Preparation for release

xenon-middleware · Jul 31, 2019 · a6fd42c · a6fd42c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,7 +1,12 @@
-Xenon 3.0.0
+Xenon 3.0.1
 -----------
 
-This is release 3.0.0 of Xenon.
+This is release 3.0.1 of Xenon.
+
+Notable changes compared to v3.0.1:
+-----------------------------------
+
+- fixed minute delay on shutdown when SSH adaptor was used (discussed as part of #654).
 
 Notable changes compared to v2.6.2:
 -----------------------------------

diff --git a/CITATION.cff b/CITATION.cff
@@ -58,7 +58,7 @@ authors:
     given-names: Arnold
     orcid: "https://orcid.org/0000-0003-1711-7961"
 cff-version: "1.0.3"
-date-released: 2019-06-13
+date-released: 2019-07-31
 doi: "10.5281/zenodo.597993"
 keywords: 
   - Java
@@ -79,4 +79,4 @@ license: Apache-2.0
 message: "If you use this software, please cite it using these metadata."
 repository-code: "https://github.com/xenon-middleware/xenon"
 title: Xenon
-version: "3.0.0"
+version: "3.0.1"
diff --git a/README.md b/README.md
@@ -92,7 +92,7 @@ and
 
 ```gradle
 	dependencies {
-	        compile group: 'nl.esciencecenter.xenon', name: 'xenon', version: '3.0.0'
+	        compile group: 'nl.esciencecenter.xenon', name: 'xenon', version: '3.0.1'
 	}
 
