Merge pull request #1 from catalystneuro/run_tests

[Testing]: Running tests after rename

.github/workflows/testing.yml

@@ -1,7 +1,7 @@
 name: Minimal and Full Tests
 on:
   schedule:
-    - cron: "0 16 * * *"  # Daily at Noon EST
+    - cron: "0 16 * * *"  # Daily at noon EST
   pull_request:
 
 env:
@@ -74,6 +74,9 @@ jobs:
         uses: crazy-max/[email protected]
         with:
           args: install git-annex --ignore-checksums
+      - if: ${{ (steps.cache-ecephys-datasets.outputs.cache-hit == false || steps.cache-ophys-datasets.outputs.cache-hit == false || steps.cache-behavior-datasets.outputs.cache-hit == false) && matrix.os == 'windows-latest' }}
+        name: Get datalad - Windows
+        run: pip install datalad==0.16.3
 
       - if: steps.cache-ecephys-datasets.outputs.cache-hit == false && (matrix.os == 'ubuntu-latest' || matrix.os == 'windows-latest')
         name: "Force GIN: ecephys download"

README.md

@@ -5,13 +5,11 @@
 [![documentation](https://readthedocs.org/projects/nwb-conversion-tools/badge/?version=main)](https://nwb-conversion-tools.readthedocs.io/en/main/)
 [![License](https://img.shields.io/pypi/l/pynwb.svg)](https://github.com/catalystneuro/nwb-conversion-tools/license.txt)
 
-# NWB conversion tools
+# NeuroConv
 
-NWB Conversion Tools is a package for creating NWB files by converting and
+NeuroConv is a package for creating NWB files by converting and
 combining neural data in proprietary formats and adding essential metadata.
 
-**Under heavy construction. API is changing rapidly.**
-
 
 Features:
 * Command line interface
@@ -27,16 +25,16 @@ pip install nwb-conversion-tools
 For more flexibility we recommend installing the latest version directly from GitHub. The following commands create an environment with all the required dependencies and the latest updates:
 
 ```shell
-git clone https://github.com/catalystneuro/nwb-conversion-tools
-cd nwb-conversion-tools
-conda env create -f make_env.yml
-conda activate nwb_conversion_env
+git clone https://github.com/catalystneuro/neuroconv
+cd neuroconv
+conda env create -f make_environment.yml
+conda activate neuroconv_environment
 ```
 Note that this will install the package in [editable mode](https://pip.pypa.io/en/stable/cli/pip_install/#editable-installs).
 
 Finally, if you prefer to avoid `conda` altogether, the following commands provide a clean installation within the current environment:
 ```shell
-pip install git+https://github.com/catalystneuro/nwb-conversion-tools.git@master
+pip install git+https://github.com/catalystneuro/neuroconv.git@master
 ```
 
 ## Dependencies
@@ -142,8 +140,8 @@ The output of these tests is, by default, stored in a temporary directory that i
 For building the documentation locally, the following procedure can be followed. Create a clean environment and type
 the following commands in your terminal:
 ```shell
-git clone https://github.com/catalystneuro/nwb-conversion-tools
-cd nwb-conversion-tools
+git clone https://github.com/catalystneuro/neuroconv
+cd neuroconv
 pip install -e .[docs]
 ```
 These commands install both the latest version of the repo and the dependencies necessary to build the documentation.

docs/conversion_examples_gallery/imaging/hdf5imaging.rst

@@ -8,7 +8,7 @@ Convert HDF5 imaging data to NWB using :py:class:`~nwb_conversion_tools.datainte
     >>> from datetime import datetime
     >>> from dateutil import tz
     >>> from pathlib import Path
-    >>> from nwb_conversion_tools import Hdf5ImagingInterface
+    >>> from neuroconv import Hdf5ImagingInterface
     >>>
     >>> file_path = OPHYS_DATA_PATH / "imaging_datasets" / "hdf5" / "demoMovie.hdf5"
     >>> interface = Hdf5ImagingInterface(file_path=file_path, verbose=False)

