more auditing of dandi to lincbrain renaming

lincbrain/cli/tests/test_service_scripts.py

@@ -14,7 +14,7 @@
 import vcr
 
 from dandi import __version__
-from dandi.tests.fixtures import SampleDandiset
+from lincbrain.tests.fixtures import SampleDandiset
 
 from ..cmd_service_scripts import service_scripts
 

lincbrain/dandiapi.py

@@ -1684,6 +1684,7 @@ def from_data(
                 raise ValueError("Asset data contains both `blob` and `zarr`'")
         else:
             raise ValueError("Asset data contains neither `blob` nor `zarr`")
+        # TODO: Aaron -- validation starts here...
         return klass(  # type: ignore[call-arg]
             client=dandiset.client,
             dandiset_id=dandiset.identifier,

lincbrain/files/__init__.py

@@ -16,9 +16,9 @@
 import os.path
 from pathlib import Path
 
-from dandi import get_logger
-from dandi.consts import BIDS_DATASET_DESCRIPTION, dandiset_metadata_file
-from dandi.exceptions import UnknownAssetError
+from lincbrain import get_logger
+from lincbrain.consts import BIDS_DATASET_DESCRIPTION, dandiset_metadata_file
+from lincbrain.exceptions import UnknownAssetError
 
 from ._private import BIDSFileFactory, DandiFileFactory
 from .bases import (

lincbrain/files/_private.py

@@ -7,12 +7,12 @@
 from typing import ClassVar
 import weakref
 
-from dandi.consts import (
+from lincbrain.consts import (
     BIDS_DATASET_DESCRIPTION,
     VIDEO_FILE_EXTENSIONS,
     ZARR_EXTENSIONS,
 )
-from dandi.exceptions import UnknownAssetError
+from lincbrain.exceptions import UnknownAssetError
 
 from .bases import DandiFile, GenericAsset, LocalAsset, NWBAsset, VideoAsset
 from .bids import (

lincbrain/files/bases.py

@@ -23,14 +23,14 @@
 from pydantic import ValidationError
 import requests
 
-import dandi
-from dandi.dandiapi import RemoteAsset, RemoteDandiset, RESTFullAPIClient
-from dandi.metadata.core import get_default_metadata
-from dandi.misctypes import DUMMY_DANDI_ETAG, Digest, LocalReadableFile, P
-from dandi.utils import yaml_load
-from dandi.validate_types import Scope, Severity, ValidationOrigin, ValidationResult
+import lincbrain
+from lincbrain.dandiapi import RemoteAsset, RemoteDandiset, RESTFullAPIClient
+from lincbrain.metadata.core import get_default_metadata
+from lincbrain.misctypes import DUMMY_DANDI_ETAG, Digest, LocalReadableFile, P
+from lincbrain.utils import yaml_load
+from lincbrain.validate_types import Scope, Severity, ValidationOrigin, ValidationResult
 
-lgr = dandi.get_logger()
+lgr = lincbrain.get_logger()
 
 # TODO -- should come from schema.  This is just a simplistic example for now
 _required_dandiset_metadata_fields = ["identifier", "name", "description"]
@@ -204,7 +204,7 @@ def get_validation_errors(
                 ValidationResult(
                     origin=ValidationOrigin(
                         name="dandi",
-                        version=dandi.__version__,
+                        version=lincbrain.__version__,
                     ),
                     severity=Severity.ERROR,
                     id="dandi.SOFTWARE_ERROR",
@@ -299,7 +299,7 @@ def get_metadata(
 
     def get_digest(self) -> Digest:
         """Calculate a dandi-etag digest for the asset"""
-        from dandi.support.digests import get_digest
+        from lincbrain.support.digests import get_digest
 
         value = get_digest(self.filepath, digest="dandi-etag")
         return Digest.dandi_etag(value)
@@ -331,7 +331,7 @@ def iter_upload(
             ``"done"`` and an ``"asset"`` key containing the resulting
             `RemoteAsset`.
         """
-        from dandi.support.digests import get_dandietag
+        from lincbrain.support.digests import get_dandietag
 
         asset_path = metadata.setdefault("path", self.path)
         client = dandiset.client
@@ -469,7 +469,7 @@ def get_metadata(
         digest: Digest | None = None,
         ignore_errors: bool = True,
     ) -> BareAsset:
-        from dandi.metadata.nwb import nwb2asset
+        from lincbrain.metadata.nwb import nwb2asset
 
         try:
             metadata = nwb2asset(self.filepath, digest=digest)
@@ -501,7 +501,7 @@ def get_validation_errors(
         """
         from nwbinspector import Importance, inspect_nwbfile, load_config
 
