From 20e4e617c8a0db723d5a1cf100297d11e60b00d8 Mon Sep 17 00:00:00 2001
From: Rebelo Alexis <rebelo.alexis@gmail.com>
Date: Fri, 14 Jun 2024 13:24:47 +0200
Subject: [PATCH 01/10] Adding docstring and type

---
 .../app/view/CustomPlotSelectionWindow.py     | 121 ++++++++++++++++--
 1 file changed, 112 insertions(+), 9 deletions(-)

diff --git a/src/silx/app/view/CustomPlotSelectionWindow.py b/src/silx/app/view/CustomPlotSelectionWindow.py
index 8a2d68d938..58ea373375 100644
--- a/src/silx/app/view/CustomPlotSelectionWindow.py
+++ b/src/silx/app/view/CustomPlotSelectionWindow.py
@@ -20,6 +20,7 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 # THE SOFTWARE.
 # ###########################################################################*/
+from __future__ import annotations
 
 """"""
 
@@ -38,10 +39,10 @@
 class _HashDropZones(qt.QStyledItemDelegate):
     """Delegate item displaying a drop zone when the item does not contain a dataset."""
 
-    def __init__(self, parent=None):
+    def __init__(self, parent: qt.QWidget | None = None):
         super(_HashDropZones, self).__init__(parent)
         self.__dropPen = qt.QPen(qt.QColor("#D0D0D0"), 2, qt.Qt.DotLine)
-        self.__highlightDropPen = qt.QPen(qt.QColor("#000000"), 2, qt.Qt.SolidLine)
+        self.__highlightDropPen = qt.QPen(qt.QColor("#000000"), 2, qt.Qt.DotLine)
         self.__dropTargetIndex = None
 
     def paint(self, painter, option, index):
@@ -66,7 +67,7 @@ def paint(self, painter, option, index):
         if isDropHighlighted:
             painter.save()
             painter.setPen(self.__highlightDropPen)
-            painter.drawRect(option.rect.adjusted(1, 1, -1, -1))
+            painter.drawRect(option.rect.adjusted(3, 3, -3, -3))
             painter.restore()
 
         if displayDropZone:
@@ -97,6 +98,12 @@ def paint(self, painter, option, index):
 
 
 class _FileListModel(qt.QStandardItemModel):
+    """
+    A model class for managing and displaying file data in a tree view structure
+
+    :param plot : Plot 1D
+    """
+
     def __init__(self, plot, parent=None):
         super().__init__(parent)
         root = self.invisibleRootItem()
@@ -124,13 +131,23 @@ def __init__(self, plot, parent=None):
 
         self.rowsAboutToBeRemoved.connect(self._rowAboutToBeRemoved)
 
-    def getXParent(self):
+    def getXParent(self) -> qt.QStandardItem:
+        """Returns the X parent item."""
         return self._xParent
 
     def getYParent(self):
+        """Returns the Y parent item.
+
+        :rtype: qt.QStandardItem
+        """
         return self._yParent
 
     def _setXFile(self, url=None, curve=None):
+        """Set X file informations to the model
+
+        :param str filename: The file name.
+        :param curve: The curve data. Defaults to None.
+        """
         if url is None:
             dataName = ""
         else:
@@ -148,6 +165,10 @@ def _setXFile(self, url=None, curve=None):
             self.setItem(xIndex, 2, removeItem)
 
     def _addYFile(self, url=None, curve=None, node="X"):
+        """Add Y file to the model
+
+        :param curve : The curve data. Defaults to None.
+        """
         if url is None:
             dataName = ""
         else:
@@ -167,6 +188,11 @@ def _addYFile(self, url=None, curve=None, node="X"):
         )
 
     def _findRowContainingText(self, text):
+        """Find the row containing the specified text.
+
+        :param str text: The text to search for.
+        """
+
         for row in range(self.rowCount()):
             item = self.item(row, 0)
             if item and item.text() == text:
@@ -174,6 +200,11 @@ def _findRowContainingText(self, text):
         return None
 
     def _createRowItems(self, filename, curve):
+        """Create row items for the file.
+
+        :param str filename : The file name.
+        :param Curve curve : The curve data
+        """
         fileItem = qt.QStandardItem(filename)
         fileItem.setData(curve, qt.Qt.UserRole)
         fileItem.setData(False, _DROP_HIGHLIGHT_ROLE)
@@ -187,6 +218,10 @@ def _createRowItems(self, filename, curve):
         return fileItem, iconItem, removeItem
 
     def fileItemExists(self, filename):
+        """Check if the file already exists in the model.
+
+        :param str filename : The file name.
+        """
         for row in range(self.getYParent().rowCount()):
             item = self.item(row, 1)
             if item and item.text() == filename:
@@ -194,6 +229,12 @@ def fileItemExists(self, filename):
         return False
 
     def addUrl(self, url, node="X"):
+        """Add a URL to the model.
+
+        :param url : The data URL.
+        :param node : The node name. Defaults to "X".
+        """
+
         if url.file_path() is not None:
             file = silx.io.open(url.file_path())
             data = file[url.data_path()]
@@ -215,7 +256,12 @@ def addUrl(self, url, node="X"):
                     curve = self._addPlot(self._xDataset, data)
                     self._addYFile(url, curve)
 
