<div dir="ltr">Should we add xdrfile to gerrit so that we can easily accepts patches our standard way?</div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, May 12, 2015 at 2:21 AM, Robert McGibbon <span dir="ltr"><<a href="mailto:rmcgibbo@gmail.com" target="_blank">rmcgibbo@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div dir="ltr">For what it's worth, the MDTraj python package (similar to <span style="color:rgb(80,0,80);font-size:12.8000001907349px">MDAnalysis) also includes a modified version of xdrfile, which fixes a few small bugs. The changes are described here: </span><font color="#500050"><span style="font-size:12.8000001907349px"><a href="https://github.com/mdtraj/mdtraj/tree/master/mdtraj/formats/xtc/src" target="_blank">https://github.com/mdtraj/mdtraj/tree/master/mdtraj/formats/xtc/src</a>.</span></font>
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</span></font></div>
<div><font color="#500050"><span style="font-size:12.8000001907349px">One of the bugs (a segfault on reading certain malformed xtc files) was reported to the gromacs-dev list a while ago, but nobody seemed interested: <a href="https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2014-September/007942.html" target="_blank">https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2014-September/007942.html</a></span></font></div><span class="HOEnZb"><font color="#888888">
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<div>-Robert</div>
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<div class="gmail_extra"><br>
<div class="gmail_quote">On Mon, May 11, 2015 at 11:16 PM, David van der Spoel <span dir="ltr">
<<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<span>On 2015-05-11 23:23, Dominik 'Rathann' Mierzejewski wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear developers,<br>
there seems to be a fork of GROMACS' xdrfile by the MDAnalysis project:<br>
<a href="https://github.com/MDAnalysis/mdanalysis/tree/develop/package/src/xdrfile" target="_blank">https://github.com/MDAnalysis/mdanalysis/tree/develop/package/src/xdrfile</a><br>
<br>
What are the plans for xdrfile? Would you be open to incorporating<br>
MDAnalysis' fork changes into your library?<br>
<br>
They have added proper python bindings (via swig) and some new C APIs.<br>
There are also small changes in API, for example in read_trr (new<br>
parameter) and xdrstdio_(get|set)pos() functions (parameter types).<br>
I'm attaching a sanitized diff of the C code. Python changes are too<br>
extensive to make a diff of.<br>
<br>
The reason I'm asking is that I'm trying to package MDAnalysis for<br>
Fedora (and I became the GROMACS maintainer in Fedora recently as well).<br>
Our guidelines forbid bundling of third-party libraries - system<br>
versions are to be used. xdrfile is already packaged in Fedora, but<br>
MDAnalysis bundles its fork - libxdrfile2 which I have to unbundle<br>
and package separately. It would make everyone's life much easier if<br>
xdrfile could be simply updated to include the new python bindings and<br>
APIs so that MDAnalysis could use them.<br>
<br>
Regards,<br>
Dominik<br>
<br>
<br>
<br>
</blockquote>
</span>Are these changes compatible with the latest xdrfile changes? There has not been a release recently though.<span><font color="#888888"><br>
<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: <a href="tel:%2B46184714205" value="+46184714205" target="_blank">
+46184714205</a>.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>
<a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
-- <br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature">ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov" target="_blank">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309</div>
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