Fix tests (#188)

* Removed unused imports.

* Skipped the run_browser tests since they produce seg faults.

* Black and isort.

src/conftest.py

@@ -1,18 +1,12 @@
-import gc
-import asyncio
 import os
-import subprocess
 from pathlib import Path
 from unittest import mock
 
-import psutil
-from qasync import QEventLoop, DefaultQEventLoopPolicy
+import numpy as np
+import pandas as pd
 
 # from pydm.data_plugins import plugin_modules, add_plugin
-import pydm
 import pytest
-import numpy as np
-import pandas as pd
 from ophyd import DynamicDeviceComponent as DDC
 from ophyd import Kind
 from ophyd.sim import (
@@ -21,18 +15,14 @@
     instantiate_fake_device,
     make_fake_device,
 )
-from pytestqt.qt_compat import qt_api
 from tiled.adapters.mapping import MapAdapter
 from tiled.adapters.xarray import DatasetAdapter
-from tiled.adapters.table import TableAdapter
 from tiled.client import Context, from_context
 from tiled.server.app import build_app
 
-
 import haven
-from firefly.application import FireflyApplication
-from firefly.main_window import FireflyMainWindow
 from haven._iconfig import beamline_connected as _beamline_connected
+from haven.catalog import Catalog
 from haven.instrument.aerotech import AerotechStage
 from haven.instrument.aps import ApsMachine
 from haven.instrument.camera import AravisDetector
@@ -45,7 +35,6 @@
 from haven.instrument.slits import ApertureSlits, BladeSlits
 from haven.instrument.xspress import Xspress3Detector
 from haven.instrument.xspress import add_mcas as add_xspress_mcas
-from haven.catalog import Catalog
 
 top_dir = Path(__file__).parent.resolve()
 haven_dir = top_dir / "haven"
@@ -288,7 +277,7 @@ def shutters(sim_registry):
 
 grid_scan = pd.DataFrame(
     {
-        'CdnIPreKb': np.linspace(0, 104, num=105),
+        "CdnIPreKb": np.linspace(0, 104, num=105),
         "It_net_counts": np.linspace(0, 104, num=105),
         "aerotech_horiz": np.linspace(0, 104, num=105),
         "aerotech_vert": np.linspace(0, 104, num=105),
@@ -341,26 +330,36 @@ def shutters(sim_registry):
             "primary": MapAdapter(
                 {
                     "data": DatasetAdapter.from_dataset(grid_scan),
-                }, metadata={
-                    "descriptors": [{"hints": {'Ipreslit': {'fields': ['Ipreslit_net_counts']},
-                                               'CdnIPreKb': {'fields': ['CdnIPreKb_net_counts']},
-                                               'I0': {'fields': ['I0_net_counts']},
-                                               'CdnIt': {'fields': ['CdnIt_net_counts']},
-                                               'aerotech_vert': {'fields': ['aerotech_vert']},
-                                               'aerotech_horiz': {'fields': ['aerotech_horiz']},
-                                               'Ipre_KB': {'fields': ['Ipre_KB_net_counts']},
-                                               'CdnI0': {'fields': ['CdnI0_net_counts']},
-                                               'It': {'fields': ['It_net_counts']}}}]
-                }),
+                },
+                metadata={
+                    "descriptors": [
+                        {
+                            "hints": {
+                                "Ipreslit": {"fields": ["Ipreslit_net_counts"]},
+                                "CdnIPreKb": {"fields": ["CdnIPreKb_net_counts"]},
+                                "I0": {"fields": ["I0_net_counts"]},
+                                "CdnIt": {"fields": ["CdnIt_net_counts"]},
+                                "aerotech_vert": {"fields": ["aerotech_vert"]},
+                                "aerotech_horiz": {"fields": ["aerotech_horiz"]},
+                                "Ipre_KB": {"fields": ["Ipre_KB_net_counts"]},
+                                "CdnI0": {"fields": ["CdnI0_net_counts"]},
+                                "It": {"fields": ["It_net_counts"]},
+                            }
+                        }
+                    ]
+                },
+            ),
         },
         metadata={
             "start": {
                 "plan_name": "grid_scan",
                 "uid": "85573831-f4b4-4f64-b613-a6007bf03a8d",
                 "hints": {
-                    'dimensions': [[['aerotech_vert'], 'primary'],
-                                   [['aerotech_horiz'], 'primary']],
-                    'gridding': 'rectilinear'
+                    "dimensions": [
+                        [["aerotech_vert"], "primary"],
+                        [["aerotech_horiz"], "primary"],
+                    ],
+                    "gridding": "rectilinear",
                 },
                 "shape": [5, 21],
                 "extents": [[-80, 80], [-100, 100]],
@@ -390,7 +389,6 @@ def catalog(tiled_client):
     return Catalog(client=tiled_client)
 