-    def _addPlot(self, x, y):
+    def _addPlot(self, x: numpy.ndarray, y):
+        """Add a curve to the plot
+
+        :param x:
+        :param y:
+        """
         if x is None:
             x = numpy.arange(len(y))
 
@@ -228,6 +274,12 @@ def _addPlot(self, x, y):
         return curve
 
     def _rowAboutToBeRemoved(self, parentIndex, first, last):
+        """Handle the event when rows are about to be removed.
+
+        :param parentIndex : the parent index.
+        :param int first : the first row to be removed.
+        :param int last : the last row to be removed.
+        """
         parentItem = self.itemFromIndex(parentIndex)
         for row in range(first, last + 1):
             fileItem = parentItem.child(row, 1)
@@ -236,6 +288,7 @@ def _rowAboutToBeRemoved(self, parentIndex, first, last):
                 self._plot1D.removeItem(curve)
 
     def _updateYCurvesWithDefaultX(self):
+        """Update Y curves with default X values"""
         for item in self._plot1D.getItems():
             y = item.getInfo()
             x = numpy.arange(len(y))
@@ -243,6 +296,7 @@ def _updateYCurvesWithDefaultX(self):
             self._plot1D.resetZoom()
 
     def clearAll(self):
+        """Clear all data from the model"""
         self._xDataset = None
 
         self._yParent.removeRows(0, self._yParent.rowCount())
@@ -280,11 +334,15 @@ def _getBasename(self, text):
 
 
 class _DropTreeView(qt.QTreeView):
-    """TreeView widget for displaying dropped file names"""
+    """TreeView widget for displaying dropped file names
+
+    :param model : _FileListModel
+    """
 
     (_DESCRIPTION_COLUMN, _FILE_COLUMN, _REMOVE_COLUMN) = range(3)
 
     def __init__(self, model, parent=None):
+        """Constructor"""
         super().__init__(parent)
         self.setModel(model)
 
@@ -292,9 +350,13 @@ def __init__(self, model, parent=None):
 
         header = self.header()
         header.setStretchLastSection(False)
-        header.setSectionResizeMode(0, qt.QHeaderView.ResizeToContents)
-        header.setSectionResizeMode(1, qt.QHeaderView.Stretch)
-        header.setSectionResizeMode(2, qt.QHeaderView.ResizeToContents)
+        header.setSectionResizeMode(
+            _DropTreeView._DESCRIPTION_COLUMN, qt.QHeaderView.ResizeToContents
+        )
+        header.setSectionResizeMode(_DropTreeView._FILE_COLUMN, qt.QHeaderView.Stretch)
+        header.setSectionResizeMode(
+            _DropTreeView._REMOVE_COLUMN, qt.QHeaderView.ResizeToContents
+        )
         self.expandAll()
 
         self.setSelectionMode(qt.QAbstractItemView.SingleSelection)
@@ -307,6 +369,11 @@ def __init__(self, model, parent=None):
         self.viewport().setAcceptDrops(True)
 
     def _createIconWidget(self, row, parentItem):
+        """Create an icon widget for the specified row.
+
+        :param row : The row index.
+        :param parentItem : The parent item.
+        """
         fileItem = parentItem.child(row, 1)
         iconItem = parentItem.child(row, 0)
         curve = fileItem.data(qt.Qt.UserRole)
@@ -321,6 +388,11 @@ def _createIconWidget(self, row, parentItem):
         self.setIndexWidget(iconItem.index(), widget)
 
     def _createRemoveButton(self, row, parentItem):
+        """Create an remove button for the specified row.
+
+        :param row : The row index.
+        :param parentItem : The parent item
+        """
         if parentItem is None:
             parentItem = self.model().getXParent()
             index = self.model().index(0, 2)
@@ -342,6 +414,11 @@ def _createRemoveButton(self, row, parentItem):
             self.setIndexWidget(removeItem.index(), button)
 
     def _removeFile(self, removeItem, parentItem):
+        """Remove the specified file from the model.
+
+        :param removeItem : The item to be removed.
+        :param parentItem : The parent item.
+        """
         if removeItem is None:
             row = 0
             removeItem = self.model().getXParent()
@@ -399,6 +476,7 @@ def dropEvent(self, event):
         event.acceptProposedAction()
 
     def acceptDragEvent(self, event):
+        """Accept the drop event if the data is valid."""
         if event.mimeData().hasFormat("application/x-silx-uri"):
             byteString = event.mimeData().data("application/x-silx-uri")
             url = silx.io.url.DataUrl(byteString.data().decode("utf-8"))
@@ -414,6 +492,10 @@ def acceptDragEvent(self, event):
             event.ignore()
 