docs/conversion_examples_gallery/imaging/scanbox.rst

@@ -8,7 +8,7 @@ Convert Scanbox imaging data to NWB using :py:class:`~nwb_conversion_tools.datai
     >>> from datetime import datetime
     >>> from dateutil import tz
     >>> from pathlib import Path
-    >>> from nwb_conversion_tools import SbxImagingInterface
+    >>> from neuroconv import SbxImagingInterface
     >>>
     >>> file_path = OPHYS_DATA_PATH / "imaging_datasets" / "Scanbox" / "sample.sbx"
     >>> interface = SbxImagingInterface(file_path=file_path, verbose=False)

docs/conversion_examples_gallery/imaging/scanimage.rst

@@ -8,7 +8,7 @@ Convert ScanImage imaging data to NWB using :py:class:`~nwb_conversion_tools.dat
     >>> from datetime import datetime
     >>> from dateutil import tz
     >>> from pathlib import Path
-    >>> from nwb_conversion_tools import ScanImageImagingInterface
+    >>> from neuroconv import ScanImageImagingInterface
     >>>
     >>> file_path = OPHYS_DATA_PATH / "imaging_datasets" / "Tif" / "sample_scanimage.tiff"
     >>> interface = ScanImageImagingInterface(file_path=file_path, verbose=False)

docs/conversion_examples_gallery/imaging/tiff.rst

@@ -8,7 +8,7 @@ Convert Tiff imaging data to NWB using :py:class:`~nwb_conversion_tools.datainte
     >>> from datetime import datetime
     >>> from dateutil import tz
     >>> from pathlib import Path
-    >>> from nwb_conversion_tools import TiffImagingInterface
+    >>> from neuroconv import TiffImagingInterface
     >>>
     >>> file_path = OPHYS_DATA_PATH / "imaging_datasets" / "Tif" / "demoMovie.tif"
     >>> interface = TiffImagingInterface(file_path=file_path, sampling_frequency=15.0, verbose=False)

docs/conversion_examples_gallery/recording/axona.rst

@@ -8,7 +8,7 @@ Convert axona data to NWB using :py:class:`~nwb_conversion_tools.datainterfaces.
     >>> from datetime import datetime
     >>> from dateutil import tz
     >>> from pathlib import Path
-    >>> from nwb_conversion_tools import AxonaRecordingExtractorInterface
+    >>> from neuroconv import AxonaRecordingExtractorInterface
     >>>
     >>> # For this interface we need to pass the location of the ``.bin`` file
     >>> file_path = f"{ECEPHY_DATA_PATH}/axona/axona_raw.bin"

docs/conversion_examples_gallery/recording/blackrock.rst

@@ -8,7 +8,7 @@ Convert Blackrock data to NWB using :py:class:`~nwb_conversion_tools.datainterfa
     >>> from datetime import datetime
     >>> from dateutil import tz
     >>> from pathlib import Path
-    >>> from nwb_conversion_tools import BlackrockRecordingExtractorInterface
+    >>> from neuroconv import BlackrockRecordingExtractorInterface
     >>>
     >>> # For this interface we need to pass the location of the ``.ns5`` file
     >>> file_path = f"{ECEPHY_DATA_PATH}/blackrock/FileSpec2.3001.ns5"

docs/conversion_examples_gallery/recording/intan.rst

@@ -7,7 +7,7 @@ Convert Intan data to NWB using :py:class:`~nwb_conversion_tools.datainterfaces.
     >>> from datetime import datetime
     >>> from dateutil import tz
     >>> from pathlib import Path
-    >>> from nwb_conversion_tools import IntanRecordingInterface
+    >>> from neuroconv import IntanRecordingInterface
     >>>
     >>> # For this data interface we need to pass the location of the `.rhd` file
     >>> suffix = "rhd" # This can also be rhs

docs/conversion_examples_gallery/recording/neuralynx.rst

@@ -8,7 +8,7 @@ Convert Neuralynx data to NWB using :py:class:`~.nwb_conversion_tools.datainterf
     >>> from datetime import datetime
     >>> from dateutil import tz
     >>> from pathlib import Path
-    >>> from nwb_conversion_tools import NeuralynxRecordingInterface
+    >>> from neuroconv import NeuralynxRecordingInterface
     >>>
     >>> # For this data interface we need to pass the folder where the data is
     >>> folder_path = f"{ECEPHY_DATA_PATH}/neuralynx/Cheetah_v5.7.4/original_data"

