Merge pull request #2 from OpenSourceBrain/master

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OpenSourceBrain · Jul 1, 2022 · 4568ed7 · 4568ed7
2 parents 467b5b1 + e89d5a2
commit 4568ed7
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diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml
@@ -3,9 +3,9 @@ name: Testing non OMV based scripts
 
 on:
   push:
-    branches: [ master, development, experimental ]
+    branches: [ master, development, experimental, pg* ]
   pull_request:
-    branches: [ master, development, experimental ]
+    branches: [ master, development, experimental, pg* ]
 
 jobs:
   build:
@@ -54,7 +54,7 @@ jobs:
     - name: Extract NeuroML2 models from NEURON files
       run: |
          pip install neuron
-         
+
          cd CellTypesDatabase/models
          nrnivmodl  NEURON
          python ParseAll.py
@@ -69,7 +69,7 @@ jobs:
          rm -rf neurotune
          export NEURON_HOME=$pythonLocation
          python tuneAllen.py -izhone
-         
+
     - name: Final version info
       run: |
         pip list

diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml
@@ -2,9 +2,9 @@ name: Continuous builds
 
 on:
   push:
-    branches: [ master, development ]
+    branches: [ master, development, experimental, pg* ]
   pull_request:
-    branches: [ master, development ]
+    branches: [ master, development, experimental, pg* ]
 
 jobs:
   build:

diff --git a/.gitignore b/.gitignore
@@ -294,3 +294,4 @@ original.v.dat
 /tests.log
 /CellTypesDatabase/data/tests.log
 /CellTypesDatabase/tune/*_analysis.json
+/CellTypesDatabase/data/tmp
diff --git a/CellTypesDatabase/data/data_helper.py b/CellTypesDatabase/data/data_helper.py
@@ -26,7 +26,7 @@
 DATASET_TARGET_SWEEPS[468120757] = [43,46,51,54,62,63,65]
 
 DATASET_TARGET_SWEEPS[476686112] = [23, 24, 25, 26, 37, 31, 36]
-DATASET_TARGET_SWEEPS[477127614] = [22, 27, 38, 41, 29, 30, 35]
+DATASET_TARGET_SWEEPS[477127614] = [22, 25, 27, 38, 30, 32, 35]
 
 
 #  Layer 5, aspiny http://celltypes.brain-map.org/mouse/experiment/electrophysiology/464198958

diff --git a/CellTypesDatabase/data/summary/CellInfo.html b/CellTypesDatabase/data/summary/CellInfo.html
@@ -14,7 +14,7 @@
             <tr> 
                 <td width="130px">
                     <p style="font-size:80%;font-family:arial"><b>464198958</b></p>
-                    <p style="font-size:80%;font-family:arial">Lateral visual area, layer 5</p>
+                    <p style="font-size:80%;font-family:arial">Primary visual area, layer 5</p>
                     <p style="font-size:80%;font-family:arial">aspiny</p>
                     <p style="font-size:80%;font-family:arial">Sst-IRES-Cre</p>
                     <p style="font-size:80%;font-family:arial"><a href="http://celltypes.brain-map.org/mouse/experiment/electrophysiology/464198958">Source data</a></p>

diff --git a/CellTypesDatabase/data/summary/README.md b/CellTypesDatabase/data/summary/README.md
@@ -3,7 +3,7 @@
 <tr>
 <td width="130px">
 <p style="font-size:80%;font-family:arial"><b>464198958</b></p>
-<p style="font-size:80%;font-family:arial">Lateral visual area, layer 5</p>
+<p style="font-size:80%;font-family:arial">Primary visual area, layer 5</p>
 <p style="font-size:80%;font-family:arial">aspiny</p>
 <p style="font-size:80%;font-family:arial">Sst-IRES-Cre</p>
 <p style="font-size:80%;font-family:arial"><a href="http://celltypes.brain-map.org/mouse/experiment/electrophysiology/464198958">Source data</a></p>

diff --git a/CellTypesDatabase/data/summary/traces_464198958.png b/CellTypesDatabase/data/summary/traces_464198958.png
diff --git a/CellTypesDatabase/data/summary/traces_477127614.png b/CellTypesDatabase/data/summary/traces_477127614.png
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472450023.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472450023.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_483108201.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_483108201.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_486556811.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_486556811.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/LEMS_472450023.xml b/CellTypesDatabase/models/NeuroML2/LEMS_472450023.xml
@@ -2,7 +2,7 @@
 
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.5.8 (libNeuroML v0.2.54)
+        This LEMS file has been automatically generated using PyNeuroML v0.7.0 (libNeuroML v0.4.0)
 
      -->
 

diff --git a/CellTypesDatabase/models/NeuroML2/LEMS_483108201.xml b/CellTypesDatabase/models/NeuroML2/LEMS_483108201.xml
@@ -2,7 +2,7 @@
 
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.5.8 (libNeuroML v0.2.54)
+        This LEMS file has been automatically generated using PyNeuroML v0.7.0 (libNeuroML v0.4.0)
 
      -->
 

diff --git a/CellTypesDatabase/models/NeuroML2/LEMS_486556811.xml b/CellTypesDatabase/models/NeuroML2/LEMS_486556811.xml
@@ -2,7 +2,7 @@
 
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.5.8 (libNeuroML v0.2.54)
+        This LEMS file has been automatically generated using PyNeuroML v0.7.0 (libNeuroML v0.4.0)
 
      -->
 

diff --git a/CellTypesDatabase/models/NeuroML2/Network_472450023.net.nml b/CellTypesDatabase/models/NeuroML2/Network_472450023.net.nml
@@ -1,4 +1,4 @@
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.1.xsd" id="NeuroML2_file_exported_from_NEURON">
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="NeuroML2_file_exported_from_NEURON">
     <notes>
 
 Export of a cell model (472450023) obtained from the Allen Institute Cell Types Database into NeuroML2

diff --git a/CellTypesDatabase/models/NeuroML2/Network_483108201.net.nml b/CellTypesDatabase/models/NeuroML2/Network_483108201.net.nml
@@ -1,4 +1,4 @@
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.1.xsd" id="NeuroML2_file_exported_from_NEURON">
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="NeuroML2_file_exported_from_NEURON">
     <notes>
 
 Export of a cell model (483108201) obtained from the Allen Institute Cell Types Database into NeuroML2

diff --git a/CellTypesDatabase/models/NeuroML2/Network_486556811.net.nml b/CellTypesDatabase/models/NeuroML2/Network_486556811.net.nml
@@ -1,4 +1,4 @@
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.1.xsd" id="NeuroML2_file_exported_from_NEURON">
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="NeuroML2_file_exported_from_NEURON">
     <notes>
 
 Export of a cell model (486556811) obtained from the Allen Institute Cell Types Database into NeuroML2