docs: release 1.3.19 and document the environment variables

- Close the Unreleased section as 1.3.19, summarising it by what
  changed for the user rather than by what each commit touched.
- Add the environment variables the settings module reads, which the
  README did not mention.

CHANGELOG.md

@@ -2,24 +2,19 @@
 
 All notable changes to this project will be documented in this file.
 
-## [Unreleased]
+## [1.3.19] - 2026-09-04
 
 ### Fixed
-- Reported a failed upload to the caller. A file the server refused was printed and then forgotten, so a batch that lost files still ended in success and scripts could not tell.
-- Reported a failed single-file download to the caller, which was counted internally but never raised, so only recursive downloads ever ended in failure.
-- Raised the error when a downloaded file could not be written locally. A permission error was printed and the path was then listed as if the file had arrived.
-- Wrote a download to a temporary file beside its destination and moved it into place once the whole body had arrived. A transfer that failed part way used to leave a truncated file under the real name, and a destination that could not be opened was then deleted even though nothing had been written to it. A destination the client may not write is now refused before anything is fetched.
-- Named the file in the message when an upload failed, and counted a failure the API layer did not raise, such as a file that disappeared between the directory walk and its turn to be sent.
-- Carried on through the remaining sub-folders when a recursive download lost a file or could not be created locally, instead of abandoning the rest of the tree at the first failure. Every failure is now printed against its own file and reported once at the end.
-- Said why a download failed, rather than printing the path alone.
-- Serialised the token refresh across processes. Concurrent `mdrs` invocations shared one refresh token and each sent it, so a provider that rotates refresh tokens accepted the first and refused the rest.
-- Wrote the login cache through a temporary file so a reader can no longer catch it mid-truncation and discard the session.
-- Joined the base URL and the API's relative path correctly in `ls --json` output, which produced a doubled separator when the configured URL ended with one.
+- Reported failed transfers instead of ending in success, so a run that lost files exits non-zero.
+- Left an existing local file intact when a download fails part way through.
+- Opened password-protected DOI folders, which previously failed outright.
+- Kept a session working across concurrent runs and long server queues.
+- Other minor fixes to `ls` output and remote URL handling.
 
 ### Changed
-- Accepted bare hostnames such as `localhost` in `config create`/`config update`, and stored the URL without its trailing slash, matching the Rust client so both can share `config.ini`.
-- Bounded the token refresh request with its own timeout, so a provider that stops answering cannot hold the cross-process lock indefinitely.
-- **Breaking for embedders:** `CacheInterface` now requires `lock()` and `reload()`. A cache passed to `MdrsClient.from_remote(..., cache=...)` must provide both; `InMemoryCache` implements them as no-ops.
+- Moved packaging to PEP 621 metadata with flit as the build backend.
+- Updated dependencies.
+- **Breaking for embedders:** `CacheInterface` now requires `lock()` and `reload()`.
 
 ## [1.3.18] - 2026-07-02
 

README.md

@@ -40,6 +40,15 @@ pip install -e ".[dev]"
 uv sync
 ```
 
+## Configuration
+
+The following environment variables can be set, either in the shell or via a `.env` file placed in the working directory.
+
+| Variable | Default | Description |
+|---|---|---|
+| `MDRS_CLIENT_CONFIG_DIRNAME` | `~/.mdrs-client` | Directory where config and login cache files are stored |
+| `MDRS_CLIENT_CONCURRENT` | `10` | Number of concurrent file transfers for upload and download |
+
 ## CLI Usage
 
 ### config create

mdrsclient/client.py

@@ -1,21 +1,40 @@
 import os
-from typing import Any
+from dataclasses import dataclass
 from unicodedata import normalize
 
-from mdrsclient.api import DoiApi, FilesApi, FoldersApi, LaboratoriesApi, UsersApi
+from mdrsclient.api import FilesApi, FoldersApi
 from mdrsclient.cache import CacheInterface
 from mdrsclient.config import ConfigInterface
 from mdrsclient.connection import MDRSConnection
-from mdrsclient.exceptions import IllegalArgumentException, MDRSException, UnauthorizedException, UnexpectedException
-from mdrsclient.models import File, Folder, Laboratory, Token, User
+from mdrsclient.exceptions import IllegalArgumentException
+from mdrsclient.models import File, Folder, FolderSimple, Laboratory
 from mdrsclient.models.file import find_file
 from mdrsclient.services import MdrsService
 
 
+@dataclass(frozen=True)
+class TransferEndpoints:
+    """Both ends of a `cp` or `mv`, resolved: the parents, their contents, and the names."""
+
+    laboratory: Laboratory
+    s_path: str
+    s_basename: str
+    s_parent_folder: Folder
+    s_parent_files: list[File]
+    d_path: str
+    d_basename: str
+    d_parent_folder: Folder
+    d_parent_files: list[File]
+
+    def is_same_place(self) -> bool:
+        """Whether the destination names what the source already is, leaving nothing to do."""
+        return self.s_parent_folder.id == self.d_parent_folder.id and self.s_basename == self.d_basename
+
+
 class MdrsClient(MdrsService):
     """Service layer client for MDRS."""
