-
Notifications
You must be signed in to change notification settings - Fork 6
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #5 from pgleeson/development
Adds morphology only export option to GUI; tests generated nml files
- Loading branch information
Showing
37 changed files
with
50,707 additions
and
22 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
|
|
||
| name: Continuous build using OMV | ||
|
|
||
| on: | ||
| schedule: | ||
| - cron: "1 1 1 */2 *" | ||
| push: | ||
| branches: [ main, development, experimental, test* ] | ||
| pull_request: | ||
| branches: [ main, development, experimental, test* ] | ||
|
|
||
| jobs: | ||
| build: | ||
|
|
||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| python-version: [ 3.9, "3.11" ] | ||
| engine: [ jNeuroML_validate, jNeuroML_NEURON, jNeuroML_EDEN ] | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v4 | ||
|
|
||
| - name: Set up Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
|
|
||
| - name: Install OMV | ||
| run: | | ||
| pip install git+https://github.com/OpenSourceBrain/osb-model-validation | ||
| - name: Run OMV tests on engine ${{ matrix.engine }} | ||
| run: | | ||
| omv all -V --engine=${{ matrix.engine }} | ||
| - name: OMV final version info | ||
| run: | | ||
| omv list -V # list installed engines | ||
| env |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,102 @@ | ||
| <neuroml xmlns="http://www.neuroml.org/schema/neuroml2" | ||
| 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_v2.3.1.xsd" | ||
| id="Case1_new"> | ||
|
|
||
| <cell id="Case1_new"> | ||
| <notes> | ||
| Neuronal morphology exported in NeuroML v2.3.1 from CVapp (NeuroMorpho.org version) | ||
| Original file: Case1_new.swc </notes> | ||
|
|
||
| <morphology id="morphology_Case1_new"> | ||
|
|
||
| <!-- First point is of a multi point soma => not spherical! --> | ||
|
|
||
| <segment id="0" name="Seg_0"> <!-- "Cable" is 0--> | ||
|
|
||
| <!-- Cylindrical soma... --> | ||
| <proximal x="0" y="-10" z="0" diameter="20"/> | ||
| <distal x="0" y="0" z="0" diameter="20"/> | ||
| </segment> | ||
|
|
||
| <segment id="1" name="Seg_1"> <!-- "Cable" is 0--> | ||
| <parent segment="0"/> | ||
| <distal x="0" y="10" z="0" diameter="20"/> | ||
| </segment> | ||
|
|
||
| <!-- Parent point is on soma! Not creating 'real' segment --> | ||
|
|
||
| <segment id="2" name="Seg_2"> <!-- "Cable" is 1--> | ||
| <parent segment="0"/> | ||
| <proximal x="10" y="0" z="0" diameter="4"/> | ||
| <distal x="30" y="0" z="0" diameter="4"/> | ||
| </segment> | ||
|
|
||
| <segment id="3" name="Seg_3"> <!-- "Cable" is 2--> | ||
| <parent segment="2"/> | ||
| <proximal x="30" y="0" z="0" diameter="4"/> | ||
| <distal x="40" y="10" z="0" diameter="4"/> | ||
| </segment> | ||
|
|
||
| <segment id="4" name="Seg_4"> <!-- "Cable" is 3--> | ||
| <parent segment="2"/> | ||
| <proximal x="30" y="0" z="0" diameter="4"/> | ||
| <distal x="40" y="-10" z="0" diameter="4"/> | ||
| </segment> | ||
|
|
||
| <segmentGroup id="Cable_0" > | ||
| <member segment="0"/> | ||
| <member segment="1"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="Cable_1" > | ||
| <member segment="2"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="Cable_2" > | ||
| <member segment="3"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="Cable_3" > | ||
| <member segment="4"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="color_white" > | ||
| <include segmentGroup="Cable_0"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="dendrite_group" > | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="soma_group" > | ||
| <include segmentGroup="Cable_0"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="basal_dendrite" > | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="color_green" > | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="all" > | ||
| <include segmentGroup="Cable_0"/> | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| </segmentGroup> | ||
|
|
||
| </morphology> | ||
|
|
||
| <!-- No biophysical properties, as this cell was generated from an SWC morphology file --> | ||
|
|
||
| </cell> | ||
| </neuroml> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,98 @@ | ||
| <neuroml xmlns="http://www.neuroml.org/schema/neuroml2" | ||
| 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_v2.3.1.xsd" | ||
| id="Case1_new_morphology"> | ||
|
|
||
| <notes> | ||
| Neuronal morphology exported in NeuroML v2.3.1 from CVapp (NeuroMorpho.org version) | ||
| Original file: Case1_new.swc </notes> | ||
|
|
||
| <morphology id="morphology_Case1_new"> | ||
|
|
||
| <!-- First point is of a multi point soma => not spherical! --> | ||
|
|
||
| <segment id="0" name="Seg_0"> <!-- "Cable" is 0--> | ||
|
|
||
| <!-- Cylindrical soma... --> | ||
| <proximal x="0" y="-10" z="0" diameter="20"/> | ||
