Merge pull request #158 from OpenSourceBrain/development

To v0.4.0; Remove brian1 features, update README and add  --exit-zero option

Author: pgleeson

.github/workflows/ci_versions.yml

@@ -44,11 +44,22 @@ jobs:
         pip install .
         pip list
 
+
+    - name: Run pytest 
+      run: |
+        pip install pytest
+        cd omv/test
+        pytest -vs
+
     - name: Run simple OMV tests
       run: |
         omv all -V --engine=jNeuroML_NEURON
         omv test -V utilities/tests/.test.exIzh.jnmlnetpyne.omt
 
+    - name: Run broken test with flag --exit-zero
+      run: |
+        # This is known to fail, but should not cause the CI to fail due to the --exit-zero flag
+        omv test -V utilities/tests/brokentest/.test.ex9.jnml.omt.broken --exit-zero
 
     - name: OMV final version info
       run: |

README.md

@@ -9,14 +9,14 @@
 
 # OSB Model Validation
 
-Tools for automated model validation in [Open Source Brain](http://www.opensourcebrain.org) projects, which can also be used for testing model behaviour on many [simulation engines](https://github.com/OpenSourceBrain/osb-model-validation/tree/master/omv/engines) both:
+Tools for automated model validation in [Open Source Brain](https://www.opensourcebrain.org) projects, which can also be used for testing model behaviour on many [simulation engines](https://github.com/OpenSourceBrain/osb-model-validation/tree/master/omv/engines) both:
 
 - on your local machine when developing models
 - on [GitHub Actions](https://github.com/features/actions), to ensure tests pass on every commit.
 
 To see this framework in action, click on some of the green buttons below:
 
-|  OSB project   |   Tests on GitHub Actions    |  Test workflow script |
+|  OSBv1 project   |   Tests on GitHub Actions    |  Test workflow script |
 |----------|:-------------:|:------:|
 |[FitzHugh Nagumo](http://www.opensourcebrain.org/projects/fitzhugh-nagumo-fitzhugh-1969) | [![Continuous build using OMV](https://github.com/OpenSourceBrain/FitzHugh-Nagumo/actions/workflows/omv-ci.yml/badge.svg)](https://github.com/OpenSourceBrain/FitzHugh-Nagumo/actions/workflows/omv-ci.yml) | [omv-ci.yml](https://github.com/OpenSourceBrain/FitzHugh-Nagumo/blob/master/.github/workflows/omv-ci.yml) |
 |[Auditory cortex network](http://www.opensourcebrain.org/projects/acnet2)| [![Continuous build using OMV](https://github.com/OpenSourceBrain/ACnet2/actions/workflows/omv-ci.yml/badge.svg)](https://github.com/OpenSourceBrain/ACnet2/actions/workflows/omv-ci.yml) | [omv-ci.yml](https://github.com/OpenSourceBrain/ACnet2/blob/master/.github/workflows/omv-ci.yml) |
@@ -54,7 +54,7 @@ Setting up validation for a model and simulation written in NeuroML2/LEMS requir
 ### Write MEP files
 
