529 Make pynwb optional dependency

.github/workflows/cov_test_workflow.yml

@@ -34,6 +34,9 @@ jobs:
         poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Install optional dependency pynwb
+      run: |
+        poetry add pynwb
     - name: Test with pytest and get coverage
       run: |
         cd syncopy/tests

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]

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

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())

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:

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):
 

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)

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
 

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.