Make morphio optional (#829)

Fixes #823

Author: apdavison

.github/workflows/full-test.yml

@@ -39,7 +39,7 @@ jobs:
     - name: Install NEURON
       if: startsWith(matrix.os, 'ubuntu')
       run: |
-        python -m pip install "neuron>=9.0.0"
+        python -m pip install "neuron>=9.0.0" morphio
         python -m pip install "nrnutils>0.2.0"
     - name: Install NEST
       if: startsWith(matrix.os, 'ubuntu')
@@ -53,7 +53,7 @@ jobs:
     - name: Install Arbor
       if: startsWith(matrix.os, 'ubuntu')
       run: |
-        python -m pip install arbor==0.9.0 libNeuroML
+        python -m pip install arbor==0.9.0 libNeuroML morphio
     - name: Install PyNN itself
       run: |
         python -m pip install -e ".[test]"

pyNN/arbor/cells.py

@@ -6,7 +6,6 @@
 from ..morphology import Morphology, NeuroMLMorphology, MorphIOMorphology, IonChannelDistribution
 from ..models import BaseCellType
 from ..parameters import ParameterSpace
-from morphio import SectionType
 
 
 def convert_point(p3d: Point3DWithDiam) -> arbor.mpoint:

pyNN/morphology.py

@@ -14,8 +14,6 @@
     have_neuroml = True
 except ImportError:
     have_neuroml = False
-import morphio
-from morphio import SectionType
 
 
 def _download_file(url):
@@ -68,6 +66,8 @@ class NeuroMLMorphology(Morphology):
     """
 
     def __init__(self, morphology):
+        from morphio import SectionType
+
         if not have_neuroml:
             raise ImportError("Please install libNeuroML to use the NeuroMLMorphology class")
         super(NeuroMLMorphology, self).__init__()
@@ -158,6 +158,9 @@ class BrianMorphology(Morphology):
 class MorphIOMorphology(Morphology):
 
     def __init__(self, morphology_file):
+        import morphio
+        from morphio import SectionType
+
         super().__init__()
         self.morphology_file = morphology_file
         self._morphology = morphio.Morphology(morphology_file)

pyNN/neuron/cells.py

@@ -14,7 +14,6 @@
 import numpy as np
 from neuron import h, nrn, hclass
 import numpy.random
-from morphio import SectionType
 
 from .. import errors
 from ..models import BaseCellType

pyNN/neuron/morphology.py

@@ -4,7 +4,6 @@
 
 """
 
-from morphio import SectionType
 import numpy as np
 from .. import morphology as base_morphology
 
@@ -38,6 +37,8 @@ class dendrites(base_morphology.dendrites):
     def __call__(self, morphology, filter_by_section=False):
         """Return an index (integer NumPy array) that can be used
         to retrieve the sections corresponding to the filter. """
+        from morphio import SectionType
+
         section_index = np.array([], dtype=int)
         for label in (SectionType.apical_dendrite, SectionType.basal_dendrite):
             if label in morphology.section_groups:
@@ -53,6 +54,8 @@ def __call__(self, morphology, filter_by_section=False):
 class apical_dendrites(base_morphology.apical_dendrites):
 
     def __call__(self, morphology, filter_by_section=False):
+        from morphio import SectionType
+
         if SectionType.apical_dendrite in morphology.section_groups:
             section_index = morphology.section_groups[SectionType.apical_dendrite]
             if filter_by_section:
@@ -66,6 +69,8 @@ def __call__(self, morphology, filter_by_section=False):
 class basal_dendrites(base_morphology.basal_dendrites):
 
     def __call__(self, morphology, filter_by_section=False):
+        from morphio import SectionType
+
         if SectionType.basal_dendrite in morphology.section_groups:
             section_index = morphology.section_groups[SectionType.basal_dendrite]
             if filter_by_section:
@@ -79,6 +84,8 @@ def __call__(self, morphology, filter_by_section=False):
 class axon(base_morphology.axon):
 
     def __call__(self, morphology, filter_by_section=False):
+        from morphio import SectionType
+
         if SectionType.axon in morphology.section_groups:
             section_index = morphology.section_groups[SectionType.axon]
             if filter_by_section:
@@ -92,6 +99,8 @@ def __call__(self, morphology, filter_by_section=False):
 class soma(base_morphology.axon):
 
     def __call__(self, morphology, filter_by_section=False):
+        from morphio import SectionType
+
         if SectionType.soma in morphology.section_groups:
             section_index = morphology.section_groups[SectionType.soma]
             if filter_by_section:

pyproject.toml

@@ -29,8 +29,7 @@ classifiers = [
 ]
 dependencies = [
   "lazyarray>=0.5.2",
-  "neo>=0.13.4",
-  "morphio"
+  "neo>=0.13.4"
 ]
 
 [project.optional-dependencies]
@@ -40,9 +39,10 @@ examples = ["matplotlib", "scipy"]
 plotting = ["matplotlib", "scipy"]
 MPI = ["mpi4py"]
 sonata = ["h5py"]
+morphologies = ["morphio"]
 neuron = ["neuron", "nrnutils"]
 brian2 = ["brian2"]
-arbor = ["arbor==0.9.0", "libNeuroML"]
+arbor = ["arbor==0.9.0", "libNeuroML", "morphio"]
 spiNNaker = ["spyNNaker"]
 neuroml = ["libNeuroML"]
 

test/system/scenarios/test_scenario5.py

@@ -1,6 +1,12 @@
 import sys
 import numpy as np
 
+try:
+    import morphio
+    have_morphio = True
+except ImportError:
+    have_morphio = False
+
 try:
     from neuroml import Morphology, Segment, Point3DWithDiam as P
     have_neuroml = True
@@ -21,6 +27,8 @@ def test_scenario5(sim):
     """
     Array of multi-compartment neurons, each injected with a different current.
     """
+    if not have_morphio:
+        pytest.skip("morphio not available")
     if not have_neuroml:
         pytest.skip("libNeuroML not available")
 

test/system/test_neuron.py

@@ -18,6 +18,11 @@
     have_neuron = False
 import pytest
 
+try:
+    import morphio
+    have_morphio = True
+except ImportError:
+    have_morphio = False
 
 try:
     from neuroml import Morphology, Segment, Point3DWithDiam as P
@@ -242,8 +247,8 @@ def test_artificial_cells():
 
 
 def test_2_compartment():
-    if not (have_neuron and have_neuroml):
-        pytest.skip("Need neuron and neuroml")
+    if not (have_neuron and have_neuroml and have_morphio):
+        pytest.skip("Need neuron, neuroml, and morphio")
     sim = pyNN.neuron
 
     sim.setup(timestep=0.025)

test/unittests/test_morphology.py

@@ -17,7 +17,12 @@
     have_neuroml = True
 except ImportError:
     have_neuroml = False
-from pyNN.morphology import load_morphology, NeuroMLMorphology, SectionType, any as morph_any
+try:
+    from pyNN.morphology import load_morphology, NeuroMLMorphology, any as morph_any
+    from morphio import SectionType
+    have_morphio = True
+except ImportError:
+    have_morphio = False
 try:
     from pyNN.neuron.morphology import (dendrites, apical_dendrites,
                                  basal_dendrites, random_section, with_label,
@@ -53,8 +58,10 @@
 def setUpModule():
     global neuroml_morph, array_morph
 
+    if not have_morphio:
+        pytest.skip("morphio not installed")
     if not have_neuroml:
-            pytest.skip("libNeuroML not installed")
+        pytest.skip("libNeuroML not installed")
 
     test_file = "morph_test.swc"
     with open(test_file, "w") as fp: