Fixed tests and linting.

src/firefly/run_browser/client.py

@@ -2,7 +2,7 @@
 import datetime as dt
 import logging
 import warnings
-from collections import OrderedDict, ChainMap
+from collections import ChainMap, OrderedDict
 from functools import partial
 from typing import Mapping, Sequence
 
@@ -162,7 +162,7 @@ async def load_all_runs(self, filters: Mapping = {}):
             all_runs.append(run_data)
         return all_runs
 
-    async def hints(self, stream: str="primary") -> tuple[list, list]:
+    async def hints(self, stream: str = "primary") -> tuple[list, list]:
         """Get hints for this stream, as two lists.
 
         (*independent_hints*, *dependent_hints*)
@@ -178,10 +178,7 @@ async def hints(self, stream: str="primary") -> tuple[list, list]:
         dhints = [hint for hints in dhints for hint in hints]
         return ihints, dhints
 
-
-
     async def signal_names(self, stream: str, *, hinted_only: bool = False):
-
         """Get a list of valid signal names (data columns) for selected runs.
 
         Parameters
@@ -258,7 +255,7 @@ async def all_signals(self, stream: str, *, hinted_only=False) -> dict:
 
     async def dataset(
         self,
-            dataset_name: str,
+        dataset_name: str,
         *,
         stream: str,
         uids: Sequence[str] | None = None,
@@ -284,7 +281,6 @@ async def dataset(
             arrays[run.uid] = arr
         return arrays
 
-
     async def signals(
         self,
         x_signal,

src/firefly/run_browser/display.py

@@ -1,14 +1,13 @@
 import asyncio
 import datetime as dt
 import logging
-from collections import Counter, ChainMap
+from collections import ChainMap, Counter
 from contextlib import contextmanager
 from functools import partial, wraps
 from typing import Mapping, Optional, Sequence
 
-import qtawesome as qta
-import yaml
 import numpy as np
+import qtawesome as qta
 from ophyd import Device as ThreadedDevice
 from ophyd_async.core import Device
 from pydm import PyDMChannel
@@ -95,7 +94,9 @@ async def change_catalog(self, catalog_name: str):
         )
 
     @asyncSlot(str)
-    async def retrieve_dataset(self, dataset_name: str, callback, task_name: str) -> np.ndarray:
+    async def retrieve_dataset(
+        self, dataset_name: str, callback, task_name: str
+    ) -> np.ndarray:
         """Retrieve a dataset from disk, and provide it to the slot.
 
         Parameters
@@ -106,9 +107,11 @@ async def retrieve_dataset(self, dataset_name: str, callback, task_name: str) ->
           Will be called with the retrieved dataset.
         task_name
           For handling parallel database tasks.
-       """
+        """
         # Retrieve data from the database
-        data = await self.db_task(self.db.dataset(dataset_name, stream=self.stream), task_name)
+        data = await self.db_task(
+            self.db.dataset(dataset_name, stream=self.stream), task_name
+        )
         # Pass it back to the slot
         callback(data)
 
@@ -414,7 +417,9 @@ async def update_data_keys(self, *args):
                 self.db_task(self.db.hints(stream), "update data hints"),
             )
         independent_hints, dependent_hints = hints
-        self.data_keys_changed.emit(data_keys, set(independent_hints), set(dependent_hints))
+        self.data_keys_changed.emit(
+            data_keys, set(independent_hints), set(dependent_hints)
+        )
 
     @asyncSlot()
     @cancellable
@@ -425,8 +430,12 @@ async def update_data_frames(self):
             assert False
             log.info("Not loading data frames for empty stream.")
         else:
-            with self.busy_hints(run_widgets=True, run_table=False, filter_widgets=False):
-                data_frames = await self.db_task(self.db.data_frames(stream), "update data frames")
+            with self.busy_hints(
+                run_widgets=True, run_table=False, filter_widgets=False
+            ):
+                data_frames = await self.db_task(
+                    self.db.data_frames(stream), "update data frames"
+                )
         self.data_frames_changed.emit(data_frames)
 
     @asyncSlot()

src/firefly/run_browser/gridplot_view.py

@@ -1,20 +1,15 @@
 import logging
-from itertools import count
 from pathlib import Path
 from typing import Mapping, Sequence
 
-from scipy.interpolate import griddata
 import numpy as np
 import pandas as pd
-import yaml
-from matplotlib.colors import TABLEAU_COLORS
-from pandas.api.types import is_numeric_dtype
-from pyqtgraph import GraphicsLayoutWidget, ImageView, PlotItem, PlotWidget
 import pyqtgraph
-import qtawesome as qta
-from qtpy import QtCore, QtWidgets, uic
-from qtpy.QtCore import Qt, Signal, Slot
-from qtpy.QtWidgets import QFileDialog, QWidget
+from matplotlib.colors import TABLEAU_COLORS
+from pyqtgraph import ImageView, PlotItem
+from qtpy import QtWidgets, uic
+from qtpy.QtCore import Slot
+from scipy.interpolate import griddata
 
