fix running in bash environment on windows

pyproject.toml

@@ -48,7 +48,8 @@ dependencies = [
   'tqdm~=4.45',
   'typing-extensions~=4.0;python_version<"3.10"',
   'upf_to_json~=0.9.2',
-  'wrapt~=1.11'
+  'wrapt~=1.11',
+  'chardet'
 ]
 description = 'AiiDA is a workflow manager for computational science with a strong focus on provenance, performance and extensibility.'
 dynamic = ['version']  # read from aiida/__init__.py

src/aiida/cmdline/commands/cmd_computer.py

@@ -136,12 +136,14 @@ def _computer_create_temp_file(transport, scheduler, authinfo, computer):
 
     transport.makedirs(workdir, ignore_existing=True)
 
-    with tempfile.NamedTemporaryFile(mode='w+') as tempf:
+    with tempfile.NamedTemporaryFile(mode='w+', delete=False) as tempf:
         fname = os.path.split(tempf.name)[1]
         remote_file_path = os.path.join(workdir, fname)
         tempf.write(file_content)
         tempf.flush()
+        tempf.close()
         transport.putfile(tempf.name, remote_file_path)
+        os.remove(tempf.name)
 
     if not transport.path_exists(remote_file_path):
         return False, f'failed to create the file `{remote_file_path}` on the remote'

src/aiida/manage/configuration/config.py

@@ -20,6 +20,7 @@
 import io
 import json
 import os
+import shutil
 import uuid
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Tuple
@@ -780,7 +781,8 @@ def _atomic_write(self, filepath=None):
                 os.umask(umask)
 
             handle.flush()
-            os.rename(handle.name, self.filepath)
+            handle.close()
+            shutil.move(handle.name, self.filepath)
 
     def filepaths(self, profile: Profile):
         """Return the filepaths used by a profile.

src/aiida/manage/profile_access.py

@@ -10,6 +10,7 @@
 
 import contextlib
 import os
+import shutil
 import typing
 from pathlib import Path
 
@@ -76,7 +77,7 @@ def request_access(self) -> None:
             # it will read the incomplete command, won't be able to correctly compare it with its running
             # process, and will conclude the record is old and clean it up.
             filepath_tmp.write_text(str(self.process.cmdline()))
-            os.rename(filepath_tmp, filepath_pid)
+            shutil.move(filepath_tmp, filepath_pid)
 
             # Check again in case a lock was created in the time between the first check and creating the
             # access record file.

src/aiida/orm/nodes/data/code/abstract.py

@@ -159,7 +159,7 @@ def can_run_on_computer(self, computer: Computer) -> bool:
         """
 
     @abc.abstractmethod
-    def get_executable(self) -> pathlib.PurePosixPath:
+    def get_executable(self) -> pathlib.PurePath:
         """Return the executable that the submission script should execute to run the code.
 
         :return: The executable to be called in the submission script.

src/aiida/orm/nodes/data/code/containerized.py

@@ -62,7 +62,7 @@ def __init__(self, engine_command: str, image_name: str, **kwargs):
         self.image_name = image_name
 
     @property
-    def filepath_executable(self) -> pathlib.PurePosixPath:
+    def filepath_executable(self) -> pathlib.PurePath:
         """Return the filepath of the executable that this code represents.
 
         .. note:: This is overridden from the base class since the path does not have to be absolute.

src/aiida/orm/nodes/data/code/installed.py

@@ -170,7 +170,7 @@ def can_run_on_computer(self, computer: Computer) -> bool:
         type_check(computer, Computer)
         return computer.pk == self.computer.pk
 
-    def get_executable(self) -> pathlib.PurePosixPath:
+    def get_executable(self) -> pathlib.PurePath:
         """Return the executable that the submission script should execute to run the code.
 
         :return: The executable to be called in the submission script.
@@ -207,12 +207,12 @@ def full_label(self) -> str:
         return f'{self.label}@{self.computer.label}'
 
     @property
-    def filepath_executable(self) -> pathlib.PurePosixPath:
+    def filepath_executable(self) -> pathlib.PurePath:
         """Return the absolute filepath of the executable that this code represents.
 
