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Merge pull request #80 from NeuroML/development
For NML v2.1 release
2 parents 7d1aa12 + 5174bf8 commit f953e6e

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‎.github/workflows/docs.yml‎

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# This workflow will build a Java project with Maven
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# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven
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name: Publish Javadocs
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on:
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push:
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branches: [ development ]
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- uses: nelonoel/[email protected]
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- name: Set up JDK 11
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uses: actions/setup-java@v1
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with:
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java-version: 11
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java-package: jdk
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- name: Set up Python 3.9
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uses: actions/setup-python@v2
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with:
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python-version: 3.9
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- name: Install GH import
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run: |
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python -m pip install --upgrade pip
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pip install ghp-import
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- name: Checkout NeuroML2
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uses: actions/checkout@v2
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with:
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repository: NeuroML/NeuroML2
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ref: development
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path: NeuroML2
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- name: Checkout org.lemsml
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uses: actions/checkout@v2
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with:
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repository: LEMS/jLEMS
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ref: development
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path: jLEMS
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- name: Checkout org.neuroml.model.injectingplugin
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uses: actions/checkout@v2
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with:
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repository: NeuroML/org.neuroml.model.injectingplugin
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ref: development
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path: org.neuroml.model.injectingplugin
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- name: Checkout org.neuroml1.model
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uses: actions/checkout@v2
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with:
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repository: NeuroML/org.neuroml1.model
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ref: development
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path: org.neuroml1.model
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- name: Checkout org.neuroml.model
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uses: actions/checkout@v2
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with:
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repository: NeuroML/org.neuroml.model
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ref: development
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path: org.neuroml.model
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- name: Checkout org.neuroml.export
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uses: actions/checkout@v2
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with:
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repository: NeuroML/org.neuroml.export
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ref: development
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path: org.neuroml.export
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- name: Checkout org.neuroml.import
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uses: actions/checkout@v2
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with:
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repository: NeuroML/org.neuroml.import
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ref: development
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path: org.neuroml.import
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- name: Install NeuroML deps
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run: |
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pushd jLEMS
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mvn install
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popd
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pushd NeuroML2
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mvn install
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popd
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pushd org.neuroml.model.injectingplugin
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mvn install
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popd
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pushd org.neuroml1.model
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mvn install
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popd
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pushd org.neuroml.model
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mvn install
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popd
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pushd org.neuroml.export
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mvn install
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popd
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pushd org.neuroml.import
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mvn install
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popd
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- name: Build docs
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run: |
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mvn javadoc:javadoc
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- name: Publish documentation on GH pages
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run: |
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ghp-import -f -m "Regenerate documentation" -b gh-pages -n -p target/site/apidocs
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‎.travis.yml‎

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dist: trusty
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sudo: false
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dist: xenial
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language: java
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jdk:
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- openjdk7
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- oraclejdk11
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- openjdk8
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- oraclejdk8
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# - oraclejdk9
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#- openjdk10 # Some non deterministic recurring error with jdk10...
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- openjdk11
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install:
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- export main_repo_branch=$TRAVIS_BRANCH
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- ls -alt
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- git branch
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- python getNeuroML.py $main_repo_branch # will call mvn install on this & other repos
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- mvn dependency:tree
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- pwd
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script:

