<div dir="ltr">Hi Markus,<div><br></div><div>Indeed, <a href="http://dials.lbl.gov">dials.lbl.gov</a> is built off of the same sources. I was more concerned about <a href="http://cctbx.sourceforge.net">cctbx.sourceforge.net</a>. We can look into that on our end.</div><div><br></div><div>As for the repositories, there are licensing issues with the way you have things set up and we would like to examine if the code duplication that is occurring can be avoided. We (Billy and I) will make up a list of dependencies and their licenses and how we think they should be hosted. Should we do a brief skype call over the next couple days? </div><div><br></div><div>Thanks,</div><div>-Aaron</div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Nov 1, 2016 at 2:04 AM, <span dir="ltr"><<a href="mailto:markus.gerstel@diamond.ac.uk" target="_blank">markus.gerstel@diamond.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div lang="EN-GB" link="blue" vlink="purple">
<div class="m_-8494258839431152153WordSection1">
<p class="MsoNormal"><a name="m_-8494258839431152153__MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Hi Aaron,<u></u><u></u></span></a></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">If you could send me your gmail addresses and I’ll share the doc.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Regarding your questions:<u></u><u></u></span></p>
<p class="m_-8494258839431152153MsoListParagraph"><u></u><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><span>1.<span style="font:7.0pt "Times New Roman"">
</span></span></span><u></u><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Syncing the repositories is done using subgit and I run this currently 4 times a day.<u></u><u></u></span></p>
<p class="m_-8494258839431152153MsoListParagraph"><u></u><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><span>2.<span style="font:7.0pt "Times New Roman"">
</span></span></span><u></u><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Yes, the repositories are copies of what we are distributing. No, I do not think we should remove them, rather we should if at all possible extend
them by adding their development history and actually point to them. Currently no changes can be made to any of those packages, and – from a distribution point of view, worse – nobody knows if and when those packages do change. What I therefore do for dials
releases is a) download all the packages, b) unpack them into the respective repositories and c) see if any changes were made before I d) tag the repository for release. As you can see this has a massive time impact and is part of the reason why releases are
currently more painful than they have to be. Therefore if the packages were recently updated this is not a problem since nobody currently refers to them outside the stable releases.
<u></u><u></u></span></p>
<p class="m_-8494258839431152153MsoListParagraph"><u></u><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><span>3.<span style="font:7.0pt "Times New Roman"">
</span></span></span><u></u><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Isn’t <a href="http://dials.lbl.gov" target="_blank">dials.lbl.gov</a> already running off the
</span><a href="https://github.com/dials/dials.github.io" target="_blank"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">https://github.com/dials/<wbr>dials.github.io</span></a><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> repository?
I am sure we can have something similar for the cctbx websites. We already generate
</span><a href="http://cctbx.github.io/" target="_blank"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">http://cctbx.github.io/</span></a><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> but I don’t atm know where <a href="http://cctbx.sourceforge.net" target="_blank">cctbx.sourceforge.net</a>
comes from.<u></u><u></u></span></p><span class="">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">-Markus<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Dr Markus Gerstel MBCS<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Postdoctoral Research Associate<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Tel: <a href="tel:%2B44%201235%20778698" value="+441235778698" target="_blank">+44 1235 778698</a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Diamond Light Source Ltd.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Diamond House<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Harwell Science & Innovation Campus<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Didcot<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Oxfordshire<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">OX11 0DE<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
