Run pyupgrade --py38-plus on source

dandi/cli/cmd_ls.py

@@ -298,7 +298,7 @@ def flatten_meta_to_pyout_v1(meta):
             continue
         if isinstance(v, dict):
             for vf, vv in flatten_meta_to_pyout_v1(v).items():
-                out["%s_%s" % (f, vf)] = flatten_v(vv)
+                out[f"{f}_{vf}"] = flatten_v(vv)
         else:
             out[f] = flatten_v(v)
     return out

dandi/cli/command.py

@@ -99,7 +99,7 @@ def main(ctx, log_level, pdb=False):
 
     logdir = platformdirs.user_log_dir("dandi-cli", "dandi")
     logfile = os.path.join(
-        logdir, "{:%Y%m%d%H%M%SZ}-{}.log".format(datetime.utcnow(), os.getpid())
+        logdir, f"{datetime.utcnow():%Y%m%d%H%M%SZ}-{os.getpid()}.log"
     )
     os.makedirs(logdir, exist_ok=True)
     handler = logging.FileHandler(logfile, encoding="utf-8")

dandi/cli/formatter.py

@@ -7,7 +7,7 @@
 lgr = get_logger()
 
 
-class Formatter(object):
+class Formatter:
     def __enter__(self):
         pass
 

dandi/dandiapi.py

@@ -438,7 +438,7 @@ def for_dandi_instance(
         instance: str | DandiInstance,
         token: str | None = None,
         authenticate: bool = False,
-    ) -> "DandiAPIClient":
+    ) -> DandiAPIClient:
         """
         Construct a client instance for the server identified by ``instance``
         (either the name of a registered Dandi Archive instance or a
@@ -530,7 +530,7 @@ def _instance_id(self) -> str:
 
     def get_dandiset(
         self, dandiset_id: str, version_id: str | None = None, lazy: bool = True
-    ) -> "RemoteDandiset":
+    ) -> RemoteDandiset:
         """
         Fetches the Dandiset with the given ``dandiset_id``.  If ``version_id``
         is not specified, the `RemoteDandiset`'s version is set to the most
@@ -556,7 +556,7 @@ def get_dandiset(
                     return d.for_version(version_id)
             return d
 
-    def get_dandisets(self) -> Iterator["RemoteDandiset"]:
+    def get_dandisets(self) -> Iterator[RemoteDandiset]:
         """
         Returns a generator of all Dandisets on the server.  For each Dandiset,
         the `RemoteDandiset`'s version is set to the most recent published
@@ -565,7 +565,7 @@ def get_dandisets(self) -> Iterator["RemoteDandiset"]:
         for data in self.paginate("/dandisets/"):
             yield RemoteDandiset.from_data(self, data)
 
-    def create_dandiset(self, name: str, metadata: dict[str, Any]) -> "RemoteDandiset":
+    def create_dandiset(self, name: str, metadata: dict[str, Any]) -> RemoteDandiset:
         """Creates a Dandiset with the given name & metadata"""
         return RemoteDandiset.from_data(
             self, self.post("/dandisets/", json={"name": name, "metadata": metadata})
@@ -596,7 +596,7 @@ def check_schema_version(self, schema_version: str | None = None) -> None:
                 " upgrade dandi and/or dandischema."
             )
 
-    def get_asset(self, asset_id: str) -> "BaseRemoteAsset":
+    def get_asset(self, asset_id: str) -> BaseRemoteAsset:
         """
         Fetch the asset with the given asset ID.  If the given asset does not
         exist, a `NotFoundError` is raised.
@@ -1026,7 +1026,7 @@ def wait_until_valid(self, max_time: float = 120) -> None:
             f"Dandiset {self.identifier} is {v.status.value}: {json.dumps(about, indent=4)}"
         )
 
-    def publish(self, max_time: float = 120) -> "RemoteDandiset":
+    def publish(self, max_time: float = 120) -> RemoteDandiset:
         """
         Publish the draft version of the Dandiset and wait at most ``max_time``
         seconds for the publication operation to complete.  If the operation
@@ -1073,7 +1073,7 @@ def get_assets(self, order: str | None = None) -> Iterator[RemoteAsset]:
                 f"No such version: {self.version_id!r} of Dandiset {self.identifier}"
             )
 
-    def get_asset(self, asset_id: str) -> "RemoteAsset":
+    def get_asset(self, asset_id: str) -> RemoteAsset:
         """
         Fetch the asset in this version of the Dandiset with the given asset
         ID.  If the given asset does not exist, a `NotFoundError` is raised.
@@ -1133,7 +1133,7 @@ def get_assets_by_glob(
                 f"No such version: {self.version_id!r} of Dandiset {self.identifier}"
             )
 