         :return: The absolute filepath of the executable.
         """
-        return pathlib.PurePosixPath(self.base.attributes.get(self._KEY_ATTRIBUTE_FILEPATH_EXECUTABLE))
+        return pathlib.PurePath(self.base.attributes.get(self._KEY_ATTRIBUTE_FILEPATH_EXECUTABLE))
 
     @filepath_executable.setter
     def filepath_executable(self, value: str) -> None:

src/aiida/orm/nodes/data/code/legacy.py

@@ -123,7 +123,7 @@ def can_run_on_computer(self, computer: Computer) -> bool:
         type_check(computer, orm.Computer)
         return computer.pk == self.get_remote_computer().pk
 
-    def get_executable(self) -> pathlib.PurePosixPath:
+    def get_executable(self) -> pathlib.PurePath:
         """Return the executable that the submission script should execute to run the code.
 
         :return: The executable to be called in the submission script.
@@ -133,7 +133,7 @@ def get_executable(self) -> pathlib.PurePosixPath:
         else:
             exec_path = self.get_remote_exec_path()
 
-        return pathlib.PurePosixPath(exec_path)
+        return pathlib.PurePath(exec_path)
 
     def hide(self):
         """Hide the code (prevents from showing it in the verdi code list)"""

src/aiida/orm/nodes/data/code/portable.py

@@ -124,7 +124,7 @@ def can_run_on_computer(self, computer: Computer) -> bool:
         """
         return True
 
-    def get_executable(self) -> pathlib.PurePosixPath:
+    def get_executable(self) -> pathlib.PurePath:
         """Return the executable that the submission script should execute to run the code.
 
         :return: The executable to be called in the submission script.
@@ -161,12 +161,12 @@ def full_label(self) -> str:
         return self.label
 
     @property
-    def filepath_executable(self) -> pathlib.PurePosixPath:
+    def filepath_executable(self) -> pathlib.PurePath:
         """Return the relative filepath of the executable that this code represents.
 
         :return: The relative filepath of the executable.
         """
-        return pathlib.PurePosixPath(self.base.attributes.get(self._KEY_ATTRIBUTE_FILEPATH_EXECUTABLE))
+        return pathlib.PurePath(self.base.attributes.get(self._KEY_ATTRIBUTE_FILEPATH_EXECUTABLE))
 
     @filepath_executable.setter
     def filepath_executable(self, value: str) -> None:
@@ -176,7 +176,7 @@ def filepath_executable(self, value: str) -> None:
         """
         type_check(value, str)
 
-        if pathlib.PurePosixPath(value).is_absolute():
+        if pathlib.PurePath(value).is_absolute():
             raise ValueError('The `filepath_executable` should not be absolute.')
 
         self.base.attributes.set(self._KEY_ATTRIBUTE_FILEPATH_EXECUTABLE, value)

src/aiida/orm/nodes/data/folder.py

@@ -23,7 +23,7 @@
 
 __all__ = ('FolderData',)
 
-FilePath = t.Union[str, pathlib.PurePosixPath]
+FilePath = t.Union[str, pathlib.PurePath]
 
 
 class FolderData(Data):
@@ -177,7 +177,7 @@ def put_object_from_tree(self, filepath: str, path: str | None = None) -> None:
         """
         return self.base.repository.put_object_from_tree(filepath, path)
 
-    def walk(self, path: FilePath | None = None) -> t.Iterable[tuple[pathlib.PurePosixPath, list[str], list[str]]]:
+    def walk(self, path: FilePath | None = None) -> t.Iterable[tuple[pathlib.PurePath, list[str], list[str]]]:
         """Walk over the directories and files contained within this repository.
 
         .. note:: the order of the dirname and filename lists that are returned is not necessarily sorted. This is in
@@ -186,11 +186,11 @@ def walk(self, path: FilePath | None = None) -> t.Iterable[tuple[pathlib.PurePos
         :param path: the relative path of the directory within the repository whose contents to walk.
         :return: tuples of root, dirnames and filenames just like ``os.walk``, with the exception that the root path is
             always relative with respect to the repository root, instead of an absolute path and it is an instance of
-            ``pathlib.PurePosixPath`` instead of a normal string
+            ``pathlib.PurePath`` instead of a normal string
         """
         yield from self.base.repository.walk(path)
 
-    def glob(self) -> t.Iterable[pathlib.PurePosixPath]:
+    def glob(self) -> t.Iterable[pathlib.PurePath]:
         """Yield a recursive list of all paths (files and directories)."""
         yield from self.base.repository.glob()
 

src/aiida/orm/nodes/data/singlefile.py

@@ -22,7 +22,7 @@
 
 __all__ = ('SinglefileData',)
 
-FilePath = t.Union[str, pathlib.PurePosixPath]
+FilePath = t.Union[str, pathlib.PurePath]
 
 
 class SinglefileData(Data):

src/aiida/orm/nodes/repository.py

@@ -20,7 +20,7 @@
 
 __all__ = ('NodeRepository',)
 
-FilePath = t.Union[str, pathlib.PurePosixPath]
+FilePath = t.Union[str, pathlib.PurePath]
 
 
 class NodeRepository:
@@ -317,7 +317,7 @@ def put_object_from_tree(self, filepath: str, path: str | None = None):
         self._repository.put_object_from_tree(filepath, path)
         self._update_repository_metadata()
 
