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Same questions here as Markus asked.. What is simtbx? First time
hear about it. How cctbx can benefit from it?<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 5/3/17 07:53,
<a class="moz-txt-link-abbreviated" href="mailto:markus.gerstel@diamond.ac.uk">markus.gerstel@diamond.ac.uk</a> wrote:<br>
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<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Hi
Nick,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Sorry,
outsider perspective here. I don’t know what simtbx does or
is supposed to do.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">What
is the benefit of having code in a repository that,
according to your earlier mail, is explicitly not used in
the project?<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Or
more bluntly: We (and ccp4) distribute dials and, as part of
it, the cctbx_project repository.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Why
should we ship dead code?<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">-Markus<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><a name="_MailEndCompose"
moz-do-not-send="true"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></a></p>
<span style="mso-bookmark:_MailEndCompose"></span>
<p class="MsoNormal"><b><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif"
lang="EN-US">From:</span></b><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif"
lang="EN-US"> <a class="moz-txt-link-abbreviated" href="mailto:cctbxbb-bounces@phenix-online.org">cctbxbb-bounces@phenix-online.org</a>
[<a class="moz-txt-link-freetext" href="mailto:cctbxbb-bounces@phenix-online.org">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 class="moz-txt-link-rfc2396E" href="mailto:cctbxbb@phenix-online.org"><cctbxbb@phenix-online.org></a><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>
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<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>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">Nick<o:p></o:p></p>
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<p class="MsoNormal"><br clear="all">
<o:p></o:p></p>
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<div>
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<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>
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<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" moz-do-not-send="true">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" moz-do-not-send="true">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" moz-do-not-send="true">
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"
moz-do-not-send="true"><span style="color:#1F497D"> </span></a><o:p></o:p></p>
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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" moz-do-not-send="true">cctbxbb-bounces@phenix-online.org</a>
[mailto:<a
href="mailto:cctbxbb-bounces@phenix-online.org"
target="_blank" moz-do-not-send="true">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" moz-do-not-send="true">Graeme.Winter@Diamond.ac.uk</a>>;
<a href="mailto:cctbxbb@phenix-online.org"
target="_blank" moz-do-not-send="true">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" moz-do-not-send="true">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>
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<p class="MsoNormal"
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<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
_______________________________________________<br>
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<p class="MsoNormal"><o:p> </o:p></p>
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<pre wrap="">_______________________________________________
cctbxbb mailing list
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