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Moved the bids-specific tools to a bids subdirectory and started writing tests
1 parent b4927fa commit 2af0d01

32 files changed

Lines changed: 2215 additions & 37 deletions

‎.github/workflows/ci.yaml‎

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- name: Lint with flake8
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run: |
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# stop the build if there are Python syntax errors or undefined names
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flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude=hedtools/hed/tools/*
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flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
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# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
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flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --exclude=hedtools/hed/tools/*
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# flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
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- name: Test with unittest
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run: |

‎hedtools/hed/tools/bids/__init__.py‎

Whitespace-only changes.

‎hedtools/hed/tools/bids/bids_dataset.py‎

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import os
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import json
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from hed.tools.data_util import get_new_dataframe
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from hed.schema.hed_schema_file import load_schema_version
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from hed.tools.bids.bids_event_files import BidsEventFiles
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class BidsDataset:
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"""Represents a bids dataset."""
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def __init__(self, root_path):
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self.root_path = os.path.abspath(root_path)
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self.dataset_description = {}
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self.participants = []
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self.hed_schema = None
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self._load_info()
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self.event_files = BidsEventFiles(root_path)
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def _load_info(self):
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part_path = os.path.join(self.root_path, "participants.tsv")
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self.participants = get_new_dataframe(part_path)
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desc_path = os.path.join(self.root_path, "dataset_description.json")
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with open(desc_path, "r") as fp:
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self.dataset_description = json.load(fp)
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hed = self.dataset_description.get("HEDVersion", None)
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if isinstance(hed, str):
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self.hed_schema = load_schema_version(xml_version_number=hed)
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if __name__ == '__main__':
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path = 'D:\\Research\\HED\\hed-examples\\datasets\\eeg_ds003654s'
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bids = BidsDataset(path)

hedtools/hed/tools/bids_dataset_summary.py renamed to hedtools/hed/tools/bids/bids_dataset_summary.py

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from hed.tools.bids_event_files import BidsEventFiles
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from hed.tools.bids.bids_event_files import BidsEventFiles
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class BidsDatasetSummary():
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hedtools/hed/tools/bids_event_file.py renamed to hedtools/hed/tools/bids/bids_event_file.py

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import os
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from bids_file import BidsFile
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from hed.models.events_input import EventsInput
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from hed.tools.bids.bids_file import BidsFile
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class BidsEventFile(BidsFile):
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name=os.path.abspath(self.file_path))
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def set_sidecars(self, sidecars):
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self.sidecars = sidecars
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if sidecars is None:
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self.sidecars = []
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elif not isinstance(sidecars, list):
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self.sidecars = [sidecars]
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else:
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self.sidecars = sidecars
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def __str__(self):
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my_str = super().__str__()

hedtools/hed/tools/bids_event_files.py renamed to hedtools/hed/tools/bids/bids_event_files.py

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import os
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from hed.errors.error_reporter import get_printable_issue_string
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from hed.schema.hed_schema_file import load_schema
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from hed.tools.bids_event_file import BidsEventFile
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from hed.tools.bids_sidecar_file import BidsSidecarFile
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from hed.tools.bids.bids_event_file import BidsEventFile
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from hed.tools.bids.bids_sidecar_file import BidsSidecarFile
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from hed.models.events_input import EventsInput
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from hed.tools.io_util import get_dir_dictionary, get_file_list, get_path_components
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from hed.validator.hed_validator import HedValidator

hedtools/hed/tools/bids_file.py renamed to hedtools/hed/tools/bids/bids_file.py

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import os
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from hed.tools.bids_util import parse_bids_filename
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from hed.tools.bids.bids_util import parse_bids_filename
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from hed.tools.io_util import get_file_list
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hedtools/hed/tools/bids_sidecar_file.py renamed to hedtools/hed/tools/bids/bids_sidecar_file.py

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import os
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from hed.models.sidecar import Sidecar
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from hed.tools.bids_file import BidsFile
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from hed.tools.bids.bids_file import BidsFile
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class BidsSidecarFile(BidsFile):

hedtools/hed/tools/bids_util.py renamed to hedtools/hed/tools/bids/bids_util.py

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hedtools/hed/tools/bids_validator.py renamed to hedtools/hed/tools/bids/bids_validator.py

File renamed without changes.

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