitem(self, tmpdir):
@@ -686,11 +689,11 @@ def setitem_list(sd, data):
 
         self.multithreaded_buffering_test(setitem_list, True, tmpdir)
 
-    @pytest.mark.xfail(
+    @pytest.mark.skipif(
+        ON_WINDOWS,
         reason=(
-            "This test sometimes fails. This may indicate a race condition. "
-            "The test fails more consistently on Windows but also appears on "
-            "Linux in CI."
+            "The JSONCollection cannot be safely used in multithreaded settings "
+            "on Windows due to https://bugs.python.org/issue46003."
         ),
     )
     def test_multithreaded_buffering_extend(self, tmpdir):
@@ -701,11 +704,11 @@ def extend_list(sd, data):
 
         self.multithreaded_buffering_test(extend_list, False, tmpdir)
 
-    @pytest.mark.xfail(
+    @pytest.mark.skipif(
+        ON_WINDOWS,
         reason=(
-            "This test sometimes fails. This may indicate a race condition. "
-            "The test fails more consistently on Windows but also appears on "
-            "Linux in CI."
+            "The JSONCollection cannot be safely used in multithreaded settings "
+            "on Windows due to https://bugs.python.org/issue46003."
         ),
     )
     def test_multithreaded_buffering_append(self, tmpdir):
@@ -717,11 +720,11 @@ def append_list(sd, data):
 
         self.multithreaded_buffering_test(append_list, False, tmpdir)
 
-    @pytest.mark.xfail(
+    @pytest.mark.skipif(
+        ON_WINDOWS,
         reason=(
-            "This test sometimes fails. This may indicate a race condition. "
-            "The test fails more consistently on Windows but also appears on "
-            "Linux in CI."
+            "The JSONCollection cannot be safely used in multithreaded settings "
+            "on Windows due to https://bugs.python.org/issue46003."
         ),
     )
     def test_multithreaded_buffering_load(self, tmpdir):

diff --git a/tests/test_synced_collections/test_json_collection.py b/tests/test_synced_collections/test_json_collection.py
@@ -9,6 +9,7 @@
 from synced_collection_test import SyncedDictTest, SyncedListTest
 
 from signac._synced_collections.backends.collection_json import (
+    ON_WINDOWS,
     JSONAttrDict,
     JSONAttrList,
     JSONDict,
@@ -42,6 +43,16 @@ def synced_collection_positional(self, tmpdir):
     def test_filename(self, synced_collection):
         assert os.path.basename(synced_collection.filename) == self._fn
 
+    @pytest.mark.skipif(
+        ON_WINDOWS,
+        reason=(
+            "The JSONCollection cannot be safely used in multithreaded settings "
+            "on Windows due to https://bugs.python.org/issue46003."
+        ),
+    )
+    def test_multithreaded(self, synced_collection):
+        return super().test_multithreaded(synced_collection)
+
 
 class TestJSONDict(JSONCollectionTest, SyncedDictTest):