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adarshpadarshp
authored
Changing linter and formatter to ruff (#571)
1 parent eeaee4f commit a03d49e

31 files changed

+433
-194
lines changed

‎human_experiments/datasette_interface/Makefile

Lines changed: 2 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,6 @@
11
lint:
2-
black .
3-
isort .
4-
autoflake -r . --in-place --remove-all-unused-imports
5-
flake8 .
2+
ruff check --fix .
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ruff format .
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75
# Datasette
86
create_datasette:

‎human_experiments/datasette_interface/bin/create_tables.py

Lines changed: 30 additions & 39 deletions
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@@ -1,47 +1,38 @@
11
#!/usr/bin/env python
22

33
from datasette_interface.database.config import Base, engine # noqa f401
4-
from datasette_interface.database.entity.base.data_validity import \
5-
DataValidity # noqa f401
6-
from datasette_interface.database.entity.base.eeg_device import \
7-
EEGDevice # noqa f401
8-
from datasette_interface.database.entity.base.group_session import \
9-
GroupSession # noqa f401
10-
from datasette_interface.database.entity.base.modality import \
11-
Modality # noqa f401
12-
from datasette_interface.database.entity.base.participant import \
13-
Participant # noqa f401
14-
from datasette_interface.database.entity.base.station import \
15-
Station # noqa f401
4+
from datasette_interface.database.entity.base.data_validity import DataValidity # noqa f401
5+
from datasette_interface.database.entity.base.eeg_device import EEGDevice # noqa f401
6+
from datasette_interface.database.entity.base.group_session import GroupSession # noqa f401
7+
from datasette_interface.database.entity.base.modality import Modality # noqa f401
8+
from datasette_interface.database.entity.base.participant import Participant # noqa f401
9+
from datasette_interface.database.entity.base.station import Station # noqa f401
1610
from datasette_interface.database.entity.base.task import Task # noqa f401
17-
from datasette_interface.database.entity.derived.eeg_sync import \
18-
EEGSync # noqa f401
19-
from datasette_interface.database.entity.derived.ekg_sync import \
20-
EKGSync # noqa f401
21-
from datasette_interface.database.entity.derived.fnirs_sync import \
22-
FNIRSSync # noqa f401
23-
from datasette_interface.database.entity.derived.gsr_sync import \
24-
GSRSync # noqa f401
25-
from datasette_interface.database.entity.signal.audio_vocalics import \
26-
AudioVocalics # noqa f401
11+
from datasette_interface.database.entity.derived.eeg_sync import EEGSync # noqa f401
12+
from datasette_interface.database.entity.derived.ekg_sync import EKGSync # noqa f401
13+
from datasette_interface.database.entity.derived.fnirs_sync import FNIRSSync # noqa f401
14+
from datasette_interface.database.entity.derived.gsr_sync import GSRSync # noqa f401
15+
from datasette_interface.database.entity.signal.audio_vocalics import AudioVocalics # noqa f401
2716
from datasette_interface.database.entity.signal.eeg import EEGRaw # noqa f401
28-
from datasette_interface.database.entity.signal.fnirs import \
29-
FNIRSRaw # noqa f401
30-
from datasette_interface.database.entity.signal.gaze import \
31-
GAZERaw # noqa f401
32-
from datasette_interface.database.entity.signal.screen_capture import \
33-
ScreenCapture # noqa f401
34-
from datasette_interface.database.entity.task.affective_task_event import \
35-
AffectiveTaskEvent # noqa f401
36-
from datasette_interface.database.entity.task.finger_tapping_task_observation import \
37-
FingerTappingTaskObservation # noqa f401
17+
from datasette_interface.database.entity.signal.fnirs import FNIRSRaw # noqa f401
18+
from datasette_interface.database.entity.signal.gaze import GAZERaw # noqa f401
19+
from datasette_interface.database.entity.signal.screen_capture import ScreenCapture # noqa f401
20+
from datasette_interface.database.entity.task.affective_task_event import (
21+
AffectiveTaskEvent,
22+
) # noqa f401
23+
from datasette_interface.database.entity.task.finger_tapping_task_observation import (
24+
FingerTappingTaskObservation,
25+
) # noqa f401
3826
from datasette_interface.database.entity.task.minecraft_task import ( # noqa f401
39-
MinecraftMission, MinecraftTestbedMessage)
40-
from datasette_interface.database.entity.task.ping_pong_competitive_task_observation import \
41-
PingPongCompetitiveTaskObservation # noqa f401
42-
from datasette_interface.database.entity.task.ping_pong_cooperative_task_observation import \
43-
PingPongCooperativeTaskObservation # noqa f401
44-
from datasette_interface.database.entity.task.rest_state_task import \
45-
RestStateTask # noqa f401
27+
MinecraftMission,
28+
MinecraftTestbedMessage,
29+
)
30+
from datasette_interface.database.entity.task.ping_pong_competitive_task_observation import (
31+
PingPongCompetitiveTaskObservation,
32+
) # noqa f401
33+
from datasette_interface.database.entity.task.ping_pong_cooperative_task_observation import (
34+
PingPongCooperativeTaskObservation,
35+
) # noqa f401
36+
from datasette_interface.database.entity.task.rest_state_task import RestStateTask # noqa f401
4637

