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python-versions = ">=3.8" files = [ @@ -2483,6 +2403,7 @@ files = [ name = "zipp" version = "3.15.0" description = "Backport of pathlib-compatible object wrapper for zip files" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2497,4 +2418,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more [metadata] lock-version = "2.0" python-versions = "^3.8" -content-hash = "fdc77781c83aec6bacfb1ab654852919bb8cb1d22253e224e100aa4e3ce6078d" +content-hash = "b295149a384026cd346e9c7f201f442fd2a4438d51b9af61078f4427e89b520a" diff --git a/pyproject.toml b/pyproject.toml index d3888086..5c7d9b0d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,7 +32,6 @@ tqdm = ">=4.31" natsort = "^8.1.0" psutil = ">=5.9" fooof = ">=1.0" -pynwb = "^2.3.2" bokeh = "^3.1.1" [tool.poetry.group.dev.dependencies] diff --git a/syncopy.yml b/syncopy.yml index 29d4ff6e..ec3497be 100644 --- a/syncopy.yml +++ b/syncopy.yml @@ -17,7 +17,6 @@ dependencies: - psutil - tqdm >= 4.31 - fooof >= 1.0 - - pynwb >= 2.3 - bokeh >= 3.1.1 # Optional packages required for running the test-suite and building the HTML docs diff --git a/syncopy/__init__.py b/syncopy/__init__.py index 62fb8934..d27736d8 100644 --- a/syncopy/__init__.py +++ b/syncopy/__init__.py @@ -88,6 +88,11 @@ def startup_print_once(message, force=False): except ImportError: __plt__ = False +try: + import pynwb + __pynwb__ = True +except ImportError: + __pynwb__ = False # Set package-wide temp directory csHome = "/cs/home/{}".format(getpass.getuser()) diff --git a/syncopy/datatype/continuous_data.py b/syncopy/datatype/continuous_data.py index 76078027..1af901c1 100644 --- a/syncopy/datatype/continuous_data.py +++ b/syncopy/datatype/continuous_data.py @@ -19,12 +19,17 @@ from .methods.definetrial import definetrial from .base_data import BaseData from syncopy.shared.parsers import scalar_parser, array_parser -from syncopy.shared.errors import SPYValueError +from syncopy.shared.errors import SPYValueError, SPYError from syncopy.shared.tools import best_match from syncopy.plotting import sp_plotting, mp_plotting from syncopy.io.nwb import _analog_timelocked_to_nwbfile from .util import TimeIndexer -from pynwb import NWBHDF5IO + + +from syncopy import __pynwb__ + +if __pynwb__: # pragma: no cover + from pynwb import NWBHDF5IO @@ -480,7 +485,12 @@ def save_nwb(self, outpath, nwbfile=None, with_trialdefinition=True, is_raw=True before calling this function if you want to export a subset only. The Syncopy NWB reader only supports the NWB raw data format. + + This function requires the optional 'pynwb' dependency to be installed. """ + if not __pynwb__: + raise SPYError("NWB support is not available. Please install the 'pynwb' package.") + nwbfile = _analog_timelocked_to_nwbfile(self, nwbfile=nwbfile, with_trialdefinition=with_trialdefinition, is_raw=is_raw) # Write the file to disk. with NWBHDF5IO(outpath, "w") as io: @@ -900,7 +910,12 @@ def save_nwb(self, outpath, with_trialdefinition=True, is_raw=True): open it using pynwb before using it with the target software. Selections are ignored, the full data is exported. Create a new Syncopy data object before calling this function if you want to export a subset only. + + This function requires the optional 'pynwb' dependency to be installed. """ + if not __pynwb__: + raise SPYError("NWB support is not available. Please install the 'pynwb' package.") + nwbfile = _analog_timelocked_to_nwbfile(self, nwbfile=None, with_trialdefinition=with_trialdefinition, is_raw=is_raw) # Write the file to disk. with NWBHDF5IO(outpath, "w") as io: diff --git a/syncopy/datatype/discrete_data.py b/syncopy/datatype/discrete_data.py index 4a445fc7..619db4c9 100644 --- a/syncopy/datatype/discrete_data.py +++ b/syncopy/datatype/discrete_data.py @@ -18,7 +18,11 @@ from syncopy.plotting import spike_plotting from syncopy.io.nwb import _spikedata_to_nwbfile -from pynwb import NWBHDF5IO + +from syncopy import __pynwb__ + +if __pynwb__: # pragma: no cover + from pynwb import NWBHDF5IO __all__ = ["SpikeData", "EventData"] @@ -631,11 +635,14 @@ def save_nwb(self, outpath, with_trialdefinition=True): Selections are ignored, the full data is exported. Create a new Syncopy data object before calling this function if you want to export a subset only. """ + if not __pynwb__: + raise SPYError("NWB support is not available. Please install the 'pynwb' package.") + nwbfile = _spikedata_to_nwbfile(self, nwbfile=None, with_trialdefinition=with_trialdefinition) # Write the file to disk. with NWBHDF5IO(outpath, "w") as io: io.write(nwbfile) - + # implement plotting def singlepanelplot(self, **show_kwargs): diff --git a/syncopy/io/load_nwb.py b/syncopy/io/load_nwb.py index 7447010c..eedf2e6c 100644 --- a/syncopy/io/load_nwb.py +++ b/syncopy/io/load_nwb.py @@ -10,17 +10,20 @@ import subprocess import numpy as np from tqdm import tqdm -import pynwb # Local imports from syncopy.datatype.continuous_data import AnalogData from syncopy.datatype.discrete_data import EventData, SpikeData from syncopy.shared.errors import SPYError, SPYTypeError, SPYValueError, SPYWarning, SPYInfo from syncopy.shared.parsers import io_parser, scalar_parser, filename_parser +from syncopy import __pynwb__ __all__ = ["load_nwb"] +if __pynwb__: + import pynwb + def _is_valid_nwb_file(filename): try: this_python = os.path.join(os.path.dirname(sys.executable), 'python') @@ -58,6 +61,8 @@ def load_nwb(filename, memuse=3000, container=None, validate=False, default_spik objects are returned as a dictionary whose keys are the base-names (sans path) of the corresponding files. """ + if not __pynwb__: + raise SPYError("NWB support is not available. Please install the 'pynwb' package.") # Check if file exists nwbPath, nwbBaseName = io_parser(filename, varname="filename", isfile=True, exists=True) diff --git a/syncopy/io/nwb.py b/syncopy/io/nwb.py index 07950c94..5f20d925 100644 --- a/syncopy/io/nwb.py +++ b/syncopy/io/nwb.py @@ -20,9 +20,15 @@ import pytz import os import shutil -from pynwb import NWBFile -from pynwb.ecephys import LFP, ElectricalSeries -from pynwb.core import DynamicTableRegion + +from syncopy import __pynwb__ + + +if __pynwb__: + import pynwb + from pynwb import NWBFile + from pynwb.ecephys import LFP, ElectricalSeries + from pynwb.core import DynamicTableRegion # Local imports diff --git a/syncopy/tests/test_spyio.py b/syncopy/tests/test_spyio.py index 92a54218..55622843 100644 --- a/syncopy/tests/test_spyio.py +++ b/syncopy/tests/test_spyio.py @@ -31,6 +31,10 @@ from syncopy.synthdata.analog import white_noise from syncopy.synthdata.spikes import poisson_noise from syncopy.io.load_nwb import _is_valid_nwb_file +from syncopy import __pynwb__ + +skip_no_pynwb = pytest.mark.skipif(not __pynwb__, reason=f"This test requires the 'pynwb' package to be installed.") + # Decorator to detect if test data dir is available on_esi = os.path.isdir('/cs/slurm/syncopy') @@ -587,6 +591,7 @@ class TestNWBImporter: nwb_filename = nwbfile break + @skip_no_pynwb def test_load_nwb_analog(self): """Test loading of an NWB file containing acquistion data into a Syncopy AnalogData object.""" @@ -632,6 +637,7 @@ class TestNWBExporter(): do_validate_NWB = True + @skip_no_pynwb def test_save_nwb_analog_no_trialdef(self): """Test saving to NWB file and re-reading data for AnalogData, without trial definition.""" @@ -658,6 +664,7 @@ def test_save_nwb_analog_no_trialdef(self): assert all(adata_reread.channel == adata.channel) # Check that channel names are saved and re-read correctly. assert np.allclose(adata.data, adata_reread.data) + @skip_no_pynwb def test_save_nwb_analog_with_trialdef(self): """Test saving to NWB file and re-reading data for AnalogData with a trial definition.""" @@ -686,6 +693,7 @@ def test_save_nwb_analog_with_trialdef(self): assert all(adata_reread.channel == adata.channel) # Check that channel names are saved and re-read correctly. assert np.allclose(adata.data, adata_reread.data) + @skip_no_pynwb def test_save_nwb_analog_with_trialdef_as_LFP(self): """Test saving to NWB file and re-reading data for AnalogData with a trial definition. Saves as LFP, as opposed to raw data.""" @@ -714,6 +722,7 @@ def test_save_nwb_analog_with_trialdef_as_LFP(self): assert all(adata_reread.channel == adata.channel) # Check that channel names are saved and re-read correctly. assert np.allclose(adata.data, adata_reread.data) + @skip_no_pynwb def test_save_nwb_analog_2(self): """Test saving to NWB file and re-reading data for 2x AnalogData.""" @@ -746,7 +755,7 @@ def test_save_nwb_analog_2(self): assert np.allclose(adata.data, adata_reread.data) assert np.allclose(adata2.data, adata2_reread.data) - + @skip_no_pynwb def test_save_nwb_timelock_with_trialdef(self): """Test saving to NWB file and re-reading data for TimeLockData with a trial definition. Currently, when the file is bering re-read, it results in an AnalogData object, not a TimeLockData object. @@ -784,7 +793,7 @@ def test_save_nwb_timelock_with_trialdef(self): assert all(adata_reread.channel == adata.channel) # Check that channel names are saved and re-read correctly. assert np.allclose(adata.data, adata_reread.data) - + @skip_no_pynwb def test_save_nwb_spikedata(self): """Test exporting SpikeData to NWB format. @@ -826,6 +835,7 @@ def test_save_nwb_spikedata(self): assert np.allclose(spdata.data[:, 0], spdata_reread.data[:, 0]) @skip_no_pynapple + @skip_no_pynwb def test_load_exported_nwb_spikes_pynapple(self, plot_spikes=True): """Test loading exported SpikeData in pynapple.