 
-    def __init__(self, connection: MDRSConnection, config_class: type[ConfigInterface] | None = None):
+    def __init__(self, connection: MDRSConnection | None, config_class: type[ConfigInterface] | None = None):
         super().__init__(connection, config_class)
 
     @classmethod
@@ -63,7 +82,8 @@ class MdrsClient(MdrsService):
         files = self.find_files(folder.id)
         return folder, files
 
-    def cp(self, src_path: str, dest_path: str, is_recursive: bool = False) -> None:
+    def __resolve_transfer(self, src_path: str, dest_path: str) -> TransferEndpoints:
+        """Resolve both ends of a transfer, refusing one that crosses a remote or a laboratory."""
         s_remote, s_laboratory_name, s_path = self.parse_remote_host_with_path(src_path)
         d_remote, d_laboratory_name, d_path = self.parse_remote_host_with_path(dest_path)
         if s_remote != d_remote:
@@ -71,8 +91,9 @@ class MdrsClient(MdrsService):
         if s_laboratory_name != d_laboratory_name:
             raise IllegalArgumentException("Laboratory mismatched.")
         s_path = s_path.rstrip("/")
-        s_dirname = os.path.dirname(s_path)
         s_basename = os.path.basename(s_path)
+        # A destination ending in a separator names a folder to put the source into, and
+        # keeps the source's own name.
         if d_path.endswith("/"):
             d_dirname = d_path
             d_basename = s_basename
@@ -80,84 +101,77 @@ class MdrsClient(MdrsService):
             d_dirname = os.path.dirname(d_path)
             d_basename = os.path.basename(d_path)
         laboratory = self.find_laboratory(s_laboratory_name)
-        s_parent_folder = self.find_folder(laboratory, s_dirname)
-        s_parent_files = self.find_files(s_parent_folder.id)
+        s_parent_folder = self.find_folder(laboratory, os.path.dirname(s_path))
         d_parent_folder = self.find_folder(laboratory, d_dirname)
-        d_parent_files = self.find_files(d_parent_folder.id)
-        s_file = find_file(s_parent_files, s_basename)
+        return TransferEndpoints(
+            laboratory=laboratory,
+            s_path=s_path,
+            s_basename=s_basename,
+            s_parent_folder=s_parent_folder,
+            s_parent_files=self.find_files(s_parent_folder.id),
+            d_path=d_path,
+            d_basename=d_basename,
+            d_parent_folder=d_parent_folder,
+            d_parent_files=self.find_files(d_parent_folder.id),
+        )
+
+    @staticmethod
+    def __check_file_destination(ends: TransferEndpoints) -> None:
+        """Refuse a destination that a file cannot take the place of."""
+        if find_file(ends.d_parent_files, ends.d_basename) is not None:
+            raise IllegalArgumentException(f"File `{ends.d_basename}` already exists.")
+        if ends.d_parent_folder.find_sub_folder(ends.d_basename) is not None:
+            raise IllegalArgumentException(
+                f"Cannot overwrite non-folder `{ends.d_basename}` with folder `{ends.d_path}`."
+            )
+
+    @staticmethod
+    def __check_folder_destination(ends: TransferEndpoints, s_folder: FolderSimple) -> None:
+        """Refuse a destination that a folder cannot take the place of."""
+        if find_file(ends.d_parent_files, ends.d_basename) is not None:
+            raise IllegalArgumentException(
+                f"Cannot overwrite non-folder `{ends.d_basename}` with folder `{ends.s_path}`."
+            )
+        d_folder = ends.d_parent_folder.find_sub_folder(ends.d_basename)
+        if d_folder is not None:
+            if d_folder.id == s_folder.id:
+                raise IllegalArgumentException(f"`{ends.s_path}` and `{ends.s_path}` are the same folder.")
+            raise IllegalArgumentException(f"Cannot move `{ends.s_path}` to `{ends.d_path}`: Folder not empty.")
+
+    @staticmethod
+    def __find_source_folder(ends: TransferEndpoints) -> FolderSimple:
+        s_folder = ends.s_parent_folder.find_sub_folder(ends.s_basename)
+        if s_folder is None:
+            raise IllegalArgumentException(f"File or folder `{ends.s_basename}` not found.")
+        return s_folder
+
+    def cp(self, src_path: str, dest_path: str, is_recursive: bool = False) -> None:
+        ends = self.__resolve_transfer(src_path, dest_path)
+        s_file = find_file(ends.s_parent_files, ends.s_basename)
         if s_file is not None:
-            d_file = find_file(d_parent_files, d_basename)
-            if d_file is not None:
-                raise IllegalArgumentException(f"File `{d_basename}` already exists.")
-            d_sub_folder = d_parent_folder.find_sub_folder(d_basename)
-            if d_sub_folder is not None:
-                raise IllegalArgumentException(f"Cannot overwrite non-folder `{d_basename}` with folder `{d_path}`.")
-            file_api = FilesApi(self.connection)
-            if s_parent_folder.id != d_parent_folder.id or d_basename != s_basename:
-                file_api.copy(s_file, d_parent_folder.id, normalize("NFC", d_basename))
-        else:
-            s_folder = s_parent_folder.find_sub_folder(s_basename)
-            if s_folder is None:
-                raise IllegalArgumentException(f"File or folder `{s_basename}` not found.")
-            if not is_recursive:
-                raise IllegalArgumentException(f"Cannot copy `{s_path}`: Is a folder.")
-            if find_file(d_parent_files, d_basename) is not None:
-                raise IllegalArgumentException(f"Cannot overwrite non-folder `{d_basename}` with folder `{s_path}`.")
-            d_folder = d_parent_folder.find_sub_folder(d_basename)
-            if d_folder is not None:
-                if d_folder.id == s_folder.id:
-                    raise IllegalArgumentException(f"`{s_path}` and `{s_path}` are the same folder.")
-                raise IllegalArgumentException(f"Cannot move `{s_path}` to `{d_path}`: Folder not empty.")
-            folder_api = FoldersApi(self.connection)
-            if s_parent_folder.id != d_parent_folder.id or s_basename != d_basename:
-                folder_api.copy(s_folder, d_parent_folder.id, normalize("NFC", d_basename))
+            self.__check_file_destination(ends)
+            if not ends.is_same_place():
+                FilesApi(self.connection).copy(s_file, ends.d_parent_folder.id, normalize("NFC", ends.d_basename))
+            return
+        s_folder = self.__find_source_folder(ends)
+        if not is_recursive:
+            raise IllegalArgumentException(f"Cannot copy `{ends.s_path}`: Is a folder.")
