OSBModelValidation 0.3.11__tar.gz → 0.4.0__tar.gz

{osbmodelvalidation-0.3.11 → osbmodelvalidation-0.4.0/OSBModelValidation.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: OSBModelValidation
-Version: 0.3.11
+Version: 0.4.0
 Summary: Open Source Brain Model validation
 Home-page: https://github.com/OpenSourceBrain/osb-model-validation
 Author: Boris Marin, Padraig Gleeson
@@ -37,14 +37,14 @@ Dynamic: license-file
 
 # 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) |
@@ -82,7 +82,7 @@ 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

{osbmodelvalidation-0.3.11 → osbmodelvalidation-0.4.0}/OSBModelValidation.egg-info/SOURCES.txt

@@ -35,7 +35,6 @@ omv/common/__init__.py
 omv/common/inout.py
 omv/engines/__init__.py
 omv/engines/arbor_.py
-omv/engines/brian1.py
 omv/engines/brian2_.py
 omv/engines/eden_.py
 omv/engines/engine.py
@@ -61,7 +60,6 @@ omv/engines/getpynn.py
 omv/engines/getxpp.py
 omv/engines/jlems.py
 omv/engines/jneuroml.py
-omv/engines/jneuromlbrian.py
 omv/engines/jneuromlbrian2.py
 omv/engines/jneuromleden.py
 omv/engines/jneuromlmoose.py
@@ -89,7 +87,6 @@ omv/engines/pyneuromlvalidatesbml.py
 omv/engines/pyneuromlxpp.py
 omv/engines/pyneuron.py
 omv/engines/pynn.py
-omv/engines/pynnbrian1.py
 omv/engines/pynnbrian2.py
 omv/engines/pynnnest.py
 omv/engines/pynnneuroml.py
@@ -120,6 +117,7 @@ omv/schemata/types/test/observable.yaml
 omv/schemata/types/test/protocol.1.yaml
 omv/schemata/types/test/protocol.2.yaml
 omv/test/__init__.py
+omv/test/test_drop_py2_bits.py
 omv/test/test_rates.py
 omv/test/test_types.py
 omv/validation/__init__.py

{osbmodelvalidation-0.3.11/OSBModelValidation.egg-info → osbmodelvalidation-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: OSBModelValidation
-Version: 0.3.11
+Version: 0.4.0
 Summary: Open Source Brain Model validation
 Home-page: https://github.com/OpenSourceBrain/osb-model-validation
 Author: Boris Marin, Padraig Gleeson
@@ -37,14 +37,14 @@ Dynamic: license-file
 
 # 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) |
@@ -82,7 +82,7 @@ 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

{osbmodelvalidation-0.3.11 → osbmodelvalidation-0.4.0}/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

{osbmodelvalidation-0.3.11 → osbmodelvalidation-0.4.0}/omv/autogen.py

@@ -80,7 +80,7 @@ def generate_dottravis(targets):
     travis = UnsortableOrderedDict(
         [
             ("language", "python"),
-            ("python", 2.7),
+            ("python", 3.12),
             ("env", engines),
             ("install", ["pip install " + repo]),
             ("script", ["omv all"]),

{osbmodelvalidation-0.3.11 → osbmodelvalidation-0.4.0}/omv/engines/__init__.py

@@ -21,7 +21,6 @@ from omv.engines.pylems import PyLemsEngine
 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.pynn import PyNNEngine
 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

{osbmodelvalidation-0.3.11 → osbmodelvalidation-0.4.0}/omv/engines/getbrian2.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:

{osbmodelvalidation-0.3.11 → osbmodelvalidation-0.4.0}/omv/engines/getnetpyne.py

@@ -2,7 +2,6 @@ from omv.common.inout import check_output
 from omv.engines.utils.wdir import working_dir
 from omv.common.inout import pip_install
 import os
-import sys
 
 
 def install_netpyne(version=None):
@@ -33,19 +32,6 @@ def install_netpyne(version=None):
             print(check_output(["pwd"]))
 
         with working_dir(path):
-            if sys.version_info.major == 2:
-                pip_install(
-                    [
-                        "kiwisolver==1.0.1",
-                        "matplotlib==2.2.4",
-                        "pandas==0.23.4",
-                        "bokeh==1.4.0",
-                        "Pillow==5.4.1",
-                        "matplotlib-scalebar==0.5.1",
-                        "scipy==1.2.2",
-                        "python-dateutil==2.8.0",
-                    ]
-                )
             pip_install(".")
 
         m = "Successfully installed NetPyNE..."

