Update dependencies including actions/cache, ruff, and pytest

.github/workflows/python-package.yml

@@ -19,7 +19,7 @@ jobs:
         python-version: [ "3.12", "3.13", "3.14" ]
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v6
         with:

.github/workflows/python-publish.yml

@@ -11,7 +11,7 @@ jobs:
   release-build:
     runs-on: ubuntu-24.04
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - uses: actions/setup-python@v6
         with:
           python-version: "3.13"
@@ -23,7 +23,7 @@ jobs:
           virtualenvs-in-project: true
           add-to-path: true
       - name: Cache Poetry virtual environment
-        uses: actions/cache@v4
+        uses: actions/cache@v6
         with:
           path: .venv
           key: venv-release-build-${{ runner.os }}-3.13-${{ hashFiles('poetry.lock') }}
@@ -66,7 +66,7 @@ jobs:
         os: [ windows-2022 ]
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - uses: actions/setup-python@v6
         with:
           python-version: "3.13"
@@ -82,7 +82,7 @@ jobs:
         shell: pwsh
         run: echo "$env:USERPROFILE\.local\bin" >> $env:GITHUB_PATH
       - name: Cache Poetry virtual environment
-        uses: actions/cache@v4
+        uses: actions/cache@v6
         with:
           path: .venv
           key: venv-pyinstaller-${{ runner.os }}-3.13-${{ hashFiles('poetry.lock') }}

README.md

@@ -22,8 +22,8 @@ Download ready-to-use executables from [Releases](https://github.com/PonyLianna/
 
 | Platform | Download |
 |----------|----------|
-| Windows CLI | [main.exe](https://github.com/PonyLianna/pythonQEPest/releases/download/v2.0.0-alpha/main.exe) |
-| Windows GUI | [gui.exe](https://github.com/PonyLianna/pythonQEPest/releases/download/v2.0.0-alpha/gui.exe) |
+| Windows CLI | [main.exe](https://github.com/PonyLianna/pythonQEPest/releases/download/v2.0.0-alpha.5/pythonQEPest-2.0.0a5-win64.exe) |
+| Windows GUI | [gui.exe](https://github.com/PonyLianna/pythonQEPest/releases/download/v2.0.0-alpha.5/pythonQEPest-GUI-2.0.0a5-win64.exe) |
 
 
 ## Installation

gui.spec

@@ -2,7 +2,7 @@
 
 
 a = Analysis(
-    ['pythonQEPest/gui/gui.py'],
+    ['pythonQEPest\\gui\\gui.py'],
     pathex=[],
     binaries=[],
     datas=[],
@@ -22,11 +22,11 @@ exe = EXE(
     a.binaries,
     a.datas,
     [],
-    name='pythonQEPest-GUI',
+    name='gui',
     debug=False,
     bootloader_ignore_signals=False,
     strip=False,
-    upx=False,
+    upx=True,
     upx_exclude=[],
     runtime_tmpdir=None,
     console=False,

main.spec

@@ -10,7 +10,7 @@ a = Analysis(
     hookspath=[],
     hooksconfig={},
     runtime_hooks=[],
-    excludes=[],
+    excludes=['rdkit'],
     noarchive=False,
     optimize=0,
 )

pyproject.toml

@@ -5,7 +5,7 @@ description = "Java QEPest but written in Python"
 readme = "README.md"
 requires-python = ">=3.12,<3.15"
 authors = [{ name = "Lina", email = "knocker767@gmail.com" }]
-dependencies = ["pydantic==2.12.5", "python-dotenv>=1.2.1,<2.0.0", "ruff (>=0.15.13,<0.16.0)"]
+dependencies = ["pydantic==2.12.5", "python-dotenv>=1.2.1,<2.0.0", "ruff (>=0.15.13,<0.16.0)", "ttkbootstrap>=1.20.4,<2.0.0"]
 
 [project.optional-dependencies]
 gui = ["pyperclip>=1.11.0,<2.0.0"]
@@ -50,3 +50,5 @@ test = "pytest"
 build-simple = "pyinstaller --onefile pythonQEPest/main.py"
 build-gui = "pyinstaller --onefile --noconsole pythonQEPest/gui/gui.py"
 publish-pypi = "twine upload --repository pythonQEPest dist/*"
+ruff_lint = "ruff check --fix"
+ruff_format = "ruff format"

pythonQEPest/gui/actions/actions_crud.py

@@ -5,26 +5,50 @@
 except ImportError:
     pyperclip = None
 
-from pythonQEPest.gui.elements.EditWindow import EditWindow
 from pythonQEPest.gui.utility.DataManager import DataManager
 
 
 class GUIActionsCRUD:
-    def __init__(self, data_tree, result_tree, save_button, index):
-        self.index = index
+    def __init__(self, data_tree, result_tree, save_button, entry_panel):
         self.data_manager = DataManager()
         self.data_tree: ttk.Treeview = data_tree
         self.result_tree: ttk.Treeview = result_tree
         self.save_button = save_button
+        self.entry_panel = entry_panel
+
+    def sync_selection_to_panel(self, *args, **kwargs):
+        selected = self.data_tree.selection()
+        if selected:
+            item_id = selected[0]
+            values = self.data_tree.item(item_id, "values")
+            self.entry_panel.load_entry(values, item_id)
 
     def edit_selected(self, *args, **kwargs):
         selected = self.data_tree.selection()
         if not selected:
             messagebox.showwarning("Select Entry", "Select Entry for editing")
             return
 