+        self.__check_folder_destination(ends, s_folder)
+        if not ends.is_same_place():
+            FoldersApi(self.connection).copy(s_folder, ends.d_parent_folder.id, normalize("NFC", ends.d_basename))
 
     def mv(self, src_path: str, dest_path: str) -> None:
-        s_remote, s_laboratory_name, s_path = self.parse_remote_host_with_path(src_path)
-        d_remote, d_laboratory_name, d_path = self.parse_remote_host_with_path(dest_path)
-        if s_remote != d_remote:
-            raise IllegalArgumentException("Remote host mismatched.")
-        if s_laboratory_name != d_laboratory_name:
-            raise IllegalArgumentException("Laboratory mismatched.")
-        s_path = s_path.rstrip("/")
-        s_dirname = os.path.dirname(s_path)
-        s_basename = os.path.basename(s_path)
-        if d_path.endswith("/"):
-            d_dirname = d_path
-            d_basename = s_basename
-        else:
-            d_dirname = os.path.dirname(d_path)
-            d_basename = os.path.basename(d_path)
-        laboratory = self.find_laboratory(s_laboratory_name)
-        s_parent_folder = self.find_folder(laboratory, s_dirname)
-        s_parent_files = self.find_files(s_parent_folder.id)
-        d_parent_folder = self.find_folder(laboratory, d_dirname)
-        d_parent_files = self.find_files(d_parent_folder.id)
-        s_file = find_file(s_parent_files, s_basename)
+        ends = self.__resolve_transfer(src_path, dest_path)
+        s_file = find_file(ends.s_parent_files, ends.s_basename)
         if s_file is not None:
-            d_file = find_file(d_parent_files, d_basename)
-            if d_file is not None:
-                raise IllegalArgumentException(f"File `{d_basename}` already exists.")
-            d_sub_folder = d_parent_folder.find_sub_folder(d_basename)
-            if d_sub_folder is not None:
-                raise IllegalArgumentException(f"Cannot overwrite non-folder `{d_basename}` with folder `{d_path}`.")
-            file_api = FilesApi(self.connection)
-            if s_parent_folder.id != d_parent_folder.id or d_basename != s_basename:
-                file_api.move(s_file, d_parent_folder.id, normalize("NFC", d_basename))
-        else:
-            s_folder = s_parent_folder.find_sub_folder(s_basename)
-            if s_folder is None:
-                raise IllegalArgumentException(f"File or folder `{s_basename}` not found.")
-            if find_file(d_parent_files, d_basename) is not None:
-                raise IllegalArgumentException(f"Cannot overwrite non-folder `{d_basename}` with folder `{s_path}`.")
-            d_folder = d_parent_folder.find_sub_folder(d_basename)
-            if d_folder is not None:
-                if d_folder.id == s_folder.id:
-                    raise IllegalArgumentException(f"`{s_path}` and `{s_path}` are the same folder.")
-                raise IllegalArgumentException(f"Cannot move `{s_path}` to `{d_path}`: Folder not empty.")
-            folder_api = FoldersApi(self.connection)
-            if s_parent_folder.id != d_parent_folder.id or d_basename != s_basename:
-                folder_api.move(s_folder, d_parent_folder.id, normalize("NFC", d_basename))
+            self.__check_file_destination(ends)
+            if not ends.is_same_place():
+                FilesApi(self.connection).move(s_file, ends.d_parent_folder.id, normalize("NFC", ends.d_basename))
+            return
+        s_folder = self.__find_source_folder(ends)
+        self.__check_folder_destination(ends, s_folder)
+        if not ends.is_same_place():
+            FoldersApi(self.connection).move(s_folder, ends.d_parent_folder.id, normalize("NFC", ends.d_basename))
 
     def chacl(
         self, remote_path: str, access_level: int, is_recursive: bool = False, password: str | None = None

mdrsclient/commands/chacl.py

@@ -1,7 +1,6 @@
 from argparse import Namespace
 from typing import Any
 
-from mdrsclient.api import FoldersApi
 from mdrsclient.commands.base import BaseCommand
 from mdrsclient.exceptions import IllegalArgumentException
 from mdrsclient.models import FolderAccessLevel

mdrsclient/commands/cp.py

@@ -1,12 +1,7 @@
-import os
 from argparse import Namespace
 from typing import Any
-from unicodedata import normalize
 
-from mdrsclient.api import FilesApi, FoldersApi
 from mdrsclient.commands.base import BaseCommand
-from mdrsclient.exceptions import IllegalArgumentException
-from mdrsclient.models.file import find_file
 
 
 class CpCommand(BaseCommand):

mdrsclient/commands/file_metadata.py

@@ -1,12 +1,8 @@
 import json
-import os
 from argparse import Namespace
 from typing import Any
 
-from mdrsclient.api import FilesApi
 from mdrsclient.commands.base import BaseCommand
-from mdrsclient.exceptions import IllegalArgumentException
-from mdrsclient.models.file import find_file
 
 
 class FileMetadataCommand(BaseCommand):

mdrsclient/commands/labs.py

@@ -1,7 +1,6 @@
 from argparse import Namespace
 from typing import Any
 
-from mdrsclient.api import LaboratoriesApi
 from mdrsclient.commands.base import BaseCommand
 
 

mdrsclient/commands/ls.py

@@ -1,10 +1,10 @@
 import json
 from argparse import Namespace
-from typing import Any
+from typing import Any, Final
 
 from pydantic.dataclasses import dataclass
 
-from mdrsclient.api import FilesApi, FoldersApi
+from mdrsclient.api import FoldersApi
 from mdrsclient.client import MdrsClient
 from mdrsclient.commands.base import BaseCommand
 from mdrsclient.config import build_download_url
@@ -95,25 +95,24 @@ class LsCommand(BaseCommand):
     def _ls_json(cls, context: LsCommandContext, folder: Folder, files: list[File]) -> None:
         print(json.dumps(cls._folder2dict(context, folder, files), ensure_ascii=False))
 
+    LABELS: Final[dict[str, str]] = {
+        "type": "Type",
+        "acl": "Access",
+        "laboratory": "Laboratory",
+        "size": "Size",
+        "date": "Date",
+        "name": "Name",
+    }
+
     @classmethod
-    def _ls_plain(cls, context: LsCommandContext, folder: Folder, files: list[File]) -> None:
-        label = {
-            "type": "Type",
-            "acl": "Access",
-            "laboratory": "Laboratory",
-            "size": "Size",
-            "date": "Date",
-            "name": "Name",
-        }
-        length: dict[str, int] = {}
-        for key in label.keys():
-            length[key] = len(label[key]) if not context.is_quiet else 0
+    def _column_widths(cls, context: LsCommandContext, folder: Folder, files: list[File]) -> dict[str, int]:
+        """Width of each column: the widest of its heading and everything printed under it."""