‎README.md‎

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11
jNeuroML
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========
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[![GitHub](https://img.shields.io/github/license/NeuroML/jNeuroML)](https://github.com/NeuroML/jNeuroML/blob/master/LICENSE.lesser)
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[![GitHub pull requests](https://img.shields.io/github/issues-pr/NeuroML/jNeuroML)](https://github.com/NeuroML/jNeuroML/pulls)
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[![GitHub issues](https://img.shields.io/github/issues/NeuroML/jNeuroML)](https://github.com/NeuroML/jNeuroML/issues)
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[![GitHub Org's stars](https://img.shields.io/github/stars/NeuroML?style=social)](https://github.com/NeuroML)
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[![Twitter Follow](https://img.shields.io/twitter/follow/NeuroML?style=social)](https://twitter.com/NeuroML)
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There are a number of repositories in active development under GitHub for handling [NeuroML](https://github.com/NeuroML)
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and [LEMS](https://github.com/LEMS) with Java. To make it easier to access all of this functionality, we've created a single package, jNeuroML, which allows access to most of this functionality through a simple command line interface and requires minimal installation.
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svn checkout svn://svn.code.sf.net/p/neuroml/code/jNeuroMLJar
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cd jNeuroMLJar
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### Fedora
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The [NeuroFedora](https://neuro.fedoraproject.org) community initiative provides jNeuroML for use on the [Fedora Linux Distribution](https://getfedora.org).
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Fedora users can install jNeuroML using the following commands:
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sudo dnf copr enable @neurofedora/neurofedora-extra
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sudo dnf install jneuroml
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Please see the [project documentation](https://docs.fedoraproject.org/en-US/neurofedora/copr/) for more information.
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Usage
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-----
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[![Build Status](https://travis-ci.com/NeuroML/jNeuroML.png?branch=master)](https://travis-ci.com/NeuroML/jNeuroML)
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This code is distributed under the terms of the GNU Lesser General Public License.
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‎getNeuroML.py‎

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import sys
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import os.path as op
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import subprocess
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from textwrap import dedent
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def main():
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"""Main"""
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# Which repos use a development branch?
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dev_branch_repos = neuroml2_spec_repo + neuroml_repos + jlems_repo
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all_repos = lems_repos + neuroml_repos
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all_repos = lems_repos + neuroml_repos
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# Set the preferred method for cloning from GitHub
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github_pref = "HTTP"
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local_dir = ".." + os.sep + repo.split("/")[1]
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if mode is "clean":
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print("------ Cleaning: %s -------"%repo)
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if mode == "clean":
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print("------ Cleaning: %s -------" % repo)
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if repo in java_repos:
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command = "mvn clean"
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print("It's a Java repository, so cleaning using Maven...")
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info = execute_command_in_dir(command, local_dir)
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78-
if mode is "update":
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print("------ Updating: %s -------" %repo)
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if mode == "update":
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print("------ Updating: %s -------" % repo)
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runMvnInstall = False
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8483
if not op.isdir(local_dir):
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command = "git clone %s%s" % (pre_gh[github_pref], repo)
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print ("Creating a new directory: %s by cloning from GitHub" % \
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(local_dir))
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print("Creating a new directory: %s by cloning from GitHub" %
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(local_dir))
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execute_command_in_dir(command, "..")
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runMvnInstall = True
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if switch_to_branch:
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if (repo in dev_branch_repos):
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command = "git checkout %s" % (switch_to_branch)
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print ("Switching to branch: %s" % (switch_to_branch))
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exit_on_fail = switch_to_branch is not "experimental"
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print("Switching to branch: %s" % (switch_to_branch))
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exit_on_fail = switch_to_branch != "experimental"
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execute_command_in_dir(command, local_dir, exit_on_fail)
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runMvnInstall = True
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107106
or not op.isdir(local_dir + os.sep + "target") \
108107
or ("jNeuroML" in repo)
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110-
if (repo in java_repos or repo in neuroml2_spec_repo) and runMvnInstall:
109+
if (repo in java_repos or repo in neuroml2_spec_repo) \
110+
and runMvnInstall:
111111
command = "mvn install"
112112
print("It's a Java repository, so installing using Maven...")
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info = execute_command_in_dir(command, local_dir)
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#The code below needs a non trivial rewrite due to python3 differences.
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#
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# The code below needs a non trivial rewrite due to python3
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# differences.
118117
if str("BUILD SUCCESS") in str(info):
119-
print("Successful installation using : %s!" %command)
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print("Successful installation using : %s!" % command)
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else:
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print("Problem installing using : %s!" %command)
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print("Problem installing using : %s!" % command)
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print(info)
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exit(1)
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125-
if mode is "update":
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if mode == "update":
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print("All repositories successfully updated & Java modules built!")
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print("You should be able to run some examples straight " \
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"away using jnml: ")
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if os.name is not 'nt':
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print(" ./jnml "\
131-
"-validate ../NeuroML2/examples/NML2_FullNeuroML.nml")
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print(" ./jnml " \
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"../NeuroML2/LEMSexamples/LEMS_NML2_Ex2_Izh.xml")
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print("You should be able to run examples straight away using jnml: ")
127+
if os.name != 'nt':
128+
print(" ./jnml " +
129+
"-validate ../NeuroML2/examples/NML2_FullNeuroML.nml")
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print(" ./jnml " +
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"../NeuroML2/LEMSexamples/LEMS_NML2_Ex2_Izh.xml")
134132
else:
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print(" jnml -validate " \
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"..\\NeuroML2\\examples\\NML2_FullNeuroML.nml")
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print(" jnml " \
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"..\\NeuroML2\\LEMSexamples\\LEMS_NML2_Ex2_Izh.xml")
139-
if mode is "clean":
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print(" jnml -validate " +
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"..\\NeuroML2\\examples\\NML2_FullNeuroML.nml")
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print(" jnml " +
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"..\\NeuroML2\\LEMSexamples\\LEMS_NML2_Ex2_Izh.xml")
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if mode == "clean":
140138
print("All repositories successfully cleaned!")
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145141
def execute_command_in_dir(command, directory, exit_on_fail=True):
146142
"""Execute a command in specific working directory"""
147143
if os.name == 'nt':
148144
directory = os.path.normpath(directory)
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150-
print(">>> Executing: (%s) in dir: %s (%s)" % (command, directory, os.path.abspath(directory)))
146+
print(">>> Executing: (%s) in dir: %s (%s)" %
147+
(command, directory, os.path.abspath(directory)))
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152-
p = subprocess.Popen(command, cwd=directory, shell=True, stdout=subprocess.PIPE)
149+
p = subprocess.Popen(command, cwd=directory, shell=True,
150+
stdout=subprocess.PIPE)
153151
return_str = p.communicate()
154152

