make tests compatible with having correct soma (#122)

* many "contour" soma had only a single point
BlueBrain · Dec 15, 2023 · a30b235 · a30b235
1 parent c3b6621
commit a30b235
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Showing 14 changed files with 287 additions and 223 deletions.
diff --git a/tests/data/apical_test.h5 b/tests/data/apical_test.h5
diff --git a/tests/data/input-convert/simple2.asc b/tests/data/input-convert/simple2.asc
@@ -1,7 +1,10 @@
 ("CellBody"
  (Color Red)
  (CellBody)
- (0 0 0 2)
+ (0.1  0    0 2)
+ (0    0.1  0 2)
+ (-0.1 0    0 2)
+ (0    -0.1 0 2)
  )
 
  ((Dendrite)

diff --git a/tests/data/input-convert/simple3.asc b/tests/data/input-convert/simple3.asc
@@ -3,7 +3,10 @@
 ("CellBody"
  (Color Red)
  (CellBody)
- (0 0 0 2)
+ ( 0.1  0   0 2)
+ ( 0.1  0.1 0 2)
+ (-0.1  0   0 2)
+ (-0.1 -0.1 0 2)
  )
 
 ((Dendrite)

diff --git a/tests/data/nrnhines.asc b/tests/data/nrnhines.asc
@@ -0,0 +1,26 @@
+((Dendrite)
+ (0 0 0 2)
+ (0 5 0 2)
+ (
+  (-5 5 0 3)
+  (-6 5 0 3)
+  (
+    (-7 5 0 3)
+    |
+    (-8 10 0 3)
+  )
+  |
+  (6 5 0 3)
+  )
+ )
+
+
+((Axon)
+ (0 0 0 2)
+ (0 -4 0 2)
+ (
+  (6 -4 0 4)
+  |
+  (-5 -4 0 4)
+  )
+ )
diff --git a/tests/data/simple.asc b/tests/data/simple.asc
@@ -19,7 +19,10 @@
 ("CellBody"
  (Color Red)
  (CellBody)
- (0 0 0 2)
+ ( 0.1  0   0 2)
+ ( 0.1  0.1 0 2)
+ (-0.1  0   0 2)
+ (-0.1 -0.1 0 2)
  )
 
  ((Dendrite)

diff --git a/tests/data/simple.h5 b/tests/data/simple.h5
diff --git a/tests/data/simple2.asc b/tests/data/simple2.asc
@@ -1,7 +1,10 @@
 ("CellBody"
  (Color Red)
  (CellBody)
- (0 0 0 2)
+ ( 0.1  0   0 2)
+ ( 0.1  0.1 0 2)
+ (-0.1  0   0 2)
+ (-0.1 -0.1 0 2)
  )
 
  ((Dendrite)

diff --git a/tests/data/simple3.asc b/tests/data/simple3.asc
@@ -3,7 +3,10 @@
 ("CellBody"
  (Color Red)
  (CellBody)
- (0 0 0 2)
+ ( 2  0 0 2)
+ ( 0  2 0 2)
+ (-2  0 0 2)
+ ( 0 -2 0 2)
  )
 
 ((Dendrite)

diff --git a/tests/data/synthesized_cell.asc b/tests/data/synthesized_cell.asc
@@ -3,7 +3,10 @@
 ("CellBody"
  (Color Red)
  (CellBody)
- (5 5 5 1)
+ (5.5 5   5 1)
+ (5   5.5 5 1)
+ (4.5 5   5 1)
+ (5   4.5 5 1)
  )
 
 ((Dendrite)

diff --git a/tests/test_cli.py b/tests/test_cli.py
@@ -30,7 +30,7 @@ def test_convert_file(tmpdir):
 
 def test_convert_folder(tmpdir):
     runner = CliRunner()
-    result = runner.invoke(cli, ['convert', 'folder', '-ext', 'swc',
+    result = runner.invoke(cli, ['convert', 'folder', '--single-point-soma', '-ext', 'swc',
                                  str(DATA / 'input-convert'), str(tmpdir)])
     assert result.exit_code == 0, result.exc_info
 

diff --git a/tests/test_converter.py b/tests/test_converter.py
@@ -15,11 +15,14 @@
 
 
 def test_convert(tmpdir):
-    for in_ext, out_ext in it.product(['asc', 'h5', 'swc'], repeat=2):
+    for in_ext, out_ext in (('asc', 'h5'),
+                            ('asc', 'swc'),
+                            ('h5', 'asc'),
+                            ('h5', 'swc')):
         # A simple morphology
         inname = DATA / f'simple.{in_ext}'
         outname = Path(tmpdir, f'test.{out_ext}')
-        convert(inname, outname)
+        convert(inname, outname, single_point_soma=(out_ext == 'swc'))
         assert not diff(inname, outname)
 
         # A more complex one

diff --git a/tests/test_graft.py b/tests/test_graft.py
@@ -98,6 +98,7 @@ def test_graft_axon_on_synthesized_cell():
                               [[5.1272364, 5.4825425, 4.9689593],
                                [5.1272364, 1.4825425, 4.9689593]])
 
+
 def test_self_graft():
     '''Grafting a neuron with its own neuron'''
     filename = DATA / 'neuron.asc'

diff --git a/tests/test_nrnhines.py b/tests/test_nrnhines.py
@@ -5,7 +5,7 @@
 import morph_tool.nrnhines as tested
 
 DATA = Path(__file__).parent / 'data'
-SIMPLE = DATA / 'simple2.asc'
+SIMPLE = DATA / 'nrnhines.asc'
 
 
 def test_interpolate_compartments():
@@ -46,11 +46,11 @@ def test_point_to_section_end():
     assert (tested.point_to_section_end(cell.icell.all, [-8, 10, 0]) ==
                  6)
 
-    assert (tested.point_to_section_end(cell.icell.all, [-8, 10, 2]) ==
+    assert (tested.point_to_section_end(cell.icell.all, [-8, 10, 2]) is
                  None)
 
     assert (tested.point_to_section_end(cell.icell.all, [-8, 10, 2],
-                                             atol=10) ==
+                                             atol=8) ==
                  3)