🐛 FIX: aiida/repository typing

.pre-commit-config.yaml

@@ -48,6 +48,7 @@ repos:
                 aiida/manage/database/delete/nodes.py|
                 aiida/orm/nodes/node.py|
                 aiida/orm/nodes/process/.*py|
+                aiida/repository/.*py|
                 aiida/tools/graph/graph_traversers.py|
                 aiida/tools/groups/paths.py|
                 aiida/tools/importexport/archive/.*py|

aiida/backends/general/migrations/utils.py

@@ -108,7 +108,7 @@ def is_initialised(self) -> bool:
     def erase(self):
         raise NotImplementedError()
 
-    def put_object_from_filelike(self, handle: io.BufferedIOBase) -> str:
+    def _put_object_from_filelike(self, handle: io.BufferedIOBase) -> str:
         """Store the byte contents of a file in the repository.
 
         :param handle: filelike object with the byte content to be stored.

aiida/orm/nodes/repository.py

@@ -105,7 +105,7 @@ def list_object_names(self, path: str = None) -> typing.List[str]:
         return self._repository.list_object_names(path)
 
     @contextlib.contextmanager
-    def open(self, path: str, mode='r') -> io.BufferedReader:
+    def open(self, path: str, mode='r') -> typing.Iterator[typing.BinaryIO]:
         """Open a file handle to an object stored under the given key.
 
         .. note:: this should only be used to open a handle to read an existing file. To write a new file use the method

aiida/repository/__init__.py

@@ -13,4 +13,4 @@
 from .common import *
 from .repository import *
 
-__all__ = (backend.__all__ + common.__all__ + repository.__all__)
+__all__ = (backend.__all__ + common.__all__ + repository.__all__)  # type: ignore[name-defined]

aiida/repository/backend/__init__.py

@@ -5,4 +5,4 @@
 from .disk_object_store import *
 from .sandbox import *
 
-__all__ = (abstract.__all__ + disk_object_store.__all__ + sandbox.__all__)
+__all__ = (abstract.__all__ + disk_object_store.__all__ + sandbox.__all__)  # type: ignore[name-defined]

aiida/repository/backend/abstract.py

@@ -44,7 +44,7 @@ def is_initialised(self) -> bool:
         """Return whether the repository has been initialised."""
 
     @abc.abstractmethod
-    def erase(self):
+    def erase(self) -> None:
         """Delete the repository itself and all its contents.
 
         .. note:: This should not merely delete the contents of the repository but any resources it created. For
@@ -53,17 +53,23 @@ def erase(self):
         """
 
     @staticmethod
-    def is_readable_byte_stream(handle):
+    def is_readable_byte_stream(handle) -> bool:
         return hasattr(handle, 'read') and hasattr(handle, 'mode') and 'b' in handle.mode
 
-    def put_object_from_filelike(self, handle: io.BufferedIOBase) -> str:
+    def put_object_from_filelike(self, handle: typing.BinaryIO) -> str:
         """Store the byte contents of a file in the repository.
 
         :param handle: filelike object with the byte content to be stored.
         :return: the generated fully qualified identifier for the object within the repository.
+        :raises TypeError: if the handle is not a byte stream.
         """
         if not isinstance(handle, io.BytesIO) and not self.is_readable_byte_stream(handle):
             raise TypeError(f'handle does not seem to be a byte stream: {type(handle)}.')
+        return self._put_object_from_filelike(handle)
+
+    @abc.abstractmethod
+    def _put_object_from_filelike(self, handle: typing.BinaryIO) -> str:
+        pass
 
     def put_object_from_file(self, filepath: typing.Union[str, pathlib.Path]) -> str:
         """Store a new object with contents of the file located at `filepath` on this file system.
@@ -84,7 +90,7 @@ def has_object(self, key: str) -> bool:
         """
 
     @contextlib.contextmanager
-    def open(self, key: str) -> io.BufferedIOBase:
+    def open(self, key: str) -> typing.Iterator[typing.BinaryIO]:  # type: ignore[return]
         """Open a file handle to an object stored under the given key.
 
