fix arbor tests with latest arbor version

BlueBrain · Aug 20, 2024 · 3c887d7 · 3c887d7
1 parent aff67f8
commit 3c887d7
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Showing 20 changed files with 21 additions and 19 deletions.
diff --git a/bluepyopt/ephys/morphologies.py b/bluepyopt/ephys/morphologies.py
@@ -307,6 +307,8 @@ def load(morpho_filename, replace_axon):
             morpho = arbor.load_component(morpho_filename).component
         elif morpho_suffix == '.swc':
             morpho = arbor.load_swc_arbor(morpho_filename)
+            # turn loaded_morphology into morphology type
+            morpho = arbor.morphology(morpho.segment_tree)
         elif morpho_suffix == '.asc':
             morpho = arbor.load_asc(morpho_filename).morphology
         else:

diff --git a/bluepyopt/ephys/templates/acc/decor_acc_template.jinja2 b/bluepyopt/ephys/templates/acc/decor_acc_template.jinja2
@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (decor
     {%- for mech, params in global_mechs.items() %}
     {%- if mech is not none %}

diff --git a/bluepyopt/ephys/templates/acc/label_dict_acc_template.jinja2 b/bluepyopt/ephys/templates/acc/label_dict_acc_template.jinja2
@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (label-dict
   {%- for loc, label in label_dict.items() %}
     {{ label.defn }}

diff --git a/bluepyopt/tests/test_ephys/test_create_acc.py b/bluepyopt/tests/test_ephys/test_create_acc.py
@@ -537,7 +537,7 @@ def run_short_sim(cable_cell):
     arb_cell_model.properties.catalogue.extend(arbor.bbp_catalogue(), "BBP::")
 
     # Run a very short simulation to test mechanism instantiation
-    arb_cell_model.run(tfinal=0.1)
+    arb_cell_model.run(tfinal=0.1 *arbor.units.ms)
 
 
 @pytest.mark.unit

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/CCell/CCell_decor.acc b/bluepyopt/tests/test_ephys/testdata/acc/CCell/CCell_decor.acc
@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (decor
     (default (gSKv3_1bar_SKv3_1 65))
     (paint (region "soma") (gSKv3_1bar_SKv3_1 65))

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/CCell/CCell_label_dict.acc b/bluepyopt/tests/test_ephys/testdata/acc/CCell/CCell_label_dict.acc
@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (label-dict 
     (region-def "all" (all)) 
     (region-def "apic" (tag 4)) 

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/CCell/simple_axon_replacement.acc b/bluepyopt/tests/test_ephys/testdata/acc/CCell/simple_axon_replacement.acc
@@ -1,6 +1,6 @@
 (arbor-component 
   (meta-data 
-    (version "0.1-dev"))
+    (version "0.9-dev"))
   (morphology 
     (branch 0 -1 
       (segment 0 

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/expsyn/simple_cell_decor.acc b/bluepyopt/tests/test_ephys/testdata/acc/expsyn/simple_cell_decor.acc
@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (decor
     (paint (region "soma") (membrane-capacitance 0.01))
     (paint (region "soma") (density (mechanism "default::pas")))

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/expsyn/simple_cell_label_dict.acc b/bluepyopt/tests/test_ephys/testdata/acc/expsyn/simple_cell_label_dict.acc
@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (label-dict
     (region-def "all" (all))
     (region-def "soma" (tag 1))

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/l5pc/C060114A7_axon_replacement.acc b/bluepyopt/tests/test_ephys/testdata/acc/l5pc/C060114A7_axon_replacement.acc
@@ -1,6 +1,6 @@
 (arbor-component 
   (meta-data 
-    (version "0.1-dev"))
+    (version "0.9-dev"))
   (morphology 
     (branch 0 -1 
       (segment 0 

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/l5pc/C060114A7_modified.acc b/bluepyopt/tests/test_ephys/testdata/acc/l5pc/C060114A7_modified.acc
@@ -1,6 +1,6 @@
 (arbor-component 
   (meta-data 
-    (version "0.1-dev"))
+    (version "0.9-dev"))
   (morphology 
     (branch 0 -1 
       (segment 0 

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/l5pc/l5pc_decor.acc b/bluepyopt/tests/test_ephys/testdata/acc/l5pc/l5pc_decor.acc
@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (decor
     (default (membrane-potential -65))
     (default (temperature-kelvin 307.14999999999998))

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/l5pc/l5pc_label_dict.acc b/bluepyopt/tests/test_ephys/testdata/acc/l5pc/l5pc_label_dict.acc
@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (label-dict
     (region-def "all" (all))
     (region-def "soma" (tag 1))

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/l5pc_py37/l5pc_decor.acc b/bluepyopt/tests/test_ephys/testdata/acc/l5pc_py37/l5pc_decor.acc
@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (decor
     (default (membrane-potential -65))
     (default (temperature-kelvin 307.14999999999998))

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_axon_replacement.acc b/bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_axon_replacement.acc
@@ -1,6 +1,6 @@
 (arbor-component 
   (meta-data 
-    (version "0.1-dev"))
+    (version "0.9-dev"))
   (morphology 
     (branch 0 -1 
       (segment 0 

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_cell_decor.acc b/bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_cell_decor.acc
@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (decor
     (paint (region "soma") (membrane-capacitance 0.01))
     (paint (region "soma") (density (mechanism "default::hh" ("gnabar" 0.10299326453483033) ("gkbar" 0.027124836082684685))))))
diff --git a/bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_cell_label_dict.acc b/bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_cell_label_dict.acc
@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (label-dict
     (region-def "all" (all))
     (region-def "soma" (tag 1))

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_modified.acc b/bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_modified.acc
@@ -1,6 +1,6 @@
 (arbor-component 
   (meta-data 
-    (version "0.1-dev"))
+    (version "0.9-dev"))
   (morphology 
     (branch 0 -1 
       (segment 0 

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/templates/decor_acc_template.jinja2 b/bluepyopt/tests/test_ephys/testdata/acc/templates/decor_acc_template.jinja2
@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (meta-data (info "test-decor"))
   (decor
     {%- for mech, params in global_mechs.items() %}

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/templates/label_dict_acc_template.jinja2 b/bluepyopt/tests/test_ephys/testdata/acc/templates/label_dict_acc_template.jinja2
@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (meta-data (info "test-label-dict"))
   (label-dict
   {%- for loc, label in label_dict.items() %}{# this is a comment #}