Merge pull request #33 from lincbrain/ak-cli-name

Update DANDI_API_KEY to LINCBRAIN_API_KEY

DEVELOPMENT.md

@@ -55,7 +55,7 @@ development command line options.
   otherwise be hidden from the user-visible (`--help`) interface, unless this
   env variable is set to a non-empty value
 
-- `DANDI_API_KEY` -- avoids using keyrings, thus making it possible to
+- `LINCBRAIN_API_KEY` -- avoids using keyrings, thus making it possible to
   "temporarily" use another account etc for the "API" version of the server.
 
 - `DANDI_LOG_LEVEL` -- set log level. By default `INFO`, should be an int (`10` - `DEBUG`).

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/cli/tests/test_service_scripts.py

@@ -28,7 +28,7 @@ def test_reextract_metadata(
     asset_id = nwb_dandiset.dandiset.get_asset_by_path(
         "sub-mouse001/sub-mouse001.nwb"
     ).identifier
-    monkeypatch.setenv("DANDI_API_KEY", nwb_dandiset.api.api_key)
+    monkeypatch.setenv("LINCBRAIN_API_KEY", nwb_dandiset.api.api_key)
     r = CliRunner().invoke(
         service_scripts,
         ["reextract-metadata", "--when=always", nwb_dandiset.dandiset.version_api_url],
@@ -71,7 +71,7 @@ def test_update_dandiset_from_doi(
 ) -> None:
     dandiset_id = new_dandiset.dandiset_id
     repository = new_dandiset.api.instance.gui
-    monkeypatch.setenv("DANDI_API_KEY", new_dandiset.api.api_key)
+    monkeypatch.setenv("LINCBRAIN_API_KEY", new_dandiset.api.api_key)
     if os.environ.get("DANDI_TESTS_NO_VCR", ""):
         ctx = nullcontext()
     else:

lincbrain/dandiapi.py

@@ -477,7 +477,7 @@ def authenticate(self, token: str, save_to_keyring: bool = False) -> None:
     def dandi_authenticate(self) -> None:
         """
         Acquire and set the authentication token/API key used by the
-        `DandiAPIClient`.  If the :envvar:`DANDI_API_KEY` environment variable
+        `DandiAPIClient`.  If the :envvar:`LINCBRAIN_API_KEY` environment variable
         is set, its value is used as the token.  Otherwise, the token is looked
         up in the user's keyring under the service
         ":samp:`dandi-api-{INSTANCE_NAME}`" [#auth]_ and username "``key``".
@@ -488,9 +488,9 @@ def dandi_authenticate(self) -> None:
                    "``dandi-api-dandi-staging``" for the staging server
         """
         # Shortcut for advanced folks
-        api_key = os.environ.get("DANDI_API_KEY", None)
+        api_key = os.environ.get("LINCBRAIN_API_KEY", None)
         if api_key:
-            lgr.debug("Using api key from DANDI_API_KEY environment variable")
+            lgr.debug("Using api key from LINCBRAIN_API_KEY environment variable")
             self.authenticate(api_key)
             return
         client_name, app_id = self._get_keyring_ids()

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/fixtures.py

@@ -505,7 +505,7 @@ def client(self) -> DandiAPIClient:
 
     def upload(self, paths: list[str | Path] | None = None, **kwargs: Any) -> None:
         with pytest.MonkeyPatch().context() as m:
-            m.setenv("DANDI_API_KEY", self.api.api_key)
+            m.setenv("LINCBRAIN_API_KEY", self.api.api_key)
             upload(
                 paths=paths or [self.dspath],
                 dandi_instance=self.api.instance_id,

lincbrain/tests/test_dandiapi.py

@@ -123,15 +123,15 @@ 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)
 
-    monkeypatch.delenv("DANDI_API_KEY", raising=False)
+    monkeypatch.delenv("LINCBRAIN_API_KEY", raising=False)
 
     client = DandiAPIClient(local_dandi_api.api_url)
     assert "Authorization" not in client.session.headers
@@ -156,13 +156,13 @@ 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")
     confirm_spy = mocker.spy(click, "confirm")
 
-    monkeypatch.delenv("DANDI_API_KEY", raising=False)
+    monkeypatch.delenv("LINCBRAIN_API_KEY", raising=False)
 
     client = DandiAPIClient(local_dandi_api.api_url)
     assert "Authorization" not in client.session.headers
@@ -186,15 +186,15 @@ 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)
 
-    monkeypatch.delenv("DANDI_API_KEY", raising=False)
+    monkeypatch.delenv("LINCBRAIN_API_KEY", raising=False)
 
     client = DandiAPIClient(local_dandi_api.api_url)
     assert "Authorization" not in client.session.headers