<div dir="ltr">Since this is a major version, we should focus on refactoring projects which will alter the API. There are only a couple things I'm working on that fit that. <a href="https://github.com/biojava/biojava/issues/126">#126</a> is a major undertaking and will probably happen for 5.0 at the earliest. The symmetry code will consist of adding features, so this could be slated for 4.1, as could DSSP (<a href="https://github.com/biojava/biojava/issues/112">#112</a>). Of course there's no harm in including them in 4.0 if they're done, but we shouldn't wait for them.<div><br></div><div>I'll try to look through the issues and assign milestones for each, but what I see as important to finish is deciding the biojava3 issue (see other thread), finish logging (<a href="https://github.com/biojava/biojava/issues/155">#155</a>), and a minor project I've been working on to refactor the structure CLI code. Personally, I think mid November would be reasonable to shoot for. Then we can start on 4.1 development (with a 5.0 branch for any api-changing commits).</div><div><br></div><div>-Spencer</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Oct 10, 2014 at 10:37 AM, Jose Manuel Duarte <span dir="ltr"><<a href="mailto:jose.duarte@psi.ch" target="_blank">jose.duarte@psi.ch</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
To me 1 month sounds a bit early. In any case to go with the
"release early, release often" philosophy, we can really try to push
it soon, say in a couple of months. <br>
<br>
What about setting a target date of December (before the 15th)? I
think that can be helpful for everyone involved to get ready for it.<br>
<br>
The milestone 4.0 in github doesn't show so much:<br>
<br>
<a href="https://github.com/biojava/biojava/milestones/BioJava%204.0.0" target="_blank">https://github.com/biojava/biojava/milestones/BioJava%204.0.0</a><br>
<br>
But I think some other things are missing there, for instance
nice-to-haves in the structure module would be: improving structure
alignments (#126), reorganising symmetry code, finish secondary
structure implementation (#112)... All of these are of course
optional, they can always be pushed back if we can't reach them on
time.<br>
<br>
As for core and other modules I really have no clue. It would be
nice if someone can say if there are plans to add new features
there.<br>
<br>
An important issue we should really address is eliminating the
biojava3 naming that some packages now have. The reason behind those
names is apparently keeping compatibility with biojava legacy, but
by now we can probably do without that. I'd say simply eliminating
the 3 would do the trick. Otherwise take an approach like blast
where they kept a blast+ and a blast legacy. I'd favour simply
eliminating the 3, it should help to keep it simple.<span class="HOEnZb"><font color="#888888"><br>
<br>
Jose</font></span><div><div class="h5"><br>
<br>
<br>
<br>
<div>On 09/10/14 00:11, Andreas Prlic wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div class="h5">
<div dir="ltr">Hi
<div><br clear="all">
<div>The upcoming new biojava 4 series has mad a lot of
progress recently. How do people feel about trying to
release BioJava 4.0.0 in about a month? </div>
<div><br>
</div>
<div>Andreas</div>
</div>
</div>
<br>
<fieldset></fieldset>
<br>
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