e2eTests

.github/workflows/e2eTest.yml

@@ -0,0 +1,36 @@
+name: Project Tests
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      matrix:
+        python-version: ["3.6"]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniconda-version: "latest"
+          activate-environment: rec_to_binaries
+          environment-file: environment.yml
+      - name: Install rec-to-binaries
+        shell: bash -l {0}
+        run: |
+          pip install rec_to_binaries
+      - name: Make dependencies editable
+        shell: bash -l {0}
+        run: |
+          pip install -e .
+      - name: Run e2eTests
+        shell: bash -l {0}
+        run: |
+          python -m pytest rec_to_binaries/test/e2etests/

environment.yml

@@ -5,7 +5,7 @@ dependencies:
 - jupyter
 - jupyterlab
 - matplotlib
-- pandas
+- "pandas = 0.24.0"
 - numpy
 - scipy
 - "python >= 3.6"

my_file.txt

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+abc

rec_to_binaries/test/e2etests/__init__.py

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+# __init__.py

rec_to_binaries/test/e2etests/conftest.py

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+import pytest
+import os
+
+CURRENT_DIRECTORY = os.getcwd()
+
+def _clear_file_content(file_path):
+    if file_path is None or file_path.strip() == '':
+        raise FileNotFoundError
+    with open(file_path, 'r+') as file:
+        file.truncate(0)
+
+@pytest.fixture
+def e2etests_directory_path():
+    return f'{CURRENT_DIRECTORY}/rec_to_binaries/test/e2etests/'
+
+@pytest.fixture
+def current_directory():
+    return CURRENT_DIRECTORY
+
+@pytest.fixture
+def clear_file_content():
+    return _clear_file_content

rec_to_binaries/test/e2etests/test_adjust_timestamps.py

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+import pytest
+import numpy as np
+from rec_to_binaries.adjust_timestamps import (
+    fix_timestamp_lag,
+)
+
+@pytest.mark.skip(reason='not implemented')
+def test_fix_timestamp_lag_check_if_data_is_written_no_systime(e2etests_directory_path, clear_file_content):
+#     # arrange
+#     file_path = f'{e2etests_directory_path}/test_data/fix_timestamp_lag_check_if_data_is_written_no_systime.txt'
+#     clear_file_content(file_path)
+#     fake_data = np.array([
+#         ('just', 1),
+#         ('another', 2),
+#         ('part', 3)], dtype=[('one', 'b1'), ('two', '<b1')]
+#     )
+#     with open(file_path, "wb") as file:
+#         file.write(bytes(b'<Start settings>'))
+#         file.write(bytes(b'\n'))
+#         file.write(b'data: ')
+#         file.write(fake_data)
+#         file.write(bytes(b'\n'))
+#         file.write(bytes(b'<End settings>'))
+
+#     fix_timestamp_lag(file_path)
+#     # act
+
+#     # assert
+    pass