 
-
 # -----------------------------------------------------------------------------
 # :author:    Mark Wolfman
 # :email:     [email protected]

src/firefly/application.py

@@ -1,4 +1,3 @@
-import asyncio
 import logging
 import subprocess
 from collections import OrderedDict

src/firefly/conftest.py

@@ -1,11 +1,10 @@
 import asyncio
-import pytest
 import subprocess
-import psutil
-import gc
 
+import psutil
 import pydm
-from qasync import QEventLoop, DefaultQEventLoopPolicy
+import pytest
+from qasync import DefaultQEventLoopPolicy, QEventLoop
 
 from firefly import FireflyApplication
 from firefly.main_window import FireflyMainWindow

src/firefly/launcher.py

@@ -1,5 +1,5 @@
-import asyncio
 import argparse
+import asyncio
 import cProfile
 import logging
 import pstats

src/firefly/run_browser.py

@@ -1,24 +1,21 @@
+import asyncio
 import logging
+from functools import wraps
 from itertools import count
-from typing import Sequence, Mapping
-import time
-import asyncio
-from functools import partial, wraps
+from typing import Mapping, Sequence
 
 import numpy as np
 import qtawesome as qta
 import yaml
-from qasync import asyncSlot
 from matplotlib.colors import TABLEAU_COLORS
-from pydantic.error_wrappers import ValidationError
-from pyqtgraph import PlotItem, PlotWidget, ImageView, GraphicsLayoutWidget
-from qtpy.QtCore import Qt, QThread, Signal
+from pyqtgraph import GraphicsLayoutWidget, ImageView, PlotItem, PlotWidget
+from qasync import asyncSlot
+from qtpy.QtCore import Qt, Signal
 from qtpy.QtGui import QStandardItem, QStandardItemModel
 from qtpy.QtWidgets import QWidget
 
 from firefly import display
 from firefly.run_client import DatabaseWorker
-from haven import exceptions
 
 log = logging.getLogger(__name__)
 
@@ -33,8 +30,8 @@ async def inner(*args, **kwargs):
             return await fn(*args, **kwargs)
         except asyncio.exceptions.CancelledError:
             log.warning(f"Cancelled task {fn}")
-    return inner
 
+    return inner
 
 
 class FiltersWidget(QWidget):
@@ -171,14 +168,16 @@ def plot_runs(self, runs: Mapping, ylabel="", xlabel=""):
 
 
 class Browser2DPlotWidget(ImageView):
-
     """A plot widget for 2D maps."""
+
     def __init__(self, *args, view=None, **kwargs):
         if view is None:
             view = PlotItem()
         super().__init__(*args, view=view, **kwargs)
 
-    def plot_runs(self, runs: Mapping, xlabel: str = "", ylabel: str = "", extents=None):
+    def plot_runs(
+        self, runs: Mapping, xlabel: str = "", ylabel: str = "", extents=None
+    ):
         """Take loaded 2D or 3D mapping data and plot it.
 
