<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="Generator" content="Microsoft Word 14 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p
{mso-style-priority:99;
mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
{mso-style-priority:99;
mso-style-link:"Balloon Text Char";
margin:0cm;
margin-bottom:.0001pt;
font-size:8.0pt;
font-family:"Tahoma","sans-serif";}
p.m-2651995399140751371msolistparagraph, li.m-2651995399140751371msolistparagraph, div.m-2651995399140751371msolistparagraph
{mso-style-name:m_-2651995399140751371msolistparagraph;
mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
span.EmailStyle19
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
span.BalloonTextChar
{mso-style-name:"Balloon Text Char";
mso-style-priority:99;
mso-style-link:"Balloon Text";
font-family:"Tahoma","sans-serif";
mso-fareast-language:EN-GB;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-GB" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Nick<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Fine, so long as not configured by default otherwise can take out cctbx builds as a side effect (as happened earlier)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Best wishes Graeme<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<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""> Nicholas Sauter [mailto:nksauter@lbl.gov]
<br>
<b>Sent:</b> 03 May 2017 15:52<br>
<b>To:</b> cctbx mailing list<br>
<b>Cc:</b> Winter, Graeme (DLSLtd,RAL,LSCI)<br>
<b>Subject:</b> Re: [cctbxbb] simtbx<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">Markus,<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">We want option c. simtbx should be in the cctbx_project directory. No separate git repository. We need to double check we've gotten all the files in cctbx_project, then remove them from the separate repo. James, could you look into
this?<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Nick<o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal"><br clear="all">
<o:p></o:p></p>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal">Nicholas K. Sauter, Ph. D.<br>
Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division<o:p></o:p></p>
<div>
<p class="MsoNormal">Lawrence Berkeley National Laboratory<br>
1 Cyclotron Rd., Bldg. 33R0345<br>
Berkeley, CA 94720<br>
(510) 486-5713<o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Wed, May 3, 2017 at 7:49 AM, <<a href="mailto:markus.gerstel@diamond.ac.uk" target="_blank">markus.gerstel@diamond.ac.uk</a>> wrote:<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D">Hi James,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D">It looks that you now have two separate places where simtbx code is kept. One is in the simtbx repository, where you fixed the sign earlier, and the
other one is in the cctbx repository, where you just now fixed it again.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D">Simtbx repo:
<a href="https://github.com/dials/simtbx" target="_blank">https://github.com/dials/simtbx</a></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D">Simtbx folder in cctbx repo:
<a href="https://github.com/cctbx/cctbx_project/tree/master/simtbx" target="_blank">
https://github.com/cctbx/cctbx_project/tree/master/simtbx</a> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D">I guess suppose there are three options here:</span><o:p></o:p></p>
<p class="m-2651995399140751371msolistparagraph"><span style="color:#1F497D">a.</span><span style="font-size:7.0pt;color:#1F497D">
</span><span style="color:#1F497D">move simtbx into the module directory, add simtbx to the bootstrap script so it is initialised correctly.</span><o:p></o:p></p>
<p class="m-2651995399140751371msolistparagraph"><span style="color:#1F497D">b.</span><span style="font-size:7.0pt;color:#1F497D">
</span><span style="color:#1F497D">leave simtbx inside the cctbx_project directory and repository, but as its own git repository (using git submodule)</span><o:p></o:p></p>
<p class="m-2651995399140751371msolistparagraph"><span style="color:#1F497D">c.</span><span style="font-size:7.0pt;color:#1F497D">
</span><span style="color:#1F497D">leave simtbx inside the cctbx_project directory, delete the separate git repository</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D">NB: This issue is independent of resolving the dials-dependency issue.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D">-Markus</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><a name="m_-2651995399140751371__MailEndCompose"><span style="color:#1F497D"> </span></a><o:p></o:p></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span lang="EN-US">From:</span></b><span lang="EN-US">
<a href="mailto:cctbxbb-bounces@phenix-online.org" target="_blank">cctbxbb-bounces@phenix-online.org</a> [mailto:<a href="mailto:cctbxbb-bounces@phenix-online.org" target="_blank">cctbxbb-bounces@phenix-online.org</a>]
<b>On Behalf Of </b>James Holton<br>
<b>Sent:</b> 03 May 2017 15:40<br>
<b>To:</b> Winter, Graeme (DLSLtd,RAL,LSCI) <<a href="mailto:Graeme.Winter@Diamond.ac.uk" target="_blank">Graeme.Winter@Diamond.ac.uk</a>>;
<a href="mailto:cctbxbb@phenix-online.org" target="_blank">cctbxbb@phenix-online.org</a><br>
<b>Subject:</b> Re: [cctbxbb] simtbx</span><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:12.0pt"><br>
Yesterday, Aaron and I were trying to set things up so that simtbx would be available to people who aren't James Holton. It's been checked in and working for over a month now, and only a few days ago I discovered that a fresh "bootstrap" has a broken simtbx,
despite my "git status" telling me all my files are up to date. I asked Aaron and Nick for help with this.<br>
<br>
I thought what we did was make cctbx.xfel depends on simtbx, since fitting simulations to stills is the whole reason for porting my stuff into python.
<br>
<br>
I set up simtbx with a constructor that takes a dxtbx detector as input, but does that make it depend on dials? I did not expect that.<br>
<br>
Sorry, didn't mean to break anything! Would much appreciate any help on this. <br>
<br>
-James<o:p></o:p></p>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">On 5/3/2017 1:41 AM,
<a href="mailto:Graeme.Winter@Diamond.ac.uk" target="_blank">Graeme.Winter@Diamond.ac.uk</a> wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hi Folks<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">We have noticed that simtbx, part of the core cctbx now, depends on dials<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">This means if you do not have a dials build your cctbx will be broken<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">This is probably not the way we want things?<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I thought simtbx was a separate repo?<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Cheerio Graeme<o:p></o:p></p>
<p> <o:p></o:p></p>
<p>-- <o:p></o:p></p>
<p>This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt
by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.<br>
Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd.
<br>
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.<br>
Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom<br>
<o:p></o:p></p>
</blockquote>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<p> <o:p></o:p></p>
<p>-- <o:p></o:p></p>
<p>This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt
by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.<br>
Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd.
<br>
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.<br>
Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom<br>
<o:p></o:p></p>
</div>
</div>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
_______________________________________________<br>
cctbxbb mailing list<br>
<a href="mailto:cctbxbb@phenix-online.org">cctbxbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/cctbxbb" target="_blank">http://phenix-online.org/mailman/listinfo/cctbxbb</a><o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
<p align="justify"> </p>
<p align="justify">-- </p>
<p align="justify">This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.<br />Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. <br />Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.<br />Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom<br /> </p></body>
</html>