Merge pull request #147 from spc-group/fix_tests

Fixed tests. Thought using ubutnu 20.04 on CI had fixed seg-faults. But I did still see one intermittent segfault in the CI. Might still have to come back to this.
spc-group · Nov 16, 2023 · 0690bf7 · 0690bf7
2 parents 5dccc2e + fc3c319
commit 0690bf7
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -20,7 +20,7 @@ jobs:
     defaults:
       run:
         shell: bash -l {0}
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     strategy:
       max-parallel: 5
     steps:
@@ -29,20 +29,22 @@ jobs:
       uses: mamba-org/setup-micromamba@v1
       with:
         environment-file: environment.yml
-    - name: Setup X virtual frame buffer
-      run: Xvfb $DISPLAY &
     - name: Install haven
       run: pip install -e .
     - name: Environment info
       run: |
         env
         micromamba info
         micromamba list
-    - name: Lint with flake8
+    - name: Lint
       run: |
-        # stop the build if there are Python syntax errors or undefined names
+        # Check for syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # Make sure black code formatting is applied
+        black --check --preview src/
+        # Make sure import orders are correct
+        isort --check src/
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
-      run: pytest --timeout=120
+    - name: Test with pytest in Xvfb
+      run: xvfb-run python -m pytest -vv --timeout=120
diff --git a/environment.yml b/environment.yml
@@ -34,7 +34,7 @@ dependencies:
   - numba>=0.56  # Ensures 0.53 (broken) isn't installed
 
   # --- testing and quality assurance
-  - black
+  - black >=22.1
   - flake8
   - pre-commit
   - pylint
@@ -90,6 +90,7 @@ dependencies:
   - ophyd >=1.6.3
   - pcdsdevices  # For extra signal types
   - pydm >=1.18.0
+  - typhos
   - p4p
   - tiled-server
   - tiled-client >= 0.1.0a106  # 2023-10-02 to get new Cache() behavior

diff --git a/ipython_startup.py b/ipython_startup.py
@@ -1,10 +1,10 @@
-from bluesky import plans as bp, plan_stubs as bps, RunEngine, suspenders
-from bluesky.simulators import summarize_plan
-from bluesky.callbacks.best_effort import BestEffortCallback
-import databroker
-import matplotlib.pyplot as plt
+from bluesky import plans as bp, plan_stubs as bps, RunEngine, suspenders  # noqa: F401
+from bluesky.simulators import summarize_plan  # noqa: F401
+from bluesky.callbacks.best_effort import BestEffortCallback  # noqa: F401
+import databroker  # noqa: F401
+import matplotlib.pyplot as plt  # noqa: F401
 
-import haven
+import haven  # noqa: F401
 
 # Prepare the haven instrument
 config = haven.load_config()

diff --git a/pyproject.toml b/pyproject.toml
@@ -37,3 +37,6 @@ firefly_cameras = "firefly.launcher:cameras"
 [build-system]
 requires = ["setuptools>=61.0"]
 build-backend = "setuptools.build_meta"
+
+[tool.isort]
+profile = "black"
diff --git a/src/conftest.py b/src/conftest.py
@@ -1,35 +1,38 @@
-from unittest import mock
+import os
 import subprocess
-import psutil
 from pathlib import Path
-import os
+from unittest import mock
 
-from bluesky import RunEngine
+import psutil
+
+# from pydm.data_plugins import plugin_modules, add_plugin
+import pydm
 import pytest
-from ophyd import DynamicDeviceComponent as DDC, Kind
+from bluesky import RunEngine
+from ophyd import DynamicDeviceComponent as DDC
+from ophyd import Kind
 from ophyd.sim import (
+    FakeEpicsSignal,
+    fake_device_cache,
     instantiate_fake_device,
     make_fake_device,
-    fake_device_cache,
-    FakeEpicsSignal,
 )
-from pydm.data_plugins import add_plugin
 from pytestqt.qt_compat import qt_api
 
 import haven
+from firefly.application import FireflyApplication
+from firefly.main_window import FireflyMainWindow
 from haven._iconfig import beamline_connected as _beamline_connected
 from haven.instrument.aerotech import AerotechStage
 from haven.instrument.aps import ApsMachine
-from haven.instrument.shutter import Shutter
 from haven.instrument.camera import AravisDetector
 from haven.instrument.delay import EpicsSignalWithIO
-from haven.instrument.dxp import DxpDetector, add_mcas as add_dxp_mcas
+from haven.instrument.dxp import DxpDetector
+from haven.instrument.dxp import add_mcas as add_dxp_mcas
 from haven.instrument.ion_chamber import IonChamber
-from haven.instrument.xspress import Xspress3Detector, add_mcas as add_xspress_mcas
-from firefly.application import FireflyApplication
-from firefly.main_window import FireflyMainWindow
-from firefly.ophyd_plugin import OphydPlugin
-
+from haven.instrument.shutter import Shutter
+from haven.instrument.xspress import Xspress3Detector
+from haven.instrument.xspress import add_mcas as add_xspress_mcas
 
