For NML v2.1 release

.github/workflows/docs.yml

@@ -0,0 +1,116 @@
+# This workflow will build a Java project with Maven
+# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven
+
+name: Publish Javadocs
+
+on:
+  push:
+    branches: [ development ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - uses: nelonoel/branch-name@v1.0.1
+
+    - name: Set up JDK 11
+      uses: actions/setup-java@v1
+      with:
+        java-version: 11
+        java-package: jdk
+
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+
+    - name: Install GH import
+      run: |
+        python -m pip install --upgrade pip
+        pip install ghp-import
+
+    - name: Checkout NeuroML2
+      uses: actions/checkout@v2
+      with:
+        repository: NeuroML/NeuroML2
+        ref: development
+        path: NeuroML2
+
+    - name: Checkout org.lemsml
+      uses: actions/checkout@v2
+      with:
+        repository: LEMS/jLEMS
+        ref: development
+        path: jLEMS
+
+    - name: Checkout org.neuroml.model.injectingplugin
+      uses: actions/checkout@v2
+      with:
+        repository: NeuroML/org.neuroml.model.injectingplugin
+        ref: development
+        path: org.neuroml.model.injectingplugin
+
+    - name: Checkout org.neuroml1.model
+      uses: actions/checkout@v2
+      with:
+        repository: NeuroML/org.neuroml1.model
+        ref: development
+        path: org.neuroml1.model
+
+    - name: Checkout org.neuroml.model
+      uses: actions/checkout@v2
+      with:
+        repository: NeuroML/org.neuroml.model
+        ref: development
+        path: org.neuroml.model
+
+    - name: Checkout org.neuroml.export
+      uses: actions/checkout@v2
+      with:
+        repository: NeuroML/org.neuroml.export
+        ref: development
+        path: org.neuroml.export
+
+    - name: Checkout org.neuroml.import
+      uses: actions/checkout@v2
+      with:
+        repository: NeuroML/org.neuroml.import
+        ref: development
+        path: org.neuroml.import
+
+
+    - name: Install NeuroML deps
+      run: |
+        pushd jLEMS
+        mvn install
+        popd
+        pushd NeuroML2
+        mvn install
+        popd
+        pushd org.neuroml.model.injectingplugin
+        mvn install
+        popd
+        pushd org.neuroml1.model
+        mvn install
+        popd
+        pushd org.neuroml.model
+        mvn install
+        popd
+        pushd org.neuroml.export
+        mvn install
+        popd
+        pushd org.neuroml.import
+        mvn install
+        popd
+
+    - name: Build docs
+      run: |
+        mvn javadoc:javadoc
+
+    - name: Publish documentation on GH pages
+      run: |
+        ghp-import -f -m "Regenerate documentation" -b gh-pages -n -p target/site/apidocs
+

.travis.yml

@@ -1,13 +1,13 @@
-dist: trusty
-sudo: false
+dist: xenial
 
 language: java
 
 jdk:
-  - openjdk7
+  - oraclejdk11
+
   - openjdk8
-  - oraclejdk8
-  # - oraclejdk9
+  #- openjdk10 # Some non deterministic recurring error with jdk10...
+  - openjdk11
 
 install:
     - export main_repo_branch=$TRAVIS_BRANCH
@@ -18,6 +18,7 @@ install:
     - ls -alt
     - git branch
     - python getNeuroML.py $main_repo_branch  # will call mvn install on this & other repos
+    - mvn dependency:tree
     - pwd
 
 script:

README.md

@@ -1,6 +1,13 @@
 jNeuroML
 ========
 
+[![GitHub](https://img.shields.io/github/license/NeuroML/jNeuroML)](https://github.com/NeuroML/jNeuroML/blob/master/LICENSE.lesser)
+[![GitHub pull requests](https://img.shields.io/github/issues-pr/NeuroML/jNeuroML)](https://github.com/NeuroML/jNeuroML/pulls)
+[![GitHub issues](https://img.shields.io/github/issues/NeuroML/jNeuroML)](https://github.com/NeuroML/jNeuroML/issues)
+[![GitHub Org's stars](https://img.shields.io/github/stars/NeuroML?style=social)](https://github.com/NeuroML)
+[![Twitter Follow](https://img.shields.io/twitter/follow/NeuroML?style=social)](https://twitter.com/NeuroML)
+
+
 There are a number of repositories in active development under GitHub for handling [NeuroML](https://github.com/NeuroML) 
 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. 
 