-    def get_asset_by_path(self, path: str) -> "RemoteAsset":
+    def get_asset_by_path(self, path: str) -> RemoteAsset:
         """
         Fetch the asset in this version of the Dandiset whose
         `~RemoteAsset.path` equals ``path``.  If the given asset does not
@@ -1264,7 +1264,7 @@ class BaseRemoteAsset(ABC, APIBase):
 
     #: The `DandiAPIClient` instance that returned this `BaseRemoteAsset`
     #: and which the latter will use for API requests
-    client: "DandiAPIClient"
+    client: DandiAPIClient
     #: The asset identifier
     identifier: str = Field(alias="asset_id")
     #: The asset's (forward-slash-separated) path
@@ -1611,9 +1611,7 @@ def get_entry_by_path(self, path: str) -> RemoteZarrEntry:
         else:
             return entry
 
-    def rmfiles(
-        self, files: Iterable["RemoteZarrEntry"], reingest: bool = True
-    ) -> None:
+    def rmfiles(self, files: Iterable[RemoteZarrEntry], reingest: bool = True) -> None:
         """
         Delete one or more files from the Zarr.
 

dandi/download.py

@@ -423,7 +423,7 @@ def agg_done(self, done_sizes: Iterator[int]) -> list[str]:
             pref += "<"
         if self.items_summary.has_unknown_sizes:
             pref += "?"
-        v = [naturalsize(done), "%s%.2f%%" % (pref, 100 * r)]
+        v = [naturalsize(done), f"{pref}{100 * r:.2f}%"]
         if (
             done
             and self.items_summary.t0 is not None

dandi/due.py

@@ -27,7 +27,7 @@
 __version__ = "0.0.8"
 
 
-class InactiveDueCreditCollector(object):
+class InactiveDueCreditCollector:
     """Just a stub at the Collector which would not do anything"""
 
     def _donothing(self, *args, **kwargs):

dandi/organize.py

@@ -382,9 +382,9 @@ def _assign_dandi_names(metadata):
 def _get_unique_values(metadata, fields, filter_=False):
     unique_values = {}
     for field in fields:
-        unique_values[field] = set(_get_hashable(r.get(field, None)) for r in metadata)
+        unique_values[field] = {_get_hashable(r.get(field, None)) for r in metadata}
         if filter_:
-            unique_values[field] = set(v for v in unique_values[field] if v)
+            unique_values[field] = {v for v in unique_values[field] if v}
     return unique_values
 
 
@@ -998,7 +998,7 @@ def _get_metadata(path):
     if acted_upon and in_place:
         # We might need to cleanup a bit - e.g. prune empty directories left
         # by the move in in-place mode
-        dirs = set(op.dirname(e["path"]) for e in acted_upon)
+        dirs = {op.dirname(e["path"]) for e in acted_upon}
         for d in sorted(dirs)[::-1]:  # from longest to shortest
             if op.exists(d):
                 try:

dandi/pynwb_utils.py

@@ -157,7 +157,7 @@ def get_neurodata_types_to_modalities_map() -> dict[str, str]:
 
                 v_split = v_.__module__.split(".")
                 if len(v_split) != 2:
-                    print("Skipping %s coming from %s" % (v_, v_.__module__))
+                    print(f"Skipping {v_} coming from {v_.__module__}")
                     continue
                 modality = v_split[1]  # so smth like ecephys
 
@@ -247,7 +247,7 @@ def _get_pynwb_metadata(path: str | Path | Readable) -> dict[str, Any]:
                 continue
             if not f.startswith("number_of_"):
                 raise NotImplementedError(
-                    "ATM can only compute number_of_ fields. Got {}".format(f)
+                    f"ATM can only compute number_of_ fields. Got {f}"
                 )
             key = f[len("number_of_") :]
             out[f] = len(getattr(nwb, key, []) or [])

dandi/support/pyout.py

@@ -54,7 +54,7 @@ def summary_dates(values):
 
 
 def counts(values):
-    return ["{:d} {}".format(v, k) for k, v in Counter(values).items()]
+    return [f"{v:d} {k}" for k, v in Counter(values).items()]
 