</span><p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> <a href="mailto:cctbxbb-bounces@phenix-online.org" target="_blank">cctbxbb-bounces@phenix-online.<wbr>org</a> [mailto:<a href="mailto:cctbxbb-bounces@phenix-online.org" target="_blank">cctbxbb-bounces@<wbr>phenix-online.org</a>]
<b>On Behalf Of </b>Aaron Brewster<br>
<b>Sent:</b> 28 October 2016 23:48</span></p><div><div class="h5"><br>
<b>To:</b> cctbx mailing list<br>
<b>Subject:</b> Re: [cctbxbb] Git status update<u></u><u></u></div></div><p></p><div><div class="h5">
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<p class="MsoNormal">Hi Markus, <u></u><u></u></p>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Billy, Nigel and I worked through the plan you originally sent out (linked at the top of this email thread). We've added a couple questions as comments in the document (expounded on below). Also, could you make the document writeable
by Billy, Nigel and I? We want to assign some of the tasks listed.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Here are the questions:<u></u><u></u></p>
</div>
<div>
<div>
<ul type="disc">
<li class="MsoNormal">
How is the repository at <a href="https://github.com/cctbx/cctbx" target="_blank">https://github.com/cctbx/cctbx</a><wbr> being synced with the SVN version? (This is just my own curiosity :)<u></u><u></u></li><li class="MsoNormal">
We think the non-cctbx repositories there that are copies (clipper, boost, annlib, etc.) of the bundles distributed alongside cctbx need to be removed from the git cctbx organization as they are duplications of what we are currently distributing. You say they
are there so you can do tagging with the dials releases, but if Billy has updated the versions at LBL, then wouldn't these versions hosted by git already be out of date? Which would affect the dials stable releases?<u></u><u></u></li><li class="MsoNormal">
We need to think about how websites such as <a href="http://dials.lbl.gov" target="_blank">dials.lbl.gov</a> or
<a href="http://cctbx.sourceforge.net" target="_blank">cctbx.sourceforge.net</a> will be affected by moving to git. Probably it's just updating links or moving html files?<u></u><u></u></li></ul>
<div>
<p class="MsoNormal">Thanks,<u></u><u></u></p>
</div>
</div>
</div>
<div>
<p class="MsoNormal">-Aaron<u></u><u></u></p>
</div>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<p class="MsoNormal">On Tue, Aug 23, 2016 at 6:32 AM, <<a href="mailto:markus.gerstel@diamond.ac.uk" target="_blank">markus.gerstel@diamond.ac.uk</a>> wrote:<u></u><u></u></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">Hi Marcin.<br>
<br>
Currently I would say there is no plan. I do not have the history of the projects, so I could not do anything about that. I also don't use any of those repositories, so can't really comment on their status or future. I created the repositories only so I can
tag versions for the DIALS releases, otherwise someone changing the downloadable archive would affect stable releases.<br>
<br>
-Markus<br>
<br>
Dr Markus Gerstel MBCS<br>
Postdoctoral Research Associate<br>
Tel: <a href="tel:%2B44%201235%20778698" target="_blank">+44 1235 778698</a><br>
<br>
Diamond Light Source Ltd.<br>
<span class="m_-8494258839431152153im">Diamond House</span><br>
<span class="m_-8494258839431152153im">Harwell Science & Innovation Campus</span><br>
<span class="m_-8494258839431152153im">Didcot</span><br>
<span class="m_-8494258839431152153im">Oxfordshire</span><br>
<span class="m_-8494258839431152153im">OX11 0DE</span><br>
<br>
<br>
<span class="m_-8494258839431152153im">-----Original Message-----</span><br>
<span class="m_-8494258839431152153im">From: <a href="mailto:cctbxbb-bounces@phenix-online.org" target="_blank">cctbxbb-bounces@phenix-online.<wbr>org</a> [mailto:<a href="mailto:cctbxbb-bounces@phenix-online.org" target="_blank">cctbxbb-bounces@<wbr>phenix-online.org</a>] On Behalf Of Marcin Wojdyr</span><br>
<span class="m_-8494258839431152153im">Sent: 23 August 2016 14:26</span><br>
<span class="m_-8494258839431152153im">To: cctbx mailing list</span><br>
<span class="m_-8494258839431152153im">Subject: Re: [cctbxbb] Git status update</span><u></u><u></u></p>
<div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt">Hi Markus,<br>
what's the plan for the repositories that are currently imported as "copy of LBL archive" (without history).<br>
I guess the plan is to preserve the history - but will they be merged or added as submodule/subtree of the main cctbx repository?<br>
<br>
Marcin<br>
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