Fix typing issues in tests

pyproject.toml

@@ -85,11 +85,6 @@ strict = true
 show_error_codes = true
 warn_unreachable = true
 
-[[tool.mypy.overrides]]
-module = "tests.*"
-disallow_untyped_defs = false
-disallow_untyped_calls = false
-
 [tool.pydantic-mypy]
 init_forbid_extra = true
 init_typed = true

src/scitacean/testing/backend/config.py

@@ -5,10 +5,18 @@
 import json
 from dataclasses import dataclass
 from pathlib import Path
+from typing import TypedDict
+
+
+class ScicatCredentials(TypedDict):
+    """A dict with testing credentials for SciCat."""
+
+    username: str
+    password: str
 
 
 @dataclass
-class SciCatUser:
+class ScicatUser:
     """A SciCat user.
 
     Warning
@@ -24,7 +32,7 @@ class SciCatUser:
     group: str
 
     @property
-    def credentials(self) -> dict[str, str]:
+    def credentials(self) -> ScicatCredentials:
         """Return login credentials for this user.
 
         User as
@@ -51,43 +59,43 @@ def dump(self) -> dict[str, str | bool]:
 
 # see https://github.com/SciCatProject/scicat-backend-next/blob/master/src/config/configuration.ts
 USERS = {
-    "ingestor": SciCatUser(
+    "ingestor": ScicatUser(
         username="ingestor",
         password="aman",  # noqa: S106
         email="[email protected]",
         group="ingestor",
     ),
-    "user1": SciCatUser(
+    "user1": ScicatUser(
         username="user1",
         password="a609316768619f154ef58db4d847b75e",  # noqa: S106
         email="[email protected]",
         group="group1",
     ),
-    "user2": SciCatUser(
+    "user2": ScicatUser(
         username="user2",
         password="f522d1d715970073a6413474ca0e0f63",  # noqa: S106
         email="[email protected]",
         group="group2",
     ),
-    "user3": SciCatUser(
+    "user3": ScicatUser(
         username="user3",
         password="70dc489e8ee823ae815e18d664424df2",  # noqa: S106
         email="[email protected]",
         group="group3",
     ),
-    "user4": SciCatUser(
+    "user4": ScicatUser(
         username="user4",
         password="0014890e7020f515b92b767227ef2dfa",  # noqa: S106
         email="[email protected]",
         group="group4",
     ),
-    "user5.1": SciCatUser(
+    "user5.1": ScicatUser(
         username="user5.1",
         password="359a5fda99bfe5dbc42ee9b3ede77fb7",  # noqa: S106
         email="[email protected]",
         group="group5",
     ),
-    "user5.2": SciCatUser(
+    "user5.2": ScicatUser(
         username="user5.2",
         password="f3ebd2e4def95db59ef95ee32ef45242",  # noqa: S106
         email="[email protected]",
@@ -109,7 +117,7 @@ class SciCatAccess:
     """Access parameters for a local SciCat backend."""
 
     url: str
-    user: SciCatUser
+    user: ScicatUser
 
 
 def local_access(user: str) -> SciCatAccess:

src/scitacean/testing/backend/fixtures.py

@@ -52,7 +52,7 @@ def fake_client(scicat_access: SciCatAccess) -> FakeClient:
     """
     client = FakeClient.from_credentials(
         url=scicat_access.url,
-        **scicat_access.user.credentials,  # type: ignore[arg-type]
+        **scicat_access.user.credentials,
     )
     client.datasets.update(
         {ds.pid: ds for ds in seed.INITIAL_DATASETS.values()}  # type: ignore[misc]
@@ -87,7 +87,7 @@ def real_client(scicat_access: SciCatAccess, scicat_backend: bool) -> Client | N
         return None
     return Client.from_credentials(
         url=scicat_access.url,
-        **scicat_access.user.credentials,  # type: ignore[arg-type]
+        **scicat_access.user.credentials,
     )
 
 
@@ -200,7 +200,7 @@ def _seed_database(
 ) -> None:
     client = client_class.from_credentials(
         url=scicat_access.url,
-        **scicat_access.user.credentials,  # type: ignore[arg-type]
+        **scicat_access.user.credentials,
     )
     seed.seed_database(client=client, scicat_access=scicat_access)
     seed.save_seed(target_dir)

src/scitacean/testing/backend/seed.py

@@ -30,7 +30,7 @@
 )
 from ...pid import PID
 from ...thumbnail import Thumbnail
-from .config import SITE, SciCatAccess, SciCatUser
+from .config import SITE, SciCatAccess, ScicatUser
 
