Repository: spyder-ide/spyder

Issue:
PermissionError when trying to reload a file
## Description

### What steps will reproduce the problem?

<!--- You can use Markdown here --->

When I start Sypder my session it normally starts with the files I had open last session.  This time, instead of the pointer curser, I got a round circle with a cross . Oppisite sides where colored the same, but different colors adjacent.  None of my files opened. No default file was opened either,  The Save a single file button was active.  The save All files button was deactivated.

I opened the file I wanted to edit.  Since I still didn't have the pointer curser (i.e. I had the circle curser).  I decided to restart Spyder.  It seemed to come up normally.  I made about 1 minute of edits and my wife needed my help.  When I got back 30 minutes later the "Issue preporter" window was up and I started typing this problem report.



### Traceback
```python-traceback
Traceback (most recent call last):
  File "/Applications/Spyder.app/Contents/Resources/lib/python3.9/spyder/plugins/editor/widgets/editor.py", line 2290, in focus_changed
    self.refresh()
  File "/Applications/Spyder.app/Contents/Resources/lib/python3.9/spyder/plugins/editor/widgets/editor.py", line 2450, in refresh
    self.__check_file_status(index)
  File "/Applications/Spyder.app/Contents/Resources/lib/python3.9/spyder/plugins/editor/widgets/editor.py", line 2423, in __check_file_status
    self.reload(index)
  File "/Applications/Spyder.app/Contents/Resources/lib/python3.9/spyder/plugins/editor/widgets/editor.py", line 2508, in reload
    txt, finfo.encoding = encoding.read(finfo.filename)
  File "/Applications/Spyder.app/Contents/Resources/lib/python3.9/spyder/utils/encoding.py", line 304, in read
    text, encoding = decode( open(filename, 'rb').read() )
PermissionError: [Errno 1] Operation not permitted: '/Users/dave/Desktop/SynologyDrive/MyCode/RothConversion/PythonRC/main.py'
```

## Versions

* Spyder version: 5.4.4 d28269e66 (standalone)
* Python version: 3.9.14 64-bit
* Qt version: 5.15.2
* PyQt5 version: 5.15.9
* Operating System: macOS-13.4.1-x86_64-i386-64bit

### Dependencies

```
# Mandatory:
atomicwrites >=1.2.0                                                        :  1.4.1 (OK)
chardet >=2.0.0                                                             :  5.1.0 (OK)
cloudpickle >=0.5.0                                                         :  2.2.1 (OK)
cookiecutter >=1.6.0                                                        :  2.2.3 (OK)
diff_match_patch >=20181111                                                 :  20230430 (OK)
intervaltree >=3.0.2                                                        :  3.1.0 (OK)
IPython >=7.31.1,<9.0.0,!=8.8.0,!=8.9.0,!=8.10.0,!=8.11.0,!=8.12.0,!=8.12.1 :  8.14.0 (OK)
jedi >=0.17.2,<0.19.0                                                       :  0.18.2 (OK)
jellyfish >=0.7                                                             :  1.0.0 (OK)
jsonschema >=3.2.0                                                          :  4.18.4 (OK)
keyring >=17.0.0                                                            :  24.2.0 (OK)
nbconvert >=4.0                                                             :  7.7.1 (OK)
numpydoc >=0.6.0                                                            :  1.5.0 (OK)
parso >=0.7.0,<0.9.0                                                        :  0.8.3 (OK)
pexpect >=4.4.0                                                             :  4.8.0 (OK)
pickleshare >=0.4                                                           :  0.7.5 (OK)
psutil >=5.3                                                                :  5.9.5 (OK)
pygments >=2.0                                                              :  2.15.1 (OK)
pylint >=2.5.0,<3.0                                                         :  2.17.4 (OK)
pylint_venv >=3.0.2                                                         :  None (OK)
pyls_spyder >=0.4.0                                                         :  0.4.0 (OK)
pylsp >=1.7.4,<1.8.0                                                        :  1.7.4 (OK)
pylsp_black >=1.2.0,<3.0.0                                                  :  1.3.0 (OK)
qdarkstyle >=3.0.2,<3.2.0                                                   :  3.1 (OK)
qstylizer >=0.2.2                                                           :  0.2.2 (OK)
qtawesome >=1.2.1                                                           :  1.2.3 (OK)
qtconsole >=5.4.2,<5.5.0                                                    :  5.4.3 (OK)
qtpy >=2.1.0                                                                :  2.3.1 (OK)
rtree >=0.9.7                                                               :  1.0.1 (OK)
setuptools >=49.6.0                                                         :  68.0.0 (OK)
sphinx >=0.6.6                                                              :  5.1.1 (OK)
spyder_kernels >=2.4.4,<2.5.0                                               :  2.4.4 (OK)
textdistance >=4.2.0                                                        :  4.5.0 (OK)
three_merge >=0.1.1                                                         :  0.1.1 (OK)
watchdog >=0.10.3                                                           :  3.0.0 (OK)
zmq >=22.1.0                                                                :  25.1.0 (OK)

# Optional:
cython >=0.21                                                               :  3.0.0 (OK)
matplotlib >=3.0.0                                                          :  3.7.2 (OK)
numpy >=1.7                                                                 :  1.25.1 (OK)
pandas >=1.1.1                                                              :  2.0.3 (OK)
scipy >=0.17.0                                                              :  1.11.1 (OK)
sympy >=0.7.3                                                               :  1.12 (OK)

# Spyder plugins:
spyder_terminal.terminalplugin 1.2.2                                        :  1.2.2 (OK)
```



