Update to 4.2.8

cellprofiler_core/__init__.py

@@ -1 +1 @@
-__version__ = "4.2.6"
+__version__ = "4.2.8"

cellprofiler_core/__main__.py

@@ -1,55 +0,0 @@
-import os
-import pathlib
-
-import click
-
-import cellprofiler_core.commands
-
-CONTEXT_SETTINGS = dict(auto_envvar_prefix="COMPLEX")
-
-
-class Command(click.MultiCommand):
-    def get_command(self, context, name):
-        try:
-            name = f"cellprofiler_core.commands._{name}_command"
-
-            imported_module = __import__(name, None, None, ["command"])
-        except ImportError:
-            return
-
-        return imported_module.command
-
-    def list_commands(self, context):
-        command_names = []
-
-        commands_pathname = cellprofiler_core.commands.__file__
-
-        commands_directory = pathlib.Path(commands_pathname).parent
-
-        for filename in os.listdir(commands_directory):
-            if filename.endswith("_command.py") and filename.startswith("_"):
-                command_name = filename[1:-11]
-
-                command_names += [command_name]
-
-        command_names.sort()
-
-        return command_names
-
-
-class Environment:
-    def __init__(self):
-        pass
-
-
-pass_environment = click.make_pass_decorator(Environment, ensure=True)
-
-
-@click.command(cls=Command, context_settings=CONTEXT_SETTINGS)
-@pass_environment
-def main(context):
-    pass
-
-
-if __name__ == "__main__":
-    main({})

cellprofiler_core/analysis/_runner.py

@@ -102,7 +102,7 @@ def __init__(
         # should have jobserver() call load_measurements_from_buffer() rather
         # than interface() doing so.  Currently, passing measurements in this
         # way seems like it might be buggy:
-        # http://code.google.com/p/h5py/issues/detail?id=244
+        # https://github.com/h5py/h5py/issues/244
         self.received_measurements_queue = queue.Queue(maxsize=10)
 
         self.shared_dicts = None

cellprofiler_core/module/_module.py

@@ -545,7 +545,7 @@ def set_notes(self, notes):
         """Give the module new user-entered notes
 
         """
-        sanitization_dict = {"“":"\"","”":"\""}
+        sanitization_dict = {"“":"\"","”":"\"","—":"-","’":"'","`":"'"}
         self.__notes = [''.join(sanitization_dict.get(x,x) for x in note) for note in notes]
 
     notes = property(get_notes, set_notes)

cellprofiler_core/utilities/zmq/__init__.py

@@ -17,6 +17,7 @@
     LockStatusRequest,
     Request,
 )
+from ._event import PollTimeoutException
 
 NOTIFY_SOCKET_ADDR = "inproc://BoundaryNotifications"
 SD_KEY_DICT = "__keydict__"

cellprofiler_core/utilities/zmq/_event.py

@@ -0,0 +1,4 @@
+class PollTimeoutException(Exception):
+    """Exception issued by a timeout from polling"""
+
+    pass

cellprofiler_core/worker/_worker.py

@@ -29,12 +29,15 @@
 from ..constants.worker import the_zmq_context
 from ..measurement import Measurements
 from ..utilities.measurement import load_measurements_from_buffer
+from ..utilities.zmq import PollTimeoutException
 from ..pipeline import CancelledException
 from ..preferences import get_awt_headless
 from ..preferences import set_preferences_from_dict
 from ..utilities.zmq.communicable.reply.upstream_exit import UpstreamExit
 from ..workspace import Workspace
 
+LOGGER = logging.getLogger(__name__)
+
 
 class Worker:
     """An analysis worker processing work at a given address
@@ -124,6 +127,7 @@ def run(self):
                         )
                         t0 = time.time()
                     self.work_socket = the_zmq_context.socket(zmq.REQ)
+                    self.work_socket.set_hwm(2000)
                     self.work_socket.connect(self.work_request_address)
                     # fetch a job
                     the_request = Work(self.current_analysis_id)
@@ -304,26 +308,40 @@ def do_job(self, job):
                     return
 