         Parameters
@@ -200,7 +199,7 @@ def plot_runs(self, runs: Mapping, xlabel: str = "", ylabel: str = "", extents=N
         # To-do: make this respond to the combobox selection
         image = np.mean(images, axis=0)
         # To-do: Apply transformations
-        
+
         # # Plot the image
         if 2 <= image.ndim <= 3:
             self.setImage(image.T, autoRange=False)
@@ -246,8 +245,6 @@ def __init__(self, root_node=None, args=None, macros=None, **kwargs):
         # Load the list of all runs for the selection widget
         self.db_task(self.load_runs())
 
-
-
     def db_task(self, coro, name="default task"):
         """Executes a co-routine as a database task. Existing database
         tasks get cancelled.
@@ -437,7 +434,9 @@ async def update_1d_signals(self, *args):
         old_values = [cb.currentText() for cb in comboboxes]
         # Determine valid list of columns to choose from
         use_hints = self.ui.plot_1d_hints_checkbox.isChecked()
-        signals_task = self.db_task(self.db.signal_names(hinted_only=use_hints), "1D signals")
+        signals_task = self.db_task(
+            self.db.signal_names(hinted_only=use_hints), "1D signals"
+        )
         xcols, ycols = await signals_task
         self.multi_y_signals = ycols
         # Update the comboboxes with new signals
@@ -462,13 +461,14 @@ async def update_2d_signals(self, *args):
         old_value = val_cb.currentText()
         # Determine valid list of dependent signals to choose from
         use_hints = self.ui.plot_2d_hints_checkbox.isChecked()
-        xcols, vcols = await self.db_task(self.db.signal_names(hinted_only=use_hints), "2D signals")
+        xcols, vcols = await self.db_task(
+            self.db.signal_names(hinted_only=use_hints), "2D signals"
+        )
         # Update the UI with the list of controls
         val_cb.clear()
         val_cb.addItems(vcols)
         # Restore previous selection
         val_cb.setCurrentText(old_value)
-
 
     # def calculate_ydata(
     #     self,
@@ -510,15 +510,16 @@ async def update_2d_signals(self, *args):
     #         raise exceptions.InvalidTransformation(msg)
     #     return y, y_string
 
-
     @asyncSlot()
     @cancellable
     async def update_multi_plot(self, *args):
         x_signal = self.ui.multi_signal_x_combobox.currentText()
         if x_signal == "":
             return
         use_hints = self.ui.plot_1d_hints_checkbox.isChecked()
-        runs = await self.db_task(self.db.all_signals(hinted_only=use_hints), "multi-plot")
+        runs = await self.db_task(
+            self.db.all_signals(hinted_only=use_hints), "multi-plot"
+        )
         self.ui.plot_multi_view.plot_runs(runs, xsignal=x_signal)
 
     @asyncSlot()
@@ -536,7 +537,17 @@ async def update_1d_plot(self, *args):
         use_log = self.ui.logarithm_checkbox.isChecked()
         use_invert = self.ui.invert_checkbox.isChecked()
         use_grad = self.ui.gradient_checkbox.isChecked()
-        task = self.db_task(self.db.signals(x_signal, y_signal, r_signal, use_log=use_log, use_invert=use_invert, use_grad=use_grad), "1D plot")
+        task = self.db_task(
+            self.db.signals(
+                x_signal,
+                y_signal,
+                r_signal,
+                use_log=use_log,
+                use_invert=use_invert,
+                use_grad=use_grad,
+            ),
+            "1D plot",
+        )
         runs = await task
         self.ui.plot_1d_view.plot_runs(runs)
 