         .. note:: this should only be used to open a handle to read an existing file. To write a new file use the method

aiida/repository/backend/disk_object_store.py

@@ -1,7 +1,6 @@
 # -*- coding: utf-8 -*-
 """Implementation of the ``AbstractRepositoryBackend`` using the ``disk-objectstore`` as the backend."""
 import contextlib
-import io
 import shutil
 import typing
 
@@ -23,7 +22,9 @@ def __init__(self, container):
 
     def __str__(self) -> str:
         """Return the string representation of this repository."""
-        return f'DiskObjectStoreRepository: {self.container.container_id} | {self.container.get_folder()}'
+        if self.is_initialised:
+            return f'DiskObjectStoreRepository: {self.container.container_id} | {self.container.get_folder()}'
+        return 'DiskObjectStoreRepository: <uninitialised>'
 
     @property
     def uuid(self) -> typing.Optional[str]:
@@ -45,7 +46,7 @@ def is_initialised(self) -> bool:
         return self.container.is_initialised
 
     @property
-    def container(self):
+    def container(self) -> Container:
         return self._container
 
     def erase(self):
@@ -55,14 +56,13 @@ def erase(self):
         except FileNotFoundError:
             pass
 
-    def put_object_from_filelike(self, handle: io.BufferedIOBase) -> str:
+    def _put_object_from_filelike(self, handle: typing.BinaryIO) -> str:
         """Store the byte contents of a file in the repository.
 
         :param handle: filelike object with the byte content to be stored.
         :return: the generated fully qualified identifier for the object within the repository.
         :raises TypeError: if the handle is not a byte stream.
         """
-        super().put_object_from_filelike(handle)
         return self.container.add_object(handle.read())
 
     def has_object(self, key: str) -> bool:
@@ -74,7 +74,7 @@ def has_object(self, key: str) -> bool:
         return self.container.has_object(key)
 
     @contextlib.contextmanager
-    def open(self, key: str) -> io.BufferedIOBase:
+    def open(self, key: str) -> typing.Iterator[typing.BinaryIO]:
         """Open a file handle to an object stored under the given key.
 
         .. note:: this should only be used to open a handle to read an existing file. To write a new file use the method

aiida/repository/backend/sandbox.py

@@ -1,7 +1,6 @@
 # -*- coding: utf-8 -*-
 """Implementation of the ``AbstractRepositoryBackend`` using a sandbox folder on disk as the backend."""
 import contextlib
-import io
 import os
 import shutil
 import typing
@@ -16,11 +15,14 @@ class SandboxRepositoryBackend(AbstractRepositoryBackend):
     """Implementation of the ``AbstractRepositoryBackend`` using a sandbox folder on disk as the backend."""
 
     def __init__(self):
-        self._sandbox = None
+        from aiida.common.folders import SandboxFolder
+        self._sandbox: typing.Optional[SandboxFolder] = None
 
     def __str__(self) -> str:
         """Return the string representation of this repository."""
-        return f'SandboxRepository: {self._sandbox.abspath}'
+        if self.is_initialised:
+            return f'SandboxRepository: {self._sandbox.abspath if self._sandbox else "null"}'
+        return 'SandboxRepository: <uninitialised>'
 
     def __del__(self):
         """Delete the entire sandbox folder if it was instantiated and still exists."""
@@ -68,15 +70,13 @@ def erase(self):
             finally:
                 self._sandbox = None
 
-    def put_object_from_filelike(self, handle: io.BufferedIOBase) -> str:
+    def _put_object_from_filelike(self, handle: typing.BinaryIO) -> str:
         """Store the byte contents of a file in the repository.
 
         :param handle: filelike object with the byte content to be stored.
         :return: the generated fully qualified identifier for the object within the repository.
         :raises TypeError: if the handle is not a byte stream.
         """
-        super().put_object_from_filelike(handle)
-
         key = str(uuid.uuid4())
         filepath = os.path.join(self.sandbox.abspath, key)
 
@@ -94,7 +94,7 @@ def has_object(self, key: str) -> bool:
         return key in os.listdir(self.sandbox.abspath)
 
     @contextlib.contextmanager
-    def open(self, key: str) -> io.BufferedIOBase:
+    def open(self, key: str) -> typing.Iterator[typing.BinaryIO]:
         """Open a file handle to an object stored under the given key.
 
         .. note:: this should only be used to open a handle to read an existing file. To write a new file use the method