<div dir="ltr"><div class="gmail_default" style=""><font face="verdana, sans-serif">I think it would be nice if all the external dependency checks were in an external module that could be used by a user.</font></div><div class="gmail_default" style=""><font face="verdana, sans-serif">A user might what to;</font></div><div class="gmail_default" style=""><ul><li><font face="verdana, sans-serif">Make sure Biopython can find the external app and help diagnose problems.</font></li><li><font face="verdana, sans-serif">Check which version of the external app Biopython is using</font></li><li><font face="verdana, sans-serif">Might help with "modular installation" <a href="https://github.com/biopython/biopython/issues/349">https://github.com/biopython/biopython/issues/349</a></font></li></ul></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div>Vincent Davis</div><div>720-301-3003<span></span><span></span></div></div></div>
<br><div class="gmail_quote">On Thu, May 12, 2016 at 2:15 PM, Tiago Rodrigues Antao <span dir="ltr"><<a href="mailto:tra@popgen.net" target="_blank">tra@popgen.net</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Regarding free vs non-free dependencies, I would suggest marking dependencies without a license as non-free.<span class="HOEnZb"><font color="#888888"><br>
<br>
Tiago</font></span><div class="HOEnZb"><div class="h5"><br>
<br>
On Tue, 10 May 2016, Tiago Rodrigues Antao wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
On Tue, 10 May 2016, Peter Cock wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I like this idea - I guess we'd need a subclass of the missing dependency<br>
exception specifically for missing a proprietary extension?<br>
</blockquote>
<br>
That would work.<br>
Also, change run_tests and add two options, say:<br>
--check-dependencies<br>
--check-free-dependencies<br>
<br>
I can work on a PR along these lines...<br>
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</blockquote>
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