                 if worker_runs_post_group:
-                    last_workspace.interaction_handler = self.interaction_handler
-                    last_workspace.cancel_handler = self.cancel_handler
-                    last_workspace.post_group_display_handler = (
-                        self.post_group_display_handler
-                    )
-                    # There might be an exception in this call, but it will be
-                    # handled elsewhere, and there's nothing we can do for it
-                    # here.
-                    current_pipeline.post_group(
-                        last_workspace, current_measurements.get_grouping_keys()
-                    )
-                    del last_workspace
+                    if not last_workspace is None:
+                        last_workspace.interaction_handler = self.interaction_handler
+                        last_workspace.cancel_handler = self.cancel_handler
+                        last_workspace.post_group_display_handler = (
+                            self.post_group_display_handler
+                        )
+                        # There might be an exception in this call, but it will be
+                        # handled elsewhere, and there's nothing we can do for it
+                        # here.
+                        current_pipeline.post_group(
+                            last_workspace, current_measurements.get_grouping_keys()
+                        )
+                        del last_workspace
+                    else:
+                        LOGGER.error("No workspace from last image set, cannot run post group")
 
             # send measurements back to server
             req = MeasurementsReport(
                 self.current_analysis_id,
                 buf=current_measurements.file_contents(),
                 image_set_numbers=image_set_numbers,
             )
-            rep = self.send(req)
+
+            while True:
+                try:
+                    rep = self.send(req, timeout=4000)
+                    break
+                except PollTimeoutException:
+                    LOGGER.info(f"Worker sending MeasurementsReport halted, retrying for job {str(job.image_set_numbers)}")
+                    self.work_socket.close(linger=0)
+                    self.work_socket = the_zmq_context.socket(zmq.REQ)
+                    self.work_socket.set_hwm(2000)
+                    self.work_socket.connect(self.work_request_address)
+                    continue
 
         except CancelledException:
             # Main thread received shutdown signal
@@ -389,7 +407,7 @@ def omero_login_handler(self):
         rep = self.send(req)
         use_omero_credentials(rep.credentials)
 
-    def send(self, req, work_socket=None):
+    def send(self, req, work_socket=None, timeout=None):
         """Send a request and receive a reply
 
         req - request to send
@@ -410,7 +428,10 @@ def send(self, req, work_socket=None):
         req.send_only(work_socket)
         response = None
         while response is None:
-            for socket, state in poller.poll():
+            poll_res = poller.poll(timeout)
+            if len(poll_res) == 0:
+                raise PollTimeoutException
+            for socket, state in poll_res:
                 if socket == self.notify_socket and state == zmq.POLLIN:
                     notify_msg = self.notify_socket.recv()
                     if notify_msg == NOTIFY_STOP:

docs/conf.py

@@ -12,6 +12,6 @@
 
 project = "CellProfiler-core"
 
-release = "4.2.6"
+release = "4.2.8"
 
 templates_path = ["_templates"]

setup.cfg

@@ -3,6 +3,6 @@ filterwarnings =
     ignore::DeprecationWarning
     ignore::FutureWarning
 minversion =
-    4.2.6
+    4.2.8
 testpaths =
     ./tests/

setup.py

@@ -8,30 +8,28 @@
         "License :: OSI Approved :: MIT License",
         "Programming Language :: Python :: 3",
         "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
     ],
     extras_require={
         "dev": [
-            "black==19.10b0",
-            "click>=7.1.2",
-            "pre-commit==2.2.0",
-            "sphinx==3.1.2",
+            "sphinx>=3.1.2",
             "twine==3.1.1",
         ],
-        "test": ["pytest==5.4.1"],
+        "test": ["pytest~=7.4.1"],
         "wx": ["wxPython==4.1.0"],
     },
     install_requires=[
         "boto3==1.14.23",
-        "centrosome==1.2.2",
+        "centrosome==1.2.3",
         "docutils==0.15.2",
         "fsspec==2022.2.0",
         "h5py==3.6.0",  # Consider 3.2.1 if problems happen
         "matplotlib==3.1.3",
         "numpy==1.23.1",
         "prokaryote==2.4.4",
         "psutil==5.7.0",
-        "python-bioformats==4.0.7",
-        "python-javabridge==4.0.3",
+        "python-bioformats==4.1.0",
+        "python-javabridge==4.0.4",
         "pyzmq==22.3.0",
         "Pillow==8.3.2",
         "scikit-image==0.18.3",
@@ -44,6 +42,6 @@
     packages=setuptools.find_packages(exclude=["tests"]),
     python_requires=">=3.8, <4",
     url="https://github.com/CellProfiler/core",
-    version="4.2.6",
+    version="4.2.8",
     zip_safe=False,
 )