-    def walk(self, path: FilePath | None = None) -> t.Iterable[tuple[pathlib.PurePosixPath, list[str], list[str]]]:
+    def walk(self, path: FilePath | None = None) -> t.Iterable[tuple[pathlib.PurePath, list[str], list[str]]]:
         """Walk over the directories and files contained within this repository.
 
         .. note:: the order of the dirname and filename lists that are returned is not necessarily sorted. This is in
@@ -326,11 +326,11 @@ def walk(self, path: FilePath | None = None) -> t.Iterable[tuple[pathlib.PurePos
         :param path: the relative path of the directory within the repository whose contents to walk.
         :return: tuples of root, dirnames and filenames just like ``os.walk``, with the exception that the root path is
             always relative with respect to the repository root, instead of an absolute path and it is an instance of
-            ``pathlib.PurePosixPath`` instead of a normal string
+            ``pathlib.PurePath`` instead of a normal string
         """
         yield from self._repository.walk(path)
 
-    def glob(self) -> t.Iterable[pathlib.PurePosixPath]:
+    def glob(self) -> t.Iterable[pathlib.PurePath]:
         """Yield a recursive list of all paths (files and directories)."""
         for dirpath, dirnames, filenames in self.walk():
             for dirname in dirnames:

src/aiida/repository/repository.py

@@ -12,7 +12,7 @@
 
 __all__ = ('Repository',)
 
-FilePath = Union[str, pathlib.PurePosixPath]
+FilePath = Union[str, pathlib.PurePath]
 
 
 class Repository:
@@ -127,23 +127,23 @@ def hash(self) -> str:
         return make_hash(objects)
 
     @staticmethod
-    def _pre_process_path(path: Optional[FilePath] = None) -> pathlib.PurePosixPath:
-        """Validate and convert the path to instance of ``pathlib.PurePosixPath``.
+    def _pre_process_path(path: Optional[FilePath] = None) -> pathlib.PurePath:
+        """Validate and convert the path to instance of ``pathlib.PurePath``.
 
         This should be called by every method of this class before doing anything, such that it can safely assume that
-        the path is a ``pathlib.PurePosixPath`` object, which makes path manipulation a lot easier.
+        the path is a ``pathlib.PurePath`` object, which makes path manipulation a lot easier.
 
-        :param path: the path as a ``pathlib.PurePosixPath`` object or `None`.
-        :raises TypeError: if the type of path was not a str nor a ``pathlib.PurePosixPath`` instance.
+        :param path: the path as a ``pathlib.PurePath`` object or `None`.
+        :raises TypeError: if the type of path was not a str nor a ``pathlib.PurePath`` instance.
         """
         if path is None:
-            return pathlib.PurePosixPath()
+            return pathlib.PurePath()
 
         if isinstance(path, str):
-            path = pathlib.PurePosixPath(path)
+            path = pathlib.PurePath(path)
 
-        if not isinstance(path, pathlib.PurePosixPath):
-            raise TypeError('path is not of type `str` nor `pathlib.PurePosixPath`.')
+        if not isinstance(path, pathlib.PurePath):
+            raise TypeError('path is not of type `str` nor `pathlib.PurePath`.')
 
         if path.is_absolute():
             raise TypeError(f'path `{path}` is not a relative path.')
@@ -167,7 +167,7 @@ def set_backend(self, backend: AbstractRepositoryBackend) -> None:
         type_check(backend, AbstractRepositoryBackend)
         self._backend = backend
 
-    def _insert_file(self, path: pathlib.PurePosixPath, key: str) -> None:
+    def _insert_file(self, path: pathlib.PurePath, key: str) -> None:
         """Insert a new file object in the object mapping.
 