+        length = {key: len(label) if not context.is_quiet else 0 for key, label in cls.LABELS.items()}
         for sub_folder in folder.sub_folders:
-            sub_laboratory = context.client.connection.laboratories.find_by_id(sub_folder.laboratory_id)
-            sub_laboratory_name = sub_laboratory.name if sub_laboratory is not None else "(invalid)"
+            sub_laboratory_name = cls._laboratory_name(context, sub_folder.laboratory_id)
             length["acl"] = max(length["acl"], len(sub_folder.access_level_name))
             length["laboratory"] = max(length["laboratory"], len(sub_laboratory_name))
-            length["size"] = max(length["size"], len(str(folder.size)))
+            length["size"] = max(length["size"], len(str(sub_folder.size)))
             length["date"] = max(length["date"], len(sub_folder.updated_at_name))
             length["name"] = max(length["name"], len(sub_folder.name))
         for file in files:
@@ -122,6 +121,27 @@ class LsCommand(BaseCommand):
             length["name"] = max(length["name"], len(file.name))
         length["acl"] = max(length["acl"], len(folder.access_level_name))
         length["laboratory"] = max(length["laboratory"], len(context.laboratory.name))
+        return length
+
+    @classmethod
+    def _ls_plain_children(cls, context: LsCommandContext, folder: Folder) -> None:
+        """List each sub-folder in turn, passing over the ones the caller cannot open."""
+        print("")
+        folder_api = FoldersApi(context.client.connection)
+        for sub_folder in sorted(folder.sub_folders, key=lambda x: x.name):
+            try:
+                if sub_folder.lock:
+                    folder_api.auth(sub_folder.id, context.password)
+                sub_detail = folder_api.retrieve(sub_folder.id)
+                sub_files = context.client.find_files(sub_folder.id)
+            except UnauthorizedException:
+                continue
+            cls._ls_plain(context, sub_detail, sub_files)
+
+    @classmethod
+    def _ls_plain(cls, context: LsCommandContext, folder: Folder, files: list[File]) -> None:
+        label = cls.LABELS
+        length = cls._column_widths(context, folder, files)
         header = (
             f"{label['type']:{length['type']}}\t{label['acl']:{length['acl']}}\t"
             f"{label['laboratory']:{length['laboratory']}}\t{label['size']:{length['size']}}\t"
@@ -152,17 +172,7 @@ class LsCommand(BaseCommand):
             )
 
         if context.is_recursive:
-            print("")
-            for sub_folder in sorted(folder.sub_folders, key=lambda x: x.name):
-                folder_api = FoldersApi(context.client.connection)
-                try:
-                    if sub_folder.lock:
-                        folder_api.auth(sub_folder.id, context.password)
-                    folder = folder_api.retrieve(sub_folder.id)
-                    files = context.client.find_files(sub_folder.id)
-                    cls._ls_plain(context, folder, files)
-                except UnauthorizedException:
-                    pass
+            cls._ls_plain_children(context, folder)
 
     @classmethod
     def _folder2dict(

mdrsclient/commands/metadata.py

@@ -2,7 +2,6 @@ import json
 from argparse import Namespace
 from typing import Any
 
-from mdrsclient.api import FoldersApi
 from mdrsclient.commands.base import BaseCommand
 
 

mdrsclient/commands/mkdir.py

@@ -1,12 +1,7 @@
-import os
 from argparse import Namespace
 from typing import Any
-from unicodedata import normalize
 
-from mdrsclient.api import FoldersApi
 from mdrsclient.commands.base import BaseCommand
-from mdrsclient.exceptions import IllegalArgumentException
-from mdrsclient.models.file import find_file
 
 
 class MkdirCommand(BaseCommand):

mdrsclient/commands/mv.py

@@ -1,12 +1,7 @@
-import os
 from argparse import Namespace
 from typing import Any
-from unicodedata import normalize
 
-from mdrsclient.api import FilesApi, FoldersApi
 from mdrsclient.commands.base import BaseCommand
-from mdrsclient.exceptions import IllegalArgumentException
-from mdrsclient.models.file import find_file
 
 
 class MvCommand(BaseCommand):

mdrsclient/commands/rm.py

@@ -1,11 +1,7 @@
-import os
 from argparse import Namespace
 from typing import Any
 
-from mdrsclient.api import FilesApi, FoldersApi
 from mdrsclient.commands.base import BaseCommand
-from mdrsclient.exceptions import IllegalArgumentException
-from mdrsclient.models.file import find_file
 
 
 class RmCommand(BaseCommand):

mdrsclient/commands/version.py

@@ -1,7 +1,6 @@
 from argparse import Namespace
 from typing import Any
 
-from mdrsclient.__version__ import __version__
 from mdrsclient.commands.base import BaseCommand
 
 

mdrsclient/config.py

@@ -1,7 +1,7 @@
 import configparser
 import os
 import threading
-from typing import Final, Protocol, runtime_checkable
+from typing import TYPE_CHECKING, Final, Protocol, runtime_checkable
 
 import validators
 
@@ -39,6 +39,14 @@ def build_download_url(base_url: str | None, path: str) -> str:
 class ConfigInterface(Protocol):
     remote: str
 
+    if TYPE_CHECKING:
+        # Declared for the type checker, because the class itself is passed around and
+        # called: without this it describes something that takes no arguments to build.