 # Dataset models to upload to the database.
 _DATASETS: dict[str, UploadRawDataset | UploadDerivedDataset] = {
@@ -215,7 +215,7 @@
 
 
 def _apply_config_dataset(
-    dset: UploadRawDataset | UploadDerivedDataset, user: SciCatUser
+    dset: UploadRawDataset | UploadDerivedDataset, user: ScicatUser
 ) -> UploadRawDataset | UploadDerivedDataset:
     dset = deepcopy(dset)
     dset.owner = user.username
@@ -225,7 +225,7 @@ def _apply_config_dataset(
 
 
 def _apply_config_attachment(
-    attachment: UploadAttachment, user: SciCatUser
+    attachment: UploadAttachment, user: ScicatUser
 ) -> UploadAttachment:
     attachment = deepcopy(attachment)
     attachment.ownerGroup = user.group

src/scitacean/testing/transfer.py

@@ -2,10 +2,10 @@
 # Copyright (c) 2024 SciCat Project (https://github.com/SciCatProject/scitacean)
 """Fake file transfer."""
 
-from collections.abc import Iterator
+from collections.abc import Iterator, Mapping
 from contextlib import contextmanager
 from pathlib import Path
-from typing import Any
+from typing import Any, TypeVar
 
 try:
     from pyfakefs.fake_filesystem import FakeFilesystem
@@ -19,7 +19,10 @@
 from ..filesystem import RemotePath
 from ..transfer.util import source_folder_for
 
+RemotePathOrStr = TypeVar("RemotePathOrStr", RemotePath, str, RemotePath | str)
 
+
+# TODO add conditionally_disabled feature and remove custom transfers in tests
 class FakeDownloadConnection:
     """'Download' files from a fake file transfer."""
 
@@ -110,8 +113,8 @@ def __init__(
         self,
         *,
         fs: FakeFilesystem | None = None,
-        files: dict[str | RemotePath, bytes] | None = None,
-        reverted: dict[str | RemotePath, bytes] | None = None,
+        files: Mapping[RemotePathOrStr, bytes] | None = None,
+        reverted: Mapping[RemotePathOrStr, bytes] | None = None,
         source_folder: str | RemotePath | None = None,
     ):
         """Initialize a file transfer.
@@ -157,7 +160,7 @@ def connect_for_upload(self, dataset: Dataset) -> Iterator[FakeUploadConnection]
 
 
 def _remote_path_dict(
-    d: dict[str | RemotePath, bytes] | None,
+    d: Mapping[RemotePathOrStr, bytes] | None,
 ) -> dict[RemotePath, bytes]:
     if d is None:
         return {}

tests/client/attachment_client_test.py

@@ -12,9 +12,11 @@
 from scitacean.model import (
     Attachment,
     DatasetType,
+    DownloadAttachment,
     UploadAttachment,
     UploadDerivedDataset,
 )
+from scitacean.testing.backend import config as backend_config
 from scitacean.testing.backend.seed import (
     INITIAL_ATTACHMENTS,
     INITIAL_DATASETS,
@@ -27,7 +29,7 @@ def scicat_client(client: Client) -> ScicatClient:
 
 
 @pytest.fixture
-def derived_dataset(scicat_access):
+def derived_dataset(scicat_access: backend_config.SciCatAccess) -> UploadDerivedDataset:
     return UploadDerivedDataset(
         contactEmail="[email protected]",
         creationTime=parse_date("1995-11-11T11:11:11.000Z"),
@@ -44,7 +46,7 @@ def derived_dataset(scicat_access):
 
 
 @pytest.fixture
-def attachment(scicat_access):
+def attachment(scicat_access: backend_config.SciCatAccess) -> UploadAttachment:
     return UploadAttachment(
         caption="An attachment",
         thumbnail=Thumbnail(mime="image/png", data=b"9278c78a904jh"),
@@ -53,15 +55,21 @@ def attachment(scicat_access):
     )
 
