Open
Description
Describe the bug
The sources contain a bunch of undefined names that could lead to errors.
To Reproduce
Run flake8 with the following options:
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
Expected behavior
We shouldn't have undefined names in the sources.
Observed behavior
./neuroml/loaders.py:117:19: F821 undefined name 'MorphologyImportError'
raise MorphologyImportError(s)
^
./neuroml/arraymorph_load_time_benchmark.py:3:9: F821 undefined name 'self'
self.num_segments = num_segments
^
./neuroml/arraymorph_load_time_benchmark.py:9:13: F821 undefined name 'np'
x = np.linspace(0,10,num_vertices)
^
./neuroml/arraymorph_load_time_benchmark.py:10:13: F821 undefined name 'np'
y = np.zeros(num_vertices)
^
./neuroml/arraymorph_load_time_benchmark.py:11:13: F821 undefined name 'np'
z = np.zeros(num_vertices)
^
./neuroml/arraymorph_load_time_benchmark.py:12:13: F821 undefined name 'np'
d = np.linspace(1,0.01,num_vertices)
^
./neuroml/arraymorph_load_time_benchmark.py:14:20: F821 undefined name 'np'
vertices = np.array([x,y,z,d]).T
^
./neuroml/arraymorph_load_time_benchmark.py:18:26: F821 undefined name 'am'
big_arraymorph = am.ArrayMorphology(vertices = vertices,
^
./neuroml/arraymorph_load_time_benchmark.py:21:31: F821 undefined name 'np'
transposed_vertices = np.array([transposed_x,y,z,d]).T
^
./neuroml/arraymorph_load_time_benchmark.py:23:33: F821 undefined name 'am'
transposed_arraymorph = am.ArrayMorphology(vertices = transposed_vertices,
^
./neuroml/arraymorph_load_time_benchmark.py:27:27: F821 undefined name 'np'
fatter_vertices = np.array([x,y,z,bigger_d]).T
^
./neuroml/arraymorph_load_time_benchmark.py:29:29: F821 undefined name 'am'
fatter_arraymorph = am.ArrayMorphology(vertices = fatter_vertices,
^
./neuroml/arraymorph_load_time_benchmark.py:32:24: F821 undefined name 'neuroml'
neuroml_cell = neuroml.Cell(id='cell_4')
^
./neuroml/arraymorph_load_time_benchmark.py:33:30: F821 undefined name 'neuroml'
neuroml_morphology = neuroml.Morphology(id = 'my_morph')
^
./neuroml/arraymorph_load_time_benchmark.py:40:23: F821 undefined name 'neuroml'
self.cell_1 = neuroml.Cell(id='cell_1')
^
./neuroml/arraymorph_load_time_benchmark.py:41:23: F821 undefined name 'neuroml'
self.cell_2 = neuroml.Cell(id='cell_2')
^
./neuroml/arraymorph_load_time_benchmark.py:42:23: F821 undefined name 'neuroml'
self.cell_3 = neuroml.Cell(id='cell_3')
^
./neuroml/arraymorph_load_time_benchmark.py:48:25: F821 undefined name 'neuroml'
self.test_doc = neuroml.NeuroMLDocument(id='TestDocument')
^
./neuroml/benchmarks/arraymorph_benchmarks.py:21:15: E999 SyntaxError: invalid syntax
print '%r (%r, %r) %2.2f sec' % \
(method.__name__, args, kw, te-ts)
^
./neuroml/nml/nml.py:38:20: F821 undefined name 'basestring'
BaseStrType_ = basestring
^
./neuroml/nml/nml.py:418:71: F821 undefined name 'unicode'
elif sys.version_info.major == 2 and isinstance(instring, unicode):
^
1 E999 SyntaxError: invalid syntax
20 F821 undefined name 'self'
System information:
- OS: [e.g. iOS]: Fedora Linux 34
- Python version (
python --version): python 3.9 - Version of tools in use (Output of
python -c 'import neuroml; print(neuroml.__version__)'): From development at this commit 6439df7
Additional context
Most of these are easy to fix, so I'll open a PR. The one symbol I haven't been able to find the definition of is MorphologyImportError. Where/what library defines this?