-        from dandi.pynwb_utils import validate as pynwb_validate
+        from lincbrain.pynwb_utils import validate as pynwb_validate
 
         errors: list[ValidationResult] = pynwb_validate(
             self.filepath, devel_debug=devel_debug
@@ -559,7 +559,7 @@ def get_validation_errors(
                     [e], self.filepath, scope=Scope.FILE
                 )
 
-        from dandi.organize import validate_organized_path
+        from lincbrain.organize import validate_organized_path
 
         from .bids import NWBBIDSAsset
 

lincbrain/files/bids.py

@@ -66,7 +66,7 @@ def _validate(self) -> None:
         with self._lock:
             if self._dataset_errors is None:
                 # Import here to avoid circular import
-                from dandi.validate import validate_bids
+                from lincbrain.validate import validate_bids
 
                 bids_paths = [str(self.filepath)] + [
                     str(asset.filepath) for asset in self.dataset_files

lincbrain/files/zarr.py

@@ -93,7 +93,7 @@ def get_digest(self) -> Digest:
         it is a file, it will be MD5.
         """
 
-        from dandi.support.digests import get_digest, get_zarr_checksum
+        from lincbrain.support.digests import get_digest, get_zarr_checksum
 
         if self.is_dir():
             return Digest.dandi_zarr(get_zarr_checksum(self.filepath))
@@ -151,7 +151,7 @@ def stat(self) -> ZarrStat:
         """Return various details about the Zarr asset"""
 
         def dirstat(dirpath: LocalZarrEntry) -> ZarrStat:
-            from dandi.support.digests import md5file_nocache
+            from lincbrain.support.digests import md5file_nocache
 
             size = 0
             dir_md5s = {}
@@ -177,7 +177,7 @@ def dirstat(dirpath: LocalZarrEntry) -> ZarrStat:
 
     def get_digest(self) -> Digest:
         """Calculate a dandi-zarr-checksum digest for the asset"""
-        from dandi.support.digests import get_zarr_checksum
+        from lincbrain.support.digests import get_zarr_checksum
 
         return Digest.dandi_zarr(get_zarr_checksum(self.filepath))
 
@@ -594,7 +594,7 @@ def register(self, e: LocalZarrEntry, digest: str | None = None) -> None:
 
     @staticmethod
     def _mkitem(e: LocalZarrEntry) -> UploadItem:
-        from dandi.support.digests import md5file_nocache
+        from lincbrain.support.digests import md5file_nocache
 
         digest = md5file_nocache(e.filepath)
         return UploadItem.from_entry(e, digest)
@@ -646,7 +646,7 @@ def upload_request(self) -> dict[str, str]:
 def _cmp_digests(
     asset_path: str, local_entry: LocalZarrEntry, remote_digest: str
 ) -> tuple[LocalZarrEntry, str, bool]:
-    from dandi.support.digests import md5file_nocache
+    from lincbrain.support.digests import md5file_nocache
 
     local_digest = md5file_nocache(local_entry.filepath)
     if local_digest != remote_digest:

tools/migrate-dandisets.py

@@ -2,8 +2,8 @@
 import click
 import requests
 
-from dandi.dandiapi import DandiAPIClient
-from dandi.dandiset import APIDandiset
+from lincbrain.dandiapi import DandiAPIClient
+from lincbrain.dandiset import APIDandiset
 
 
 @click.command()

tox.ini

@@ -13,7 +13,7 @@ commands =
     # Using pytest-cov instead of using coverage directly leaves a bunch of
     # .coverage.$HOSTNAME.#.# files lying around for some reason
     coverage erase
-    coverage run -m pytest -v {posargs} dandi
+    coverage run -m pytest -v {posargs} lincbrain
     coverage combine
     coverage report
 
@@ -23,16 +23,16 @@ deps =
     codespell~=2.0
     flake8
 commands =
-    codespell dandi setup.py
-    flake8 --config=setup.cfg {posargs} dandi setup.py
+    codespell lincbrain setup.py
+    flake8 --config=setup.cfg {posargs} lincbrain setup.py
 
 [testenv:typing]
 deps =
     mypy
     types-python-dateutil
     types-requests
 commands =
-    mypy dandi
+    mypy lincbrain
 
 [testenv:docs]
 basepython = python3
@@ -69,7 +69,7 @@ filterwarnings =
 
 [coverage:run]
 parallel = True
-source = dandi
+source = lincbrain
 
 [coverage:report]
 precision = 2