| <distal x="0" y="0" z="0" diameter="20"/> | ||
| </segment> | ||
|
|
||
| <segment id="1" name="Seg_1"> <!-- "Cable" is 0--> | ||
| <parent segment="0"/> | ||
| <distal x="0" y="10" z="0" diameter="20"/> | ||
| </segment> | ||
|
|
||
| <!-- Parent point is on soma! Not creating 'real' segment --> | ||
|
|
||
| <segment id="2" name="Seg_2"> <!-- "Cable" is 1--> | ||
| <parent segment="0"/> | ||
| <proximal x="10" y="0" z="0" diameter="4"/> | ||
| <distal x="30" y="0" z="0" diameter="4"/> | ||
| </segment> | ||
|
|
||
| <segment id="3" name="Seg_3"> <!-- "Cable" is 2--> | ||
| <parent segment="2"/> | ||
| <proximal x="30" y="0" z="0" diameter="4"/> | ||
| <distal x="40" y="10" z="0" diameter="4"/> | ||
| </segment> | ||
|
|
||
| <segment id="4" name="Seg_4"> <!-- "Cable" is 3--> | ||
| <parent segment="2"/> | ||
| <proximal x="30" y="0" z="0" diameter="4"/> | ||
| <distal x="40" y="-10" z="0" diameter="4"/> | ||
| </segment> | ||
|
|
||
| <segmentGroup id="Cable_0" > | ||
| <member segment="0"/> | ||
| <member segment="1"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="Cable_1" > | ||
| <member segment="2"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="Cable_2" > | ||
| <member segment="3"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="Cable_3" > | ||
| <member segment="4"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="color_white" > | ||
| <include segmentGroup="Cable_0"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="dendrite_group" > | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="soma_group" > | ||
| <include segmentGroup="Cable_0"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="basal_dendrite" > | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="color_green" > | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="all" > | ||
| <include segmentGroup="Cable_0"/> | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| </segmentGroup> | ||
|
|
||
| </morphology> | ||
|
|
||
| </neuroml> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,94 @@ | ||
| <neuroml xmlns="http://www.neuroml.org/schema/neuroml2" | ||
| 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_v2.3.1.xsd" | ||
| id="Case1_orig"> | ||
|
|
||
| <cell id="Case1_orig"> | ||
| <notes> | ||
| Neuronal morphology exported in NeuroML v2.3.1 from CVapp (NeuroMorpho.org version) | ||
| Original file: Case1_orig.swc </notes> | ||
|
|
||
| <morphology id="morphology_Case1_orig"> | ||
|
|
||
| <!-- First point is of a multi point soma => not spherical! --> | ||
|
|
||
| <segment id="0" name="Seg_0"> <!-- "Cable" is 0--> | ||
|
|
||
| <!-- Cylindrical soma... --> | ||
| <proximal x="-10" y="10" z="0" diameter="0.2"/> | ||
| <distal x="10" y="10" z="0" diameter="0.2"/> | ||
| </segment> | ||
|
|
||
| <segment id="1" name="Seg_1"> <!-- "Cable" is 0--> | ||
| <parent segment="0"/> | ||
| <distal x="10" y="-10" z="0" diameter="0.2"/> | ||
| </segment> | ||
|
|
||
| <segment id="2" name="Seg_2"> <!-- "Cable" is 0--> | ||
| <parent segment="1"/> | ||
| <distal x="-10" y="-10" z="0" diameter="0.2"/> | ||
| </segment> | ||
|
|
||
| <segment id="3" name="Seg_3"> <!-- "Cable" is 0--> | ||
| <parent segment="2"/> | ||
| <distal x="-10" y="10" z="0" diameter="0.2"/> | ||
| </segment> | ||
|
|
||
| <!-- Parent point is on soma! Not creating 'real' segment --> | ||
|
|
||
| <!-- Parent point is on soma! Not creating 'real' segment --> | ||
|
|
||
| <!-- Parent point is on soma! Not creating 'real' segment --> | ||
|
|
||
| <!-- Parent point is on soma! Not creating 'real' segment --> | ||
|
|
||
| <segmentGroup id="Cable_0" > | ||
| <member segment="0"/> | ||
| <member segment="1"/> | ||
| <member segment="2"/> | ||
| <member segment="3"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="dendrite_group" > | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| <include segmentGroup="Cable_4"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="soma_group" > | ||
| <include segmentGroup="Cable_0"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="color_green" > | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| <include segmentGroup="Cable_4"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="basal_dendrite" > | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| <include segmentGroup="Cable_4"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="all" > | ||
| <include segmentGroup="Cable_0"/> | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| <include segmentGroup="Cable_4"/> | ||
| </segmentGroup> | ||
|
|
||
| <segmentGroup id="color_white" > | ||
| <include segmentGroup="Cable_0"/> | ||
| </segmentGroup> | ||
|
|
||
| </morphology> | ||
|
|
||
| <!-- No biophysical properties, as this cell was generated from an SWC morphology file --> | ||
|
|
||
| </cell> | ||
| </neuroml> |
Oops, something went wrong.