4738
Base.metadata.create_all(engine, checkfirst=True)

‎human_experiments/datasette_interface/bin/populate_raw_tables.py

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@@ -4,25 +4,29 @@
44
import os
55

66
from datasette_interface.database.config import SQLALCHEMY_DATABASE_URI
7-
from datasette_interface.raw.process_affective_task_data import \
8-
process_affective_task_data
7+
from datasette_interface.raw.process_affective_task_data import (
8+
process_affective_task_data,
9+
)
910
from datasette_interface.raw.process_base_tables import process_base_tables
1011
from datasette_interface.raw.process_eeg_raw_data import process_eeg_raw_data
11-
from datasette_interface.raw.process_finger_tapping_task_data import \
12-
process_finger_tapping_task_data
13-
from datasette_interface.raw.process_fnirs_raw_data import \
14-
process_fnirs_raw_data
12+
from datasette_interface.raw.process_finger_tapping_task_data import (
13+
process_finger_tapping_task_data,
14+
)
15+
from datasette_interface.raw.process_fnirs_raw_data import process_fnirs_raw_data
1516
from datasette_interface.raw.process_gaze_raw_data import process_gaze_raw_data
16-
from datasette_interface.raw.process_minecraft_data import \
17-
process_minecraft_data
18-
from datasette_interface.raw.process_ping_pong_competitive_data import \
19-
process_ping_pong_competitive_task_data
20-
from datasette_interface.raw.process_ping_pong_cooperative_data import \
21-
process_ping_pong_cooperative_task_data
22-
from datasette_interface.raw.process_rest_state_task_data import \
23-
process_rest_state_task_data
24-
from datasette_interface.raw.process_screen_capture_data import \
25-
process_screen_capture_data
17+
from datasette_interface.raw.process_minecraft_data import process_minecraft_data
18+
from datasette_interface.raw.process_ping_pong_competitive_data import (
19+
process_ping_pong_competitive_task_data,
20+
)
21+
from datasette_interface.raw.process_ping_pong_cooperative_data import (
22+
process_ping_pong_cooperative_task_data,
23+
)
24+
from datasette_interface.raw.process_rest_state_task_data import (
25+
process_rest_state_task_data,
26+
)
27+
from datasette_interface.raw.process_screen_capture_data import (
28+
process_screen_capture_data,
29+
)
2630
from datasette_interface.raw.process_vocalics import process_vocalics
2731

2832
TABLES = {

‎human_experiments/datasette_interface/bin/sync_raw_signals.py

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@@ -16,8 +16,7 @@
1616

1717
from datasette_interface.common.config import LOG_DIR
1818
from datasette_interface.common.constants import STATIONS
19-
from datasette_interface.database.config import (SQLALCHEMY_DATABASE_URI,
20-
engine, get_db)
19+
from datasette_interface.database.config import SQLALCHEMY_DATABASE_URI, engine, get_db
2120
from datasette_interface.database.entity.base.group_session import GroupSession
2221
from datasette_interface.derived.helper.factory import create_modality_helper
2322
from datasette_interface.derived.main_clock import get_main_clock_timestamps
@@ -179,7 +178,7 @@ def sync_raw_signals_single_job(
179178
modality_helper.filter()
180179
except Exception as ex:
181180
error(f"Error while filtering the signals ({ex}).")
182-
info(f"Skipping.")
181+
info("Skipping.")
183182
continue
184183

185184
info("Up-sampling.")

‎human_experiments/datasette_interface/datasette_interface.egg-info/PKG-INFO

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Metadata-Version: 1.0
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Name: datasette-interface
3+
Version: 0.0.0
4+
Summary: UNKNOWN
5+
Home-page: UNKNOWN
6+
Author: UNKNOWN
7+
Author-email: UNKNOWN
8+
License: UNKNOWN
9+
Description: UNKNOWN
10+
Platform: UNKNOWN

‎human_experiments/datasette_interface/datasette_interface.egg-info/SOURCES.txt

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README.md
2+
setup.py
3+
datasette_interface/__init__.py
4+
datasette_interface.egg-info/PKG-INFO
5+
datasette_interface.egg-info/SOURCES.txt
6+
datasette_interface.egg-info/dependency_links.txt
7+
datasette_interface.egg-info/top_level.txt
8+
datasette_interface/common/__init__.py
9+
datasette_interface/common/config.py
10+
datasette_interface/common/constants.py
11+
datasette_interface/common/experiments_crawler.py
12+
datasette_interface/common/extract_signal_xdf.py
13+
datasette_interface/common/utils.py
14+
datasette_interface/database/__init__.py
15+
datasette_interface/database/config.py
16+
datasette_interface/database/entity/__init__.py
17+
datasette_interface/database/entity/base/__init__.py
18+
datasette_interface/database/entity/base/data_validity.py
19+
datasette_interface/database/entity/base/eeg_device.py
20+
datasette_interface/database/entity/base/group_session.py
21+
datasette_interface/database/entity/base/modality.py
22+
datasette_interface/database/entity/base/participant.py
23+
datasette_interface/database/entity/base/station.py
24+
datasette_interface/database/entity/base/task.py
25+
datasette_interface/database/entity/derived/__init__.py
26+
datasette_interface/database/entity/derived/eeg_sync.py
27+
datasette_interface/database/entity/derived/ekg_sync.py
28+
datasette_interface/database/entity/derived/fnirs_sync.py
29+
datasette_interface/database/entity/derived/gsr_sync.py
30+
datasette_interface/database/entity/signal/__init__.py
31+
datasette_interface/database/entity/signal/audio_vocalics.py
32+
datasette_interface/database/entity/signal/eeg.py
33+
datasette_interface/database/entity/signal/fnirs.py
34+
datasette_interface/database/entity/signal/gaze.py
35+
datasette_interface/database/entity/signal/screen_capture.py
36+
datasette_interface/database/entity/task/__init__.py
37+
datasette_interface/database/entity/task/affective_task_event.py
38+
datasette_interface/database/entity/task/finger_tapping_task_observation.py
39+
datasette_interface/database/entity/task/minecraft_task.py
40+
datasette_interface/database/entity/task/ping_pong_competitive_task_observation.py
41+
datasette_interface/database/entity/task/ping_pong_cooperative_task_observation.py
42+
datasette_interface/database/entity/task/rest_state_task.py
43+
datasette_interface/derived/__init__.py
44+
datasette_interface/derived/label_transcriptions.py
45+
datasette_interface/derived/main_clock.py
46+
datasette_interface/derived/helper/__init__.py
47+
datasette_interface/derived/helper/eeg.py
48+
datasette_interface/derived/helper/ekg.py
49+
datasette_interface/derived/helper/factory.py
50+
datasette_interface/derived/helper/fnirs.py
51+
datasette_interface/derived/helper/gsr.py
52+
datasette_interface/derived/helper/modality.py
53+
datasette_interface/model/__init__.py
54+
datasette_interface/model/audio/__init__.py
55+
datasette_interface/model/audio/pcm_audio.py
56+
datasette_interface/model/audio/praat_annotation.py
57+
datasette_interface/model/audio/sentence_labeler.py
58+
datasette_interface/model/audio/transcriber.py
59+
datasette_interface/raw/__init__.py
60+
datasette_interface/raw/process_affective_task_data.py
61+
datasette_interface/raw/process_base_tables.py
62+
datasette_interface/raw/process_eeg_raw_data.py
63+
datasette_interface/raw/process_finger_tapping_task_data.py
64+
datasette_interface/raw/process_fnirs_raw_data.py
65+
datasette_interface/raw/process_gaze_raw_data.py
66+
datasette_interface/raw/process_minecraft_data.py
67+
datasette_interface/raw/process_ping_pong_competitive_data.py
68+
datasette_interface/raw/process_ping_pong_cooperative_data.py
69+
datasette_interface/raw/process_rest_state_task_data.py
70+
datasette_interface/raw/process_screen_capture_data.py
71+
datasette_interface/raw/process_vocalics.py
72+
datasette_interface/raw/common/__init__.py
73+
datasette_interface/raw/common/label_data.py
74+
datasette_interface/raw/common/process_image_data.py
75+
datasette_interface/raw/common/process_raw_signals.py