 Depending on the size of your model, you can run validation on the full fledged model, or you can create smaller stripped down versions that test particular aspects of the model.
-Here is an example LEMS file for the FitzHugh-Nagumo model on Open Source Brain: [LEMS_FitzHugNagamo.xml](https://github.com/OpenSourceBrain/FitzHugh-Nagumo/blob/master/NeuroML2/LEMS_FitzHughNagumo.xml).
+Here is an example LEMS file for the FitzHugh-Nagumo model on Open Source Brain: [LEMS_FitzHughNagumo.xml](https://github.com/OpenSourceBrain/FitzHugh-Nagumo/blob/master/NeuroML2/LEMS_FitzHughNagumo.xml).
 
 ``` yaml
 # Script for running automated tests on OSBrain, see https://github.com/OpenSourceBrain/osb-model-validation

omv/engines/__init__.py

@@ -21,7 +21,6 @@
 from omv.engines.pylemsnml2 import PyLemsNeuroML2Engine
 from omv.engines.genesis import GenesisEngine
 
-# from omv.engines.brian1 import Brian1Engine
 from omv.engines.brian2_ import Brian2Engine
 from omv.engines.arbor_ import ArborEngine
 from omv.engines.xpp import XppEngine
@@ -33,7 +32,6 @@
 from omv.engines.pynnneuron import PyNNNRNEngine
 from omv.engines.pyneuron import PyNRNEngine
 
-# from omv.engines.pynnbrian1 import PyNNBrian1Engine
 from omv.engines.pynnbrian2 import PyNNBrian2Engine
 from omv.engines.pynnnest import PyNNNestEngine
 from omv.engines.pynnneuroml import PyNNNeuroMLEngine

omv/engines/brian1.py

@@ -1,7 +1,5 @@
 from omv.common.inout import pip_install
 
-from omv.engines.getbrian1 import check_scipy_dev
-
 
 def install_brian2(version):
     if not version:

omv/engines/getbrian2.py

@@ -2,9 +2,9 @@
 ============================================
 
   Usage:
-    omv all [-V | --verbose] [--engine=engine] [--ignore-non-py3]
-    omv all_ [-V | --verbose] [--engine=engine]
-    omv test <testMe.omt> [-V | --verbose]
+    omv all [-V | --verbose] [--engine=engine] [--ignore-non-py3] [--exit-zero]
+    omv all_ [-V | --verbose] [--engine=engine] [--ignore-non-py3] [--exit-zero]
+    omv test <testMe.omt> [-V | --verbose] [--exit-zero]
     omv autogen [options]
     omv install <engine>
     omv find
@@ -20,6 +20,7 @@
     -V --verbose      Display additional diagnosis messages [default: False].
     --version         Show version.
     --ignore-non-py3  If Python 3, ignore tests on non Py3 compatible engines [default: False]
+    --exit-zero       Run tests as normal and report failures, but always exit with code 0 [default: False]
     -y                Auto-select default options (non-interactive mode)
 """
 
@@ -46,12 +47,15 @@ def main():
     if arguments["--verbose"]:
         set_verbosity(1)
 
+    exit_zero = arguments["--exit-zero"]
+
     if arguments["test"]:
         try:
             test_one(arguments["<testMe.omt>"])
         except AssertionError:
             inform("Failed due to non passing tests")
-            exit(1)
+            if not exit_zero:
+                exit(1)
 
     elif arguments["all"]:
         try:
@@ -74,7 +78,8 @@ def main():
             )
         except AssertionError:
             inform("Failed due to non passing tests")
-            exit(1)
+            if not exit_zero:
+                exit(1)
 
     # Includes *.omt_, i.e. temporary test files
     elif arguments["all_"]:
@@ -86,7 +91,8 @@ def main():
             )
         except AssertionError:
             inform("Failed due to non passing tests")
-            exit(1)
+            if not exit_zero:
+                exit(1)
 
     elif arguments["find"]:
         try:
@@ -364,15 +370,6 @@ def _install_engine(eng):
 
             install_netpyne(engine_version)
 
-        elif eng.lower() == "Brian".lower():
-            if engine_version is not None:
-                raise Exception(
-                    "Currently, cannot install a specific version of engine %s" % eng
-                )
-            from omv.engines.getbrian1 import install_brian
-
-            install_brian()
-
         elif eng.lower() == "Brian2".lower():
             from omv.engines.brian2_ import Brian2Engine as ee
 

omv/engines/jneuromlbrian.py

@@ -1,6 +1,6 @@
 [metadata]
 name = OSBModelValidation
-version = 0.3.11
+version = 0.4.0
 author = Boris Marin, Padraig Gleeson
 author_email = borismarin@gmail.com
 url = https://github.com/OpenSourceBrain/osb-model-validation

omv/engines/pynnbrian1.py

@@ -0,0 +1,26 @@
+# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
+ 
+target: ../LEMS_NML2_Ex9_FN.xml 
+engine: jNeuroML
+mep: .test.ex9.mep
+experiments:
+  V:
+    observables:
+      spike times:
+        file: 
+          path: ../ex9.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection: 
+          method: derivative
+        tolerance: 0.004099
+  W:
+    observables:
+      spike times:
+        file: 
+          path: ../ex9.dat
+          columns: [0,2]
+          scaling: [1000, 1]
+        spike detection: 
+          method: derivative
+        tolerance: 0.000616