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<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">Shower notwithstanding, I think what happened over here is this took out our build, the board went red and surprise was expressed and questions were raised.<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">If I broke Phenix by bundling in xia2 into something, or some other project, I would expect the same level of questioning from LBL coming my way…<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">But sounds like you can resolve this with people in the same building then let us know over here what the conclusion was.
<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""> cctbxbb-bounces@phenix-online.org [mailto:cctbxbb-bounces@phenix-online.org]
<b>On Behalf Of </b>Nicholas Sauter<br>
<b>Sent:</b> 03 May 2017 15:59<br>
<b>To:</b> cctbx mailing list<br>
<b>Subject:</b> Re: [cctbxbb] simtbx<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I'm stepping in the shower now. Pavel, I can answer about simtbx later. Never knew that we had to explain ourselves to everyone? What is mmtbx? What is scitbx?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Nick<o:p></o:p></p>
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<p class="MsoNormal">Nicholas K. Sauter, Ph. D.<br>
Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division<o:p></o:p></p>
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<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>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Wed, May 3, 2017 at 7:57 AM, Pavel Afonine <<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">Same questions here as Markus asked.. What is simtbx? First time hear about it. How cctbx can benefit from it?<span style="color:#888888"><br>
<span class="hoenzb">Pavel</span></span><o:p></o:p></p>
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<p class="MsoNormal">On 5/3/17 07:53, <a href="mailto:markus.gerstel@diamond.ac.uk" target="_blank">
markus.gerstel@diamond.ac.uk</a> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Nick,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Sorry, outsider perspective here. I don’t know what simtbx does or is supposed to do.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">What is the benefit of having code in a repository that, according to your earlier mail, is explicitly
not used in the project?</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Or more bluntly: We (and ccp4) distribute dials and, as part of it, the cctbx_project repository.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Why should we ship dead code?</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">-Markus</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><a name="m_301122395722103726__MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span></a><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">
<a href="mailto:cctbxbb-bounces@phenix-online.org" target="_blank">cctbxbb-bounces@phenix-online.org</a> [<a href="mailto:cctbxbb-bounces@phenix-online.org" target="_blank">mailto:cctbxbb-bounces@phenix-online.org</a>]
<b>On Behalf Of </b>Nicholas Sauter<br>
<b>Sent:</b> 03 May 2017 15:52<br>
<b>To:</b> cctbx mailing list <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>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Markus,<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Nick<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Nicholas K. Sauter, Ph. D.<br>
Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Lawrence Berkeley National Laboratory<br>
1 Cyclotron Rd., Bldg. 33R0345<br>
Berkeley, CA 94720<br>
<a href="tel:(510)%20486-5713" target="_blank">(510) 486-5713</a><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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>
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<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="m301122395722103726m-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="m301122395722103726m-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="m301122395722103726m-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_301122395722103726_m_-2651995399140751"><span style="color:#1F497D"> </span></a><o:p></o:p></p>
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<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>
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<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.
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<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>
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<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>
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<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>
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<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>
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