Refactor: Replace deprecated IOError with OSError (#6441)

PEP 3151 reworked the builtin exception hierarchy and `IOError` was
deprecated (kept as an alias) in favor of `OSError`. The change was
implemented in Python 3.3: https://peps.python.org/pep-3151

.github/workflows/check_release_tag.py

@@ -11,7 +11,7 @@ def get_version_from_module(content: str) -> str:
     try:
         module = ast.parse(content)
     except SyntaxError as exc:
-        raise IOError(f'Unable to parse module: {exc}')
+        raise OSError(f'Unable to parse module: {exc}')
     try:
         return next(
             ast.literal_eval(statement.value)
@@ -21,7 +21,7 @@ def get_version_from_module(content: str) -> str:
             if isinstance(target, ast.Name) and target.id == '__version__'
         )
     except StopIteration:
-        raise IOError('Unable to find __version__ in module')
+        raise OSError('Unable to find __version__ in module')
 
 
 if __name__ == '__main__':

docs/source/topics/calculations/include/snippets/calcjobs/arithmetic_add_parser.py

@@ -10,7 +10,7 @@ def parse(self, **kwargs):
         try:
             with output_folder.open(self.node.get_option('output_filename'), 'r') as handle:
                 result = self.parse_stdout(handle)
-        except (OSError, IOError):
+        except OSError:
             return self.exit_codes.ERROR_READING_OUTPUT_FILE
 
         if result is None:

docs/source/topics/transport_template.py

@@ -18,7 +18,7 @@ def chdir(self, path):
         """Change directory to 'path'.
 
         :param str path: path to change working directory into.
-        :raises: IOError, if the requested path does not exist
+        :raises: OSError, if the requested path does not exist
         :rtype: string
         """
 
@@ -35,7 +35,7 @@ def copy(self, remotesource, remotedestination, *args, **kwargs):
         :param str remotesource: path of the remote source directory / file
         :param str remotedestination: path of the remote destination directory / file
 
-        :raises: IOError, if source or destination does not exist
+        :raises: OSError, if source or destination does not exist
         """
 
     def copyfile(self, remotesource, remotedestination, *args, **kwargs):
@@ -44,7 +44,7 @@ def copyfile(self, remotesource, remotedestination, *args, **kwargs):
         :param str remotesource: path of the remote source directory / file
         :param str remotedestination: path of the remote destination directory / file
 
-        :raises IOError: if one of src or dst does not exist
+        :raises OSError: if one of src or dst does not exist
         """
 
     def copytree(self, remotesource, remotedestination, *args, **kwargs):
@@ -53,7 +53,7 @@ def copytree(self, remotesource, remotedestination, *args, **kwargs):
         :param str remotesource: path of the remote source directory / file
         :param str remotedestination: path of the remote destination directory / file
 
-        :raise IOError: if one of src or dst does not exist
+        :raise OSError: if one of src or dst does not exist
         """
 
     def exec_command_wait_bytes(self, command, stdin=None, **kwargs):
@@ -177,7 +177,7 @@ def normalize(self, path='.'):
         "current folder".
 
         :param str path: path to be normalized
-        :raise IOError: if the path can't be resolved on the server
+        :raise OSError: if the path can't be resolved on the server
         """
 
     def put(self, localpath, remotepath, *args, **kwargs):
@@ -214,7 +214,7 @@ def rename(self, src, dst):
 
         :param str oldpath: existing name of the file or folder
         :param str newpath: new name for the file or folder
-        :raises IOError: if src/dst is not found
+        :raises OSError: if src/dst is not found
         :raises ValueError: if src/dst is not a valid string
         """
 
@@ -224,7 +224,7 @@ def remove(self, path):
         This only works on files; for removing folders (directories), use rmdir.
 
