More test fixes for patching in test suite

lincbrain/cli/tests/data/update_dandiset_from_doi/biorxiv.json

@@ -13,7 +13,7 @@
     ],
     "version": "draft",
     "@context": "https://raw.githubusercontent.com/dandi/schema/master/releases/0.6.4/context.json",
-    "citation": "Aguillon-Rodriguez, Valeria; Angelaki, Dora E.; Bayer, Hannah M.; Bonacchi, Niccol\u00f2; Carandini, Matteo; Cazettes, Fanny; Chapuis, Gaelle A.; Churchland, Anne K.; Dan, Yang; Dewitt, Eric E. J.; Faulkner, Mayo; Forrest, Hamish; Haetzel, Laura M.; Hausser, Michael; Hofer, Sonja B.; Hu, Fei; Khanal, Anup; Krasniak, Christopher S.; Laranjeira, In\u00eas; Mainen, Zachary F.; Meijer, Guido T.; Miska, Nathaniel J.; Mrsic-Flogel, Thomas D.; Murakami, Masayoshi; Noel, Jean-Paul; Pan-Vazquez, Alejandro; Rossant, Cyrille; Sanders, Joshua I.; Socha, Karolina Z.; Terry, Rebecca; Urai, Anne E.; Vergara, Hernando M.; Wells, Miles J.; Wilson, Christian J.; Witten, Ilana B.; Wool, Lauren E.; Zador, Anthony (2023) Standardized and reproducible measurement of decision-making in mice (Version draft) [Data set]. DANDI archive. http://localhost:8085/dandiset/000001/draft",
+    "citation": "Aguillon-Rodriguez, Valeria; Angelaki, Dora E.; Bayer, Hannah M.; Bonacchi, Niccol\u00f2; Carandini, Matteo; Cazettes, Fanny; Chapuis, Gaelle A.; Churchland, Anne K.; Dan, Yang; Dewitt, Eric E. J.; Faulkner, Mayo; Forrest, Hamish; Haetzel, Laura M.; Hausser, Michael; Hofer, Sonja B.; Hu, Fei; Khanal, Anup; Krasniak, Christopher S.; Laranjeira, In\u00eas; Mainen, Zachary F.; Meijer, Guido T.; Miska, Nathaniel J.; Mrsic-Flogel, Thomas D.; Murakami, Masayoshi; Noel, Jean-Paul; Pan-Vazquez, Alejandro; Rossant, Cyrille; Sanders, Joshua I.; Socha, Karolina Z.; Terry, Rebecca; Urai, Anne E.; Vergara, Hernando M.; Wells, Miles J.; Wilson, Christian J.; Witten, Ilana B.; Wool, Lauren E.; Zador, Anthony (2024) Standardized and reproducible measurement of decision-making in mice (Version draft) [Data set]. DANDI archive. http://localhost:8085/dandiset/000001/draft",
     "schemaKey": "Dandiset",
     "identifier": "DANDI:000001",
     "repository": "http://localhost:8085",

lincbrain/cli/tests/data/update_dandiset_from_doi/elife.json

@@ -13,7 +13,7 @@
     ],
     "version": "draft",
     "@context": "https://raw.githubusercontent.com/dandi/schema/master/releases/0.6.4/context.json",
-    "citation": "Chowdhury, Raeed H; Glaser, Joshua I; Miller, Lee E (2023) Area 2 of primary somatosensory cortex encodes kinematics of the whole arm (Version draft) [Data set]. DANDI archive. http://localhost:8085/dandiset/000004/draft",
+    "citation": "Chowdhury, Raeed H; Glaser, Joshua I; Miller, Lee E (2024) Area 2 of primary somatosensory cortex encodes kinematics of the whole arm (Version draft) [Data set]. DANDI archive. http://localhost:8085/dandiset/000004/draft",
     "schemaKey": "Dandiset",
     "identifier": "DANDI:000004",
     "repository": "http://localhost:8085",

lincbrain/cli/tests/data/update_dandiset_from_doi/jneurosci.json

@@ -13,7 +13,7 @@
     ],
     "version": "draft",
     "@context": "https://raw.githubusercontent.com/dandi/schema/master/releases/0.6.4/context.json",
-    "citation": "Ito, Makoto; Doya, Kenji (2023) Validation of Decision-Making Models and Analysis of Decision Variables in the Rat Basal Ganglia (Version draft) [Data set]. DANDI archive. http://localhost:8085/dandiset/000002/draft",
+    "citation": "Ito, Makoto; Doya, Kenji (2024) Validation of Decision-Making Models and Analysis of Decision Variables in the Rat Basal Ganglia (Version draft) [Data set]. DANDI archive. http://localhost:8085/dandiset/000002/draft",
     "schemaKey": "Dandiset",
     "identifier": "DANDI:000002",
     "repository": "http://localhost:8085",