docs/conversion_examples_gallery/recording/neuroscope.rst

@@ -8,7 +8,7 @@ Convert Neuroscope data to NWB using :py:class:`~nwb_conversion_tools.datainterf
     >>> from datetime import datetime
     >>> from dateutil import tz
     >>> from pathlib import Path
-    >>> from nwb_conversion_tools import NeuroscopeRecordingInterface
+    >>> from neuroconv import NeuroscopeRecordingInterface
     >>>
     >>> # For Neuroscope we need to pass the location of the `.dat` file
     >>> file_path = f"{ECEPHY_DATA_PATH}/neuroscope/test1/test1.dat"

docs/conversion_examples_gallery/recording/openephys.rst

@@ -9,7 +9,7 @@ Convert OpenEphys data to NWB using :py:class:`~nwb_conversion_tools.datainterfa
     >>> from dateutil import tz
     >>> from pathlib import Path
     >>>
-    >>> from nwb_conversion_tools import OpenEphysRecordingExtractorInterface
+    >>> from neuroconv import OpenEphysRecordingExtractorInterface
     >>>
     >>> folder_path = f"{ECEPHY_DATA_PATH}/openephysbinary/v0.4.4.1_with_video_tracking"
     >>> # Change the folder_path to the appropiate location in your system

docs/conversion_examples_gallery/recording/spikegadgets.rst

@@ -8,7 +8,7 @@ Convert spikegadgets data to NWB using :py:class:`~nwb_conversion_tools.datainte
     from datetime import datetime
     from dateutil import tz
     from pathlib import Path
-    from nwb_conversion_tools import SpikeGadgetsRecordingInterface
+    from neuroconv import SpikeGadgetsRecordingInterface
 
     # For this interface we need to pass the specific path to the files.
     file_path = f"{ECEPHY_DATA_PATH}/spikegadgets/20210225_em8_minirec2_ac.rec"

docs/conversion_examples_gallery/recording/spikeglx.rst

@@ -8,7 +8,7 @@ Convert spikeglx data to NWB using :py:class:`~nwb_conversion_tools.datainterfac
     >>> from datetime import datetime
     >>> from dateutil import tz
     >>> from pathlib import Path
-    >>> from nwb_conversion_tools import SpikeGLXRecordingInterface
+    >>> from neuroconv import SpikeGLXRecordingInterface
     >>>
     >>> # For this interface we need to pass the location of the ``.bin`` file
     >>> file_path = f"{ECEPHY_DATA_PATH}/spikeglx/Noise4Sam_g0/Noise4Sam_g0_imec0/Noise4Sam_g0_t0.imec0.ap.bin"

docs/conversion_examples_gallery/sorting/cellexplorer.rst

@@ -8,7 +8,7 @@ Convert cell explorer sorting data to NWB using :py:class:`~nwb_conversion_tools
     >>> from datetime import datetime
     >>> from dateutil import tz
     >>> from pathlib import Path
-    >>> from nwb_conversion_tools import CellExplorerSortingInterface
+    >>> from neuroconv import CellExplorerSortingInterface
     >>>
     >>> # For this interface we need to pass the location of the ``cellinfo.mat`` file
     >>> file_path = f"{ECEPHY_DATA_PATH}/cellexplorer/dataset_1/20170311_684um_2088um_170311_134350.spikes.cellinfo.mat"

docs/conversion_examples_gallery/sorting/kilosort.rst

@@ -9,7 +9,7 @@ Convert Kilosort data to NWB using :py:class:`~nwb_conversion_tools.datainterfac
     >>> from dateutil import tz
     >>> from pathlib import Path
     >>>
-    >>> from nwb_conversion_tools import KilosortSortingInterface
+    >>> from neuroconv import KilosortSortingInterface
     >>>
     >>> folder_path = f"{ECEPHY_DATA_PATH}/phy/phy_example_0"
     >>> # Change the file_path to the location of the data in your system