‎human_experiments/datasette_interface/datasette_interface.egg-info/dependency_links.txt

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‎human_experiments/datasette_interface/datasette_interface.egg-info/top_level.txt

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datasette_interface

‎human_experiments/datasette_interface/datasette_interface/common/experiments_crawler.py

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@@ -5,7 +5,9 @@
55

66
from datasette_interface.common.config import settings
77
from datasette_interface.common.utils import (
8-
is_directory_with_unified_xdf_files, should_ignore_directory)
8+
is_directory_with_unified_xdf_files,
9+
should_ignore_directory,
10+
)
911

1012

1113
class ExperimentsCrawler:

‎human_experiments/datasette_interface/datasette_interface/database/entity/signal/audio_vocalics.py

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -4,8 +4,7 @@
44
from datasette_interface.database.config import Base
55
from datasette_interface.database.entity.base.group_session import GroupSession
66
from datasette_interface.database.entity.base.station import Station
7-
from datasette_interface.database.entity.task.minecraft_task import \
8-
MinecraftMission
7+
from datasette_interface.database.entity.task.minecraft_task import MinecraftMission
98

109

1110
class AudioVocalics(Base):

‎human_experiments/datasette_interface/datasette_interface/derived/helper/eeg.py

Lines changed: 7 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -7,10 +7,12 @@
77
from sqlalchemy import Engine, func, select
88
from sqlalchemy.orm import Session
99

10-
from datasette_interface.common.constants import (EEG_FREQUENCY,
11-
EEG_NOTCH_FILTER_FREQUENCY,
12-
EEG_NOTCH_WIDTH,
13-
EEG_TRANSISION_BANDWIDTH)
10+
from datasette_interface.common.constants import (
11+
EEG_FREQUENCY,
12+
EEG_NOTCH_FILTER_FREQUENCY,
13+
EEG_NOTCH_WIDTH,
14+
EEG_TRANSISION_BANDWIDTH,
15+
)
1416
from datasette_interface.common.utils import convert_unix_timestamp_to_iso8601
1517
from datasette_interface.database.entity.derived.eeg_sync import EEGSync
1618
from datasette_interface.database.entity.signal.eeg import EEGRaw
@@ -90,7 +92,7 @@ def load_data(self):
9092
EEGRaw.fc6,
9193
EEGRaw.fcz,
9294
EEGRaw.f8,
93-
EEGRaw.aff2h
95+
EEGRaw.aff2h,
9496
)
9597
.where(
9698
EEGRaw.group_session_id == self.group_session,

‎human_experiments/datasette_interface/datasette_interface/derived/helper/ekg.py

Lines changed: 4 additions & 3 deletions
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@@ -8,7 +8,6 @@
88

99
from datasette_interface.common.constants import EEG_FREQUENCY
1010
from datasette_interface.common.utils import convert_unix_timestamp_to_iso8601
11-
from datasette_interface.database.entity.derived.eeg_sync import EEGSync
1211
from datasette_interface.database.entity.derived.ekg_sync import EKGSync
1312
from datasette_interface.database.entity.signal.eeg import EEGRaw
1413
from datasette_interface.derived.helper.modality import ModalityHelper
@@ -85,9 +84,11 @@ def filter(self) -> pd.DataFrame:
8584
"""
8685
super().filter()
8786