lincbrain/cli/tests/data/update_dandiset_from_doi/nature.json

@@ -13,7 +13,7 @@
     ],
     "version": "draft",
     "@context": "https://raw.githubusercontent.com/dandi/schema/master/releases/0.6.4/context.json",
-    "citation": "Sit, Kevin K.; Goard, Michael J. (2023) Coregistration of heading to visual cues in retrosplenial cortex (Version draft) [Data set]. DANDI archive. http://localhost:8085/dandiset/000005/draft",
+    "citation": "Sit, Kevin K.; Goard, Michael J. (2024) Coregistration of heading to visual cues in retrosplenial cortex (Version draft) [Data set]. DANDI archive. http://localhost:8085/dandiset/000005/draft",
     "schemaKey": "Dandiset",
     "identifier": "DANDI:000005",
     "repository": "http://localhost:8085",

lincbrain/cli/tests/test_download.py

@@ -11,7 +11,7 @@
 
 
 def test_download_defaults(mocker):
-    mock_download = mocker.patch("dandi.download.download")
+    mock_download = mocker.patch("lincbrain.download.download")
     r = CliRunner().invoke(download)
     assert r.exit_code == 0
     mock_download.assert_called_once_with(
@@ -29,7 +29,7 @@ def test_download_defaults(mocker):
 
 
 def test_download_all_types(mocker):
-    mock_download = mocker.patch("dandi.download.download")
+    mock_download = mocker.patch("lincbrain.download.download")
     r = CliRunner().invoke(download, ["--download", "all"])
     assert r.exit_code == 0
     mock_download.assert_called_once_with(
@@ -47,7 +47,7 @@ def test_download_all_types(mocker):
 
 
 def test_download_metadata_only(mocker):
-    mock_download = mocker.patch("dandi.download.download")
+    mock_download = mocker.patch("lincbrain.download.download")
     r = CliRunner().invoke(download, ["--download", "dandiset.yaml"])
     assert r.exit_code == 0
     mock_download.assert_called_once_with(
@@ -65,7 +65,7 @@ def test_download_metadata_only(mocker):
 
 
 def test_download_assets_only(mocker):
-    mock_download = mocker.patch("dandi.download.download")
+    mock_download = mocker.patch("lincbrain.download.download")
     r = CliRunner().invoke(download, ["--download", "assets"])
     assert r.exit_code == 0
     mock_download.assert_called_once_with(
@@ -83,7 +83,7 @@ def test_download_assets_only(mocker):
 
 
 def test_download_bad_type(mocker):
-    mock_download = mocker.patch("dandi.download.download")
+    mock_download = mocker.patch("lincbrain.download.download")
     r = CliRunner().invoke(download, ["--download", "foo"], standalone_mode=False)
     assert r.exit_code != 0
     assert isinstance(r.exception, click.UsageError)
@@ -95,7 +95,7 @@ def test_download_bad_type(mocker):
 
 
 def test_download_gui_instance_in_dandiset(mocker):
-    mock_download = mocker.patch("dandi.download.download")
+    mock_download = mocker.patch("lincbrain.download.download")
     runner = CliRunner()
     with runner.isolated_filesystem():
         Path(dandiset_metadata_file).write_text("identifier: '123456'\n")
@@ -120,7 +120,7 @@ def test_download_gui_instance_in_dandiset(mocker):
     reason="this instance now has GUI URL",
 )
 def test_download_api_instance_in_dandiset(mocker):
-    mock_download = mocker.patch("dandi.download.download")
+    mock_download = mocker.patch("lincbrain.download.download")
     runner = CliRunner()
     with runner.isolated_filesystem():
         Path(dandiset_metadata_file).write_text("identifier: '123456'\n")
@@ -141,7 +141,7 @@ def test_download_api_instance_in_dandiset(mocker):
 
 
 def test_download_url_instance_match(mocker):
-    mock_download = mocker.patch("dandi.download.download")
+    mock_download = mocker.patch("lincbrain.download.download")
     r = CliRunner().invoke(
         download,
         [
@@ -166,7 +166,7 @@ def test_download_url_instance_match(mocker):
 