         :param str path: path to file to remove
-        :raise IOError: if the path is a directory
+        :raise OSError: if the path is a directory
         """
 
     def rmdir(self, path):

src/aiida/cmdline/commands/cmd_calcjob.py

@@ -139,7 +139,7 @@ def calcjob_remotecat(calcjob, path):
             remote_folder.getfile(path, tmp_path.name)
             with open(tmp_path.name, 'rb') as handle:
                 shutil.copyfileobj(handle, sys.stdout.buffer)
-        except IOError as exception:
+        except OSError as exception:
             echo.echo_critical(str(exception))
 
 

src/aiida/cmdline/commands/cmd_computer.py

@@ -135,7 +135,7 @@ def _computer_create_temp_file(transport, scheduler, authinfo, computer):
 
     try:
         transport.chdir(workdir)
-    except IOError:
+    except OSError:
         transport.makedirs(workdir)
         transport.chdir(workdir)
 

src/aiida/cmdline/commands/cmd_data/cmd_cif.py

@@ -91,7 +91,7 @@ def cif_content(data):
     for node in data:
         try:
             echo.echo(node.get_content())
-        except IOError as exception:
+        except OSError as exception:
             echo.echo_warning(f'could not read the content for CifData<{node.pk}>: {exception!s}')
 
 

src/aiida/cmdline/commands/cmd_data/cmd_remote.py

@@ -39,7 +39,7 @@ def remote_ls(ls_long, path, datum):
 
     try:
         content = datum.listdir_withattributes(path=path)
-    except (IOError, OSError) as err:
+    except OSError as err:
         echo.echo_critical(f'Unable to access the remote folder or file, check if it exists.\nOriginal error: {err!s}')
     for metadata in content:
         if ls_long:
@@ -71,7 +71,7 @@ def remote_cat(datum, path):
             datum.getfile(path, tmpf.name)
             with open(tmpf.name, encoding='utf8') as fhandle:
                 sys.stdout.write(fhandle.read())
-    except IOError as err:
+    except OSError as err:
         echo.echo_critical(f'{err.errno}: {err!s}')
 
     try:

src/aiida/cmdline/commands/cmd_data/cmd_singlefile.py

@@ -25,5 +25,5 @@ def singlefile_content(datum):
     """Show the content of the file."""
     try:
         echo.echo(datum.get_content())
-    except (IOError, OSError) as exception:
+    except OSError as exception:
         echo.echo_critical(f'could not read the content for SinglefileData<{datum.pk}>: {exception!s}')

src/aiida/common/files.py

@@ -18,7 +18,7 @@ def md5_from_filelike(filelike, block_size_factor=128):
     :param block_size_factor: the file is read at chunks of size ``block_size_factor * md5.block_size``, where
         ``md5.block_size`` is the block_size used internally by the hashlib module.
     :returns: a string with the hexdigest md5.
-    :raises: no checks are done on the filelike object, so it may raise IOError if it cannot be read from.
+    :raises: no checks are done on the filelike object, so it may raise OSError if it cannot be read from.
     """
     md5 = hashlib.md5()
 
@@ -37,7 +37,7 @@ def md5_file(filepath, block_size_factor=128):
         ``md5.block_size`` is the block_size used internally by the hashlib module.
     :returns: a string with the hexdigest md5.
     :raises: No checks are done on the file, so if it doesn't exists it may
-        raise IOError.
+        raise OSError.
     """
     with open(filepath, 'rb', encoding=None) as handle:
         return md5_from_filelike(handle, block_size_factor=block_size_factor)
@@ -55,7 +55,7 @@ def sha1_file(filename, block_size_factor=128):
     :returns: a string with the hexdigest sha1.
 
     :raises: No checks are done on the file, so if it doesn't exists it may
-        raise IOError.
+        raise OSError.
     """
     sha1 = hashlib.sha1()
     with open(filename, 'rb', encoding=None) as fhandle:

src/aiida/common/folders.py

@@ -184,7 +184,7 @@ def insert_path(self, src, dest_name=None, overwrite=True):
                     # This automatically overwrites files
                     shutil.copyfile(src, dest_abs_path)
                 else:
-                    raise IOError(f'destination already exists: {os.path.join(dest_abs_path)}')
+                    raise OSError(f'destination already exists: {os.path.join(dest_abs_path)}')
             else:
                 shutil.copyfile(src, dest_abs_path)
         elif os.path.isdir(src):
@@ -197,7 +197,7 @@ def insert_path(self, src, dest_name=None, overwrite=True):
                     # This automatically overwrites files
                     shutil.copytree(src, dest_abs_path)
                 else:
-                    raise IOError(f'destination already exists: {os.path.join(dest_abs_path)}')
+                    raise OSError(f'destination already exists: {os.path.join(dest_abs_path)}')
             else:
                 shutil.copytree(src, dest_abs_path)
         else:
@@ -339,11 +339,11 @@ def replace_with_folder(self, srcdir, move=False, overwrite=False):
         :param move: if True, the srcdir is moved to the repository. Otherwise, it is only copied.
         :type move: bool
         :param overwrite: if True, the folder will be erased first.
-            if False, an IOError is raised if the folder already exists.
+            if False, an OSError is raised if the folder already exists.
             Whatever the value of this flag, parent directories will be created, if needed.
         :type overwrite: bool
 
