Merge pull request #422 from dandi/cleanup-code

Assorted code cleanup

dandi/__init__.py

@@ -41,8 +41,6 @@ def set_logger_level(lgr, level):
     lgr.setLevel(level)
 
 
-_DEFAULT_LOG_FORMAT = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
-
 lgr = get_logger()
 # Basic settings for output, for now just basic
 set_logger_level(lgr, os.environ.get("DANDI_LOG_LEVEL", logging.INFO))

dandi/dandiset.py

@@ -1,5 +1,4 @@
 """Classes/utilities for support of a dandiset"""
-import json
 import os
 from pathlib import Path
 
@@ -149,6 +148,4 @@ def _load_metadata(self):
         # models as metadata, so we take dict representation
         # Do R/T through json since it then maps types, although
         # "access" has a side-effect: https://github.com/dandi/dandi-cli/issues/343
-        self.metadata = json.loads(
-            migrate2newschema(self.metadata).json(exclude_unset=True, exclude_none=True)
-        )
+        self.metadata = migrate2newschema(self.metadata).json_dict()

dandi/tests/test_organize.py

@@ -179,7 +179,7 @@ def test_organize_nwb_test_data(nwb_test_data, tmpdir, clirunner, mode):
         assert not any(op.islink(p) for p in produced_paths)
 
 
-def test_ambigous(simple2_nwb, tmp_path, clirunner):
+def test_ambiguous(simple2_nwb, tmp_path, clirunner):
     copy2 = copy_nwb_file(simple2_nwb, tmp_path)
     outdir = str(tmp_path / "organized")
     args = ["--files-mode", "copy", "-d", outdir, simple2_nwb, copy2]
@@ -198,7 +198,7 @@ def test_ambigous(simple2_nwb, tmp_path, clirunner):
     )
 
 
-def test_ambiguos_probe1():
+def test_ambiguous_probe1():
     base = dict(subject_id="1", session="2", extension="nwb")
     # fake filenames should be ok since we never should get to reading them for object_id
     metadata = [

dandi/utils.py

@@ -152,19 +152,13 @@ def ensure_strtime(t, isoformat=True):
     raise TypeError(f"Do not know how to convert {t_orig!r} to string datetime")
 
 
-def fromisoformat(t, impl=None):
-    if impl is None:
-        # datetime parser "does not support parsing arbitrary ISO 8601 strings"
-        # https://docs.python.org/3/library/datetime.html
-        # In particular it does not parse time zone suffix which was recently
-        # introduced into datetime's provided by API
-        impl = "dateutil"
-    if impl == "datetime":
-        return datetime.datetime.fromisoformat(t)
-    elif impl == "dateutil":
-        return dateutil.parser.isoparse(t)
-    else:
-        raise ValueError(impl)
+def fromisoformat(t):
+    # datetime.fromisoformat "does not support parsing arbitrary ISO 8601
+    # strings" <https://docs.python.org/3/library/datetime.html>.  In
+    # particular, it does not parse the time zone suffixes recently
+    # introduced into timestamps provided by the API.  Hence, we need to use
+    # dateutil instead.
+    return dateutil.parser.isoparse(t)
 
 
 def ensure_datetime(t, strip_tzinfo=False, tz=None):

setup.cfg

@@ -21,8 +21,6 @@ description = Command line client for interaction with DANDI archive elements
 long_description = file:README.md
 long_description_content_type = text/markdown; charset=UTF-8
 platforms = OS Independent
-provides =
-    dandi
 project_urls =
     Source Code = https://github.com/dandi/dandi-cli
 

tox.ini

@@ -6,6 +6,7 @@ extras = test
 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 combine
     coverage report