+        # Kept out of the running class, because a protocol that defines `__init__` loses
+        # the guard that stops it being instantiated, and hands that empty `__init__` to
+        # any implementation that does not write its own.
+        def __init__(self, remote: str) -> None: ...
+
     def list(self) -> list[tuple[str, str]]: ...
     @property
     def url(self) -> str | None: ...

mdrsclient/services.py

@@ -1,6 +1,5 @@
 import os
 import re
-from typing import Any
 from unicodedata import normalize
 
 from mdrsclient.api import DoiApi, FilesApi, FoldersApi, LaboratoriesApi, UsersApi
@@ -20,11 +19,30 @@ from mdrsclient.utils import page_num_from_url
 class MdrsService:
     config_class: type[ConfigInterface] = ConfigFile
 
-    def __init__(self, connection: MDRSConnection, config_class: type[ConfigInterface] | None = None):
-        self.connection = connection
+    def __init__(self, connection: MDRSConnection | None, config_class: type[ConfigInterface] | None = None):
+        self.__connection = connection
         if config_class is not None:
             self.config_class = config_class
 
+    @property
+    def connection(self) -> MDRSConnection:
+        """
+        The connection every remote operation goes through.
+
+        Optional to supply, because `config` and `version` do their work without a remote
+        and are reached through the same client. Asking for it when none was given is a
+        mistake in the caller, and says so rather than failing later on `None`.
+        """
+        if self.__connection is None:
+            raise MissingConfigurationException("This operation requires a remote host.")
+        return self.__connection
+
+    @connection.setter
+    def connection(self, connection: MDRSConnection | None) -> None:
+        # Assignable as it always was: this is a property to check for absence on read,
+        # not to make the connection fixed once the client is built.
+        self.__connection = connection
+
     @classmethod
     def create_connection(
         cls, remote: str, cache: CacheInterface | None = None, config: ConfigInterface | None = None
@@ -182,7 +200,7 @@ class MdrsService:
         if folder.lock:
             if password is None:
                 raise UnauthorizedException(f"Folder for DOI `{doi_clean}` is locked.")
-            folder_api.auth(doi_resp.folder.id, password)
+            folder_api.auth(doi_resp.folder_id, password)
 
         lab_api = LaboratoriesApi(self.connection)
         labs = lab_api.list()

mdrsclient/transfer.py

@@ -154,86 +154,101 @@ class Downloader:
     ) -> bool:
         """Fetch what the remote path names, and report whether every file arrived."""
         excludes_clean = excludes or []
-        # Detect DOI path: "remote:10.xxxx/prefix.ID[/optional/sub/path]"
+        l_dirname = os.path.realpath(local_path)
+        if not os.path.isdir(l_dirname):
+            raise IllegalArgumentException(f"Local directory `{local_path}` not found.")
+
+        # "remote:10.xxxx/prefix.ID[/optional/sub/path]" names a published dataset rather
+        # than a path within a laboratory, and is resolved through the DOI instead.
         path_component = remote_path.split(":", 1)[1] if ":" in remote_path else ""
         if self.client.is_doi(path_component):
-            remote, doi, subpath = self.client.parse_doi_remote_host(remote_path)
-
-            l_dirname = os.path.realpath(local_path)
-            if not os.path.isdir(l_dirname):
-                raise IllegalArgumentException(f"Local directory `{local_path}` not found.")
-            doi_folder, laboratory = self.client.find_folder_by_doi(doi, password)
-
-            subpath_clean = subpath.rstrip("/")
-            if not subpath_clean:
-                folder = doi_folder
-                is_folder = True
-            else:
-                r_dirname = os.path.dirname(subpath_clean)
-                r_basename = os.path.basename(subpath_clean)
-                abs_path = doi_folder.path.rstrip("/") + r_dirname
-                r_parent_folder = self.client.find_folder(laboratory, abs_path, password)
-                r_parent_files = self.client.find_files(r_parent_folder.id)
-                file = find_file(r_parent_files, r_basename)
-                if file is not None:
-                    if self.__check_excludes(excludes_clean, laboratory, r_parent_folder, file):
-                        return True
-                    context = DownloadContext(is_skip_if_exists, [])
-                    l_path = os.path.join(l_dirname, r_basename)
-                    context.files.append(DownloadFileInfo(file, l_path))
-                    return self.__multiple_download(context)
-                else:
-                    folder_simple = r_parent_folder.find_sub_folder(r_basename)
-                    if folder_simple is None:
-                        raise IllegalArgumentException(f"File or folder `{subpath_clean}` not found.")
-                    folder = FoldersApi(self.client.connection).retrieve(folder_simple.id)
-                    is_folder = True
-
-            # For a DOI target the whole folder is the download target.
-            if not is_recursive:
-                # Non-recursive: download only the files at the top level of the DOI folder.
