debugs

src/nwbinspector/__init__.py

@@ -11,17 +11,7 @@
 from ._inspection import inspect_nwb  # TODO: remove after 7/1/2023
 from ._formatting import format_messages, print_to_console, save_report, MessageFormatter, FormatterOptions
 from ._organization import organize_messages
-from .checks.ecephys import *
-from .checks.general import *
-from .checks.image_series import *
-from .checks.images import *
-from .checks.nwb_containers import *
-from .checks.nwbfile_metadata import *
-from .checks.ogen import *
-from .checks.ophys import *
-from .checks.tables import *
-from .checks.time_series import *
-from .checks.icephys import *
+from .checks import *
 
 default_check_registry = {check.__name__: check for check in available_checks}
 

src/nwbinspector/_formatting.py

@@ -11,8 +11,9 @@
 
 import numpy as np
 
-from ._registration import InspectorMessage, Importance
-from .utils._utils import get_package_version, FilePathType
+from ._types import InspectorMessage, Importance
+from ._organization import organize_messages
+from .utils import get_package_version, FilePathType
 
 
 def _get_report_header():

src/nwbinspector/_inspection.py

@@ -14,7 +14,7 @@
 from tqdm import tqdm
 from natsort import natsorted
 
-from . import available_checks
+from . import available_checks, configure_checks
 from ._registration import InspectorMessage, Importance
 from .tools import get_s3_urls_and_dandi_paths
 from .utils import (

src/nwbinspector/_inspection_cli.py

@@ -9,18 +9,9 @@
 
 import click
 
-from ._formatting import (
-    _get_report_header,
-    format_messages,
-    print_to_console,
-    save_report,
-)
-from ._registration import Importance
-from nwbinspector.utils._utils import (
-    strtobool,
-)
-
-from ._inspection import inspect_all
+from ._formatting import _get_report_header
+from . import Importance, inspect_all, format_messages, print_to_console, save_report, __version__
+from .utils import strtobool
 
 
 @click.command()

src/nwbinspector/checks/__init__.py

@@ -0,0 +1,11 @@
+from .ecephys import *
+from .general import *
+from .image_series import *
+from .images import *
+from .nwb_containers import *
+from .nwbfile_metadata import *
+from .ogen import *
+from .ophys import *
+from .tables import *
+from .time_series import *
+from .icephys import *

src/nwbinspector/testing/__init__.py

@@ -7,7 +7,7 @@
     update_testing_config,
     generate_testing_files,
     generate_image_series_testing_files,
-    make_minimal_nwbfilem,
+    make_minimal_nwbfile,
     TESTING_CONFIG_FILE_PATH,
 )
 
@@ -20,6 +20,6 @@
     "update_testing_config",
     "generate_testing_files",
     "generate_image_series_testing_files",
-    "make_minimal_nwbfilem",
+    "make_minimal_nwbfile",
     "TESTING_CONFIG_FILE_PATH",
 ]

tests/test_inspector.py

@@ -14,17 +14,24 @@
 
 from nwbinspector import (
     Importance,
+    Severity,
+    InspectorMessage,
+    register_check,
+    load_config,
+    inspect_all,
+    inspect_nwbfile,
+    inspect_nwbfile_object,
+    available_checks,
+)
+from nwbinspector.checks import (
     check_small_dataset_compression,
     check_regular_timestamps,
     check_data_orientation,
     check_timestamps_match_first_dimension,
     check_subject_exists,
-    load_config,
 )
-from nwbinspector import inspect_all, inspect_nwbfile, inspect_nwbfile_object, available_checks
-from nwbinspector._registration import Severity, InspectorMessage, register_check
-from nwbinspector.tools import make_minimal_nwbfile
-from nwbinspector.utils._utils import FilePathType
+from nwbinspector.testing import make_minimal_nwbfile
+from nwbinspector.utils import FilePathType
 
 
 def add_big_dataset_no_compression(nwbfile: NWBFile):
@@ -120,6 +127,7 @@ def assertFileExists(self, path: FilePathType):
     def assertLogFileContentsEqual(
         self, test_file_path: FilePathType, true_file_path: FilePathType, skip_first_newlines: bool = False
     ):
+        skip_first_n_lines = 0
         with open(file=test_file_path, mode="r") as test_file:
             with open(file=true_file_path, mode="r") as true_file:
                 test_file_lines = test_file.readlines()

tests/test_tools.py

@@ -5,9 +5,8 @@
 import pynwb
 from hdmf.testing import TestCase
 
+from nwbinspector import InspectorMessage, Importance, Severity, organize_messages
 from nwbinspector.tools import all_of_type
-from nwbinspector._formatting import organize_messages
-from nwbinspector._registration import InspectorMessage, Importance, Severity
 
 
 def test_all_of_type():

tests/unit_tests/test_image_series.py

@@ -15,8 +15,7 @@
     check_image_series_data_size,
     check_timestamps_match_first_dimension,
 )
-from nwbinspector.tools import make_minimal_nwbfile
-from nwbinspector.testing._testing import load_testing_config
+from nwbinspector.testing import make_minimal_nwbfile, load_testing_config
 
 try:
     testing_config = load_testing_config()

tests/unit_tests/test_nwbfile_metadata.py

@@ -25,7 +25,7 @@
     check_session_start_time_future_date,
     PROCESSING_MODULE_CONFIG,
 )
-from nwbinspector.tools import make_minimal_nwbfile
+from nwbinspector.testing import make_minimal_nwbfile
 
 
 minimal_nwbfile = make_minimal_nwbfile()

tests/unit_tests/test_time_series.py

@@ -18,9 +18,8 @@
     check_timestamp_of_the_first_sample_is_not_negative,
     check_rate_is_not_zero,
 )
-from nwbinspector.tools import make_minimal_nwbfile
-from nwbinspector.testing._testing import check_streaming_tests_enabled
-from nwbinspector.utils._utils import get_package_version, robust_s3_read
+from nwbinspector.testing import make_minimal_nwbfile, check_streaming_tests_enabled
+from nwbinspector.utils import get_package_version, robust_s3_read
 
 STREAMING_TESTS_ENABLED, DISABLED_STREAMING_TESTS_REASON = check_streaming_tests_enabled()