-        item_id = selected[0]
-        EditWindow(item_id=item_id, tree=self.data_tree, child_tree=self.result_tree)
+        self.sync_selection_to_panel()
+
+    def undo(self, *args, **kwargs):
+        if self.data_manager.undo() is None:
+            return
+        self._rebuild_from_data_manager()
+
+    def _rebuild_from_data_manager(self):
+        self.data_tree.delete(*self.data_tree.get_children())
+        self.result_tree.delete(*self.result_tree.get_children())
+
+        for row in self.data_manager.file_data:
+            self.data_tree.insert("", "end", values=tuple(str(v) for v in row))
+        for row in self.data_manager.result_data:
+            self.result_tree.insert("", "end", values=tuple(str(v) for v in row))
+
+        self.entry_panel.cancel()
+        self.save_button.config(
+            state="normal" if self.data_manager.result_data else "disabled"
+        )
 
     def copy_selected(self, *args, **kwargs):
         selected_data_tree = self.data_tree.selection()
@@ -83,14 +107,18 @@ def paste_entries(self, *args, **kwargs):
         lines = clipboard_text.strip().splitlines()
         count_added = 0
 
+        self.data_manager.push_undo()
         for line in lines:
             parts = line.strip().split("\t")
             if len(parts) == 7:
-                idx = self.index
+                try:
+                    float(parts[1])
+                except ValueError:
+                    continue
+                idx = self.data_manager.next_file_id
                 self.data_manager.add_file((idx, *parts))
                 self.data_tree.insert("", "end", values=(idx, *parts))
                 count_added += 1
-                self.index += 1
 
         if count_added:
             messagebox.showinfo(
@@ -99,33 +127,44 @@ def paste_entries(self, *args, **kwargs):
             )
 
     def delete_selected(self, *args, **kwargs):
-        selected = self.data_tree.selection()
-        if not selected:
+        selected_data = self.data_tree.selection()
+        selected_result = self.result_tree.selection()
+
+        if not selected_data and not selected_result:
             messagebox.showwarning("Select Entry", "Select the entry to delete.")
             return
 
         idxs_to_remove = []
-        for item in selected:
-            values = self.data_tree.item(item, "values")
-            idx_to_remove = int(values[0])
-            idxs_to_remove.append(idx_to_remove)
 
+        self.data_manager.push_undo()
+        for item in selected_data:
+            values = self.data_tree.item(item, "values")
+            idxs_to_remove.append(int(values[0]))
             self.data_tree.delete(item)
 
-            if self.result_tree.exists(item):
-                self.result_tree.delete(item)
+        for item in selected_result:
+            values = self.result_tree.item(item, "values")
+            idxs_to_remove.append(int(values[0]))
+            self.result_tree.delete(item)
+
+        for child in self.result_tree.get_children(""):
+            if int(self.result_tree.set(child, "ID")) in idxs_to_remove:
+                self.result_tree.delete(child)
+
+        for child in self.data_tree.get_children(""):
+            if int(self.data_tree.set(child, "ID")) in idxs_to_remove:
+                self.data_tree.delete(child)
 
         self.data_manager.remove_result_by_ids(idxs_to_remove)
         self.data_manager.remove_file_by_ids(idxs_to_remove)
 
         messagebox.showinfo("Deleted", "The selected records have been deleted.")
 
-        if not self.data_manager:
-            self.save_button.config(state="disabled")
-
     def clear_everything(self, *args, **kwargs):
+        self.data_manager.push_undo()
         self.data_manager.clear_file()
         self.data_manager.clear_result()
 
         self.data_tree.delete(*self.data_tree.get_children())
         self.result_tree.delete(*self.result_tree.get_children())
+        self.save_button.config(state="disabled")

pythonQEPest/gui/actions/actions_other.py

@@ -1,20 +1,20 @@
-import tkinter as tk
 from tkinter import filedialog, messagebox
 
 from pythonQEPest.dto.QEPestInput import QEPestInput
 from pythonQEPest.gui.utility.DataManager import DataManager
 
 
 class GUIActionsOther:
-    def __init__(self, root, data_tree, result_tree, save_button, qepest):
+    def __init__(self, root, data_tree, result_tree, save_button, qepest, entry_panel):
         self.data_manager = DataManager()
         self.root = root
         self.data_tree = data_tree
         self.result_tree = result_tree
         self.save_button = save_button
         self.qepest = qepest
+        self.entry_panel = entry_panel
 
