Merge pull request #140 from BCDA-APS/107-bug-test-files-some-crash-t…

…he-app

Solve performance issues when loading folders

.github/workflows/docs.yml

@@ -68,7 +68,7 @@ jobs:
         name: mdaviz-docs
         path: docs/build/html
         # ${{ steps.deployment.outputs.artifact }}
-    
+
     - name: Publish (push gh-pages branch) only on demand
       uses: peaceiris/actions-gh-pages@v4
       if: ${{ github.event.inputs.deploy }}

.gitignore

@@ -172,4 +172,5 @@ dev_*.py
 mdaviz/resources/*.py
 
 # temporary files from Microsoft
-~*
+~*
+Untitled.ipynb

.pre-commit-config.yaml

@@ -0,0 +1,24 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-toml
+      - id: check-ast
+      - id: check-merge-conflict
+      - id: check-added-large-files
+      - id: mixed-line-ending
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.7.1
+    hooks:
+      - id: nbstripout
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.3.2
+    hooks:
+      # Run the linter.
+      - id: ruff
+        args: [--fix]
+      # Run the formatter.
+      - id: ruff-format

README.md

@@ -3,7 +3,7 @@
 Python Qt5 application to visualize mda data.
 
 GH tag | GH release | PyPI
---- | --- | --- 
+--- | --- | ---
 [![tag](https://img.shields.io/github/tag/BCDA-APS/mdaviz.svg)](https://github.com/BCDA-APS/mdaviz/tags) | [![release](https://img.shields.io/github/release/BCDA-APS/mdaviz.svg)](https://github.com/BCDA-APS/mdaviz/releases) | [![PyPi](https://img.shields.io/pypi/v/mdaviz.svg)](https://pypi.python.org/pypi/mdaviz)
 
 Python version(s) | Unit Tests | Code Coverage | License
@@ -20,5 +20,5 @@ For complete installation guide, see [https://bcda-aps.github.io/mdaviz/](https:
 
 ## Acknowledgements
 
-"This product includes software produced by UChicago Argonne, LLC 
+"This product includes software produced by UChicago Argonne, LLC
 under Contract No. DE-AC02-06CH11357 with the Department of Energy."

docs/source/changes.rst

@@ -3,4 +3,4 @@
 Changes
 =======
 
-TODO
+TODO

docs/source/index.rst

@@ -36,8 +36,8 @@ Documentation
    :align: center
    :figclass: align-center
    :figwidth: 100%
-   
-   Screenshot of the mdaviz GUI displaying sample data. 
+
+   Screenshot of the mdaviz GUI displaying sample data.
 
 .. toctree::
    :maxdepth: 1
@@ -68,5 +68,5 @@ About
 Acknowledgements
 ================
 
-"This product includes software produced by UChicago Argonne, LLC 
+"This product includes software produced by UChicago Argonne, LLC
 under Contract No. DE-AC02-06CH11357 with the Department of Energy."

docs/source/license.rst

@@ -4,4 +4,4 @@ License
 =======
 
 .. literalinclude:: ../../mdaviz/LICENSE
-   :language: text
+   :language: text

mdaviz/LICENSE

@@ -9,27 +9,27 @@ BCDA, Advanced Photon Source, Argonne National Laboratory
 
 OPEN SOURCE LICENSE
 
-Redistribution and use in source and binary forms, with or without 
+Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:
 
-1. Redistributions of source code must retain the above copyright notice, 
-   this list of conditions and the following disclaimer.  Software changes, 
-   modifications, or derivative works, should be noted with comments and 
+1. Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.  Software changes,
+   modifications, or derivative works, should be noted with comments and
    the author and organization's name.
 
 2. Redistributions in binary form must reproduce the above copyright notice,
-   this list of conditions and the following disclaimer in the documentation 
+   this list of conditions and the following disclaimer in the documentation
    and/or other materials provided with the distribution.
 
-3. Neither the names of UChicago Argonne, LLC or the Department of Energy 
-   nor the names of its contributors may be used to endorse or promote 
-   products derived from this software without specific prior written 
+3. Neither the names of UChicago Argonne, LLC or the Department of Energy
+   nor the names of its contributors may be used to endorse or promote
+   products derived from this software without specific prior written
    permission.
 
-4. The software and the end-user documentation included with the 
+4. The software and the end-user documentation included with the
    redistribution, if any, must include the following acknowledgment:
 
-   "This product includes software produced by UChicago Argonne, LLC 
+   "This product includes software produced by UChicago Argonne, LLC
    under Contract No. DE-AC02-06CH11357 with the Department of Energy."
 
 ****************************************************************************
@@ -38,11 +38,11 @@ DISCLAIMER
 
 THE SOFTWARE IS SUPPLIED "AS IS" WITHOUT WARRANTY OF ANY KIND.
 