{osbmodelvalidation-0.3.11 → osbmodelvalidation-0.4.0}/omv/engines/getnrn.py

@@ -1,20 +1,24 @@
 import os
 import sys
+import re
 from subprocess import check_output as co
 from omv.common.inout import inform
 from omv.common.inout import pip_install
 
 from omv.engines.utils.wdir import working_dir
 
+DEFAULT_NEURON_VERSION = "8.2.7"
+
+
+def _supports_pip_install(version):
+    return bool(re.match(r"^7\.8($|\.)|^8\.", version))
+
 
 def install_neuron(version):
     if not version:
-        if sys.version_info.major == 3:
-            version = "8.2.7"  
-        else:
-            version = "7.6"
+        version = DEFAULT_NEURON_VERSION
 
-    if sys.version_info.major == 3 and ("7.8" in version or "8." in version):
+    if _supports_pip_install(version):
         pip_install("neuron==%s" % version)
         import neuron
 
@@ -31,12 +35,6 @@ def install_neuron(version):
             )
             dl_file = "nrn-%s.tar.gz" % version
 
-            # See below re 7.8 on py2...
-            if "7.8" in version or "8.0" in version:
-                nrn_url = "https://github.com/neuronsimulator/nrn/archive/%s.tar.gz" % (
-                    version
-                )
-                dl_file = "%s.tar.gz" % version
             print(co(["wget", "-nv", nrn_url]))
             print(co(["tar", "xzvf", dl_file]))
             print(co(["mv", "nrn-%s" % version, "nrn"]))

{osbmodelvalidation-0.3.11 → osbmodelvalidation-0.4.0}/omv/engines/neuron_.py

@@ -1,5 +1,4 @@
 import os
-import sys
 from glob import glob
 import platform
 import subprocess as sp
@@ -175,10 +174,7 @@ class NeuronEngine(OMVEngine):
                 self.modelpath,
                 "\n".join(self.extra_pars),
             )
-            if sys.version_info[0] == 3:
-                c = dedent(cmd).encode()
-            else:
-                c = dedent(cmd)
+            c = dedent(cmd).encode()
             stdout, stderr = p.communicate(c)
             # with open('/tmp/omv_test.nrn.stdout', 'w') as f:
             #     f.write(stdout)

{osbmodelvalidation-0.3.11 → osbmodelvalidation-0.4.0}/omv/engines/pyneuron.py

@@ -2,7 +2,6 @@ import subprocess as sp
 from textwrap import dedent
 from omv.engines.utils.wdir import working_dir
 from os.path import dirname
-import sys
 
 from omv.engines.neuron_ import NeuronEngine
 
@@ -73,10 +72,7 @@ class PyNRNEngine(NeuronEngine):
             cmd = """\
             %s
             """ % ("\n".join(self.extra_pars))
-            if sys.version_info[0] == 3:
-                c = dedent(cmd).encode()
-            else:
-                c = dedent(cmd)
+            c = dedent(cmd).encode()
             stdout, stderr = p.communicate(c)
             # with open('/tmp/omv_test.nrn.stdout', 'w') as f:
             #     f.write(stdout)

{osbmodelvalidation-0.3.11 → osbmodelvalidation-0.4.0}/omv/omv_util.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
 

{osbmodelvalidation-0.3.11 → osbmodelvalidation-0.4.0}/omv/parse_omt.py

@@ -3,7 +3,6 @@ from omv.engines.engine import EngineInstallationError, EngineExecutionError
 from omv.omt_mep_parser import OMVTestParser
 from omv.common.inout import inform, check, trim_path
 from omv.tally import Tallyman
-import sys
 import platform
 
 
@@ -67,10 +66,7 @@ def parse_omt(omt_path, do_not_run=False, engine_version=None, ignore_non_py3=Fa
                     indent=3,
                 )
                 for rn, rv in results.items():
-                    if sys.version_info >= (3, 0):
-                        inform("{:<30}{:^20}".format(rn, check(rv)), indent=3)
-                    else:
-                        inform("{:<30}{:^20}".format(rn, check(rv)), indent=3)
+                    inform("{:<30}{:^20}".format(rn, check(rv)), indent=3)
                     if not rv:
                         some_failed = True
                 tally.add_experiment(exp, results)