rec_to_binaries/test/e2etests/test_binary_utils.py

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+import pytest
+from rec_to_binaries.binary_utils import (
+    TrodesBinaryFormatError,
+    TrodesBinaryReader,
+    TrodesLFPBinaryLoader,
+    TrodesTimestampBinaryLoader,
+    TrodesSpikeBinaryLoader,
+    TrodesPosBinaryLoader,
+    TrodesDIOBinaryLoader,
+)
+
+def test_TrodesBinaryReader_first_line_not_Start_settings_error(e2etests_directory_path):
+    file_path = f'{e2etests_directory_path}/test_data/TrodesBinaryReader_test_first_line_exception.txt'
+
+    with pytest.raises(TrodesBinaryFormatError) as ex:
+        trodes_binary_reader = TrodesBinaryReader(file_path)
+
+
+def test_TrodesBinaryReader_more_than_1000_length_error(e2etests_directory_path):
+    file_path = f'{e2etests_directory_path}/test_data/TrodesBinaryReader_test_more_than_1000_line_exception.txt'
+
+    with pytest.raises(TrodesBinaryFormatError):
+        trodes_binary_reader = TrodesBinaryReader(file_path)
+
+def test_TrodesBinaryReader_check_if_valid_file_is_read(e2etests_directory_path):
+    file_path = f'{e2etests_directory_path}/test_data/TrodesBinaryReader_check_if_valid_file_is_read.txt'
+    trodes_binary_reader = TrodesBinaryReader(file_path)
+
+    assert trodes_binary_reader.data_start_byte == 43
+    assert trodes_binary_reader.header_params == {'a': '1', 'data': '2'}
+
+def test_TrodesLFPBinaryLoader_check_if_file_can_be_read(e2etests_directory_path):
+    file_path = f'{e2etests_directory_path}/test_data/TrodesLFPBinaryLoader_test_file_read.txt'
+    trodes_LFP_binary_loader = TrodesLFPBinaryLoader(file_path)
+
+    assert trodes_LFP_binary_loader.header_params['Original_file'] == 'test_Original_file'
+    assert trodes_LFP_binary_loader.header_params['Trode_ID'] == 'test_Trode_ID'
+    assert trodes_LFP_binary_loader.header_params['Trode_channel'] == 'test_Trode_channel'
+    assert trodes_LFP_binary_loader.header_params['Clock rate'] == 'test_Clock rate'
+    assert trodes_LFP_binary_loader.header_params['Voltage_scaling'] == 'test_Voltage_scaling'
+    assert trodes_LFP_binary_loader.header_params['Decimation'] == 'test_Decimation'
+    assert trodes_LFP_binary_loader.header_params['First_timestamp'] == 'test_First_timestamp'
+    assert trodes_LFP_binary_loader.header_params['Reference'] == 'test_Reference'
+    assert trodes_LFP_binary_loader.header_params['Low_pass_filter'] == 'test_Low_pass_filter'
+    assert trodes_LFP_binary_loader.header_params['Fields'] == 'test_Fields'
+
+def test_TrodesTimestampBinaryLoader_check_if_file_can_be_read(e2etests_directory_path):
+    file_path = f'{e2etests_directory_path}/test_data/TrodesTimestampBinaryLoader_test_file_read.txt'
+    trodes_timestamp_binary_loader = TrodesTimestampBinaryLoader(file_path)
+
+    assert trodes_timestamp_binary_loader.header_params['Byte_order'] == 'test_Byte_order'
+    assert trodes_timestamp_binary_loader.header_params['Original_file'] == 'test_Original_file'
+    assert trodes_timestamp_binary_loader.header_params['Clock rate'] == 'test_Clock rate'
+    assert trodes_timestamp_binary_loader.header_params['Decimation'] == 'test_Decimation'
+    assert trodes_timestamp_binary_loader.header_params['Time_offset'] == 'test_Time_offset'
+    assert trodes_timestamp_binary_loader.header_params['Fields'] == 'test_Fields'
+
+def test_TrodesSpikeBinaryLoader_check_if_data_file_is_read(e2etests_directory_path):
+    file_path = f'{e2etests_directory_path}/test_data/TrodesSpikeBinaryLoader_test_file_read.txt'
+    trodes_spike_binary_loader = TrodesSpikeBinaryLoader(file_path)
+
+
+    assert trodes_spike_binary_loader.header_params['Original_file'] == 'test_Original_file'
+    assert trodes_spike_binary_loader.header_params['nTrode_ID'] == '1'
+    assert trodes_spike_binary_loader.num_channels == 10
+    assert trodes_spike_binary_loader.header_params['Clock rate'] == '3'
+    assert trodes_spike_binary_loader.header_params['Voltage_scaling'] == 'v'
+    assert trodes_spike_binary_loader.header_params['Time_offset'] == '4'
+    assert trodes_spike_binary_loader.header_params['Threshold'] == '5'
+    assert trodes_spike_binary_loader.header_params['Spike_invert'] == 't'
+    assert trodes_spike_binary_loader.header_params['Reference'] == '6'
+    assert trodes_spike_binary_loader.header_params['ReferenceNTrode'] == '7'
+    assert trodes_spike_binary_loader.header_params['ReferenceChannel'] == '8'
+    assert trodes_spike_binary_loader.header_params['Filter'] == 't'
+    assert trodes_spike_binary_loader.header_params['lowPassFilter'] == 'y'
+    assert trodes_spike_binary_loader.header_params['highPassFilter'] == 'n'
+    assert trodes_spike_binary_loader.header_params['Fields'] == 'test_field'
+    assert trodes_spike_binary_loader.spike_rec_size == 804
+
+@pytest.mark.skip(reason="I have to figure out why pos_list stays empty")
+def test_TrodesPosBinaryLoader_check_if_data_file_is_read(e2etests_directory_path):
+    file_path = f'{e2etests_directory_path}/test_data/TrodesPosBinaryLoader_check_if_data_file_is_read.txt'
+    trodes_pos_binary_loader = TrodesPosBinaryLoader(file_path)
+
+    breakpoint()
+
+    assert trodes_pos_binary_loader.header_params['threshold'] == 'test_threshold'
+    assert trodes_pos_binary_loader.header_params['dark'] == 'test_dark'
+    assert trodes_pos_binary_loader.header_params['clockrate'] == 'test_clockrate'
+    assert trodes_pos_binary_loader.header_params['field_str'] == 'test_Fields'
+    assert trodes_pos_binary_loader.rec_size == 12
+    assert trodes_pos_binary_loader.unpack_format == 'IHHHH'
+
+@pytest.mark.skip(reason="I have to figure out why pos_list stays empty")
+def test_TrodesDIOBinaryLoader_check_if_data_file_is_read(e2etests_directory_path):
+    file_path = f'{e2etests_directory_path}/test_data/TrodesPosBinaryLoader_check_if_data_file_is_read.txt'
+    trodes_pos_binary_loader = TrodesDIOBinaryLoader(file_path)
+
+    assert True

rec_to_binaries/test/e2etests/test_core.py

@@ -0,0 +1,24 @@
+import pytest
+from rec_to_binaries.core import (
+    extract_trodes_rec_file,
+    convert_binaries_to_hdf5,
+)
+
+@pytest.mark.skip(reason='Got to figure out the many cases')
+def extract_trodes_rec_file():
+    pass
+
+@pytest.mark.skip(reason='Got to figure out - type object \'object\' has no attribute \'dtype')
+def test_convert_binaries_to_hdf5_rec_file_write_to_file(e2etests_directory_path):
+    data_dir = e2etests_directory_path
+    animal = 'test_animal'
+    convert_binaries_to_hdf5(data_dir,
+                             animal,
+                             out_dir=None,
+                             dates=None,
+                             parallel_instances=1,
+                             convert_dio=False,
+                             convert_lfp=False,
+                             convert_pos=False,
+                             convert_spike=False
+    )

rec_to_binaries/test/e2etests/test_create_system_time.py

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+import pytest
+
+@pytest.mark.skip(reason='not implemented')
+def test_infer_systime():
+    pass
+
+@pytest.mark.skip(reason='not implemented')
+def test_create_systime():
+    pass

rec_to_binaries/test/e2etests/test_data/TrodesBinaryReader_check_if_valid_file_is_read.txt

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+<Start settings>
+a:1
+data:2
+<End settings>

rec_to_binaries/test/e2etests/test_data/TrodesBinaryReader_test_first_line_exception.txt

@@ -0,0 +1 @@
+<test>