-Neither the United States GOVERNMENT, nor the United States Department 
-of Energy, NOR uchicago argonne, LLC, nor any of their employees, makes 
-any warranty, express or implied, or assumes any legal liability or 
-responsibility for the accuracy, completeness, or usefulness of any 
-information, data, apparatus, product, or process disclosed, or 
+Neither the United States GOVERNMENT, nor the United States Department
+of Energy, NOR uchicago argonne, LLC, nor any of their employees, makes
+any warranty, express or implied, or assumes any legal liability or
+responsibility for the accuracy, completeness, or usefulness of any
+information, data, apparatus, product, or process disclosed, or
 represents that its use would not infringe privately owned rights.
 
 ****************************************************************************

mdaviz/app.py

@@ -23,9 +23,7 @@ def gui(directory):
 
     app = QtWidgets.QApplication(sys.argv)
     main_window = MainWindow(directory=directory)
-    main_window.setStatus(
-        f"Application started, loading {pathlib.Path(directory).absolute()} ..."
-    )
+    main_window.setStatus(f"Application started, loading {pathlib.Path(directory).absolute()} ...")
     main_window.show()
     sys.exit(app.exec())
 
@@ -74,16 +72,12 @@ def main():  # for future command-line options
 
     # Ensure the path is absolute (starts with a "/")
     if not directory.startswith("/"):
-        print(
-            f"\n\nERROR: The specified directory is not an absolute path:\n\t{directory}\n"
-        )
+        print(f"\n\nERROR: The specified directory is not an absolute path:\n\t{directory}\n")
         sys.exit(1)
 
     # Check if the directory exists
     if not directory_path.exists() or not directory_path.is_dir():
-        print(
-            f"\n\nERROR: The specified directory does not exist or is not a directory:\n\t{directory}\n"
-        )
+        print(f"\n\nERROR: The specified directory does not exist or is not a directory:\n\t{directory}\n")
         sys.exit(1)
 
     logging.basicConfig(level=options.log.upper())

mdaviz/chartview.py

@@ -6,7 +6,6 @@
 from functools import partial
 from itertools import cycle
 import numpy
-from pathlib import Path
 from PyQt5 import QtCore, QtWidgets
 from . import utils
 
@@ -414,11 +413,7 @@ def calculateBasicMath(self, x_data, y_data):
         x_at_y_min = x_array[y_min_index]
         x_at_y_max = x_array[y_max_index]
         # Calculate x_com and y_mean
-        x_com = (
-            numpy.sum(x_array * y_array) / numpy.sum(y_array)
-            if numpy.sum(y_array) != 0
-            else None
-        )
+        x_com = numpy.sum(x_array * y_array) / numpy.sum(y_array) if numpy.sum(y_array) != 0 else None
         y_mean = numpy.mean(y_array)
         return (x_at_y_min, y_min), (x_at_y_max, y_max), x_com, y_mean
 
@@ -430,9 +425,7 @@ def onRemoveCursor(self, cursor_num):
             cross.remove()
             self.cursors[cursor_num] = None
             self.cursors[f"pos{cursor_num}"] = None
-            self.cursors[f"text{cursor_num}"] = (
-                "middle click" if cursor_num == 1 else "right click"
-            )
+            self.cursors[f"text{cursor_num}"] = "middle click" if cursor_num == 1 else "right click"
         self.cursors["diff"] = "n/a"
         self.cursors["midpoint"] = "n/a"
         self.updateCursorInfo()
@@ -493,12 +486,8 @@ def calculateCursors(self):
             delta_y = y2 - y1
             midpoint_x = (x1 + x2) / 2
             midpoint_y = (y1 + y2) / 2
-            self.cursors["diff"] = (
-                f"({utils.num2fstr(delta_x)}, {utils.num2fstr(delta_y)})"
-            )
-            self.cursors["midpoint"] = (
-                f"({utils.num2fstr(midpoint_x)}, {utils.num2fstr(midpoint_y)})"
-            )
+            self.cursors["diff"] = f"({utils.num2fstr(delta_x)}, {utils.num2fstr(delta_y)})"
+            self.cursors["midpoint"] = f"({utils.num2fstr(midpoint_x)}, {utils.num2fstr(midpoint_y)})"
         self.updateCursorInfo()
 
     def updateCursorInfo(self):
@@ -525,9 +514,7 @@ class CurveManager(QtCore.QObject):
     curveUpdated = QtCore.pyqtSignal(
         str, bool, bool
     )  # Emit curveID, recompute_y (bool) & update_x (bool) when a curve is updated
-    allCurvesRemoved = QtCore.pyqtSignal(
-        bool
-    )  # Emit a doNotClearCheckboxes bool when all curve are removed
+    allCurvesRemoved = QtCore.pyqtSignal(bool)  # Emit a doNotClearCheckboxes bool when all curve are removed
 
     def __init__(self, parent=None):
         super().__init__(parent)

mdaviz/data_table_view.py

@@ -1,11 +1,9 @@
-from PyQt5 import QtCore, QtWidgets
-from . import utils
+from PyQt5 import QtWidgets
 
 HEADERS = ["X", "Y"]
 
 
 class DataTableView(QtWidgets.QWidget):
-
     def __init__(self, data, parent):
         """
         This class is responsible for setting up a table view widget, managing the data displayed within it,