osbmodelvalidation-0.4.0/omv/test/test_drop_py2_bits.py

@@ -0,0 +1,57 @@
+from contextlib import contextmanager
+import sys
+import types
+
+import pytest
+
+from omv.engines import getnetpyne, getnrn
+
+
+def test_install_neuron_defaults_to_modern_version(monkeypatch):
+    pip_calls = []
+
+    monkeypatch.setattr(getnrn, "pip_install", lambda spec: pip_calls.append(spec))
+    monkeypatch.setattr(getnrn, "inform", lambda *args, **kwargs: None)
+    monkeypatch.setitem(sys.modules, "neuron", types.SimpleNamespace())
+
+    getnrn.install_neuron(None)
+
+    assert pip_calls == [f"neuron=={getnrn.DEFAULT_NEURON_VERSION}"]
+
+
+@pytest.mark.parametrize("version", ["7.8.1", "8.2.7"])
+def test_install_neuron_supported_versions_use_pip(monkeypatch, version):
+    pip_calls = []
+
+    monkeypatch.setattr(getnrn, "pip_install", lambda spec: pip_calls.append(spec))
+    monkeypatch.setattr(getnrn, "inform", lambda *args, **kwargs: None)
+    monkeypatch.setitem(sys.modules, "neuron", types.SimpleNamespace())
+
+    getnrn.install_neuron(version)
+
+    assert pip_calls == [f"neuron=={version}"]
+
+
+@pytest.mark.parametrize(
+    "version,expected",
+    [("7.8", True), ("7.8.1", True), ("8.2.7", True), ("7.80", False), ("7.7.2", False)],
+)
+def test_supports_pip_install_matches_supported_families(version, expected):
+    assert getnrn._supports_pip_install(version) is expected
+
+
+def test_install_netpyne_without_version_only_installs_package(monkeypatch):
+    pip_calls = []
+
+    @contextmanager
+    def no_op_working_dir(_):
+        yield
+
+    monkeypatch.setattr(getnetpyne.os.path, "isdir", lambda _: True)
+    monkeypatch.setattr(getnetpyne, "working_dir", no_op_working_dir)
+    monkeypatch.setattr(getnetpyne, "check_output", lambda *_: "")
+    monkeypatch.setattr(getnetpyne, "pip_install", lambda spec: pip_calls.append(spec))
+
+    getnetpyne.install_netpyne()
+
+    assert pip_calls == ["."]

{osbmodelvalidation-0.3.11 → osbmodelvalidation-0.4.0}/setup.cfg

@@ -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

osbmodelvalidation-0.3.11/omv/engines/brian1.py

@@ -1,59 +0,0 @@
-import os
-import subprocess as sp
-
-from omv.common.inout import inform, trim_path, check_output, is_verbose
-from omv.engines.engine import OMVEngine, EngineExecutionError
-
-
-class Brian1Engine(OMVEngine):
-    name = "Brian"
-
-    python3_compatible = False
-
-    @staticmethod
-    def is_installed():
-        ret = False
-        try:
-            import brian
-
-            if is_verbose():
-                inform(
-                    "Brian version %s is correctly installed..." % brian.__version__,
-                    indent=2,
-                )
-
-            ret = "v%s" % brian.__version__
-
-        except Exception as err:
-            inform("Couldn't import Brian into Python: ", err, indent=1)
-            ret = False
-        return ret
-
-    @staticmethod
-    def install(version):
-        from omv.engines.getbrian1 import install_brian
-
-        home = os.environ["HOME"]
-        inform("Will fetch and install the latest Brian (version 1.x)", indent=2)
-        install_brian()
-        inform("Done...", indent=2)
-
-    def run(self):
-        try:
-            inform(
-                "Running file %s with %s" % (trim_path(self.modelpath), self.name),
-                indent=1,
-            )
-            self.stdout = check_output(
-                ["python", self.modelpath, "-nogui"],
-                cwd=os.path.dirname(self.modelpath),
-            )
-            self.returncode = 0
-        except sp.CalledProcessError as err:
-            self.returncode = err.returncode
-            self.stdout = err.output
-            raise EngineExecutionError
-        except Exception as err:
-            inform("Another error with running %s: " % self.name, err, indent=1)
-            self.returncode = -1
-            self.stdout = "???"