docs/conversion_examples_gallery/sorting/neuroscope.rst

@@ -8,7 +8,7 @@ Convert Neuroscope sorting data to NWB using :py:class:`~nwb_conversion_tools.da
     >>> from datetime import datetime
     >>> from dateutil import tz
     >>> from pathlib import Path
-    >>> from nwb_conversion_tools import NeuroscopeSortingInterface
+    >>> from neuroconv import NeuroscopeSortingInterface
     >>>
     >>> folder_path = f"{ECEPHY_DATA_PATH}/neuroscope/dataset_1"
     >>> xml_file_path = folder_path + "/YutaMouse42-151117.xml"

docs/conversion_examples_gallery/sorting/phy.rst

@@ -9,7 +9,7 @@ Convert Phy data to NWB using :py:class:`~.nwb_conversion_tools.datainterfaces.e
     >>> from dateutil import tz
     >>> from pathlib import Path
     >>>
-    >>> from nwb_conversion_tools import PhySortingInterface
+    >>> from neuroconv import PhySortingInterface
     >>>
     >>> folder_path = f"{ECEPHY_DATA_PATH}/phy/phy_example_0"
     >>> # Change the file_path to the location of the data in your system

make_env.yml → make_environment.yml

@@ -1,4 +1,4 @@
-name: nwb_conversion_env
+name: neuroconv_environment
 channels:
 - defaults
 - anaconda

setup.py

@@ -26,14 +26,14 @@
     copy(src=gin_config_file_base, dst=gin_config_file_local)
 
 setup(
-    name="nwb-conversion-tools",
-    version="0.11.38",
+    name="neuroconv",
+    version="0.1.0",
     description="Convert data from proprietary formats to NWB format.",
     long_description=long_description,
     long_description_content_type="text/markdown",
-    author="Ben Dichter, Cody Baker, and Luiz Tauffer",
+    author="Cody Baker, Szonja Weigl, Heberto Mayorquin, Luiz Tauffer, and Ben Dichter.",
     author_email="[email protected]",
-    url="https://github.com/catalystneuro/nwb-conversion-tools",
+    url="https://github.com/catalystneuro/neuroconv",
     keywords="nwb",
     packages=find_packages(where="src"),
     package_dir={"": "src"},
@@ -43,7 +43,7 @@
     extras_require=extras_require,
     entry_points={
         "console_scripts": [
-            "nwbct-run-conversion = nwb_conversion_tools.tools.yaml_conversion_specification.yaml_conversion_specification:run_conversion_from_yaml_cli",
+            "neuroconv = neuroconv.tools.yaml_conversion_specification.yaml_conversion_specification:run_conversion_from_yaml_cli",
         ],
     },
 )

src/nwb_conversion_tools/datainterfaces/behavior/movie/moviedatainterface.py → src/neuroconv/datainterfaces/behavior/movie/moviedatainterface.py

@@ -10,12 +10,11 @@
 from pynwb import NWBFile
 from pynwb.image import ImageSeries
 from tqdm import tqdm
-from nwb_conversion_tools.utils import calculate_regular_series_rate
 
 from .movie_utils import VideoCaptureContext
 from ....basedatainterface import BaseDataInterface
 from ....tools.nwb_helpers import get_module
-from ....utils import get_schema_from_hdmf_class, get_base_schema
+from ....utils import get_schema_from_hdmf_class, get_base_schema, calculate_regular_series_rate
 
 
 def _check_duplicates(movies_metadata, file_paths):
@@ -37,7 +36,6 @@ def _check_duplicates(movies_metadata, file_paths):
     file_paths_list: List[List[str]]
         len(file_paths_list)==len(movies_metadata_unique)
     """
-
     keys_set = []
     movies_metadata_unique = []
     file_paths_list = []

src/nwb_conversion_tools/tools/roiextractors/roiextractors.py → src/neuroconv/tools/roiextractors/roiextractors.py

@@ -25,7 +25,7 @@
 from hdmf.backends.hdf5.h5_utils import H5DataIO
 
 from ..nwb_helpers import get_default_nwbfile_metadata, make_nwbfile_from_metadata, make_or_load_nwbfile
-from nwb_conversion_tools.utils import (
+from ...utils import (
     FilePathType,
     OptionalFilePathType,
     dict_deep_update,

src/nwb_conversion_tools/tools/yaml_conversion_specification/yaml_conversion_specification.py → src/neuroconv/tools/yaml_conversion_specification/yaml_conversion_specification.py