@@ -21,6 +28,18 @@ You can also check out the most recent verson of the jar file using:
     svn checkout svn://svn.code.sf.net/p/neuroml/code/jNeuroMLJar
     cd jNeuroMLJar
 
+
+### Fedora
+
+The [NeuroFedora](https://neuro.fedoraproject.org) community initiative provides jNeuroML for use on the [Fedora Linux Distribution](https://getfedora.org).
+Fedora users can install jNeuroML using the following commands:
+
+    sudo dnf copr enable @neurofedora/neurofedora-extra
+    sudo dnf install jneuroml
+
+Please see the [project documentation](https://docs.fedoraproject.org/en-US/neurofedora/copr/) for more information.
+
+
 Usage
 -----
 
@@ -76,10 +95,3 @@ If you prefer using/installing/coding in Python, try out [pyNeuroML](https://git
 [![Build Status](https://travis-ci.com/NeuroML/jNeuroML.png?branch=master)](https://travis-ci.com/NeuroML/jNeuroML)
 
 This code is distributed under the terms of the GNU Lesser General Public License.
-
-
-
-
-
-
-

getNeuroML.py

@@ -4,6 +4,8 @@
 import sys
 import os.path as op
 import subprocess
+from textwrap import dedent
+
 
 def main():
     """Main"""
@@ -50,9 +52,7 @@ def main():
     # Which repos use a development branch?
     dev_branch_repos = neuroml2_spec_repo + neuroml_repos + jlems_repo
 
-
-    all_repos = lems_repos  + neuroml_repos 
-
+    all_repos = lems_repos + neuroml_repos
 
     # Set the preferred method for cloning from GitHub
     github_pref = "HTTP"
@@ -68,32 +68,31 @@ def main():
 
         local_dir = ".." + os.sep + repo.split("/")[1]
 
-        if mode is "clean":
-            print("------ Cleaning: %s -------"%repo)
+        if mode == "clean":
+            print("------ Cleaning: %s -------" % repo)
             if repo in java_repos:
                 command = "mvn clean"
                 print("It's a Java repository, so cleaning using Maven...")
                 info = execute_command_in_dir(command, local_dir)
 
-        if mode is "update":
-
-            print("------ Updating: %s -------" %repo)
+        if mode == "update":
+            print("------ Updating: %s -------" % repo)
 
             runMvnInstall = False
 
             if not op.isdir(local_dir):
                 command = "git clone %s%s" % (pre_gh[github_pref], repo)
-                print ("Creating a new directory: %s by cloning from GitHub" % \
-                    (local_dir))
+                print("Creating a new directory: %s by cloning from GitHub" %
+                      (local_dir))
                 execute_command_in_dir(command, "..")
 
                 runMvnInstall = True
 
             if switch_to_branch:
                 if (repo in dev_branch_repos):
                     command = "git checkout %s" % (switch_to_branch)
-                    print ("Switching to branch: %s" % (switch_to_branch))
-                    exit_on_fail = switch_to_branch is not "experimental"
+                    print("Switching to branch: %s" % (switch_to_branch))
+                    exit_on_fail = switch_to_branch != "experimental"
                     execute_command_in_dir(command, local_dir, exit_on_fail)
                     runMvnInstall = True
 
@@ -107,55 +106,54 @@ def main():
                 or not op.isdir(local_dir + os.sep + "target") \
                 or ("jNeuroML" in repo)
 
-            if (repo in java_repos or repo in neuroml2_spec_repo) and runMvnInstall:
+            if (repo in java_repos or repo in neuroml2_spec_repo) \
+                    and runMvnInstall:
                 command = "mvn install"
                 print("It's a Java repository, so installing using Maven...")
                 info = execute_command_in_dir(command, local_dir)
 