 ```

diff --git a/RELEASE.md b/RELEASE.md
@@ -38,10 +38,10 @@ to generate the metadata as used by Zenodo. Install ``cffconvert`` as follows:
 
 ```bash
 # install cffconvert in user space from PyPI
-pip install --user cffconvert
+pip3 install --user cffconvert
 
-# change directory
-cd <directory where the CITATION.cff lives>
+# change directory to xenon root dir (if needed)
+# cd <directory where the CITATION.cff lives>
 
 # check if the CITATION.cff file is valid (if there is no output, that 
 # means it's all good)
@@ -74,7 +74,7 @@ you should get something like this:
     Untracked files:
     (use "git add <file>..." to include in what will be committed)
 
-	docs/versions/3.0.0/
+	docs/versions/3.0.1/
 
 Add and commit these files using `git add` and `git commit` and `git push`.
 

diff --git a/build.gradle b/build.gradle
@@ -61,10 +61,10 @@ dependencies {
     compile group: 'com.google.guava', name: 'guava', version: '19.0'
 
     // webdav
-    compile group: 'javax.xml.bind', name: 'jaxb-api', version: '2.3.0'
-    compile group: 'com.sun.xml.bind', name: 'jaxb-core', version: '2.3.0'
-    compile group: 'com.sun.xml.bind', name: 'jaxb-impl', version: '2.3.0'
-    compile group: 'javax.activation', name: 'activation', version: '1.1.1'
+//    compile group: 'javax.xml.bind', name: 'jaxb-api', version: '2.3.0'
+//    compile group: 'com.sun.xml.bind', name: 'jaxb-core', version: '2.3.0'
+//    compile group: 'com.sun.xml.bind', name: 'jaxb-impl', version: '2.3.0'
+//    compile group: 'javax.activation', name: 'activation', version: '1.1.1'
     compile group: 'com.github.lookfirst', name: 'sardine', version: '5.8'
 
 //    compile group: 'joda-time', name: 'joda-time', version: '2.8.1'

diff --git a/docs/_data/version.yml b/docs/_data/version.yml
@@ -1 +1 @@
-current: 3.0.0
+current: 3.0.1
diff --git a/docs/versions/3.0.1/javadoc-devel/allclasses-index.html b/docs/versions/3.0.1/javadoc-devel/allclasses-index.html
diff --git a/docs/versions/3.0.1/javadoc-devel/allclasses.html b/docs/versions/3.0.1/javadoc-devel/allclasses.html
diff --git a/docs/versions/3.0.1/javadoc-devel/allpackages-index.html b/docs/versions/3.0.1/javadoc-devel/allpackages-index.html
@@ -0,0 +1,246 @@
+<!DOCTYPE HTML>
+<!-- NewPage -->
+<html lang="en">
+<head>
+<!-- Generated by javadoc -->
+<title>All Packages (xenon 3.0.1 API for Xenon developers)</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
+<link rel="stylesheet" type="text/css" href="jquery/jquery-ui.css" title="Style">
+<script type="text/javascript" src="script.js"></script>
+<script type="text/javascript" src="jquery/jszip/dist/jszip.min.js"></script>
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+<!--[if IE]>
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+<![endif]-->
+<script type="text/javascript" src="jquery/jquery-3.3.1.js"></script>
+<script type="text/javascript" src="jquery/jquery-migrate-3.0.1.js"></script>
+<script type="text/javascript" src="jquery/jquery-ui.js"></script>
+</head>
+<body>
+<script type="text/javascript"><!--
+    try {
+        if (location.href.indexOf('is-external=true') == -1) {
+            parent.document.title="All Packages (xenon 3.0.1 API for Xenon developers)";
+        }
+    }
+    catch(err) {
+    }
+//-->
+var pathtoroot = "./";
+var useModuleDirectories = true;
+loadScripts(document, 'script');</script>
+<noscript>
+<div>JavaScript is disabled on your browser.</div>
+</noscript>
+<header role="banner">
+<nav role="navigation">
+<div class="fixedNav">
+<!-- ========= START OF TOP NAVBAR ======= -->
+<div class="topNav"><a id="navbar.top">
+<!--   -->
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+<div class="skipNav"><a href="#skip.navbar.top" title="Skip navigation links">Skip navigation links</a></div>
+<a id="navbar.top.firstrow">
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+<ul class="navList" title="Navigation">
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+<li>Package</li>
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+<li><a href="deprecated-list.html">Deprecated</a></li>
+<li><a href="index-all.html">Index</a></li>
+<li><a href="help-doc.html">Help</a></li>
+</ul>
+</div>
+<div class="subNav">
+<ul class="navList" id="allclasses_navbar_top">
+<li><a href="allclasses.html">All&nbsp;Classes</a></li>
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+<ul class="navListSearch">
+<li><label for="search">SEARCH:</label>
+<input type="text" id="search" value="search" disabled="disabled">
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+<script type="text/javascript"><!--
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+<div class="navPadding">&nbsp;</div>
+<script type="text/javascript"><!--
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+</nav>
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+<main role="main">
+<div class="header">
+<h1 title="All&amp;nbsp;Packages" class="title">All&nbsp;Packages</h1>
+</div>
+<div class="allPackagesContainer">
+<ul class="blockList">
+<li class="blockList">
+<table class="packagesSummary">
+<caption><span>Package Summary</span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Package</th>
+<th class="colLast" scope="col">Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<th class="colFirst" scope="row"><a href="nl/esciencecenter/xenon/package-summary.html">nl.esciencecenter.xenon</a></th>
+<td class="colLast">
+<div class="block">This package is the main entry point into the Xenon API.</div>
+</td>
+</tr>
+<tr class="rowColor">
+<th class="colFirst" scope="row"><a href="nl/esciencecenter/xenon/adaptors/package-summary.html">nl.esciencecenter.xenon.adaptors</a></th>
+<td class="colLast">&nbsp;</td>
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+<tr class="altColor">
+<th class="colFirst" scope="row"><a href="nl/esciencecenter/xenon/adaptors/filesystems/package-summary.html">nl.esciencecenter.xenon.adaptors.filesystems</a></th>
+<td class="colLast">&nbsp;</td>
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+<th class="colFirst" scope="row"><a href="nl/esciencecenter/xenon/adaptors/filesystems/ftp/package-summary.html">nl.esciencecenter.xenon.adaptors.filesystems.ftp</a></th>
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+<th class="colFirst" scope="row"><a href="nl/esciencecenter/xenon/adaptors/filesystems/local/package-summary.html">nl.esciencecenter.xenon.adaptors.filesystems.local</a></th>
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+<td class="colLast">&nbsp;</td>
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+<tr class="rowColor">
+<th class="colFirst" scope="row"><a href="nl/esciencecenter/xenon/adaptors/schedulers/torque/package-summary.html">nl.esciencecenter.xenon.adaptors.schedulers.torque</a></th>
+<td class="colLast">&nbsp;</td>
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+<tr class="altColor">
+<th class="colFirst" scope="row"><a href="nl/esciencecenter/xenon/adaptors/shared/ssh/package-summary.html">nl.esciencecenter.xenon.adaptors.shared.ssh</a></th>
+<td class="colLast">&nbsp;</td>
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+<tr class="rowColor">
+<th class="colFirst" scope="row"><a href="nl/esciencecenter/xenon/credentials/package-summary.html">nl.esciencecenter.xenon.credentials</a></th>
+<td class="colLast">
+<div class="block">This package contains classes and interfaces for managing credentials.</div>
+</td>
+</tr>
+<tr class="altColor">
+<th class="colFirst" scope="row"><a href="nl/esciencecenter/xenon/filesystems/package-summary.html">nl.esciencecenter.xenon.filesystems</a></th>
+<td class="colLast">
+<div class="block">This package contains classes and interfaces for manipulating files.</div>
+</td>
+</tr>
+<tr class="rowColor">
+<th class="colFirst" scope="row"><a href="nl/esciencecenter/xenon/schedulers/package-summary.html">nl.esciencecenter.xenon.schedulers</a></th>
+<td class="colLast">
+<div class="block">This package contains the classes and interfaces used to run jobs.</div>
+</td>
+</tr>
+<tr class="altColor">
+<th class="colFirst" scope="row"><a href="nl/esciencecenter/xenon/utils/package-summary.html">nl.esciencecenter.xenon.utils</a></th>
+<td class="colLast">
+<div class="block">This package is contains several utility classes.</div>
+</td>
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