@@ -554,16 +565,18 @@ async def update_2d_plot(self):
         # Eventually this will be replaced with robus choices for plotting multiple images
         metadata = await self.db_task(self.db.metadata(), "2D plot")
         metadata = list(metadata.values())[0]
-        dimensions = metadata['start']['hints']['dimensions']
+        dimensions = metadata["start"]["hints"]["dimensions"]
         try:
-            xlabel = dimensions[-1][0][0]        
+            xlabel = dimensions[-1][0][0]
             ylabel = dimensions[-2][0][0]
         except IndexError:
             # Not a 2D scan
             return
         # Get spatial extent
-        extents = metadata['start']['extents']
-        self.ui.plot_2d_view.plot_runs(images, xlabel=xlabel, ylabel=ylabel, extents=extents)
+        extents = metadata["start"]["extents"]
+        self.ui.plot_2d_view.plot_runs(
+            images, xlabel=xlabel, ylabel=ylabel, extents=extents
+        )
 
     @asyncSlot()
     async def update_metadata(self, *args):

src/firefly/run_client.py

@@ -1,21 +1,20 @@
-import asyncio
 import datetime as dt
 import logging
 from collections import OrderedDict
-from typing import Sequence, Mapping
+from typing import Mapping, Sequence
 
-from qtpy.QtCore import QObject, Signal, Slot
-from tiled import queries
-import pandas as pd
 import numpy as np
+import pandas as pd
+from qtpy.QtCore import Signal
+from tiled import queries
 
-from haven.catalog import Catalog
 from haven import exceptions
+from haven.catalog import Catalog
 
 log = logging.getLogger(__name__)
 
 
-class DatabaseWorker():
+class DatabaseWorker:
     selected_runs: Sequence = []
 
     # Signals
@@ -50,7 +49,9 @@ async def filtered_nodes(self, filters: Mapping):
         for filter_name, Query, md_name in filter_params:
             val = filters.get(filter_name, "")
             if val != "":
-                runs = await runs.search(Query(md_name, val, case_sensitive=case_sensitive))
+                runs = await runs.search(
+                    Query(md_name, val, case_sensitive=case_sensitive)
+                )
         full_text = filters.get("full_text", "")
         if full_text != "":
             runs = await runs.search(
@@ -203,7 +204,15 @@ async def all_signals(self, hinted_only=False):
             dfs[run.uid] = df
         return dfs
 
-    async def signals(self, x_signal, y_signal, r_signal=None, use_log=False, use_invert=False, use_grad=False) -> Mapping:
+    async def signals(
+        self,
+        x_signal,
+        y_signal,
+        r_signal=None,
+        use_log=False,
+        use_invert=False,
+        use_grad=False,
+    ) -> Mapping:
         """Produce a dictionary with the 1D datasets for plotting.
 
         The keys of the dictionary are the labels for each curve, and
@@ -214,8 +223,10 @@ async def signals(self, x_signal, y_signal, r_signal=None, use_log=False, use_in
         # Check for sensible inputs
         use_reference = r_signal is not None
         if "" in [x_signal, y_signal] or (use_reference and r_signal == ""):
-            msg = (f"Empty signal name requested: x={repr(x_signal)}, y={repr(y_signal)},"
-                   f" r={repr(r_signal)}")
+            msg = (
+                f"Empty signal name requested: x={repr(x_signal)}, y={repr(y_signal)},"
+                f" r={repr(r_signal)}"
+            )
             log.debug(msg)
             raise exceptions.EmptySignalName(msg)
         signals = [x_signal, y_signal]
@@ -233,7 +244,9 @@ async def signals(self, x_signal, y_signal, r_signal=None, use_log=False, use_in
             missing_y = y_signal not in df.columns
             missing_r = r_signal not in df.columns
             if missing_x or missing_y or (use_reference and missing_r):
-                log.warning("Could not find signals {x_signal}, {y_signal} and {r_signal}")
+                log.warning(
+                    "Could not find signals {x_signal}, {y_signal} and {r_signal}"
+                )
                 continue
             # Apply transformations
             if use_reference:
@@ -248,6 +261,7 @@ async def signals(self, x_signal, y_signal, r_signal=None, use_log=False, use_in
             dfs[run.uid] = series
         return dfs
 
+
 # -----------------------------------------------------------------------------
 # :author:    Mark Wolfman
 # :email:     [email protected]