@@ -112,7 +112,7 @@ def run_conversion_from_yaml(
     global_data_interfaces = specification.get("data_interfaces")
     nwb_conversion_tools = import_module(
         name=".",
-        package="nwb_conversion_tools",  # relative import, but named and referenced as if it were absolute
+        package="neuroconv",  # relative import, but named and referenced as if it were absolute
     )
     file_counter = 0
     for experiment in specification["experiments"].values():

tests/test_internals/test_converter.py

@@ -5,14 +5,15 @@
 
 from pynwb import NWBFile
 
+from neuroconv import NWBConverter
+from neuroconv.basedatainterface import BaseDataInterface
+
 try:
     from ndx_events import LabeledEvents
 
     HAVE_NDX_EVENTS = True
 except ImportError:
     HAVE_NDX_EVENTS = False
-from nwb_conversion_tools import NWBConverter
-from nwb_conversion_tools.basedatainterface import BaseDataInterface
 
 
 def test_converter():

tests/test_internals/test_globbing_utils.py

@@ -1,6 +1,6 @@
 from hdmf.testing import TestCase
 
-from nwb_conversion_tools.utils import decompose_f_string, parse_f_string
+from neuroconv.utils import decompose_f_string, parse_f_string
 
 
 class TestGlobbingAssertions(TestCase):

tests/test_internals/test_hdmf.py

@@ -1,7 +1,7 @@
 import numpy as np
 from hdmf.testing import TestCase
 
-from nwb_conversion_tools.tools.hdmf import SliceableDataChunkIterator
+from neuroconv.tools.hdmf import SliceableDataChunkIterator
 
 
 class TestIteratorAssertions(TestCase):

tests/test_internals/test_interfaces.py

@@ -5,21 +5,23 @@
 from tempfile import mkdtemp
 from pathlib import Path
 from datetime import datetime
+
 import numpy as np
 import pytest
 import spikeextractors as se
 from spikeextractors.testing import check_recordings_equal, check_sortings_equal
 from hdmf.testing import TestCase
 from pynwb import NWBHDF5IO
-from nwb_conversion_tools import (
+
+from neuroconv import (
     NWBConverter,
     RecordingTutorialInterface,
     SortingTutorialInterface,
     SIPickleRecordingExtractorInterface,
     SIPickleSortingExtractorInterface,
     CEDRecordingInterface,
 )
-from nwb_conversion_tools.datainterfaces.ecephys.basesortingextractorinterface import BaseSortingExtractorInterface
+from neuroconv.datainterfaces.ecephys.basesortingextractorinterface import BaseSortingExtractorInterface
 
 
 class TestAssertions(TestCase):

tests/test_internals/test_json_schema_utils.py

@@ -4,7 +4,7 @@
 from typing import Union
 from copy import deepcopy
 
-from nwb_conversion_tools.utils import (
+from neuroconv.utils import (
     get_schema_from_method_signature,
     dict_deep_update,
     fill_defaults,

tests/test_internals/test_movie_interface.py

@@ -8,7 +8,7 @@
 import numpy as np
 from pynwb import NWBHDF5IO
 
-from nwb_conversion_tools import NWBConverter, MovieInterface
+from neuroconv import NWBConverter, MovieInterface
 
 try:
     import cv2

tests/test_internals/test_movie_utils.py

@@ -9,8 +9,8 @@
 from datetime import datetime
 from hdmf.backends.hdf5.h5_utils import H5DataIO
 
-from nwb_conversion_tools.datainterfaces.behavior.movie.movie_utils import VideoCaptureContext, MovieDataChunkIterator
-from nwb_conversion_tools.tools.nwb_helpers import make_nwbfile_from_metadata
+from neuroconv.datainterfaces.behavior.movie.movie_utils import VideoCaptureContext, MovieDataChunkIterator
+from neuroconv.tools.nwb_helpers import make_nwbfile_from_metadata
 
 try:
     import cv2