 
 def test_download_url_instance_conflict(mocker):
-    mock_download = mocker.patch("dandi.download.download")
+    mock_download = mocker.patch("lincbrain.download.download")
     r = CliRunner().invoke(
         download,
         ["-i", "dandi", "http://localhost:8000/api/dandisets/123456/"],

lincbrain/cli/tests/test_move.py

@@ -76,14 +76,14 @@
 def test_move_command(
     mocker: MockerFixture, cmdline: list[str], srcs: list[str], kwargs: dict[str, Any]
 ) -> None:
-    mock_move = mocker.patch("dandi.move.move")
+    mock_move = mocker.patch("lincbrain.move.move")
     r = CliRunner().invoke(move, cmdline)
     assert r.exit_code == 0
     mock_move.assert_called_once_with(*srcs, **kwargs)
 
 
 def test_move_command_too_few_paths(mocker: MockerFixture) -> None:
-    mock_move = mocker.patch("dandi.move.move")
+    mock_move = mocker.patch("lincbrain.move.move")
     r = CliRunner().invoke(move, ["foo"], standalone_mode=False)
     assert r.exit_code != 0
     # This is a ClickException when map_to_click_exceptions is in effect and a

lincbrain/support/digests.py

@@ -28,7 +28,7 @@
 from .threaded_walk import threaded_walk
 from ..utils import Hasher, exclude_from_zarr
 
-lgr = logging.getLogger("dandi.support.digests")
+lgr = logging.getLogger("lincbrain.support.digests")
 
 
 @dataclass

lincbrain/tests/test_dandiapi.py

@@ -123,11 +123,11 @@ def test_authenticate_bad_key_good_key_input(
 
     backend_mock = mocker.Mock(spec=["set_password"])
     keyring_lookup_mock = mocker.patch(
-        "dandi.dandiapi.keyring_lookup", return_value=(backend_mock, None)
+        "lincbrain.dandiapi.keyring_lookup", return_value=(backend_mock, None)
     )
-    input_mock = mocker.patch("dandi.dandiapi.input", side_effect=[bad_key, good_key])
+    input_mock = mocker.patch("lincbrain.dandiapi.input", side_effect=[bad_key, good_key])
     is_interactive_mock = mocker.patch(
-        "dandi.dandiapi.is_interactive", return_value=True
+        "lincbrain.dandiapi.is_interactive", return_value=True
     )
     confirm_mock = mocker.patch("click.confirm", return_value=True)
 
@@ -156,7 +156,7 @@ def test_authenticate_good_key_keyring(
 
     backend_mock = mocker.Mock(spec=["set_password"])
     keyring_lookup_mock = mocker.patch(
-        "dandi.dandiapi.keyring_lookup", return_value=(backend_mock, good_key)
+        "lincbrain.dandiapi.keyring_lookup", return_value=(backend_mock, good_key)
     )
     input_spy = mocker.spy(builtins, "input")
     is_interactive_spy = mocker.spy(dandiapi, "is_interactive")
@@ -186,11 +186,11 @@ def test_authenticate_bad_key_keyring_good_key_input(
 
     backend_mock = mocker.Mock(spec=["set_password"])
     keyring_lookup_mock = mocker.patch(
-        "dandi.dandiapi.keyring_lookup", return_value=(backend_mock, bad_key)
+        "lincbrain.dandiapi.keyring_lookup", return_value=(backend_mock, bad_key)
     )
-    input_mock = mocker.patch("dandi.dandiapi.input", return_value=good_key)
+    input_mock = mocker.patch("lincbrain.dandiapi.input", return_value=good_key)
     is_interactive_mock = mocker.patch(
-        "dandi.dandiapi.is_interactive", return_value=True
+        "lincbrain.dandiapi.is_interactive", return_value=True
     )
     confirm_mock = mocker.patch("click.confirm", return_value=True)
 