osbmodelvalidation-0.3.11/omv/engines/jneuromlbrian.py

@@ -1,65 +0,0 @@
-import os
-import subprocess as sp
-
-from omv.engines.jneuroml import JNeuroMLEngine
-from omv.engines.brian1 import Brian1Engine
-from omv.common.inout import inform, trim_path, check_output, is_verbose
-from omv.engines.engine import EngineExecutionError
-
-
-class JNeuroMLBrianEngine(JNeuroMLEngine):
-    name = "jNeuroML_Brian"
-
-    python3_compatible = Brian1Engine.python3_compatible
-
-    @staticmethod
-    def is_installed():
-        if is_verbose():
-            inform(
-                "Checking whether %s is installed..." % JNeuroMLBrianEngine.name,
-                indent=1,
-            )
-        return JNeuroMLEngine.is_installed() and Brian1Engine.is_installed()
-
-    @staticmethod
-    def install(version):
-        if not JNeuroMLEngine.is_installed():
-            JNeuroMLEngine.install(None)
-        if not Brian1Engine.is_installed():
-            Brian1Engine.install(version)
-
-        JNeuroMLBrianEngine.path = JNeuroMLEngine.path + ":" + Brian1Engine.path
-        JNeuroMLBrianEngine.environment_vars = {}
-        JNeuroMLBrianEngine.environment_vars.update(JNeuroMLEngine.environment_vars)
-        JNeuroMLBrianEngine.environment_vars.update(Brian1Engine.environment_vars)
-        inform("PATH: " + JNeuroMLBrianEngine.path)
-        inform("Env vars: %s" % JNeuroMLBrianEngine.environment_vars)
-
-    def run(self):
-        try:
-            inform(
-                "Running file %s with %s"
-                % (trim_path(self.modelpath), JNeuroMLBrianEngine.name),
-                indent=1,
-            )
-
-            from omv.engines.jneuroml import JNeuroMLEngine
-
-            jnml = JNeuroMLEngine.get_executable()
-
-            self.stdout = check_output(
-                [jnml, self.modelpath, "-brian"],
-                cwd=os.path.dirname(self.modelpath),
-                env=JNeuroMLEngine.get_environment(),
-            )
-            self.stdout += check_output(
-                ["python", self.modelpath.replace(".xml", "_brian.py"), "-nogui"],
-                cwd=os.path.dirname(self.modelpath),
-            )
-            inform("Success with running ", JNeuroMLBrianEngine.name, indent=1)
-            self.returncode = 0
-        except sp.CalledProcessError as err:
-            inform("Error with ", JNeuroMLBrianEngine.name, indent=1)
-            self.returncode = err.returncode
-            self.stdout = err.output
-            raise EngineExecutionError

osbmodelvalidation-0.3.11/omv/engines/pynnbrian1.py

@@ -1,59 +0,0 @@
-import os
-import subprocess as sp
-
-from omv.engines.brian1 import Brian1Engine
-from omv.engines.pynn import PyNNEngine
-
-from omv.common.inout import inform, trim_path, check_output, is_verbose
-from omv.engines.engine import EngineExecutionError
-
-
-class PyNNBrian1Engine(PyNNEngine):
-    name = "PyNN_Brian1"
-    python3_compatible = Brian1Engine.python3_compatible
-
-    @staticmethod
-    def is_installed():
-        if is_verbose():
-            inform(
-                "Checking whether %s is installed..." % PyNNBrian1Engine.name, indent=1
-            )
-        return PyNNEngine.is_installed() and Brian1Engine.is_installed()
-
-    @staticmethod
-    def install(version):
-        if not Brian1Engine.is_installed():
-            Brian1Engine.install(version)  # interpret version as version of Brian!
-            inform(
-                "%s installed Brian..." % PyNNBrian1Engine.name, indent=2, verbosity=1
-            )
-        if not PyNNEngine.is_installed():
-            PyNNEngine.install(None)
-            inform(
-                "%s installed PyNN..." % PyNNBrian1Engine.name, indent=2, verbosity=1
-            )
-
-        PyNNBrian1Engine.path = PyNNEngine.path + ":" + Brian1Engine.path
-        PyNNBrian1Engine.environment_vars = {}
-        PyNNBrian1Engine.environment_vars.update(PyNNEngine.environment_vars)
-        PyNNBrian1Engine.environment_vars.update(Brian1Engine.environment_vars)
-        inform("PATH: " + PyNNBrian1Engine.path)
-
-    def run(self):
-        try:
-            inform(
-                "Running file %s with %s" % (trim_path(self.modelpath), self.name),
-                indent=1,
-            )
-            self.stdout = check_output(
-                ["python", self.modelpath, "brian"], cwd=os.path.dirname(self.modelpath)
-            )
-            self.returncode = 0
-        except sp.CalledProcessError as err:
-            self.returncode = err.returncode
-            self.stdout = err.output
-            raise EngineExecutionError
-        except Exception as err:
-            inform("Another error with running %s: " % self.name, err, indent=1)
-            self.returncode = -1
-            self.stdout = "???"