Discussion:
More Information.  I noticed some .py files used the ^M (Carriage return) for EOL and some files used \r (Line feed) for EOL.  Since I'm on a Mac I changed all files to \r.  Now everything is working fine.
Hey @dgervasio, thanks for erporting. You said:

> When I start Sypder my session it normally starts with the files I had open last session. This time, instead of the pointer curser, I got a round circle with a cross . Oppisite sides where colored the same, but different colors adjacent. None of my files opened. No default file was opened either, The Save a single file button was active. The save All files button was deactivated.

I really don't know what generated this problem, but I'm glad to read that you managed to solve it by changing the line endings of your files.

> When I got back 30 minutes later the "Issue preporter" window was up and I started typing this problem report.

We'll solve that error in our next version (5.5.0), to be released in a couple of months.

Resolving patch:
diff --git a/spyder/plugins/editor/widgets/editor.py b/spyder/plugins/editor/widgets/editor.py
--- a/spyder/plugins/editor/widgets/editor.py
+++ b/spyder/plugins/editor/widgets/editor.py
@@ -2401,26 +2401,44 @@ def __check_file_status(self, index):
             # Else, testing if it has been modified elsewhere:
             lastm = QFileInfo(finfo.filename).lastModified()
             if str(lastm.toString()) != str(finfo.lastmodified.toString()):
-                if finfo.editor.document().isModified():
+                # Catch any error when trying to reload a file and close it if
+                # that's the case to prevent users from destroying external
+                # changes in Spyder.
+                # Fixes spyder-ide/spyder#21248
+                try:
+                    if finfo.editor.document().isModified():
+                        self.msgbox = QMessageBox(
+                            QMessageBox.Question,
+                            self.title,
+                            _("The file <b>{}</b> has been modified outside "
+                              "Spyder."
+                              "<br><br>"
+                              "Do you want to reload it and lose all your "
+                              "changes?").format(name),
+                            QMessageBox.Yes | QMessageBox.No,
+                            self
+                        )
+
+                        answer = self.msgbox.exec_()
+                        if answer == QMessageBox.Yes:
+                            self.reload(index)
+                        else:
+                            finfo.lastmodified = lastm
+                    else:
+                        self.reload(index)
+                except Exception:
                     self.msgbox = QMessageBox(
-                        QMessageBox.Question,
+                        QMessageBox.Warning,
                         self.title,
-                        _("The file <b>%s</b> has been modified outside "
-                          "Spyder."
+                        _("The file <b>{}</b> has been modified outside "
+                          "Spyder but it was not possible to reload it."
                           "<br><br>"
-                          "Do you want to reload it and lose all your "
-                          "changes?") % name,
-                        QMessageBox.Yes | QMessageBox.No,
+                          "Therefore, it will be closed.").format(name),
+                        QMessageBox.Ok,
                         self
                     )
-
-                    answer = self.msgbox.exec_()
-                    if answer == QMessageBox.Yes:
-                        self.reload(index)
-                    else:
-                        finfo.lastmodified = lastm
-                else:
-                    self.reload(index)
+                    self.msgbox.exec_()
+                    self.close_file(index, force=True)
 
         # Finally, resetting temporary flag:
         self.__file_status_flag = False


Test patch: