<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN" "http://www.w3.org/TR/REC-html40/loose.dtd">
<html lang="en">
<head>
<meta content="text/html; charset=US-ASCII" http-equiv="Content-Type">
<title>
GitLab
</title>
<style>img {
max-width: 100%; height: auto;
}
</style>
</head>
<body>
<div class="content">
<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/biojava-live">Debian Med / biojava-live</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/d7e7285ea56ee15806ccbb412c3254390f68335e">d7e7285e</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-26T15:24:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.9.5</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/23b0edf696803e2eae3e0ab6a2ebec911b834251">23b0edf6</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-26T15:24:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.9.5'
Update to upstream version '1.9.5'
with Debian dir 0a2a07a1b7b6fc5e43b167a5cf0bbeddcf25f546</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/fb2983aa9f96767d704b23ee947d93a926964305">fb2983aa</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-26T20:53:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removing obsolete get-orig-source target in d/rules
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/890e1a9109f2a2b0b35ed6f178c5f96311923e96">890e1a91</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-27T11:30:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">The previously referenced doc files have been suppressed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/26d52d7df362df92dd7799cb7879c79afcd0c952">26d52d7d</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-27T14:50:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refreshing d/copyright
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/efad86b30756e81dcdd56b4f6cbb100211de2348">efad86b3</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-27T15:30:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Now upstream uses Maven
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/af8654b365b33f8fe97a181b64b4295f6eda197f">af8654b3</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-27T15:30:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Providing Bug and Repository fields in d/u/metadata
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/cb77b1147d5ae4e33470a24d728ebb33ef0b608f">cb77b114</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-27T15:31:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Stripping d/rules of obsolete contents now that we use Maven
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/5a083b8ff3fcee1367244f4713d42a0c9c45b03c">5a083b8f</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-27T15:32:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refreshing the list of (build-)dependencies and setting it up for Maven
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/5d25021882e4c6bcaba9b4ea9a9e3744db73f15e">5d250218</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-27T15:32:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Installing the javadoc built by Maven and altering paths accordingly
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/03097eb08eafd0d283503a033f6e60469a871dae">03097eb0</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-27T15:37:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Now the docs are installed under apidocs/ instead of api/
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/c0bc02c1ed1a90bed675adb9088c53894ed3bee8">c0bc02c1</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-27T15:37:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removing obsolete d/*.dirs files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/cc937561e64c4cf5ad19cba3d8221eba66a2cc61">cc937561</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-27T15:39:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removing urchinTracker() in the javadoc to enhance privacy
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/697165cbf0e978b505fff8946b72376d82c75f09">697165cb</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-27T15:39:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Setting myself as uploader
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/ce4624341caadd9ebbef6dfe407a5fc562e5a5a0">ce462434</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-27T15:52:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Raising Standards version to 4.6.0 (no change)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/3527f6db2ecce20b2fe520a91a4329e6ab5115ec">3527f6db</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-27T20:42:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Stop shipping the -demos package, as demos are no more provided by upstream
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/b8642877fa5c0d37922d1dd076e495aff16a5be0">b8642877</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-27T20:43:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">html-browser does not exist anymore
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/e532241989fd55129a42347bb685ab3cbb0e7fd2">e5322419</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-28T18:07:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Filling in the classpath for the built jars
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/6e41d0f4d22bdc0c4b22b3a80f859909b43c87ba">6e41d0f4</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-28T18:07:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Excluding tests with problematic data
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/2ecd458852519d41bb99b1c3550ba32c2b6e5405">2ecd4588</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-28T18:08:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/efb8c4bfa2ea607baae943578ba13ce40f1b1f73">efb8c4bf</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-28T20:51:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Using '1.x' instead of 'debian' for the installation of Maven artifacts
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/02814fb4969001998073bf93982eb2d522f25b11">02814fb4</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-03-28T20:45:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Now building the package libbiojava1.9-java instead of libbiojava1.7-java
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/4be4d06af8a0a765cbf640e4be9caf08991e0af6">4be4d06a</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-03-28T21:12:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Expliciting that libbiojava-java is a dependency package
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/0769f89ce5c12d00297cfcd8fb9119929c15f785">0769f89c</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-03-28T21:13:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use secure URI in Homepage field.
Changes-By: lintian-brush
Fixes: lintian: homepage-field-uses-insecure-uri
See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/5ae85cdcc20b4951f0cf173f0bbb18f47360053e">5ae85cdc</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-03-28T21:18:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Marking the doc package as Multi-Arch: foreign
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava-live/-/commit/7220fa8d880077d24388e3beb8012daccda37c9f">7220fa8d</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-03-28T23:07:05+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to NEW, targetting experimental
</pre>
</li>
</ul>
<h4>21 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.cvsignore
→
.gitignore
</a>
</li>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
<span class="new-file">
+
.travis.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#ac97fd8044e211b8965191abd3e1372d4a6075d6">
<span class="new-file">
+
KEYS
</span>
</a>
</li>
<li class="file-stats">
<a href="#0398ccd0f49298b10a3d76a47800d2ebecd49859">
<span class="deleted-file">
−
LICENSE
</span>
</a>
</li>
<li class="file-stats">
<a href="#01fd5f2e100a5aa4b370b9fd5d48fce9b3de3a55">
<span class="deleted-file">
−
LICENSE.COMMONS
</span>
</a>
</li>
<li class="file-stats">
<a href="#69e27356ef629022720d868ab0c0e3394775b6c1">
<span class="deleted-file">
−
README
</span>
</a>
</li>
<li class="file-stats">
<a href="#fd0339305ff0de616eaf3cb9b865f9e0aed035cc">
<span class="deleted-file">
−
README.biosql
</span>
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<span class="new-file">
+
README.md
</span>
</a>
</li>
<li class="file-stats">
<a href="#488d4afe671d6abf30636006b4231062e2bffc1d">
<span class="new-file">
+
alignment/pom.xml
</span>
</a>
</li>
<li class="file-stats">
<a href="#3188b6f3caa01305a236f91feed6d9f61e3a168e">
src/org/biojava/bio/alignment/ARAlignment.java
→
alignment/src/main/java/org/biojava/bio/alignment/ARAlignment.java
</a>
</li>
<li class="file-stats">
<a href="#00cf2b3acb9ab6bc4e6ff1f5801dca335f5cef9b">
<span class="new-file">
+
alignment/src/main/java/org/biojava/bio/alignment/AbstractULAlignment.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#c5113fba08b5cd0057847fe036aaeb54753e7686">
<span class="new-file">
+
alignment/src/main/java/org/biojava/bio/alignment/AlignmentAlgorithm.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#c7e97574ae09e83e037adfaf75aab8d0a83670b9">
src/org/biojava/bio/alignment/AlignmentElement.java
→
alignment/src/main/java/org/biojava/bio/alignment/AlignmentElement.java
</a>
</li>
<li class="file-stats">
<a href="#1ef81247c223302814f0416481ad0e3d740aa25e">
<span class="new-file">
+
alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#68ad9b9bd3540e4cdce5208474643c242cd2a41b">
src/org/biojava/bio/alignment/EditableAlignment.java
→
alignment/src/main/java/org/biojava/bio/alignment/EditableAlignment.java
</a>
</li>
<li class="file-stats">
<a href="#58ca31500f0569a8c5fe7402e9933ac7f2d44738">
<span class="new-file">
+
alignment/src/main/java/org/biojava/bio/alignment/FlexibleAlignment.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#db665b62386979ef2df5da8d68c3d6aa351a762c">
src/org/biojava/bio/alignment/IllegalAlignmentEditException.java
→
alignment/src/main/java/org/biojava/bio/alignment/IllegalAlignmentEditException.java
</a>
</li>
<li class="file-stats">
<a href="#bc1fcd09178286a1ba206a15e3f704cc95734ff4">
<span class="new-file">
+
alignment/src/main/java/org/biojava/bio/alignment/NeedlemanWunsch.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#99e18d54dbbe151edd90643cc3d03f6091462c02">
src/org/biojava/bio/alignment/QualitativeAlignment.java
→
alignment/src/main/java/org/biojava/bio/alignment/QualitativeAlignment.java
</a>
</li>
<li class="file-stats">
<a href="#466c4f953915eea8d621c142ce1c452e08a2fdc2">
src/org/biojava/bio/alignment/SimpleAlignmentElement.java
→
alignment/src/main/java/org/biojava/bio/alignment/SimpleAlignmentElement.java
</a>
</li>
<li class="file-stats">
<a href="#32c7ef52abd8429d6d5aa54c0a570d256bdfcf2c">
src/org/biojava/bio/alignment/SmithWaterman.java
→
alignment/src/main/java/org/biojava/bio/alignment/SmithWaterman.java
</a>
</li>
</ul>
<h5>The diff was not included because it is too large.</h5>
</div>
<div class="footer" style="margin-top: 10px;">
<p style="font-size: small; color: #666;">
—
<br>
<a href="https://salsa.debian.org/med-team/biojava-live/-/compare/66c526c486e72f8585f8636ccd074fa5c40689ee...7220fa8d880077d24388e3beb8012daccda37c9f">View it on GitLab</a>.
<br>
You're receiving this email because of your account on salsa.debian.org.
If you'd like to receive fewer emails, you can
adjust your notification settings.
</p>
</div>
</body>
</html>