     def setX(self, url):
+        """Set the X data from the URL.
+
+        :param url : The data URL.
+        """
         targetNode = "X"
         node = self.model().getXParent()
         self.model().addUrl(url, targetNode)
@@ -421,6 +503,10 @@ def setX(self, url):
         self.model()._plot1D.resetZoom()
 
     def addY(self, url):
+        """Add the Y data from the URL.
+
+        :param url : The data URL.
+        """
         targetNode = "Y"
         node = self.model().getYParent()
         self.model().addUrl(url, targetNode)
@@ -429,11 +515,15 @@ def addY(self, url):
         self.model()._plot1D.resetZoom()
 
     def clear(self):
+        """Clear all data from the tree view."""
         self.model().clearAll()
         index = self.model().index(0, 2)
         self.setIndexWidget(index, None)
 
     def setDropHighlight(self, value):
+        """Set the drop highlight for the specified value.
+
+        :param value : The value to highlight ("X" or "Y")"""
         xDropFileItem = self.model().itemFromIndex(
             self.model().sibling(
                 0, 1, self.model().indexFromItem(self.model().getXParent())
@@ -447,12 +537,19 @@ def setDropHighlight(self, value):
 
 
 class _DropPlot1D(plot.Plot1D):
+    """A plot widget with drag-and-drop functionality for adding data."""
+
     def __init__(self, parent=None):
+        """Constructor"""
         super().__init__(parent)
         self.setAcceptDrops(True)
         self._treeView = None
 
     def setTreeView(self, treeView):
+        """Set the tree view for the plot.
+
+        :param treeview :
+        """
         self._treeView = treeView
 
     def dragEnterEvent(self, event):
@@ -485,10 +582,16 @@ def setXAxisLabel(self, label):
 
 
 class _PlotToolBar(qt.QToolBar):
+    """"""
+
     def __init__(self, parent=None):
         super().__init__(parent)
 
     def addClearAction(self, treeView):
+        """Add a clear action to the ToolBar
+
+        :param treeview :
+        """
         icon = self.style().standardIcon(qt.QStyle.SP_TrashIcon)
         clearAction = qt.QAction(icon, "Clear All", self)
         clearAction.triggered.connect(treeView.clear)

From 8533a204bfe658afbaf462144585612bb2de041e Mon Sep 17 00:00:00 2001
From: Rebelo Alexis <rebelo.alexis@gmail.com>
Date: Tue, 18 Jun 2024 15:25:01 +0200
Subject: [PATCH 02/10] Adding docString and type

---
 .../app/view/CustomPlotSelectionWindow.py     | 199 +++++++-----------
 1 file changed, 73 insertions(+), 126 deletions(-)

diff --git a/src/silx/app/view/CustomPlotSelectionWindow.py b/src/silx/app/view/CustomPlotSelectionWindow.py
index 58ea373375..cae5b2ed17 100644
--- a/src/silx/app/view/CustomPlotSelectionWindow.py
+++ b/src/silx/app/view/CustomPlotSelectionWindow.py
@@ -20,19 +20,22 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 # THE SOFTWARE.
 # ###########################################################################*/
-from __future__ import annotations
 
-""""""
+"""Custom plot selection window for selecting 1D datasets to plot."""
 
 from silx.gui import qt, plot, icons
+import silx.gui
+import silx.gui.plot
+import silx.gui.plot.items
 import silx.io
 import numpy
 import functools
 from silx.gui.plot.LegendSelector import LegendIcon
+import silx.io.url
 import silx.io.utils
 from silx.gui.hdf5 import _utils
 
-
+# Custom role for highlighting the drop zones
 _DROP_HIGHLIGHT_ROLE = qt.Qt.UserRole + 1
 
 
@@ -42,7 +45,7 @@ class _HashDropZones(qt.QStyledItemDelegate):
     def __init__(self, parent: qt.QWidget | None = None):
         super(_HashDropZones, self).__init__(parent)
         self.__dropPen = qt.QPen(qt.QColor("#D0D0D0"), 2, qt.Qt.DotLine)
-        self.__highlightDropPen = qt.QPen(qt.QColor("#000000"), 2, qt.Qt.DotLine)
+        self.__highlightDropPen = qt.QPen(qt.QColor("#000000"), 2, qt.Qt.SolidLine)
         self.__dropTargetIndex = None
 
     def paint(self, painter, option, index):
@@ -67,7 +70,7 @@ def paint(self, painter, option, index):
         if isDropHighlighted:
             painter.save()
             painter.setPen(self.__highlightDropPen)
-            painter.drawRect(option.rect.adjusted(3, 3, -3, -3))
+            painter.drawRect(option.rect.adjusted(1, 1, -1, -1))
             painter.restore()
 
         if displayDropZone:
@@ -98,11 +101,7 @@ def paint(self, painter, option, index):
 
 
 class _FileListModel(qt.QStandardItemModel):
-    """
-    A model class for managing and displaying file data in a tree view structure
-
-    :param plot : Plot 1D
-    """
+    """Model for displaying dropped file names in a TreeView widget"""
 
     def __init__(self, plot, parent=None):
         super().__init__(parent)
@@ -129,25 +128,18 @@ def __init__(self, plot, parent=None):
 
         self.addUrl(silx.io.url.DataUrl())
 