-    def load_file(self):
+    def load_file(self, *args):
         file_path = filedialog.askopenfilename(
             filetypes=[("Text files", "*.txt"), ("CSV files", "*.csv")]
         )
@@ -23,12 +23,18 @@ def load_file(self):
 
         try:
             with open(file_path, encoding="utf-8") as file:
+                self.data_manager.push_undo()
                 self.data_manager.clear_file()
                 self.data_tree.delete(*self.data_tree.get_children())
 
-                for idx, line in enumerate(file):
+                for line in file:
                     parts = line.strip().split("\t")
                     if len(parts) == 7:
+                        try:
+                            float(parts[1])
+                        except ValueError:
+                            continue
+                        idx = self.data_manager.next_file_id
                         self.data_manager.add_file((idx, *parts))
                         self.data_tree.insert("", "end", values=(idx, *parts))
 
@@ -39,53 +45,58 @@ def load_file(self):
             messagebox.showerror("Loading error", str(e))
 
     def add_entry(self):
-        form = tk.Toplevel(self.root)
-        form.title("Add entry")
-        form.transient(self.root)
-        form.grab_set()
-
-        entries = {}
-        fields = ["Name", "MW", "LogP", "HBA", "HBD", "RB", "arR"]
-
-        for idx, field in enumerate(fields):
-            tk.Label(form, text=field).grid(
-                row=idx, column=0, padx=5, pady=5, sticky="e"
-            )
-            entry = tk.Entry(form)
-            entry.grid(row=idx, column=1, padx=5, pady=5)
-            entries[field] = entry
-
-        def submit():
-            values = []
-            for field in fields:
-                val = entries[field].get().strip()
-                if not val:
-                    messagebox.showwarning("Error", f"The field {field} not filled.")
-                    return
-                values.append(val)
-
-            idx = len(self.data_manager.file_data)
-            self.data_manager.add_file((idx, *values))
-            self.data_tree.insert("", "end", values=(idx, *values))
-            form.destroy()
+        next_id = self.data_manager.next_file_id
+        self.entry_panel.clear_for_add(next_id)
+
+    def save_from_panel(self, mode, item_id, values):
+        self.data_manager.push_undo()
+        if mode == "add":
+            self.data_manager.add_file(tuple(values))
+            self.data_tree.insert("", "end", values=tuple(str(v) for v in values))
+            next_id = self.data_manager.next_file_id
+            self.entry_panel.reset_after_save(next_id)
             messagebox.showinfo(
                 "Added",
                 "The entry has been added. Process the data to update the result.",
             )
+        elif mode == "edit" and item_id:
+            str_values = [str(v) for v in values]
+            self.data_tree.item(item_id, values=tuple(str_values))
 
-        tk.Button(form, text="Add", command=submit).grid(
-            row=len(fields), column=0, columnspan=2, pady=10
-        )
+            old_id = int(self.data_tree.set(item_id, self.data_tree["columns"][0]))
+
+            if self.result_tree.exists(item_id):
+                child_values = list(self.result_tree.item(item_id, "values"))
+                child_values[0] = str(values[0])
+                child_values[1] = str(values[1])
+                self.result_tree.item(item_id, values=tuple(child_values))
 
-        form.wait_window()
+                res_matches = [
+                    x for x in self.data_manager.result_data if x[0] == old_id
+                ]
+                if res_matches:
+                    ridx = self.data_manager.result_data.index(res_matches[0])
+                    updated = list(self.data_manager.result_data[ridx])
+                    updated[0] = int(values[0])
+                    updated[1] = str(values[1])
+                    self.data_manager.update_result(
+                        index=ridx, new_entry=tuple(updated)
+                    )
+
+            matches = [x for x in self.data_manager.file_data if x[0] == old_id]
+            if matches:
+                idx = self.data_manager.file_data.index(matches[0])
+                self.data_manager.update_file(index=idx, new_entry=values)
+            messagebox.showinfo("Saved", "The entry has been updated.")
 
     def process_data(self):
         if not self.data_manager.file_data:
             messagebox.showwarning("No data", "Please add or upload data first.")
             return
 
-        # self.result_data = []
-        # self.result_tree.delete(*self.result_tree.get_children())
+        self.data_manager.push_undo()
+        self.data_manager.clear_result()
+        self.result_tree.delete(*self.result_tree.get_children())
 
         for row in self.data_manager.file_data:
             try:
@@ -103,7 +114,7 @@ def process_data(self):
 
         self.save_button.config(state="normal")
 
-    def save_result(self):
+    def save_result(self, *args):
         if not self.data_manager.result_data:
             messagebox.showwarning("No result", "Process the data first.")
             return