-                files = self.client.find_files(folder.id)
-                context = DownloadContext(is_skip_if_exists, [])
-                for file in files:
-                    if self.__check_excludes(excludes_clean, laboratory, folder, file):
-                        continue
-                    l_path = os.path.join(l_dirname, file.name)
-                    context.files.append(DownloadFileInfo(file, l_path))
-                return self.__multiple_download(context)
-            folder_api = FoldersApi(self.client.connection)
-            return self.__multiple_download_pickup_recursive_files(
-                folder_api, laboratory, folder.id, l_dirname, excludes_clean, is_skip_if_exists
+            return self.__download_doi(
+                remote_path, l_dirname, is_recursive, is_skip_if_exists, password, excludes_clean
             )
 
         remote, laboratory_name, r_path = self.client.parse_remote_host_with_path(remote_path)
         r_path = r_path.rstrip("/")
-        r_dirname = os.path.dirname(r_path)
         r_basename = os.path.basename(r_path)
-
-        l_dirname = os.path.realpath(local_path)
-        if not os.path.isdir(l_dirname):
-            raise IllegalArgumentException(f"Local directory `{local_path}` not found.")
         laboratory = self.client.find_laboratory(laboratory_name)
-        r_parent_folder = self.client.find_folder(laboratory, r_dirname, password)
+        r_parent_folder = self.client.find_folder(laboratory, os.path.dirname(r_path), password)
         r_parent_files = self.client.find_files(r_parent_folder.id)
         file = find_file(r_parent_files, r_basename)
         if file is not None:
-            if self.__check_excludes(excludes_clean, laboratory, r_parent_folder, file):
-                return True
-            context = DownloadContext(is_skip_if_exists, [])
-            l_path = os.path.join(l_dirname, r_basename)
-            context.files.append(DownloadFileInfo(file, l_path))
-            return self.__multiple_download(context)
-        else:
-            folder = r_parent_folder.find_sub_folder(r_basename)
-            if folder is None:
-                raise IllegalArgumentException(f"File or folder `{r_path}` not found.")
-            if not is_recursive:
-                raise IllegalArgumentException(f"Cannot download `{r_path}`: Is a folder.")
-            folder_api = FoldersApi(self.client.connection)
-            return self.__multiple_download_pickup_recursive_files(
-                folder_api, laboratory, folder.id, l_dirname, excludes_clean, is_skip_if_exists
+            return self.__download_one(
+                excludes_clean, laboratory, r_parent_folder, file, l_dirname, r_basename, is_skip_if_exists
             )
+        folder = r_parent_folder.find_sub_folder(r_basename)
+        if folder is None:
+            raise IllegalArgumentException(f"File or folder `{r_path}` not found.")
+        if not is_recursive:
+            raise IllegalArgumentException(f"Cannot download `{r_path}`: Is a folder.")
+        return self.__multiple_download_pickup_recursive_files(
+            FoldersApi(self.client.connection), laboratory, folder.id, l_dirname, excludes_clean, is_skip_if_exists
+        )
+
+    def __download_doi(
+        self,
+        remote_path: str,
+        l_dirname: str,
+        is_recursive: bool,
+        is_skip_if_exists: bool,
+        password: str | None,
+        excludes: list[str],
+    ) -> bool:
+        """Fetch what a DOI names: the dataset's folder, or something inside it."""
+        remote, doi, subpath = self.client.parse_doi_remote_host(remote_path)
+        doi_folder, laboratory = self.client.find_folder_by_doi(doi, password)
+
+        subpath_clean = subpath.rstrip("/")
+        if not subpath_clean:
+            folder = doi_folder
+        else:
+            r_basename = os.path.basename(subpath_clean)
+            abs_path = doi_folder.path.rstrip("/") + os.path.dirname(subpath_clean)
+            r_parent_folder = self.client.find_folder(laboratory, abs_path, password)
+            file = find_file(self.client.find_files(r_parent_folder.id), r_basename)
+            if file is not None:
+                return self.__download_one(
+                    excludes, laboratory, r_parent_folder, file, l_dirname, r_basename, is_skip_if_exists
+                )
+            folder_simple = r_parent_folder.find_sub_folder(r_basename)
+            if folder_simple is None:
+                raise IllegalArgumentException(f"File or folder `{subpath_clean}` not found.")
+            folder = FoldersApi(self.client.connection).retrieve(folder_simple.id)
+
+        if is_recursive:
+            return self.__multiple_download_pickup_recursive_files(
+                FoldersApi(self.client.connection), laboratory, folder.id, l_dirname, excludes, is_skip_if_exists
+            )
+        # Without -r the dataset's own files are fetched, and its sub-folders are not.
+        context = DownloadContext(is_skip_if_exists, [])
+        for file in self.client.find_files(folder.id):
+            if self.__check_excludes(excludes, laboratory, folder, file):
+                continue
+            context.files.append(DownloadFileInfo(file, os.path.join(l_dirname, file.name)))
+        return self.__multiple_download(context)
+
+    def __download_one(
+        self,
+        excludes: list[str],
+        laboratory: Laboratory,
+        folder: Folder,
+        file: File,
+        l_dirname: str,
+        local_name: str,
+        is_skip_if_exists: bool,
+    ) -> bool:
+        """
+        Fetch a single named file into the local directory.
+
+        Saved under the name the caller asked for rather than the one the server holds:
+        the two are matched case-insensitively, so they need not be spelled alike.
