Merge branch 'master' into test_mac

Author: pgleeson

.github/workflows/ci.yml

@@ -48,13 +48,15 @@ jobs:
           - jNeuroML_validatev1
           - Py_neuroConstruct
           - pyNeuroML
+          - pyNeuroML_validate_sbml
           - jNeuroML_Moose
-          - MOOSE
+          - MOOSE:3.1.5
+          - XPP
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python  ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version:  ${{ matrix.python-version }}
 

.github/workflows/ci_versions.yml

@@ -0,0 +1,53 @@
+name: Test across versions
+
+on:
+  push:
+    branches: [ master, development, experimental, test* ]
+  pull_request:
+    branches: [ master, development, experimental, test* ]
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.runs-on }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        runs-on: [ubuntu-latest, macos-latest, macos-14]
+        exclude:
+          - runs-on: macos-14
+            python-version: "3.9"
+
+    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 HDF5 for pytables on macos-14
+      run: |
+        # if [[  ${{ matrix.python-version }} == "3.11" ]] || [[  ${{ matrix.python-version }} == "3.12" ]]; then 
+        if [[  ${{ matrix.runs-on }} == "macos-14" ]]; then brew install hdf5 ; fi;
+        #fi;
+
+
+    - name: Install OMV
+      run: |
+        pip install .
+        pip list
+
+    - name: Run simple OMV tests
+      run: |
+        omv install pyNeuroML
+        omv test -V utilities/tests/.test.ex9.jnmlbrian2.omt
+
+
+    - name: OMV final version info
+      run: |
+        omv list -V # list installed engines
+        env
+        pip list

.github/workflows/python-publish.yml

@@ -0,0 +1,51 @@
+# https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+name: Publish on PyPi
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/OSBModelValidation
+    permissions:
+      id-token: write
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

LICENSE.lesser

@@ -0,0 +1,166 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
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+   Library is used in it and that the Library and its use are
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+  4. Combined Works.
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+  You may convey a Combined Work under terms of your choice that,
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+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
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+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version.
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.
+

README.md

@@ -1,4 +1,10 @@
 [![Continuous builds](https://github.com/OpenSourceBrain/osb-model-validation/actions/workflows/ci.yml/badge.svg)](https://github.com/OpenSourceBrain/osb-model-validation/actions/workflows/ci.yml)
+[![PyPI](https://img.shields.io/pypi/v/OSBModelValidation)](https://pypi.org/project/OSBModelValidation/)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/OSBModelValidation)](https://pypi.org/project/OSBModelValidation/)
+[![GitHub](https://img.shields.io/github/license/OpenSourceBrain/osb-model-validation)](https://github.com/OpenSourceBrain/osb-model-validation/blob/master/LICENSE.lesser)
+[![GitHub pull requests](https://img.shields.io/github/issues-pr/OpenSourceBrain/osb-model-validation)](https://github.com/OpenSourceBrain/osb-model-validation/pulls)
+[![GitHub issues](https://img.shields.io/github/issues/OpenSourceBrain/osb-model-validation)](https://github.com/OpenSourceBrain/osb-model-validation/issues)
+[![Gitter](https://badges.gitter.im/NeuroML/community.svg)](https://gitter.im/NeuroML/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
 ------------------------------------------
 
 # OSB Model Validation
@@ -18,38 +24,20 @@ To see this framework in action, click on some of the green buttons below:
 
 This framework has been used to test the 30+ NeuroML and PyNN models described in the [Open Source Brain paper (Gleeson et al. 2019)](https://www.cell.com/neuron/fulltext/S0896-6273(19)30444-1), and [many more](https://github.com/OpenSourceBrain/.github/blob/main/testsheet/README.md).
 
-Note: [Travis-CI](https://travis-ci.com) is no longer the preferred testing platform due to limitations with number of free test runs, all CI testing has been migrated to [GitHub Actions](https://github.com/features/actions).
-
 ## Installation
 
 Quick system-wide install:
 
 ``` bash
-pip install git+https://github.com/OpenSourceBrain/osb-model-validation
+pip install osb-model-validation
 ```
 
-System-wide install from cloned repository:
+Or you can install from cloned repository (preferably in a virtual environment):
 
 ``` bash
 git clone https://github.com/OpenSourceBrain/osb-model-validation.git
 cd osb-model-validation
-sudo python setup.py install
-```
-
-If you'd like to install only in a virtual environment in the `.venv` directory:
-
-``` bash
-git clone https://github.com/OpenSourceBrain/osb-model-validation.git
-cd osb-model-validation
-
-# Create the virtual environment
-python -m venv .venv
-# Activate the virtual environment
-source .venv/bin/activate
-python setup.py install
-
-# To deactivate the virtual environment:
-deactivate
+pip install .
 ```
 
 ## Instructions
@@ -165,6 +153,6 @@ Running validation tests locally ensures that you can quickly check if any chang
 Since you can run the validation with different [engines](https://github.com/OpenSourceBrain/osb-model-validation/tree/master/omv/engines) to use different simulators, this also allows you to quickly verify that your model gives similar results using these different tools.
 
 
-### Running tests automatically on ~~Travis-CI~~
+### Running tests automatically on GitHub Actions
 
-**Note: Travis-CI is no longer the preferred platform for testing, [GitHub Actions](https://github.com/features/actions) is. To use OMV with GHA, copy an existing configuration file, e.g. https://github.com/OpenSourceBrain/ACnet2/blob/master/.github/workflows/omv-ci.yml**
+To use OMV with GHA, copy an existing configuration file, e.g. https://github.com/OpenSourceBrain/ACnet2/blob/master/.github/workflows/omv-ci.yml and place it in the required repository.

omv/common/inout.py

@@ -121,8 +121,8 @@ def check_output(cmds, cwd=".", shell=False, verbosity=0, env=None):
 
     except sp.CalledProcessError as err:
         inform(
-            "Error running commands: %s in %s (return code: %s)"
-            % (cmds, cwd, err.returncode),
+            "CalledProcessError running commands: %s in %s (return code: %s), output:\n%s"
+            % (cmds, cwd, err.returncode, err.output),
             indent=2,
             verbosity=verbosity,
         )

omv/engines/__init__.py

@@ -23,6 +23,7 @@
 # from omv.engines.brian1 import Brian1Engine
 from omv.engines.brian2_ import Brian2Engine
 from omv.engines.arbor_ import ArborEngine
+from omv.engines.xpp import XppEngine
 from omv.engines.eden_ import EdenEngine
 from omv.engines.nestsli import NestEngine
 from omv.engines.pynest import PyNestEngine
@@ -41,6 +42,7 @@
 from omv.engines.netpyne__np2 import NetPyNENP2Engine
 from omv.engines.pyneuroconstruct import PyneuroConstructEngine
 from omv.engines.pyneuroml_ import PyNeuroMLEngine
+from omv.engines.pyneuromlvalidatesbml import PyNeuroMLValidateSBMLEngine
 
 
 OMVEngines = {

omv/engines/brian2_.py

@@ -17,7 +17,7 @@ def is_installed():
             inform(
                 "Brian2 version %s is correctly installed..." % brian2.__version__,
                 indent=2,
-                verbosity=2,
+                verbosity=1,
             )
 
             ret = "v%s" % brian2.__version__

omv/engines/getarbor.py

@@ -3,7 +3,7 @@
 
 def install_arbor(version=None):
     if not version:
-        version = "0.8.1"
+        version = "0.9.0"
     try:
         pip_install("arbor==%s" % version)
         import arbor