 top_dir = Path(__file__).parent.resolve()
 haven_dir = top_dir / "haven"
@@ -113,27 +116,29 @@ def kill_process(process_name):
 def sim_registry(monkeypatch):
     # mock out Ophyd connections so devices can be created
     modules = [
-        haven.instrument.fluorescence_detector,
-        haven.instrument.monochromator,
         haven.instrument.ion_chamber,
-        haven.instrument.motor,
         haven.instrument.device,
     ]
     for mod in modules:
         monkeypatch.setattr(mod, "await_for_connection", mock.AsyncMock())
     monkeypatch.setattr(
         haven.instrument.ion_chamber, "caget", mock.AsyncMock(return_value="I0")
     )
-    # Clean the registry so we can restore it later
+    # Save the registry so we can restore it later
     registry = haven.registry
+    use_typhos = registry.use_typhos
     objects_by_name = registry._objects_by_name
     objects_by_label = registry._objects_by_label
     registry.clear()
     # Run the test
-    yield registry
-    # Restore the previous registry components
-    registry._objects_by_name = objects_by_name
-    registry._objects_by_label = objects_by_label
+    try:
+        yield registry
+    finally:
+        # Restore the previous registry components
+        registry.clear(clear_typhos=True)
+        registry._objects_by_name = objects_by_name
+        registry._objects_by_label = objects_by_label
+        registry.use_typhos = use_typhos
 
 
 @pytest.fixture()
@@ -265,7 +270,7 @@ def shutters(sim_registry):
 
 @pytest.fixture(scope="session")
 def pydm_ophyd_plugin():
-    return add_plugin(OphydPlugin)
+    return pydm.data_plugins.plugin_for_address("sig://")
 
 
 qs_status = {

diff --git a/src/firefly/__init__.py b/src/firefly/__init__.py
@@ -1,3 +1,2 @@
-from . import display
-
-from .application import FireflyApplication
+from . import display  # noqa: F401
+from .application import FireflyApplication  # noqa: F401
diff --git a/src/firefly/application.py b/src/firefly/application.py
@@ -1,29 +1,24 @@
 import logging
+import subprocess
 from collections import OrderedDict
-from pathlib import Path
-from dataclasses import dataclass, field
-from typing import Optional, Union, Mapping, Sequence
 from functools import partial
-import subprocess
+from pathlib import Path
+from typing import Mapping, Sequence
 
-from qtpy import QtWidgets, QtCore
-from qtpy.QtWidgets import QAction
-from qtpy.QtCore import Slot, QThread, Signal, QObject
-from PyQt5.QtWidgets import QStyleFactory
-import qtawesome as qta
 import pydm
+import pyqtgraph as pg
+import qtawesome as qta
 from pydm.application import PyDMApplication
-from pydm.display import load_file
 from pydm.utilities.stylesheet import apply_stylesheet
-from bluesky_queueserver_api import BPlan
-from bluesky_queueserver_api.zmq import REManagerAPI
-import pyqtgraph as pg
+from PyQt5.QtWidgets import QStyleFactory
+from qtpy import QtCore, QtWidgets
+from qtpy.QtCore import Signal
+from qtpy.QtWidgets import QAction
 
+from haven import HavenMotor, load_config, registry
 from haven.exceptions import ComponentNotFound
-from haven import HavenMotor, registry, load_config
-import haven
+
 from .main_window import FireflyMainWindow, PlanMainWindow
-from .ophyd_plugin import OphydPlugin
 from .queue_client import QueueClient, QueueClientThread, queueserver_api
 
 generator = type((x for x in []))
@@ -51,6 +46,8 @@ class FireflyApplication(PyDMApplication):
     show_runs_window_action: QtWidgets.QAction
     show_energy_window_action: QtWidgets.QAction
     show_bss_window_action: QtWidgets.QAction
+    show_voltmeters_window_action: QtWidgets.QAction
+    show_logs_window_action: QtWidgets.QAction
     launch_queuemonitor_action: QtWidgets.QAction
 