 
 # class mapped_counts(object):
@@ -148,9 +148,7 @@ def get_style(hide_if_missing=True):
         "errors": dict(
             align="center",
             color=dict(interval=[[0, 1, "green"], [1, None, "red"]]),
-            aggregate=lambda x: (
-                "{} with errors".format(sum(map(bool, x))) if any(x) else ""
-            ),
+            aggregate=lambda x: (f"{sum(map(bool, x))} with errors" if any(x) else ""),
         ),
         "status": dict(
             color=dict(lookup={"skipped": "yellow", "done": "green", "error": "red"}),

dandi/tests/fixtures.py

@@ -435,7 +435,7 @@ def docker_compose_setup() -> Iterator[dict[str, str]]:
             ],
             cwd=str(LOCAL_DOCKER_DIR),
             env=env,
-            universal_newlines=True,
+            text=True,
         )
         m = re.search(r"^Generated token (\w+) for user admin@nil.nil$", r, flags=re.M)
         if not m:

dandi/tests/skip.py

@@ -181,7 +181,7 @@ class NamespaceAttributeError(AttributeError):
     """
 
 
-class Namespace(object, metaclass=abc.ABCMeta):
+class Namespace(metaclass=abc.ABCMeta):
     """Provide namespace skip conditions in CONDITION_FNS."""
 
     fns = {c.__name__: c for c in CONDITION_FNS}
@@ -231,12 +231,12 @@ def attr_value(self, condition_func):
     def __getattr__(self, item):
         if item.startswith("skipif_"):
             try:
-                return super(Mark, self).__getattr__(item[len("skipif_") :])
+                return super().__getattr__(item[len("skipif_") :])
             except NamespaceAttributeError:
                 # Fall back to the original item name so that the attribute
                 # error message doesn't confusingly drop "skipif_".
                 pass
-        return super(Mark, self).__getattr__(item)
+        return super().__getattr__(item)
 
 
 mark = Mark()

dandi/tests/test_keyring.py

@@ -36,7 +36,7 @@ def test_dandi_authenticate_no_env_var(
     )
     DandiAPIClient(local_dandi_api.api_url).dandi_authenticate()
     inputmock.assert_called_once_with(
-        "Please provide API Key for {}: ".format(local_dandi_api.instance_id)
+        f"Please provide API Key for {local_dandi_api.instance_id}: "
     )
 
 

dandi/tests/test_upload.py

@@ -28,9 +28,9 @@ def test_upload_download(
 ) -> None:
     d = new_dandiset.dandiset
     dspath = new_dandiset.dspath
-    (nwb_file,) = [
+    (nwb_file,) = (
         p for p in list_paths(organized_nwb_dir) if p.name != dandiset_metadata_file
-    ]
+    )
     assert nwb_file.suffix == ".nwb"
     parent, name = nwb_file.relative_to(organized_nwb_dir).parts
     (dspath / parent).mkdir()
@@ -299,7 +299,7 @@ def test_upload_bids_zarr(bids_zarr_dandiset: SampleDandiset) -> None:
     bids_zarr_dandiset.upload()
     assets = list(bids_zarr_dandiset.dandiset.get_assets())
     assert len(assets) > 10  # it is a bigish dataset
-    (asset,) = [a for a in assets if a.path.endswith(".zarr")]
+    (asset,) = (a for a in assets if a.path.endswith(".zarr"))
     assert isinstance(asset, RemoteZarrAsset)
     assert asset.asset_type is AssetType.ZARR
     assert asset.path.endswith(".zarr")

dandi/utils.py

@@ -234,16 +234,15 @@ def flattened(it: Iterable) -> list:
 
 def load_jsonl(filename: AnyPath) -> list:
     """Load json lines formatted file"""
-    with open(filename, "r") as f:
+    with open(filename) as f:
         return list(map(json.loads, f))
 
 
 _encoded_dirsep = re.escape(os.sep)
-_VCS_REGEX = r"%s\.(?:git|gitattributes|svn|bzr|hg)(?:%s|$)" % (
-    _encoded_dirsep,
-    _encoded_dirsep,
+_VCS_REGEX = (
+    rf"{_encoded_dirsep}\.(?:git|gitattributes|svn|bzr|hg)(?:{_encoded_dirsep}|$)"
 )
-_DATALAD_REGEX = r"%s\.(?:datalad)(?:%s|$)" % (_encoded_dirsep, _encoded_dirsep)
+_DATALAD_REGEX = rf"{_encoded_dirsep}\.(?:datalad)(?:{_encoded_dirsep}|$)"
 
 
 def find_files(
@@ -374,7 +373,7 @@ def copy_file(src: AnyPath, dst: AnyPath) -> None:
             ["cp", "--help"],
             stdout=subprocess.PIPE,
             stderr=subprocess.STDOUT,
-            universal_newlines=True,
+            text=True,
         )
         # Ignore command failures (e.g., if cp doesn't support --help), as the
         # command will still likely output its usage info.