155-
if p.returncode != 0:
156-
print("Error: %s" % p.returncode)
153+
if p.returncode != 0:
154+
print("Error: %s" % p.returncode)
157155
print(return_str[0])
158-
if exit_on_fail:
156+
if exit_on_fail:
159157
exit(p.returncode)
160158
if (sys.version_info > (3, 0)):
161159
return return_str[0].decode("utf-8")
@@ -164,15 +162,27 @@ def execute_command_in_dir(command, directory, exit_on_fail=True):
164162

165163

166164
def help_info():
167-
print("\nUsage:\n\n python getNeuroML.py\n " \
168-
"Pull (or clone) the latest version of all NeuroML 2 repos & " \
169-
"compile/install with Maven if applicable\n\n" \
170-
" python getNeuroML.py clean\n "
171-
"Run 'mvn clean' on all Java repos\n\n" \
172-
" python getNeuroML.py master\n " \
173-
"Switch all repos to master branch\n\n" \
174-
" python getNeuroML.py development\n " \
175-
"Switch relevant repos to development branch\n\n")
165+
usage = (
166+
"""\
167+
Usage: python getNeuroML.py [OPTION]
168+
Script to install NeuroML libraries.
169+
Note: requires internet connectivity.
170+
171+
python getNeuroML.py
172+
Pull (or clone) the latest version of all NeuroML 2 repos &
173+
compile/install with Maven if applicable
174+
175+
python getNeuroML.py clean
176+
Run 'mvn clean' on all Java repos
177+
178+
python getNeuroML.py master
179+
Switch all repos to master branch
180+
181+
python getNeuroML.py development
182+
Switch relevant repos to development branch
183+
"""
184+
)
185+
print(dedent(usage))
176186

177187

178188
if __name__ == "__main__":

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