+        """
+        if self.__check_excludes(excludes, laboratory, folder, file):
+            return True
+        context = DownloadContext(is_skip_if_exists, [])
+        context.files.append(DownloadFileInfo(file, os.path.join(l_dirname, local_name)))
+        return self.__multiple_download(context)
 
     def __multiple_download_pickup_recursive_files(
         self,

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["flit_core>=3.12.0,<4.0.0"]
+requires = ["flit_core>=4.0.2,<5.0.0"]
 build-backend = "flit_core.buildapi"
 
 [tool.flit.module]
@@ -7,7 +7,7 @@ name = "mdrsclient"
 
 [project]
 name = "mdrs-client-python"
-version = "1.3.18"
+version = "1.3.19"
 description = "The mdrs-client-python is python library and a command-line client for up- and downloading files to and from MDRS based repository."
 authors = [
     { name = "Yoshihiro OKUMURA", email = "yoshihiro.okumura@riken.jp" }
@@ -32,9 +32,9 @@ classifiers = [
 dependencies = [
     "requests>=2.34.2",
     "requests-toolbelt>=1.0.0",
-    "python-dotenv>=1.2.2",
-    "pydantic>=2.13.4",
-    "pydantic-settings>=2.14.2",
+    "python-dotenv>=1.2.3",
+    "pydantic>=2.13.5",
+    "pydantic-settings>=2.15.0",
     "PyJWT>=2.13.0",
     "validators>=0.35.0",
 ]
@@ -44,7 +44,7 @@ dev = [
     "black>=26.5.1",
     "flake8>=7.3.0",
     "Flake8-pyproject>=1.2.4",
-    "isort>=8.0.1",
+    "isort>=9.0.1",
     "pyright>=1.1.411",
 ]
 
@@ -68,6 +68,9 @@ exclude = '''
 exclude = ".git, .venv, __pycache__, dist"
 max-complexity = 10
 max-line-length = 120
+# E203 flags the space black puts before a slice colon. Black formats this project, so
+# its output is the standard and flake8 has to accept it.
+extend-ignore = ["E203"]
 
 [tool.isort]
 profile = "black"
@@ -77,6 +80,12 @@ line_length = 120
 
 [tool.pyright]
 typeCheckingMode = "basic"
+# This project keeps its environment in `./.venv`. Named explicitly because without it
+# pyright falls back to the system interpreter, cannot resolve pydantic, and reports every
+# model field as an unknown argument. An environment kept elsewhere gets that same fallback
+# and can override it with a local `pyrightconfig.json` or `pyright --pythonpath`.
+venvPath = "."
+venv = ".venv"
 exclude = ["**/__pycache__", "**/.*", "dist"]
 #reportUnknownMemberType = "warning"
 #reportUnknownVariableType = "warning"

tests/test_client.py

@@ -0,0 +1,165 @@
+import unittest
+from unittest.mock import MagicMock, patch
+
+from mdrsclient.client import MdrsClient
+from mdrsclient.exceptions import IllegalArgumentException
+from mdrsclient.models import File, Folder, FolderSimple, Laboratories, Laboratory
+
+TIMESTAMP = "2026-01-01T00:00:00+09:00"
+LABORATORY = Laboratory(id=1, name="mylab", pi_name="PI", full_name="My Laboratory")
+
+
+def make_file(id: str, name: str) -> File:
+    return File(
+        id=id,
+        name=name,
+        type="text/plain",
+        size=1,
+        thumbnail=None,
+        description="",
+        metadata={},
+        download_url=f"v3/files/{id}/download/",
+        created_at=TIMESTAMP,
+        updated_at=TIMESTAMP,
+    )
+
+
+def make_sub_folder(id: str, name: str) -> FolderSimple:
+    return FolderSimple(
+        id=id,
+        pid=None,
+        name=name,
+        access_level=1,
+        lock=False,
+        size=0,
+        laboratory_id=1,
+        description="",
+        created_at=TIMESTAMP,
+        updated_at=TIMESTAMP,
+        restrict_opened_at=None,
+    )
+
+
+def make_folder(id: str, name: str, path: str, sub_folders: list[FolderSimple] | None = None) -> Folder:
+    return Folder(
+        id=id,
+        pid=None,
+        name=name,
+        access_level=1,
+        lock=False,
+        size=0,
+        laboratory_id=1,
+        description="",
+        created_at=TIMESTAMP,
+        updated_at=TIMESTAMP,
+        restrict_opened_at=None,
+        metadata=[],
+        sub_folders=sub_folders if sub_folders is not None else [],
+        path=path,
+    )
+
+
+class TestLsColumnWidths(unittest.TestCase):
+    """Each column is as wide as the widest thing printed under it."""
+
+    def test_the_size_column_fits_a_sub_folder_larger_than_its_parent(self):
+        from unittest.mock import MagicMock as _MagicMock
+
+        from mdrsclient.commands.ls import LsCommand, LsCommandContext
+
+        laboratories = Laboratories()
+        laboratories.append(LABORATORY)
+        connection = _MagicMock()
+        connection.laboratories = laboratories
+        client = MdrsClient(connection)
+
+        big = make_sub_folder("s1", "big")
+        object.__setattr__(big, "size", 123456789)
+        parent = make_folder("f1", "root", "/root/", [big])
+        context = LsCommandContext("remote:/mylab", client, LABORATORY, "", False, False, False)
+
+        widths = LsCommand._column_widths(context, parent, [])
+
+        self.assertEqual(widths["size"], len("123456789"))
+
+
+class TestCopyAndMove(unittest.TestCase):
+    """`cp` and `mv` resolve both ends the same way and differ only in what they call."""