88-
pre_processed_df = pd.DataFrame(nk.ecg_process(
87+
pre_processed_df = pd.DataFrame(
88+
nk.ecg_process(
8989
self._data["ekg"].values, sampling_rate=self.original_frequency
90-
)[0])
90+
)[0]
91+
)
9192

9293
# Copy data and timestamps to a Data frame
9394
df = pd.DataFrame(

‎human_experiments/datasette_interface/datasette_interface/derived/helper/factory.py

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@@ -6,12 +6,7 @@
66
from datasette_interface.derived.helper.ekg import EKGHelper
77
from datasette_interface.derived.helper.modality import ModalityHelper
88

9-
MODALITIES = [
10-
"eeg",
11-
"fnirs",
12-
"gsr",
13-
"ekg"
14-
]
9+
MODALITIES = ["eeg", "fnirs", "gsr", "ekg"]
1510

1611

1712
def create_modality_helper(

‎human_experiments/datasette_interface/datasette_interface/derived/helper/fnirs.py

Lines changed: 5 additions & 2 deletions
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@@ -7,8 +7,11 @@
77
from sqlalchemy.orm import Session
88

99
from datasette_interface.common.constants import (
10-
FNIRS_BANDPASS_FILTER_METHOD, FNIRS_FREQUENCY,
11-
FNIRS_HIGH_FREQUENCY_THRESHOLD, FNIRS_LOW_FREQUENCY_THRESHOLD)
10+
FNIRS_BANDPASS_FILTER_METHOD,
11+
FNIRS_FREQUENCY,
12+
FNIRS_HIGH_FREQUENCY_THRESHOLD,
13+
FNIRS_LOW_FREQUENCY_THRESHOLD,
14+
)
1215
from datasette_interface.common.utils import convert_unix_timestamp_to_iso8601
1316
from datasette_interface.database.entity.derived.fnirs_sync import FNIRSSync
1417
from datasette_interface.database.entity.signal.fnirs import FNIRSRaw

‎human_experiments/datasette_interface/datasette_interface/derived/helper/gsr.py

Lines changed: 5 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,6 @@
88

99
from datasette_interface.common.constants import EEG_FREQUENCY
1010
from datasette_interface.common.utils import convert_unix_timestamp_to_iso8601
11-
from datasette_interface.database.entity.derived.eeg_sync import EEGSync
1211
from datasette_interface.database.entity.derived.gsr_sync import GSRSync
1312
from datasette_interface.database.entity.signal.eeg import EEGRaw
1413
from datasette_interface.derived.helper.modality import ModalityHelper
@@ -84,9 +83,11 @@ def filter(self) -> pd.DataFrame:
8483
"""
8584
super().filter()
8685

87-
pre_processed_df = pd.DataFrame(nk.eda_process(
88-
self._data["gsr"].values, sampling_rate=self.original_frequency
89-
)[0])
86+
pre_processed_df = pd.DataFrame(
87+
nk.eda_process(
88+
self._data["gsr"].values, sampling_rate=self.original_frequency
89+
)[0]
90+
)
9091

9192
# Copy data and timestamps to a Data frame
9293
df = pd.DataFrame(

‎human_experiments/datasette_interface/datasette_interface/derived/main_clock.py

Lines changed: 5 additions & 6 deletions
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@@ -4,12 +4,11 @@
44
from sqlalchemy import func, select
55
from sqlalchemy.orm import Session
66

7-
from datasette_interface.database.entity.task.minecraft_task import \
8-
MinecraftMission
9-
from datasette_interface.database.entity.task.ping_pong_cooperative_task_observation import \
10-
PingPongCooperativeTaskObservation
11-
from datasette_interface.database.entity.task.rest_state_task import \
12-
RestStateTask
7+
from datasette_interface.database.entity.task.minecraft_task import MinecraftMission
8+
from datasette_interface.database.entity.task.ping_pong_cooperative_task_observation import (
9+
PingPongCooperativeTaskObservation,
10+
)
11+
from datasette_interface.database.entity.task.rest_state_task import RestStateTask
1312

1413

1514
def get_main_clock_timestamps(

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