 log = logging.getLogger(__name__)
 colors = list(TABLEAU_COLORS.values())
@@ -32,6 +27,7 @@ def __init__(self, *args, view=None, **kwargs):
 
 class GridplotView(QtWidgets.QWidget):
     """Handles the plotting of tabular data that was taken on a grid."""
+
     ui_file = Path(__file__).parent / "gridplot_view.ui"
     shape = ()
     extent = ()
@@ -46,7 +42,7 @@ def __init__(self, parent=None):
         self.ui = uic.loadUi(self.ui_file, self)
         # Prepare plotting style
         vbox = self.ui.plot_widget.ui.roiPlot.getPlotItem().getViewBox()
-        vbox.setBackgroundColor('k')
+        vbox.setBackgroundColor("k")
         # Connect internal signals/slots
         self.ui.use_hints_checkbox.stateChanged.connect(self.update_signal_widgets)
         self.ui.regrid_checkbox.stateChanged.connect(self.update_signal_widgets)
@@ -67,8 +63,8 @@ def set_image_dimensions(self, metadata: Sequence):
             return
         md = list(metadata.values())[0]
         try:
-            self.shape = md['start']['shape']
-            self.extent = md['start']['extents']
+            self.shape = md["start"]["shape"]
+            self.extent = md["start"]["extents"]
         except KeyError as exc:
             self.shape = ()
             self.extent = ()
@@ -116,7 +112,9 @@ def update_signal_widgets(
             self.ui.value_signal_combobox,
             self.ui.r_signal_combobox,
         ]
-        for combobox, new_cols in zip(comboboxes, [new_xcols, new_xcols, new_ycols, new_ycols]):
+        for combobox, new_cols in zip(
+            comboboxes, [new_xcols, new_xcols, new_ycols, new_ycols]
+        ):
             old_cols = [combobox.itemText(idx) for idx in range(combobox.count())]
             if old_cols != new_cols:
                 old_value = combobox.currentText()
@@ -173,13 +171,11 @@ def prepare_plotting_data(self, df: pd.DataFrame) -> tuple[np.ndarray, np.ndarra
         return img
 
     def regrid(self, points: np.ndarray, values: np.ndarray):
-        """Calculate a new image with a shape based on metadata.
-
-        """
+        """Calculate a new image with a shape based on metadata."""
         # Prepare new regular grid to interpolate to
         (ymin, ymax), (xmin, xmax) = self.extent
         ystep, xstep = (npts * 1j for npts in self.shape)
-        yy, xx = np.mgrid[ymin:ymax:ystep,xmin:xmax:xstep]
+        yy, xx = np.mgrid[ymin:ymax:ystep, xmin:xmax:xstep]
         xi = np.c_[yy.flatten(), xx.flatten()]
         # Interpolate
         new_values = griddata(points, values, xi, method="cubic")
@@ -218,7 +214,9 @@ def plot(self, dataframes: Mapping | None = None):
         try:
             ylabel, xlabel = self.independent_hints
         except ValueError:
-            log.warning(f"Could not determine grid labels from hints: {self.independent_hints}")
+            log.warning(
+                f"Could not determine grid labels from hints: {self.independent_hints}"
+            )
         else:
             view = self.ui.plot_widget.view
             view.setLabels(left=ylabel, bottom=xlabel)
@@ -233,54 +231,3 @@ def plot(self, dataframes: Mapping | None = None):
     def clear_plot(self):
         self.ui.plot_widget.getImageItem().clear()
         self.data_items = {}
-
-
-# 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
-#     ):
-#         """Take loaded 2D or 3D mapping data and plot it.
-
-#         Parameters
-#         ==========
-#         runs
-#           Dictionary with pandas series for each curve. The keys
-#           should be the curve labels, the series' indexes are the x
-#           values and the series' values are the y data.
-#         xlabel
-#           The label for the horizontal axis.
-#         ylabel
-#           The label for the vertical axis.
-#         extents
-#           Spatial extents for the map as ((-y, +y), (-x, +x)).
-
-#         """
-#         images = np.asarray(list(runs.values()))
-#         # Combine the different runs into one image
-#         # 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)
-#         else:
-#             log.info(f"Could not plot image of dataset with shape {image.shape}.")
-#             return
-#         # Determine the axes labels
-#         self.view.setLabel(axis="bottom", text=xlabel)
-#         self.view.setLabel(axis="left", text=ylabel)
-#         # Set axes extent
-#         yextent, xextent = extents
-#         x = xextent[0]
-#         y = yextent[0]
-#         w = xextent[1] - xextent[0]
-#         h = yextent[1] - yextent[0]
-#         self.getImageItem().setRect(x, y, w, h)

src/firefly/run_browser/lineplot_view.py

@@ -1,18 +1,14 @@
 import logging
-from itertools import count
 from pathlib import Path
 from typing import Mapping, Sequence
 