-        self.rowsAboutToBeRemoved.connect(self._rowAboutToBeRemoved)
+        self.rowsAboutToBeRemoved.connect(self._rowsAboutToBeRemoved)
 
     def getXParent(self) -> qt.QStandardItem:
-        """Returns the X parent item."""
+        """Return the parent item for the X dataset"""
         return self._xParent
 
-    def getYParent(self):
-        """Returns the Y parent item.
-
-        :rtype: qt.QStandardItem
-        """
+    def getYParent(self) -> qt.QStandardItem:
+        """Return the parent item for the Y datasets"""
         return self._yParent
 
-    def _setXFile(self, url=None, curve=None):
-        """Set X file informations to the model
-
-        :param str filename: The file name.
-        :param curve: The curve data. Defaults to None.
-        """
+    def _setXFile(self, url: silx.io.url.DataUrl | None = None, curve: None = None):
+        """Set the X dataset file in the model"""
         if url is None:
             dataName = ""
         else:
@@ -164,17 +156,19 @@ def _setXFile(self, url=None, curve=None):
             self.setItem(xIndex, 1, fileItem)
             self.setItem(xIndex, 2, removeItem)
 
-    def _addYFile(self, url=None, curve=None, node="X"):
-        """Add Y file to the model
-
-        :param curve : The curve data. Defaults to None.
-        """
+    def _addYFile(
+        self,
+        url: silx.io.url.DataUrl | None = None,
+        curve: silx.gui.plot.items.Curve | None = None,
+    ):
+        """Add a Y dataset file to the model"""
         if url is None:
             dataName = ""
         else:
             dataName = self._getBasename(url.data_path())
         fileItem, iconItem, removeItem = self._createRowItems(dataName, curve)
         if not dataName:
+            # provide size hint for 'empty' item
             fileItem.setData(qt.QSize(0, 30), qt.Qt.SizeHintRole)
 
         fileItem.setData(self._createToolTip(url), qt.Qt.ToolTipRole)
@@ -187,24 +181,18 @@ def _addYFile(self, url=None, curve=None, node="X"):
             self.getYParent().rowCount() - 1, [iconItem, fileItem, removeItem]
         )
 
-    def _findRowContainingText(self, text):
-        """Find the row containing the specified text.
-
-        :param str text: The text to search for.
-        """
-
+    def _findRowContainingText(self, text: str) -> int | None:
+        """Return the row index containing the given text, or None if not found."""
         for row in range(self.rowCount()):
             item = self.item(row, 0)
             if item and item.text() == text:
                 return row
         return None
 
-    def _createRowItems(self, filename, curve):
-        """Create row items for the file.
-
-        :param str filename : The file name.
-        :param Curve curve : The curve data
-        """
+    def _createRowItems(
+        self, filename: str, curve: silx.gui.plot.items.Curve
+    ) -> tuple[qt.QStandardItem, qt.QStandardItem, qt.QStandardItem]:
+        """Create the items for a row in the model"""
         fileItem = qt.QStandardItem(filename)
         fileItem.setData(curve, qt.Qt.UserRole)
         fileItem.setData(False, _DROP_HIGHLIGHT_ROLE)
@@ -217,24 +205,16 @@ def _createRowItems(self, filename, curve):
 
         return fileItem, iconItem, removeItem
 
-    def fileItemExists(self, filename):
-        """Check if the file already exists in the model.
-
-        :param str filename : The file name.
-        """
+    def fileItemExists(self, filename: str) -> bool:
+        """Return if a file item with the given filename exists in the model for the Y datasets."""
         for row in range(self.getYParent().rowCount()):
             item = self.item(row, 1)
             if item and item.text() == filename:
                 return True
         return False
 
-    def addUrl(self, url, node="X"):
-        """Add a URL to the model.
-
-        :param url : The data URL.
-        :param node : The node name. Defaults to "X".
-        """
-
+    def addUrl(self, url: silx.io.url.DataUrl, node: str = "X"):
+        """Add a dataset to the model"""
         if url.file_path() is not None:
             file = silx.io.open(url.file_path())
             data = file[url.data_path()]
@@ -256,12 +236,10 @@ def addUrl(self, url, node="X"):
                     curve = self._addPlot(self._xDataset, data)
                     self._addYFile(url, curve)
 
-    def _addPlot(self, x: numpy.ndarray, y):
-        """Add a curve to the plot
-
-        :param x:
-        :param y:
-        """
+    def _addPlot(
+        self, x: numpy.ndarray | None, y: numpy.ndarray
+    ) -> silx.gui.plot.items.Curve:
+        """Add a curve to the plot with the given x and y data."""
         if x is None:
             x = numpy.arange(len(y))
 
@@ -273,13 +251,8 @@ def _addPlot(self, x: numpy.ndarray, y):
         curve.setInfo(y[()])
         return curve
 