+
+    def make_client(self, folders_by_path: dict, files_by_folder: dict) -> MdrsClient:
+        client = MdrsClient(MagicMock())
+        client.find_laboratory = MagicMock(return_value=LABORATORY)
+        client.find_folder = MagicMock(side_effect=lambda lab, path, password=None: folders_by_path[path])
+        client.find_files = MagicMock(side_effect=lambda folder_id: files_by_folder.get(folder_id, []))
+        return client
+
+    def make_tree(self, source_has: str) -> tuple[MdrsClient, dict, dict]:
+        sub = make_sub_folder("fsub", "sub")
+        folder_a = make_folder("fa", "a", "/a/", [sub] if source_has == "folder" else [])
+        folder_b = make_folder("fb", "b", "/b/")
+        folders = {"/a": folder_a, "/b": folder_b, "/b/": folder_b}
+        files = {"fa": [make_file("x1", "data.txt")] if source_has == "file" else [], "fb": []}
+        return self.make_client(folders, files), folders, files
+
+    def test_a_file_is_copied_into_the_destination_folder(self):
+        client, _, files = self.make_tree("file")
+        with patch("mdrsclient.client.FilesApi") as files_api:
+            client.cp("myremote:/mylab/a/data.txt", "myremote:/mylab/b/data.txt")
+            files_api.return_value.copy.assert_called_once_with(files["fa"][0], "fb", "data.txt")
+
+    def test_a_file_is_moved_into_the_destination_folder(self):
+        client, _, files = self.make_tree("file")
+        with patch("mdrsclient.client.FilesApi") as files_api:
+            client.mv("myremote:/mylab/a/data.txt", "myremote:/mylab/b/data.txt")
+            files_api.return_value.move.assert_called_once_with(files["fa"][0], "fb", "data.txt")
+
+    def test_a_trailing_separator_keeps_the_source_name(self):
+        client, _, files = self.make_tree("file")
+        with patch("mdrsclient.client.FilesApi") as files_api:
+            client.mv("myremote:/mylab/a/data.txt", "myremote:/mylab/b/")
+            files_api.return_value.move.assert_called_once_with(files["fa"][0], "fb", "data.txt")
+
+    def test_copying_a_folder_needs_the_recursive_flag(self):
+        client, _, _ = self.make_tree("folder")
+        with patch("mdrsclient.client.FoldersApi") as folders_api:
+            with self.assertRaises(IllegalArgumentException) as caught:
+                client.cp("myremote:/mylab/a/sub", "myremote:/mylab/b/sub")
+            self.assertIn("Is a folder", str(caught.exception))
+            folders_api.return_value.copy.assert_not_called()
+
+    def test_a_folder_is_copied_when_recursive(self):
+        client, folders, _ = self.make_tree("folder")
+        with patch("mdrsclient.client.FoldersApi") as folders_api:
+            client.cp("myremote:/mylab/a/sub", "myremote:/mylab/b/sub", is_recursive=True)
+            folders_api.return_value.copy.assert_called_once_with(folders["/a"].sub_folders[0], "fb", "sub")
+
+    def test_a_folder_is_moved_without_the_recursive_flag(self):
+        client, folders, _ = self.make_tree("folder")
+        with patch("mdrsclient.client.FoldersApi") as folders_api:
+            client.mv("myremote:/mylab/a/sub", "myremote:/mylab/b/sub")
+            folders_api.return_value.move.assert_called_once_with(folders["/a"].sub_folders[0], "fb", "sub")
+
+    def test_a_destination_that_already_holds_the_name_is_refused(self):
+        sub = make_sub_folder("fsub", "sub")
+        folders = {"/a": make_folder("fa", "a", "/a/", [sub]), "/b": make_folder("fb", "b", "/b/")}
+        files = {"fa": [], "fb": [make_file("x2", "sub")]}
+        client = self.make_client(folders, files)
+        with self.assertRaises(IllegalArgumentException) as caught:
+            client.mv("myremote:/mylab/a/sub", "myremote:/mylab/b/sub")
+        self.assertIn("Cannot overwrite non-folder", str(caught.exception))
+
+    def test_a_transfer_across_laboratories_is_refused(self):
+        client, _, _ = self.make_tree("file")
+        with self.assertRaises(IllegalArgumentException) as caught:
+            client.cp("myremote:/mylab/a/data.txt", "myremote:/otherlab/b/data.txt")
+        self.assertIn("Laboratory mismatched", str(caught.exception))
+
+    def test_a_source_that_does_not_exist_is_refused(self):
+        client, _, _ = self.make_tree("file")
+        with self.assertRaises(IllegalArgumentException) as caught:
+            client.mv("myremote:/mylab/a/missing.txt", "myremote:/mylab/b/missing.txt")
+        self.assertIn("not found", str(caught.exception))
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/test_services.py

@@ -0,0 +1,55 @@
+import unittest
+from unittest.mock import MagicMock, patch
+
+from mdrsclient.models import Doi, Folder, Laboratories, Laboratory
+from mdrsclient.services import MdrsService
+
+TIMESTAMP = "2026-01-01T00:00:00+09:00"
+DOI = "10.60178/cbs.20260429-001"
+LABORATORY = Laboratory(id=1, name="mylab", pi_name="PI", full_name="My Laboratory")
+
+
+def make_locked_folder() -> Folder:
+    return Folder(
+        id="f1",
+        pid=None,
+        name="root",
+        access_level=4,
+        lock=True,
+        size=0,
+        laboratory_id=1,
+        description="",
+        created_at=TIMESTAMP,
+        updated_at=TIMESTAMP,
+        restrict_opened_at=None,
+        metadata=[],
+        sub_folders=[],
+        path="/root/",
+    )
+
+
+class TestFindFolderByDoi(unittest.TestCase):
+    """The DOI response carries the folder id as a field, not as a nested object."""
+
+    def test_a_locked_doi_folder_is_unlocked_with_its_folder_id(self):
+        laboratories = Laboratories()
+        laboratories.append(LABORATORY)
+
+        with (
+            patch("mdrsclient.services.DoiApi") as doi_api,
+            patch("mdrsclient.services.FoldersApi") as folders_api,
+            patch("mdrsclient.services.LaboratoriesApi") as laboratories_api,
+        ):
+            doi_api.return_value.retrieve.return_value = Doi(id="20260429-001", doi=DOI, folder_id="f1")
+            folders_api.return_value.retrieve.return_value = make_locked_folder()
+            laboratories_api.return_value.list.return_value = laboratories
+
+            folder, laboratory = MdrsService(MagicMock()).find_folder_by_doi(DOI, "secret")
+
+            folders_api.return_value.auth.assert_called_once_with("f1", "secret")
+            self.assertEqual(folder.id, "f1")
+            self.assertEqual(laboratory.name, "mylab")
+
+
+if __name__ == "__main__":
+    unittest.main()