-        :raises IOError: in case of problems accessing or writing the files.
+        :raises OSError: in case of problems accessing or writing the files.
         :raises OSError: in case of problems accessing or writing the files (from ``shutil`` module).
         :raises ValueError: if the section is not recognized.
         """
@@ -352,7 +352,7 @@ def replace_with_folder(self, srcdir, move=False, overwrite=False):
         if overwrite:
             self.erase()
         elif self.exists():
-            raise IOError(f'Location {self.abspath} already exists, and overwrite is set to False')
+            raise OSError(f'Location {self.abspath} already exists, and overwrite is set to False')
 
         # Create parent dir, if needed, with the right mode
         pardir = os.path.dirname(self.abspath)

src/aiida/engine/daemon/client.py

@@ -192,7 +192,7 @@ def get_circus_port(self) -> int:
             try:
                 with open(self.circus_port_file, 'r', encoding='utf8') as fhandle:
                     return int(fhandle.read().strip())
-            except (ValueError, IOError):
+            except (ValueError, OSError):
                 raise RuntimeError('daemon is running so port file should have been there but could not read it')
         else:
             port = self.get_available_port()
@@ -241,7 +241,7 @@ def get_circus_socket_directory(self) -> str:
                 with open(self.circus_socket_file, 'r', encoding='utf8') as fhandle:
                     content = fhandle.read().strip()
                 return content
-            except (ValueError, IOError):
+            except (ValueError, OSError):
                 raise RuntimeError('daemon is running so sockets file should have been there but could not read it')
         else:
             # The SOCKET_DIRECTORY is already set, a temporary directory was already created and the same should be used
@@ -265,7 +265,7 @@ def get_daemon_pid(self) -> int | None:
                 with open(self.circus_pid_file, 'r', encoding='utf8') as fhandle:
                     content = fhandle.read().strip()
                 return int(content)
-            except (ValueError, IOError):
+            except (ValueError, OSError):
                 return None
         else:
             return None

src/aiida/engine/daemon/execmanager.py

@@ -116,7 +116,7 @@ def upload_calculation(
         # If it already exists, no exception is raised
         try:
             transport.chdir(remote_working_directory)
-        except IOError:
+        except OSError:
             logger.debug(
                 f'[submission of calculation {node.pk}] Unable to '
                 f'chdir in {remote_working_directory}, trying to create it'
@@ -296,7 +296,7 @@ def _copy_remote_files(logger, node, computer, transport, remote_copy_list, remo
                     f'[submission of calculation {node.pk}] Unable to copy remote '
                     f'resource from {remote_abs_path} to {dest_rel_path}! NOT Stopping but just ignoring!.'
                 )
-            except (IOError, OSError):
+            except OSError:
                 logger.warning(
                     f'[submission of calculation {node.pk}] Unable to copy remote '
                     f'resource from {remote_abs_path} to {dest_rel_path}! Stopping.'
@@ -318,14 +318,14 @@ def _copy_remote_files(logger, node, computer, transport, remote_copy_list, remo
             try:
                 transport.makedirs(remote_dirname, ignore_existing=True)
                 transport.symlink(remote_abs_path, dest_rel_path)
-            except (IOError, OSError):
+            except OSError:
                 logger.warning(
                     f'[submission of calculation {node.pk}] Unable to create remote symlink '
                     f'from {remote_abs_path} to {dest_rel_path}! Stopping.'
                 )
                 raise
         else:
-            raise IOError(
+            raise OSError(
                 f'It is not possible to create a symlink between two different machines for calculation {node.pk}'
             )
 