-    def _rowAboutToBeRemoved(self, parentIndex, first, last):
-        """Handle the event when rows are about to be removed.
-
-        :param parentIndex : the parent index.
-        :param int first : the first row to be removed.
-        :param int last : the last row to be removed.
-        """
+    def _rowsAboutToBeRemoved(self, parentIndex: qt.QModelIndex, first: int, last: int):
+        """Remove the curves from the plot when a row is removed from the model."""
         parentItem = self.itemFromIndex(parentIndex)
         for row in range(first, last + 1):
             fileItem = parentItem.child(row, 1)
@@ -288,7 +261,7 @@ def _rowAboutToBeRemoved(self, parentIndex, first, last):
                 self._plot1D.removeItem(curve)
 
     def _updateYCurvesWithDefaultX(self):
-        """Update Y curves with default X values"""
+        """Update the Y curves with the default X dataset."""
         for item in self._plot1D.getItems():
             y = item.getInfo()
             x = numpy.arange(len(y))
@@ -296,7 +269,7 @@ def _updateYCurvesWithDefaultX(self):
             self._plot1D.resetZoom()
 
     def clearAll(self):
-        """Clear all data from the model"""
+        """Clear all datasets from the model and the plot."""
         self._xDataset = None
 
         self._yParent.removeRows(0, self._yParent.rowCount())
@@ -311,6 +284,7 @@ def clearAll(self):
         self._updateYCurvesWithDefaultX()
 
     def _reset(self):
+        """Reset the model to its initial state."""
         self._xDataset = None
 
         self._setXFile()
@@ -334,15 +308,11 @@ def _getBasename(self, text):
 
 
 class _DropTreeView(qt.QTreeView):
-    """TreeView widget for displaying dropped file names
-
-    :param model : _FileListModel
-    """
+    """TreeView widget for displaying dropped file names"""
 
     (_DESCRIPTION_COLUMN, _FILE_COLUMN, _REMOVE_COLUMN) = range(3)
 
     def __init__(self, model, parent=None):
-        """Constructor"""
         super().__init__(parent)
         self.setModel(model)
 
@@ -350,13 +320,9 @@ def __init__(self, model, parent=None):
 
         header = self.header()
         header.setStretchLastSection(False)
-        header.setSectionResizeMode(
-            _DropTreeView._DESCRIPTION_COLUMN, qt.QHeaderView.ResizeToContents
-        )
-        header.setSectionResizeMode(_DropTreeView._FILE_COLUMN, qt.QHeaderView.Stretch)
-        header.setSectionResizeMode(
-            _DropTreeView._REMOVE_COLUMN, qt.QHeaderView.ResizeToContents
-        )
+        header.setSectionResizeMode(0, qt.QHeaderView.ResizeToContents)
+        header.setSectionResizeMode(1, qt.QHeaderView.Stretch)
+        header.setSectionResizeMode(2, qt.QHeaderView.ResizeToContents)
         self.expandAll()
 
         self.setSelectionMode(qt.QAbstractItemView.SingleSelection)
@@ -368,12 +334,8 @@ def __init__(self, model, parent=None):
         self.setDragEnabled(False)
         self.viewport().setAcceptDrops(True)
 
-    def _createIconWidget(self, row, parentItem):
-        """Create an icon widget for the specified row.
-
-        :param row : The row index.
-        :param parentItem : The parent item.
-        """
+    def _createIconWidget(self, row: int, parentItem: qt.QStandardItem):
+        """Create the icon widget for a row in the model"""
         fileItem = parentItem.child(row, 1)
         iconItem = parentItem.child(row, 0)
         curve = fileItem.data(qt.Qt.UserRole)
@@ -387,12 +349,10 @@ def _createIconWidget(self, row, parentItem):
         layout.setContentsMargins(4, 0, 4, 0)
         self.setIndexWidget(iconItem.index(), widget)
 
-    def _createRemoveButton(self, row, parentItem):
-        """Create an remove button for the specified row.
+    def _createRemoveButton(self, row: int, parentItem: qt.QStandardItem | None):
+        """Create the remove button for a row in the model"""
 
-        :param row : The row index.
-        :param parentItem : The parent item
-        """
+        # If the parentItem is None, the remove button is for the X dataset
         if parentItem is None:
             parentItem = self.model().getXParent()
             index = self.model().index(0, 2)
@@ -404,6 +364,7 @@ def _createRemoveButton(self, row, parentItem):
             self.setIndexWidget(index, button)
             return
 
+        # If the parentItem is not None, the remove button is for a Y dataset
         removeItem = parentItem.child(row, 2)
         if removeItem:
             button = qt.QToolButton(self)
@@ -413,12 +374,12 @@ def _createRemoveButton(self, row, parentItem):
             )
             self.setIndexWidget(removeItem.index(), button)
 
-    def _removeFile(self, removeItem, parentItem):
-        """Remove the specified file from the model.
+    def _removeFile(
+        self, removeItem: qt.QStandardItem | None, parentItem: qt.QStandardItem
+    ):
+        """Remove a file from the model and the plot."""
 