 
-def compare_attachment_after_upload(uploaded, downloaded):
+def compare_attachment_after_upload(
+    uploaded: UploadAttachment, downloaded: DownloadAttachment
+) -> None:
     for key, expected in uploaded:
         # The database populates a number of fields that are None in uploaded.
         # But we don't want to test those here as we don't want to test the database.
         if expected is not None:
             assert expected == dict(downloaded)[key], f"key = {key}"
 
 
-def test_create_attachment_for_dataset(scicat_client, attachment, derived_dataset):
+def test_create_attachment_for_dataset(
+    scicat_client: ScicatClient,
+    attachment: UploadAttachment,
+    derived_dataset: UploadDerivedDataset,
+) -> None:
     attachment1 = deepcopy(attachment)
     attachment2 = deepcopy(attachment)
     attachment2.caption = "Another attachment"
@@ -82,8 +90,11 @@ def test_create_attachment_for_dataset(scicat_client, attachment, derived_datase
 
 
 def test_create_attachment_for_dataset_with_existing_id(
-    real_client, attachment, derived_dataset, require_scicat_backend
-):
+    real_client: Client,
+    attachment: UploadAttachment,
+    derived_dataset: UploadDerivedDataset,
+    require_scicat_backend: None,
+) -> None:
     scicat_client = real_client.scicat
 
     dataset_id = scicat_client.create_dataset_model(derived_dataset).pid
@@ -95,17 +106,19 @@ def test_create_attachment_for_dataset_with_existing_id(
 
 
 def test_cannot_create_attachment_for_dataset_for_nonexistent_dataset(
-    scicat_client, attachment
-):
+    scicat_client: ScicatClient, attachment: UploadAttachment
+) -> None:
     with pytest.raises(ScicatCommError):
         scicat_client.create_attachment_for_dataset(
             attachment, dataset_id=PID(pid="nonexistent-id")
         )
 
 
 def test_create_attachment_for_dataset_for_dataset_populates_ids(
-    scicat_client, attachment, derived_dataset
-):
+    scicat_client: ScicatClient,
+    attachment: UploadAttachment,
+    derived_dataset: UploadDerivedDataset,
+) -> None:
     assert attachment.id is None
     assert attachment.datasetId is None
     assert attachment.sampleId is None
@@ -123,28 +136,30 @@ def test_create_attachment_for_dataset_for_dataset_populates_ids(
     assert finalized.proposalId is None
 
 
-def test_get_attachments_for_dataset(scicat_client):
+def test_get_attachments_for_dataset(scicat_client: ScicatClient) -> None:
     dset = INITIAL_DATASETS["derived"]
     attachments = scicat_client.get_attachments_for_dataset(dset.pid)
     assert attachments == INITIAL_ATTACHMENTS["derived"]
 
 
-def test_get_attachments_for_dataset_no_attachments(scicat_client):
+def test_get_attachments_for_dataset_no_attachments(
+    scicat_client: ScicatClient,
+) -> None:
     assert INITIAL_ATTACHMENTS.get("raw") is None
     dset = INITIAL_DATASETS["raw"]
     attachments = scicat_client.get_attachments_for_dataset(dset.pid)
     assert attachments == []
 
 
 @pytest.mark.parametrize("key", ["raw", "derived"])
-def test_get_dataset_does_not_initialise_attachments(client, key):
+def test_get_dataset_does_not_initialise_attachments(client: Client, key: str) -> None:
     dset = INITIAL_DATASETS["derived"]
     downloaded = client.get_dataset(dset.pid)
     assert downloaded.attachments is None
 
 
 @pytest.mark.parametrize("key", ["raw", "derived"])
-def test_download_attachments_for_dataset(client, key):
+def test_download_attachments_for_dataset(client: Client, key: str) -> None:
     dset = INITIAL_DATASETS[key]
     downloaded = client.get_dataset(dset.pid)
     with_attachments = client.download_attachments_for(downloaded)
@@ -156,7 +171,7 @@ def test_download_attachments_for_dataset(client, key):
 
 
 @pytest.mark.parametrize("key", ["raw", "derived"])
-def test_get_dataset_with_attachments(client, key):
+def test_get_dataset_with_attachments(client: Client, key: str) -> None:
     dset = INITIAL_DATASETS[key]
     downloaded = client.get_dataset(dset.pid, attachments=True)
     expected = [