         .. note:: this assumes the path is a valid relative path, so should be checked by the caller.
@@ -334,10 +334,10 @@ def put_object_from_tree(self, filepath: FilePath, path: Optional[FilePath] = No
         path = self._pre_process_path(path)
 
         if isinstance(filepath, str):
-            filepath = pathlib.PurePosixPath(filepath)
+            filepath = pathlib.PurePath(filepath)
 
-        if not isinstance(filepath, pathlib.PurePosixPath):
-            raise TypeError(f'filepath `{filepath}` is not of type `str` nor `pathlib.PurePosixPath`.')
+        if not isinstance(filepath, pathlib.PurePath):
+            raise TypeError(f'filepath `{filepath}` is not of type `str` nor `pathlib.PurePath`.')
 
         if not filepath.is_absolute():
             raise TypeError(f'filepath `{filepath}` is not an absolute path.')
@@ -347,7 +347,7 @@ def put_object_from_tree(self, filepath: FilePath, path: Optional[FilePath] = No
             self.create_directory(path)
 
         for root_str, dirnames, filenames in os.walk(filepath):
-            root = pathlib.PurePosixPath(root_str)
+            root = pathlib.PurePath(root_str)
 
             for dirname in dirnames:
                 self.create_directory(path / root.relative_to(filepath) / dirname)
@@ -457,7 +457,7 @@ def clone(self, source: 'Repository') -> None:
                 with source.open(root / filename) as handle:
                     self.put_object_from_filelike(handle, root / filename)
 
-    def walk(self, path: Optional[FilePath] = None) -> Iterable[Tuple[pathlib.PurePosixPath, List[str], List[str]]]:
+    def walk(self, path: Optional[FilePath] = None) -> Iterable[Tuple[pathlib.PurePath, List[str], List[str]]]:
         """Walk over the directories and files contained within this repository.
 
         .. note:: the order of the dirname and filename lists that are returned is not necessarily sorted. This is in
@@ -466,7 +466,7 @@ def walk(self, path: Optional[FilePath] = None) -> Iterable[Tuple[pathlib.PurePo
         :param path: the relative path of the directory within the repository whose contents to walk.
         :return: tuples of root, dirnames and filenames just like ``os.walk``, with the exception that the root path is
             always relative with respect to the repository root, instead of an absolute path and it is an instance of
-            ``pathlib.PurePosixPath`` instead of a normal string
+            ``pathlib.PurePath`` instead of a normal string
         """
         path = self._pre_process_path(path)
 

src/aiida/storage/sqlite_zip/migrations/legacy_to_main.py

@@ -13,7 +13,7 @@
 from contextlib import contextmanager
 from datetime import datetime
 from hashlib import sha256
-from pathlib import Path, PurePosixPath
+from pathlib import Path, PurePath
 from typing import Any, Callable, ContextManager, Dict, Iterator, List, Optional, Tuple, Union
 
 from archive_path import ZipPath
@@ -96,7 +96,7 @@ def _in_archive_context(_inpath):
                 if len(parts) < 6 or parts[0] != 'nodes' or parts[4] not in ('raw_input', 'path'):
                     continue
                 uuid = ''.join(parts[1:4])
-                posix_rel = PurePosixPath(*parts[5:])
+                posix_rel = PurePath(*parts[5:])
                 hashkey = None
                 if subpath.is_file():
                     with subpath.open('rb') as handle:
@@ -270,7 +270,7 @@ def _create_repo_metadata(paths: List[Tuple[str, Optional[str]]]) -> Dict[str, A
     """
     top_level = File()
     for _path, hashkey in paths:
-        path = PurePosixPath(_path)
+        path = PurePath(_path)
         if hashkey is None:
             _create_directory(top_level, path)
         else:
@@ -279,7 +279,7 @@ def _create_repo_metadata(paths: List[Tuple[str, Optional[str]]]) -> Dict[str, A
     return top_level.serialize()
 
 
-def _create_directory(top_level: File, path: PurePosixPath) -> File:
+def _create_directory(top_level: File, path: PurePath) -> File:
     """Create a new directory with the given path.
 
     :param path: the relative path of the directory.

src/aiida/transports/plugins/local.py

@@ -15,6 +15,7 @@
 import os
 import shutil
 import subprocess
+import sys
 from typing import Optional
 
 from aiida.common.warnings import warn_deprecation
@@ -777,9 +778,14 @@ def _exec_command_internal(self, command, workdir: Optional[TransportPath] = Non
         else:
             cwd = self.getcwd()
 
+        if sys.platform == 'win32':
+            shell = False
+        else:
+            shell = True
+
         with subprocess.Popen(
             command,
-            shell=True,
+            shell=shell,
             stdin=subprocess.PIPE,
             stdout=subprocess.PIPE,
             stderr=subprocess.PIPE,