-        :param removeItem : The item to be removed.
-        :param parentItem : The parent item.
-        """
+        # If removeItem is None, the file to remove is the X dataset
         if removeItem is None:
             row = 0
             removeItem = self.model().getXParent()
@@ -426,6 +387,7 @@ def _removeFile(self, removeItem, parentItem):
         if removeItem:
             row = removeItem.row()
 
+            # If the parentItem is None, the file to remove is the X dataset
             if parentItem is None:
                 parentItem = self.model().getXParent()
 
@@ -476,7 +438,8 @@ def dropEvent(self, event):
         event.acceptProposedAction()
 
     def acceptDragEvent(self, event):
-        """Accept the drop event if the data is valid."""
+        """Accept the drag event if the mime data contains a 1D dataset."""
+
         if event.mimeData().hasFormat("application/x-silx-uri"):
             byteString = event.mimeData().data("application/x-silx-uri")
             url = silx.io.url.DataUrl(byteString.data().decode("utf-8"))
@@ -491,22 +454,16 @@ def acceptDragEvent(self, event):
         else:
             event.ignore()
 
-    def setX(self, url):
-        """Set the X data from the URL.
-
-        :param url : The data URL.
-        """
+    def setX(self, url: silx.io.url.DataUrl):
+        """Set the X dataset in the model and the plot."""
         targetNode = "X"
         node = self.model().getXParent()
         self.model().addUrl(url, targetNode)
         self._createRemoveButton(node, None)
         self.model()._plot1D.resetZoom()
 
-    def addY(self, url):
-        """Add the Y data from the URL.
-
-        :param url : The data URL.
-        """
+    def addY(self, url: silx.io.url.DataUrl):
+        """Add a Y dataset to the model and the plot."""
         targetNode = "Y"
         node = self.model().getYParent()
         self.model().addUrl(url, targetNode)
@@ -515,15 +472,13 @@ def addY(self, url):
         self.model()._plot1D.resetZoom()
 
     def clear(self):
-        """Clear all data from the tree view."""
+        """Clear all datasets from the model and the plot."""
         self.model().clearAll()
         index = self.model().index(0, 2)
         self.setIndexWidget(index, None)
 
-    def setDropHighlight(self, value):
-        """Set the drop highlight for the specified value.
-
-        :param value : The value to highlight ("X" or "Y")"""
+    def setDropHighlight(self, value: str | None):
+        """Set the drop highlight for the X and Y datasets."""
         xDropFileItem = self.model().itemFromIndex(
             self.model().sibling(
                 0, 1, self.model().indexFromItem(self.model().getXParent())
@@ -537,19 +492,15 @@ def setDropHighlight(self, value):
 
 
 class _DropPlot1D(plot.Plot1D):
-    """A plot widget with drag-and-drop functionality for adding data."""
+    """Plot1D widget for displaying 1D datasets that can accept drops."""
 
     def __init__(self, parent=None):
-        """Constructor"""
         super().__init__(parent)
         self.setAcceptDrops(True)
         self._treeView = None
 
-    def setTreeView(self, treeView):
-        """Set the tree view for the plot.
-
-        :param treeview :
-        """
+    def setTreeView(self, treeView: qt.QTreeView):
+        """Set the TreeView widget for the plot."""
         self._treeView = treeView
 
     def dragEnterEvent(self, event):
@@ -576,22 +527,18 @@ def dropEvent(self, event):
         self.resetZoom()
         event.acceptProposedAction()
 
-    def setXAxisLabel(self, label):
+    def setXAxisLabel(self, label: str):
+        """Set the label for the X axis."""
         xAxis = self.getXAxis()
         xAxis.setLabel(label)
 
 
 class _PlotToolBar(qt.QToolBar):
-    """"""
-
     def __init__(self, parent=None):
         super().__init__(parent)
 
-    def addClearAction(self, treeView):
-        """Add a clear action to the ToolBar
-
-        :param treeview :
-        """
+    def addClearAction(self, treeView: qt.QTreeView):
+        """Add the clear action to the toolbar."""
         icon = self.style().standardIcon(qt.QStyle.SP_TrashIcon)
         clearAction = qt.QAction(icon, "Clear All", self)
         clearAction.triggered.connect(treeView.clear)

From 487f56dabd12d419ee036928122e8ebaa6cc6479 Mon Sep 17 00:00:00 2001
From: Rebelo Alexis <rebelo.alexis@gmail.com>
Date: Wed, 19 Jun 2024 15:05:03 +0200
Subject: [PATCH 03/10] Added missing doc

---
 src/silx/app/view/CustomPlotSelectionWindow.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/silx/app/view/CustomPlotSelectionWindow.py b/src/silx/app/view/CustomPlotSelectionWindow.py
index cae5b2ed17..86a653a2e7 100644
--- a/src/silx/app/view/CustomPlotSelectionWindow.py
+++ b/src/silx/app/view/CustomPlotSelectionWindow.py
@@ -293,7 +293,8 @@ def _reset(self):
         self._plot1D.clear()
         self._updateYCurvesWithDefaultX()
 