 import numpy as np
 import pandas as pd
-import yaml
-from matplotlib.colors import TABLEAU_COLORS
-from pandas.api.types import is_numeric_dtype
-from pyqtgraph import GraphicsLayoutWidget, ImageView, PlotItem, PlotWidget
 import qtawesome as qta
-from qtpy import QtCore, QtWidgets, uic
-from qtpy.QtCore import Qt, Signal, Slot
-from qtpy.QtWidgets import QFileDialog, QWidget
+from matplotlib.colors import TABLEAU_COLORS
+from pyqtgraph import PlotItem, PlotWidget
+from qtpy import QtWidgets, uic
+from qtpy.QtCore import Signal, Slot
 
 log = logging.getLogger(__name__)
 colors = list(TABLEAU_COLORS.values())
@@ -148,7 +144,7 @@ def axis_labels(self):
         use_reference = self.ui.r_signal_checkbox.checkState()
         inverted = self.ui.invert_checkbox.checkState()
         logarithm = self.ui.logarithm_checkbox.checkState()
-        gradient =  self.ui.gradient_checkbox.checkState()
+        gradient = self.ui.gradient_checkbox.checkState()
         if use_reference and inverted:
             ylabel = f"{rlabel}/{ylabel}"
         elif use_reference:

src/firefly/run_browser/metadata_view.py

@@ -2,8 +2,7 @@
 from typing import Mapping
 
 import yaml
-from qtpy import QtCore, QtWidgets, uic
-from qtpy.QtCore import Signal
+from qtpy import QtWidgets, uic
 
 
 class MetadataView(QtWidgets.QWidget):

src/firefly/run_browser/multiplot_view.py

@@ -1,22 +1,15 @@
 import logging
 from itertools import count
-from typing import Mapping, Sequence
 from pathlib import Path
+from typing import Mapping, Sequence
 
-import yaml
-from qtpy import QtCore, QtWidgets, uic
-from qtpy.QtCore import Signal, Slot
-import numpy as np
-from matplotlib.colors import TABLEAU_COLORS
 from pandas.api.types import is_numeric_dtype
-from pyqtgraph import GraphicsLayoutWidget, ImageView, PlotItem, PlotWidget
-from qtpy.QtCore import Qt, Signal
-from qtpy.QtWidgets import QFileDialog, QWidget
-
-
+from qtpy import QtWidgets, uic
+from qtpy.QtCore import Slot
 
 log = logging.getLogger(__name__)
 
+
 class MultiplotView(QtWidgets.QWidget):
     _multiplot_items: Mapping
     ui_file = Path(__file__).parent / "multiplot_view.ui"
@@ -155,4 +148,3 @@ def multiplot_items(self, n_cols: int = 3):
             # view.resize(int(width), int(plot_width * row))
             view.setFixedHeight(1200)
             yield new_item
-

src/firefly/run_browser/tests/test_client.py

@@ -26,6 +26,7 @@ async def test_data_frames(worker):
     # Check the results
     assert uids[0] in data_keys.keys()
 
+
 @pytest.mark.asyncio
 async def test_hints(worker):
     uids = (await worker.catalog.client).keys()

src/firefly/run_browser/tests/test_display.py

@@ -3,11 +3,9 @@
 from functools import partial
 from unittest.mock import AsyncMock, MagicMock
 
-import numpy as np
 import pytest
 import time_machine
 from ophyd.sim import instantiate_fake_device
-from pyqtgraph import ImageItem, ImageView, PlotItem, PlotWidget
 from qtpy.QtWidgets import QFileDialog
 
 from firefly.run_browser.display import RunBrowserDisplay
@@ -103,37 +101,6 @@ async def test_metadata(display, qtbot):
         await display.update_selected_runs()
 
 
-@pytest.mark.xfail
-async def test_update_2d_plot(catalog, display):
-    display.plot_2d_item.setRect = MagicMock()
-    # Load test data
-    run = await catalog["85573831-f4b4-4f64-b613-a6007bf03a8d"]
-    display.db.selected_runs = [run]
-    await display.update_1d_signals()
-    # Set the controls to describe the data we want to test
-    val_combobox = display.ui.signal_value_combobox
-    val_combobox.addItem("It_net_counts")
-    val_combobox.setCurrentText("It_net_counts")
-    display.ui.logarithm_checkbox_2d.setChecked(True)
-    display.ui.invert_checkbox_2d.setChecked(True)
-    display.ui.gradient_checkbox_2d.setChecked(True)
-    # Update the plots
-    await display.update_2d_plot()
-    # Determine what the image data should look like
-    expected_data = await run.__getitem__("It_net_counts", stream="primary")
-    expected_data = expected_data.reshape((5, 21)).T
-    # Check that the data were added
-    image = display.plot_2d_item.image
-    np.testing.assert_almost_equal(image, expected_data)
-    # Check that the axes were formatted correctly
-    axes = display.plot_2d_view.view.axes
-    xaxis = axes["bottom"]["item"]
-    yaxis = axes["left"]["item"]
-    assert xaxis.labelText == "aerotech_horiz"
-    assert yaxis.labelText == "aerotech_vert"
-    display.plot_2d_item.setRect.assert_called_with(-100, -80, 200, 160)
-
-
 def test_busy_hints_run_widgets(display):
     """Check that the display widgets get disabled during DB hits."""
     with display.busy_hints(run_widgets=True, run_table=False):