     # Keep track of motors
@@ -174,6 +171,18 @@ def setup_window_actions(self):
             text="Scheduling (&BSS)",
             slot=self.show_bss_window,
         )
+        # Launch ion chamber voltmeters window
+        self._setup_window_action(
+            action_name="show_voltmeters_window_action",
+            text="&Voltmeters",
+            slot=self.show_voltmeters_window,
+        )
+        # Launch log window
+        self._setup_window_action(
+            action_name="show_logs_window_action",
+            text="Logs",
+            slot=self.show_logs_window,
+        )
         # Launch energy window
         self._setup_window_action(
             action_name="show_energy_window_action",
@@ -266,14 +275,13 @@ def _prepare_device_windows(self, device_label: str, attr_name: str):
         window_slots = []
         setattr(self, f"{attr_name}_window_slots", window_slots)
         setattr(self, f"{attr_name}_windows", {})
-        # if attr_name == "ion_chamber":
-        #     breakpoint()
         for device in devices:
+            # Create the window action
             action = QtWidgets.QAction(self)
             action.setObjectName(f"actionShow_{attr_name}_{device.name}")
             action.setText(device.name)
             actions[device.name] = action
-            # Create a slot for opening the motor window
+            # Create a slot for opening the device window
             slot = getattr(self, f"show_{attr_name}_window")
             slot = partial(slot, device=device)
             action.triggered.connect(slot)
@@ -341,7 +349,11 @@ def prepare_queue_client(self, api=None):
             thread = QueueClientThread()
             self._queue_thread = thread
         # Create the client object
-        client = QueueClient(api=api, autoplay_action=self.queue_autoplay_action, open_environment_action=self.queue_open_environment_action)
+        client = QueueClient(
+            api=api,
+            autoplay_action=self.queue_autoplay_action,
+            open_environment_action=self.queue_open_environment_action,
+        )
         client.moveToThread(thread)
         thread.timer.timeout.connect(client.update)
         self._queue_client = client
@@ -429,9 +441,7 @@ def connect_menu_signals(self, window):
         and setup code.
 
         """
-        window.actionShow_Log_Viewer.triggered.connect(self.show_log_viewer_window)
         window.actionShow_Xafs_Scan.triggered.connect(self.show_xafs_scan_window)
-        window.actionShow_Voltmeters.triggered.connect(self.show_voltmeters_window)
         window.actionShow_Sample_Viewer.triggered.connect(
             self.show_sample_viewer_window
         )
@@ -540,7 +550,7 @@ def show_run_browser(self):
         )
 
     @QtCore.Slot()
-    def show_log_viewer_window(self):
+    def show_logs_window(self):
         self.show_window(FireflyMainWindow, ui_dir / "log_viewer.ui", name="log_viewer")
 
     @QtCore.Slot()

diff --git a/src/firefly/area_detector_overlay.ui b/src/firefly/area_detector_overlay.ui
@@ -44,7 +44,7 @@
         <string/>
        </property>
        <property name="channel" stdset="0">
-        <string>oph://${AD}.overlays.overlay_${OV}.use</string>
+        <string>sig://${AD}.overlays.overlay_${OV}.use</string>
        </property>
       </widget>
      </item>
@@ -61,7 +61,7 @@
         <string/>
        </property>
        <property name="channel" stdset="0">
-        <string>oph://${AD}.overlays.overlay_${OV}.shape</string>
+        <string>sig://${AD}.overlays.overlay_${OV}.shape</string>
        </property>
       </widget>
      </item>
@@ -75,7 +75,7 @@
         <string/>
        </property>
        <property name="channel" stdset="0">
-        <string>oph://${AD}.overlays.overlay_${OV}.position_y</string>
+        <string>sig://${AD}.overlays.overlay_${OV}.position_y</string>
        </property>
        <property name="orientation" stdset="0">
         <enum>Qt::Vertical</enum>
@@ -100,7 +100,7 @@
           <string/>
          </property>
          <property name="channel" stdset="0">
-          <string>oph://${AD}.overlays.overlay_${OV}.position_x</string>
+          <string>sig://${AD}.overlays.overlay_${OV}.position_x</string>
          </property>
          <property name="step_size" stdset="0">
           <number>0</number>
@@ -132,7 +132,7 @@
         <string/>
        </property>
        <property name="channel" stdset="0">
-        <string>oph://${AD}.overlays.overlay_${OV}.size_y</string>
+        <string>sig://${AD}.overlays.overlay_${OV}.size_y</string>
        </property>
        <property name="orientation" stdset="0">
         <enum>Qt::Vertical</enum>
@@ -157,7 +157,7 @@
           <string/>
          </property>
          <property name="channel" stdset="0">
-          <string>oph://${AD}.overlays.overlay_${OV}.size_x</string>
+          <string>sig://${AD}.overlays.overlay_${OV}.size_x</string>
          </property>
         </widget>
        </item>