-    def _createToolTip(self, url):
+    def _createToolTip(self, url: silx.io.url.DataUrl) -> str:
+        """Create the tooltip for a dataset."""
         if url is None:
             return ""
         attrs = {
@@ -303,7 +304,8 @@ def _createToolTip(self, url):
         }
         return _utils.htmlFromDict(attrs, title="HDF5 Dataset")
 
-    def _getBasename(self, text):
+    def _getBasename(self, text: str) -> str:
+        """Return the basename of a file path."""
         return text.split("/")[-1]
 
 

From 4f5dc39d89b30eab77413a910cedebae75ffcd25 Mon Sep 17 00:00:00 2001
From: Rebelo Alexis <102356226+RebeloAlexis@users.noreply.github.com>
Date: Wed, 19 Jun 2024 15:06:48 +0200
Subject: [PATCH 04/10] Update src/silx/app/view/CustomPlotSelectionWindow.py

Co-authored-by: Thomas VINCENT <thomas.vincent@esrf.fr>
---
 src/silx/app/view/CustomPlotSelectionWindow.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/silx/app/view/CustomPlotSelectionWindow.py b/src/silx/app/view/CustomPlotSelectionWindow.py
index 86a653a2e7..2e0638bd04 100644
--- a/src/silx/app/view/CustomPlotSelectionWindow.py
+++ b/src/silx/app/view/CustomPlotSelectionWindow.py
@@ -21,6 +21,7 @@
 # THE SOFTWARE.
 # ###########################################################################*/
 
+from __future__ import annotations
 """Custom plot selection window for selecting 1D datasets to plot."""
 
 from silx.gui import qt, plot, icons

From 1d58794d6b8c279d928c2b2060f7564979456f46 Mon Sep 17 00:00:00 2001
From: Rebelo Alexis <102356226+RebeloAlexis@users.noreply.github.com>
Date: Wed, 19 Jun 2024 15:11:35 +0200
Subject: [PATCH 05/10] Update src/silx/app/view/CustomPlotSelectionWindow.py

Co-authored-by: Thomas VINCENT <thomas.vincent@esrf.fr>
---
 src/silx/app/view/CustomPlotSelectionWindow.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/silx/app/view/CustomPlotSelectionWindow.py b/src/silx/app/view/CustomPlotSelectionWindow.py
index 2e0638bd04..ded8985581 100644
--- a/src/silx/app/view/CustomPlotSelectionWindow.py
+++ b/src/silx/app/view/CustomPlotSelectionWindow.py
@@ -207,7 +207,7 @@ def _createRowItems(
         return fileItem, iconItem, removeItem
 
     def fileItemExists(self, filename: str) -> bool:
-        """Return if a file item with the given filename exists in the model for the Y datasets."""
+        """Return True if a file item with the given filename exists in the Y datasets of the model."""
         for row in range(self.getYParent().rowCount()):
             item = self.item(row, 1)
             if item and item.text() == filename:

From 84eb170e7ab56eaf78313578d27dfb8eb243bbb3 Mon Sep 17 00:00:00 2001
From: Rebelo Alexis <102356226+RebeloAlexis@users.noreply.github.com>
Date: Wed, 19 Jun 2024 15:12:00 +0200
Subject: [PATCH 06/10] Update src/silx/app/view/CustomPlotSelectionWindow.py

Co-authored-by: Thomas VINCENT <thomas.vincent@esrf.fr>
---
 src/silx/app/view/CustomPlotSelectionWindow.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/silx/app/view/CustomPlotSelectionWindow.py b/src/silx/app/view/CustomPlotSelectionWindow.py
index ded8985581..9737ebd358 100644
--- a/src/silx/app/view/CustomPlotSelectionWindow.py
+++ b/src/silx/app/view/CustomPlotSelectionWindow.py
@@ -25,8 +25,6 @@
 """Custom plot selection window for selecting 1D datasets to plot."""
 
 from silx.gui import qt, plot, icons
-import silx.gui
-import silx.gui.plot
 import silx.gui.plot.items
 import silx.io
 import numpy

From 9f4c116188f5292db7ab119143094b57cb65e094 Mon Sep 17 00:00:00 2001
From: Rebelo Alexis <rebelo.alexis@gmail.com>
Date: Wed, 19 Jun 2024 15:15:48 +0200
Subject: [PATCH 07/10] Added PR suggestions

---
 src/silx/app/view/CustomPlotSelectionWindow.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/silx/app/view/CustomPlotSelectionWindow.py b/src/silx/app/view/CustomPlotSelectionWindow.py
index 2e0638bd04..26849faeb9 100644
--- a/src/silx/app/view/CustomPlotSelectionWindow.py
+++ b/src/silx/app/view/CustomPlotSelectionWindow.py
@@ -21,7 +21,6 @@
 # THE SOFTWARE.
 # ###########################################################################*/
 
