<div dir="ltr">Hi everyone,<div><br></div><div>The bootstrap.py script has been updated to pull sources from GitHub. As a consequence, your svn copy of cctbx_project will not be automatically updated by bootstrap.py.</div><div><br></div><div>To manually update your cctbx_project directory (since you should still be committing changes with svn), please run</div><div><br></div><div><font face="monospace, monospace">svn update</font></div><div><br></div><div>while in the cctbx_project directory.</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8000001907349px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Tel: (510) 486-5709</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Fri, Nov 4, 2016 at 10:24 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_-4909600053124116167WordSection1">
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Hello everyone,<u></u><u></u></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><u></u> <u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">As Aaron requested – here is an update regarding the move to GitHub.<u></u><u></u></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><u></u> <u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">At this time if you want to commit code: *<b>keep committing to Sourceforge*</b>.<u></u><u></u></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Do not worry about leaving uncommitted changes in your SVN tree. Those can be migrated later.<u></u><u></u></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><u></u> <u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">The Sourceforge cctbx repository history has now been migrated to GitHub. The repository lives at</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">
<a href="https://github.com/cctbx/cctbx" target="_blank">https://github.com/cctbx/cctbx</a><span style="color:#1f497d"><wbr>. Please do not commit to this repository yet!</span></span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Over the next few days the bootstrap script will be modified alongside the build servers to point to the GitHub repository. This means
there will only be limited testing, and the produced builds will lag behind the development effort.<u></u><u></u></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><u></u> <u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">To be listed as a developer on</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">
<a href="https://github.com/cctbx" target="_blank">https://github.com/cctbx</a><span style="color:#1f497d"> you need to set your visibility to public at</span><a> https://github.com/orgs/cctbx/<wbr>people</a><span style="color:#1f497d">.</span></span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">You can also view some fancy graphs about the cctbx project history at</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><a>
https://github.com/cctbx/<wbr>cctbx/graphs/contributors</a></span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">If you haven’t done it before, now is a good time to set up your local installation of git to use your name and mail address with</span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Courier New";color:#1f497d">git config --global <a href="http://user.name" target="_blank">user.name</a> "John Doe"</span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Courier New";color:#1f497d">git config --global user.email
</span><span style="font-size:10.0pt;font-family:"Courier New";color:black"><a href="mailto:your_email@example.com" target="_blank">your_email@example.com</a></span><span style="font-size:10.0pt;font-family:"Courier New""><u></u><u></u></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">as well as this setting to avoid merge commits:</span><span style="font-size:10.0pt;font-family:"Courier New";color:#1f497d"><u></u><u></u></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Courier New";color:#1f497d">git config --global pull.rebase true</span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Note that you must set these on every computer you use! You may want to keep a copy of those commands around in case you ever get a new
computer.<u></u><u></u></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">You should use mail addresses registered with your github account, or – if you enable it in your github account – the anonymous address
offered by github.</span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><u></u> <u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">You may want to use the time to sort out your ssh access keys with your GitHub account, and play around with git a bit. You can test
that everything works using the temporary sandbox repository of cctbx. Here are some commands to get you started:</span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Courier New";color:#1f497d">git clone
</span><span style="font-size:10.0pt;font-family:"Courier New";color:black">git@github.com:cctbx/cctbx-<wbr>playground.git</span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Courier New";color:#1f497d">cd cctbx-playground</span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Courier New";color:#1f497d">echo some text >> some-file</span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Courier New";color:#1f497d">git add some-file</span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Courier New";color:#1f497d">git commit –m "some commit"</span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Courier New";color:#1f497d">git push</span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Courier New";color:#1f497d">git log</span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Then go to
<a href="https://github.com/cctbx/cctbx-playground/commits/master" target="_blank">https://github.com/cctbx/<wbr>cctbx-playground/commits/<wbr>master</a> to see how other people will see your commits.<u></u><u></u></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">The next steps:<u></u><u></u></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><u></u> <u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">*Tuesday 8<sup>th</sup> November 2016, 11:59pm Pacific Time*<u></u><u></u></span></b></p>
<p style="margin:0cm;margin-bottom:.0001pt"><b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">*= Wednesday 9<sup>th</sup> November 2016, 07:59am GMT:*<u></u><u></u></span></b></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Sourceforge:
</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#00b050">Committing allowed</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">. GitHub:
</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#00b050">Checkout/Cloning allowed,</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">
</span><b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#c00000">*Read-only</span></b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#c00000">*.</span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">We will update our build servers and the bootstrap script to refer to the git repositories.<u></u><u></u></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">All commits still run into Sourceforge, and will be copied over to GitHub automatically<u></u><u></u></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">every couple of hours. Since the build servers will only see code on GitHub,<u></u><u></u></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">testing and deployment will be limited during this period.</span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><u></u> <u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">*Tuesday 22<sup>nd</sup> November 2016, 11:59pm Pacific Time*<u></u><u></u></span></b></p>
<p style="margin:0cm;margin-bottom:.0001pt"><b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">*= Wednesday 23<sup>rd</sup> November 2016, 07:59am GMT:*<u></u><u></u></span></b></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Sourceforge:
</span><b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#c00000">*Read-only</span></b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#c00000">*</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">.
GitHub: </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#00b050">Committing allowed</span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">We should have achieved a stable build on both Jenkins and Buildbot by this time.</span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Change any website pointers from SF to GitHub.</span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Instructions to migrate local developer repositories will be sent around.</span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">All future commits should go to GitHub only.</span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Remaining commits on Sourceforge will be migrated to GitHub.</span><u></u><u></u></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">-Markus</span><u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span>Dr Markus Gerstel MBCS<u></u><u></u></span></p>
<p class="MsoNormal"><span>Postdoctoral Research Associate<u></u><u></u></span></p>
<p class="MsoNormal"><span>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><u></u> <u></u></span></p>
<p class="MsoNormal"><span>Diamond Light Source Ltd.<u></u><u></u></span></p>
<p class="MsoNormal"><span>Diamond House<u></u><u></u></span></p>
<p class="MsoNormal"><span>Harwell Science & Innovation Campus<u></u><u></u></span></p>
<p class="MsoNormal"><span>Didcot<u></u><u></u></span></p>
<p class="MsoNormal"><span>Oxfordshire<u></u><u></u></span></p>
<p class="MsoNormal"><span>OX11 0DE<span class="HOEnZb"><font color="#888888"><u></u><u></u></font></span></span></p><span class="HOEnZb"><font color="#888888">
<p class="MsoNormal"><u></u> <u></u></p>
</font></span></div><span class="HOEnZb"><font color="#888888">
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