@@ -459,7 +459,7 @@ def stash_calculation(calculation: CalcJobNode, transport: Transport) -> None:
 
             try:
                 transport.copy(str(source_filepath), str(target_filepath))
-            except (IOError, ValueError) as exception:
+            except (OSError, ValueError) as exception:
                 EXEC_LOGGER.warning(f'failed to stash {source_filepath} to {target_filepath}: {exception}')
             else:
                 EXEC_LOGGER.debug(f'stashed {source_filepath} to {target_filepath}')

src/aiida/engine/processes/workchains/restart.py

@@ -424,7 +424,7 @@ def on_terminated(self):
                 try:
                     called_descendant.outputs.remote_folder._clean()
                     cleaned_calcs.append(str(called_descendant.pk))
-                except (IOError, OSError, KeyError):
+                except (OSError, OSError, KeyError):
                     pass
 
         if cleaned_calcs:

src/aiida/orm/nodes/data/remote/base.py

@@ -60,8 +60,8 @@ def is_empty(self):
         with transport:
             try:
                 transport.chdir(self.get_remote_path())
-            except IOError:
-                # If the transport IOError the directory no longer exists and was deleted
+            except OSError:
+                # If the transport OSError the directory no longer exists and was deleted
                 return True
 
             return not transport.listdir()
@@ -78,9 +78,9 @@ def getfile(self, relpath, destpath):
             try:
                 full_path = os.path.join(self.get_remote_path(), relpath)
                 transport.getfile(full_path, destpath)
-            except IOError as exception:
+            except OSError as exception:
                 if exception.errno == 2:  # file does not exist
-                    raise IOError(
+                    raise OSError(
                         'The required remote file {} on {} does not exist or has been deleted.'.format(
                             full_path, self.computer.label
                         )
@@ -99,9 +99,9 @@ def listdir(self, relpath='.'):
             try:
                 full_path = os.path.join(self.get_remote_path(), relpath)
                 transport.chdir(full_path)
-            except IOError as exception:
+            except OSError as exception:
                 if exception.errno in (2, 20):  # directory not existing or not a directory
-                    exc = IOError(
+                    exc = OSError(
                         f'The required remote folder {full_path} on {self.computer.label} does not exist, is not a '
                         'directory or has been deleted.'
                     )
@@ -112,9 +112,9 @@ def listdir(self, relpath='.'):
 
             try:
                 return transport.listdir()
-            except IOError as exception:
+            except OSError as exception:
                 if exception.errno in (2, 20):  # directory not existing or not a directory
-                    exc = IOError(
+                    exc = OSError(
                         f'The required remote folder {full_path} on {self.computer.label} does not exist, is not a '
                         'directory or has been deleted.'
                     )
@@ -135,9 +135,9 @@ def listdir_withattributes(self, path='.'):
             try:
                 full_path = os.path.join(self.get_remote_path(), path)
                 transport.chdir(full_path)
-            except IOError as exception:
+            except OSError as exception:
                 if exception.errno in (2, 20):  # directory not existing or not a directory
-                    exc = IOError(
+                    exc = OSError(
                         f'The required remote folder {full_path} on {self.computer.label} does not exist, is not a '
                         'directory or has been deleted.'
                     )
@@ -148,9 +148,9 @@ def listdir_withattributes(self, path='.'):
 
             try:
                 return transport.listdir_withattributes()
-            except IOError as exception:
+            except OSError as exception:
                 if exception.errno in (2, 20):  # directory not existing or not a directory
-                    exc = IOError(
+                    exc = OSError(
                         f'The required remote folder {full_path} on {self.computer.label} does not exist, is not a '
                         'directory or has been deleted.'
                     )

src/aiida/orm/nodes/process/calculation/calcjob.py

@@ -520,7 +520,7 @@ def get_scheduler_stdout(self) -> Optional[AnyStr]:
 
         try:
             stdout = retrieved_node.base.repository.get_object_content(filename)
-        except IOError:
+        except OSError:
             stdout = None
 
         return stdout
@@ -538,7 +538,7 @@ def get_scheduler_stderr(self) -> Optional[AnyStr]:
 
         try:
             stderr = retrieved_node.base.repository.get_object_content(filename)
-        except IOError:
+        except OSError:
             stderr = None
 
         return stderr

src/aiida/orm/utils/mixins.py

@@ -45,7 +45,7 @@ def store_source_info(self, func) -> None:
 
         try:
             source_list, starting_line_number = inspect.getsourcelines(func)
-        except (IOError, OSError):
+        except OSError:
             pass
         else:
             self._set_function_starting_line_number(starting_line_number)
@@ -63,7 +63,7 @@ def store_source_info(self, func) -> None:
                     self.base.repository.put_object_from_filelike(  # type: ignore[attr-defined]
                         handle, self.FUNCTION_SOURCE_FILE_PATH
                     )
-        except (IOError, OSError):
+        except OSError:
             pass
 
     @property