-from __future__ import annotations
 """Custom plot selection window for selecting 1D datasets to plot."""
 
 from silx.gui import qt, plot, icons
@@ -139,7 +138,7 @@ def getYParent(self) -> qt.QStandardItem:
         """Return the parent item for the Y datasets"""
         return self._yParent
 
-    def _setXFile(self, url: silx.io.url.DataUrl | None = None, curve: None = None):
+    def _setXFile(self, url: silx.io.url.DataUrl | None = None):
         """Set the X dataset file in the model"""
         if url is None:
             dataName = ""
@@ -147,7 +146,7 @@ def _setXFile(self, url: silx.io.url.DataUrl | None = None, curve: None = None):
             dataName = self._getBasename(url.data_path())
             self._plot1D.setXAxisLabel(dataName)
 
-        fileItem, iconItem, removeItem = self._createRowItems(dataName, curve)
+        fileItem, iconItem, removeItem = self._createRowItems(dataName, None)
         fileItem.setData(qt.QSize(0, 30), qt.Qt.SizeHintRole)
 
         fileItem.setData(self._createToolTip(url), qt.Qt.ToolTipRole)
@@ -191,7 +190,7 @@ def _findRowContainingText(self, text: str) -> int | None:
         return None
 
     def _createRowItems(
-        self, filename: str, curve: silx.gui.plot.items.Curve
+        self, filename: str, curve: silx.gui.plot.items.Curve | None
     ) -> tuple[qt.QStandardItem, qt.QStandardItem, qt.QStandardItem]:
         """Create the items for a row in the model"""
         fileItem = qt.QStandardItem(filename)

From 39bc37cbd5badaccee5e5134e506053297d9e13b Mon Sep 17 00:00:00 2001
From: Rebelo Alexis <rebelo.alexis@gmail.com>
Date: Wed, 19 Jun 2024 15:19:22 +0200
Subject: [PATCH 08/10] Added PR suggestions

---
 src/silx/app/view/CustomPlotSelectionWindow.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/silx/app/view/CustomPlotSelectionWindow.py b/src/silx/app/view/CustomPlotSelectionWindow.py
index 5d5661e325..26849faeb9 100644
--- a/src/silx/app/view/CustomPlotSelectionWindow.py
+++ b/src/silx/app/view/CustomPlotSelectionWindow.py
@@ -24,6 +24,8 @@
 """Custom plot selection window for selecting 1D datasets to plot."""
 
 from silx.gui import qt, plot, icons
+import silx.gui
+import silx.gui.plot
 import silx.gui.plot.items
 import silx.io
 import numpy
@@ -204,7 +206,7 @@ def _createRowItems(
         return fileItem, iconItem, removeItem
 
     def fileItemExists(self, filename: str) -> bool:
-        """Return True if a file item with the given filename exists in the Y datasets of the model."""
+        """Return if a file item with the given filename exists in the model for the Y datasets."""
         for row in range(self.getYParent().rowCount()):
             item = self.item(row, 1)
             if item and item.text() == filename:

From a774f640c04e14ed3d8da42f7bc2ded5d6fe6ab5 Mon Sep 17 00:00:00 2001
From: Rebelo Alexis <rebelo.alexis@gmail.com>
Date: Wed, 19 Jun 2024 15:28:57 +0200
Subject: [PATCH 09/10] Adding import annotations

---
 src/silx/app/view/CustomPlotSelectionWindow.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/silx/app/view/CustomPlotSelectionWindow.py b/src/silx/app/view/CustomPlotSelectionWindow.py
index 26849faeb9..0baca585b8 100644
--- a/src/silx/app/view/CustomPlotSelectionWindow.py
+++ b/src/silx/app/view/CustomPlotSelectionWindow.py
@@ -22,6 +22,7 @@
 # ###########################################################################*/
 
 """Custom plot selection window for selecting 1D datasets to plot."""
+from __future__ import annotations
 
 from silx.gui import qt, plot, icons
 import silx.gui

From 1d9d779413e376cfdabf76f6fa3c69d8842106bd Mon Sep 17 00:00:00 2001
From: Rebelo Alexis <rebelo.alexis@gmail.com>
Date: Mon, 24 Jun 2024 11:26:42 +0200
Subject: [PATCH 10/10] Added short description of CustomPlotSelectionWindow

---
 src/silx/app/view/CustomPlotSelectionWindow.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/silx/app/view/CustomPlotSelectionWindow.py b/src/silx/app/view/CustomPlotSelectionWindow.py
index 0baca585b8..8c722dd2da 100644
--- a/src/silx/app/view/CustomPlotSelectionWindow.py
+++ b/src/silx/app/view/CustomPlotSelectionWindow.py
@@ -549,6 +549,8 @@ def addClearAction(self, treeView: qt.QTreeView):
 
 
 class CustomPlotSelectionWindow(qt.QMainWindow):
+    """A customized plot selection window allowing the user to select and display 1D data sets."""
+
     sigVisibilityChanged = qt.Signal(bool)
 
     def __init__(self, parent=None):