-                #The code below needs a non trivial rewrite due to python3 differences.
-
-                #                
+                # The code below needs a non trivial rewrite due to python3
+                # differences.
                 if str("BUILD SUCCESS") in str(info):
-                    print("Successful installation using : %s!" %command)
+                    print("Successful installation using : %s!" % command)
                 else:
-                    print("Problem installing using : %s!" %command)
+                    print("Problem installing using : %s!" % command)
                     print(info)
                     exit(1)
 
-    if mode is "update":
+    if mode == "update":
         print("All repositories successfully updated & Java modules built!")
-        print("You should be able to run some examples straight " \
-              "away using jnml: ")
-        if os.name is not 'nt':
-            print("  ./jnml "\
-                "-validate ../NeuroML2/examples/NML2_FullNeuroML.nml")
-            print("  ./jnml " \
-                "../NeuroML2/LEMSexamples/LEMS_NML2_Ex2_Izh.xml")
+        print("You should be able to run examples straight away using jnml: ")
+        if os.name != 'nt':
+            print("  ./jnml " +
+                  "-validate ../NeuroML2/examples/NML2_FullNeuroML.nml")
+            print("  ./jnml " +
+                  "../NeuroML2/LEMSexamples/LEMS_NML2_Ex2_Izh.xml")
         else:
-            print("  jnml -validate " \
-                "..\\NeuroML2\\examples\\NML2_FullNeuroML.nml")
-            print("  jnml " \
-                "..\\NeuroML2\\LEMSexamples\\LEMS_NML2_Ex2_Izh.xml")
-    if mode is "clean":
+            print("  jnml -validate " +
+                  "..\\NeuroML2\\examples\\NML2_FullNeuroML.nml")
+            print("  jnml " +
+                  "..\\NeuroML2\\LEMSexamples\\LEMS_NML2_Ex2_Izh.xml")
+    if mode == "clean":
         print("All repositories successfully cleaned!")
 
 
-
-
 def execute_command_in_dir(command, directory, exit_on_fail=True):
     """Execute a command in specific working directory"""
     if os.name == 'nt':
         directory = os.path.normpath(directory)
 
-    print(">>>  Executing: (%s) in dir: %s (%s)" % (command, directory, os.path.abspath(directory)))
+    print(">>>  Executing: (%s) in dir: %s (%s)" %
+          (command, directory, os.path.abspath(directory)))
 
-    p = subprocess.Popen(command, cwd=directory, shell=True, stdout=subprocess.PIPE)
+    p = subprocess.Popen(command, cwd=directory, shell=True,
+                         stdout=subprocess.PIPE)
     return_str = p.communicate()
 
-    if p.returncode != 0:       
-        print("Error: %s" % p.returncode)          
+    if p.returncode != 0:
+        print("Error: %s" % p.returncode)
         print(return_str[0])
-        if exit_on_fail: 
+        if exit_on_fail:
             exit(p.returncode)
     if (sys.version_info > (3, 0)):
         return return_str[0].decode("utf-8")
@@ -164,15 +162,27 @@ def execute_command_in_dir(command, directory, exit_on_fail=True):
 
 
 def help_info():
-    print("\nUsage:\n\n    python getNeuroML.py\n        " \
-        "Pull (or clone) the latest version of all NeuroML 2 repos & " \
-        "compile/install with Maven if applicable\n\n" \
-        "    python getNeuroML.py clean\n        " 
-        "Run 'mvn clean' on all Java repos\n\n" \
-        "    python getNeuroML.py master\n       " \
-        "Switch all repos to master branch\n\n" \
-        "    python getNeuroML.py development\n       " \
-        "Switch relevant repos to development branch\n\n")
+    usage = (
+        """\
+        Usage: python getNeuroML.py [OPTION]
+        Script to install NeuroML libraries.
+        Note: requires internet connectivity.
+
+        python getNeuroML.py
+            Pull (or clone) the latest version of all NeuroML 2 repos &
+            compile/install with Maven if applicable
+
+        python getNeuroML.py clean
+            Run 'mvn clean' on all Java repos
+
+        python getNeuroML.py master
+            Switch all repos to master branch
+
+        python getNeuroML.py development
+            Switch relevant repos to development branch
+        """
+    )
+    print(dedent(usage))
 
 
 if __name__ == "__main__":