lincbrain/tests/test_download.py

@@ -218,7 +218,7 @@ def test_download_sync(
     dspath = tmp_path / text_dandiset.dandiset_id
     os.rename(text_dandiset.dspath, dspath)
     confirm_mock = mocker.patch(
-        "dandi.download.abbrev_prompt", return_value="yes" if confirm else "no"
+        "lincbrain.download.abbrev_prompt", return_value="yes" if confirm else "no"
     )
     download(
         f"dandi://{text_dandiset.api.instance_id}/{text_dandiset.dandiset_id}",
@@ -238,7 +238,7 @@ def test_download_sync_folder(
 ) -> None:
     text_dandiset.dandiset.get_asset_by_path("file.txt").delete()
     text_dandiset.dandiset.get_asset_by_path("subdir2/banana.txt").delete()
-    confirm_mock = mocker.patch("dandi.download.abbrev_prompt", return_value="yes")
+    confirm_mock = mocker.patch("lincbrain.download.abbrev_prompt", return_value="yes")
     download(
         f"dandi://{text_dandiset.api.instance_id}/{text_dandiset.dandiset_id}/subdir2/",
         text_dandiset.dspath,
@@ -259,7 +259,7 @@ def test_download_sync_list(
     text_dandiset.dandiset.get_asset_by_path("file.txt").delete()
     dspath = tmp_path / text_dandiset.dandiset_id
     os.rename(text_dandiset.dspath, dspath)
-    input_mock = mocker.patch("dandi.utils.input", side_effect=["list", "yes"])
+    input_mock = mocker.patch("lincbrain.utils.input", side_effect=["list", "yes"])
     download(
         f"dandi://{text_dandiset.api.instance_id}/{text_dandiset.dandiset_id}",
         tmp_path,
@@ -280,7 +280,7 @@ def test_download_sync_zarr(
     zarr_dandiset.dandiset.get_asset_by_path("sample.zarr").delete()
     dspath = tmp_path / zarr_dandiset.dandiset_id
     os.rename(zarr_dandiset.dspath, dspath)
-    confirm_mock = mocker.patch("dandi.download.abbrev_prompt", return_value="yes")
+    confirm_mock = mocker.patch("lincbrain.download.abbrev_prompt", return_value="yes")
     download(
         zarr_dandiset.dandiset.version_api_url,
         tmp_path,
@@ -856,7 +856,7 @@ def test_download_sync_glob(
 ) -> None:
     text_dandiset.dandiset.get_asset_by_path("file.txt").delete()
     text_dandiset.dandiset.get_asset_by_path("subdir2/banana.txt").delete()
-    confirm_mock = mocker.patch("dandi.download.abbrev_prompt", return_value="yes")
+    confirm_mock = mocker.patch("lincbrain.download.abbrev_prompt", return_value="yes")
     download(
         f"{text_dandiset.dandiset.version_api_url}assets/?glob=s*.Txt",
         text_dandiset.dspath,

lincbrain/tests/test_keyring.py

@@ -32,7 +32,7 @@ def test_dandi_authenticate_no_env_var(
     monkeypatch.delenv("DANDI_API_KEY", raising=False)
     monkeypatch.setenv("PYTHON_KEYRING_BACKEND", "keyring.backends.null.Keyring")
     inputmock = mocker.patch(
-        "dandi.dandiapi.input", return_value=local_dandi_api.api_key
+        "lincbrain.dandiapi.input", return_value=local_dandi_api.api_key
     )
     DandiAPIClient(local_dandi_api.api_url).dandi_authenticate()
     inputmock.assert_called_once_with(
@@ -145,7 +145,7 @@ def test_keyring_lookup_default_no_password(
 ) -> None:
     monkeypatch.delenv("PYTHON_KEYRING_BACKEND", raising=False)
     kb0 = null.Keyring()
-    get_keyring = mocker.patch("dandi.keyring.get_keyring", return_value=kb0)
+    get_keyring = mocker.patch("lincbrain.keyring.get_keyring", return_value=kb0)
     kb, password = keyring_lookup("testservice", "testusername")
     assert kb is kb0
     assert password is None
@@ -159,7 +159,7 @@ def test_keyring_lookup_default_password(
     monkeypatch.delenv("PYTHON_KEYRING_BACKEND", raising=False)
     kb0 = keyfile.PlaintextKeyring()
     kb0.set_password("testservice", "testusername", "testpassword")
-    get_keyring = mocker.patch("dandi.keyring.get_keyring", return_value=kb0)
+    get_keyring = mocker.patch("lincbrain.keyring.get_keyring", return_value=kb0)
     kb, password = keyring_lookup("testservice", "testusername")
     assert kb is kb0
     assert password == "testpassword"
@@ -176,7 +176,7 @@ def test_keyring_lookup_fail_default_encrypted(
 ) -> None:
     monkeypatch.delenv("PYTHON_KEYRING_BACKEND", raising=False)
     get_keyring = mocker.patch(
-        "dandi.keyring.get_keyring", return_value=EncryptedFailure()
+        "lincbrain.keyring.get_keyring", return_value=EncryptedFailure()
     )
     with pytest.raises(KeyringError):
         keyring_lookup("testservice", "testusername")