<div dir="ltr">I would like to get #2399 - my internal coordinates work - into 1.77 if it can get signed off. I'm still working on speeding it up, but don't expect any user API changes from this and probably have this part finished by Weds 13 May.<div>Rob.</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, May 8, 2020 at 9:35 PM Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Good work on this documentation fix Chris - something I was hoping we'd fixed for the next release:<div><br><div><a href="https://github.com/biopython/biopython/issues/2502" target="_blank">https://github.com/biopython/biopython/issues/2502</a><br></div></div><div><br></div><div>Another important task (which on re-reading might be made even more explicit) is running all the tests locally, including the online tests (since we skip those on TravisCI and AppVeyor). This occasionally throws up nasty surprises:</div><div><br></div><div><a href="https://biopython.org/wiki/Building_a_release" target="_blank">https://biopython.org/wiki/Building_a_release</a><br></div><div><br></div><div>Peter</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, May 7, 2020 at 5:03 PM Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Sounds good Chris,</div><div><br></div><div>Let's start with putting together a list of any blocking issues or pull requests. Community suggestions are welcome too, that's why we're discussing it openly on the mailing list.</div><div><br></div><div>Also to all our regular contributors - please say now if have something nearly ready which you are hoping to get included.</div><div><br></div><div>Thanks all,</div><div><br></div><div>Peter</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, May 7, 2020 at 2:56 PM Daley, Christopher <<a href="mailto:dalchr28@evergreen.edu" target="_blank">dalchr28@evergreen.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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Hi Peter,</div>
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Yes, that's me. I've been wanting to contribute more but this year hasn't exactly gone to plan...
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I'm happy to start today and go through the issues and pull requests and we can set up a workflow that you feel is the most manageable.</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Cheers</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Chris<br>
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<div id="gmail-m_5634063817524550212gmail-m_4745488177747252685gmail-m_7377791612198749394divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>><br>
<b>Sent:</b> Wednesday, May 6, 2020 8:40 AM<br>
<b>To:</b> Daley, Christopher <<a href="mailto:dalchr28@evergreen.edu" target="_blank">dalchr28@evergreen.edu</a>><br>
<b>Cc:</b> Michiel de Hoon <<a href="mailto:mjldehoon@yahoo.com" target="_blank">mjldehoon@yahoo.com</a>>; <a href="mailto:biopython@biopython.org" target="_blank">biopython@biopython.org</a> <<a href="mailto:biopython@biopython.org" target="_blank">biopython@biopython.org</a>><br>
<b>Subject:</b> Re: [Biopython] Volunteers for making Biopython release 1.77</font>
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<div dir="ltr">Hi Christopher, is this you on GitHub with one pull request to Biopython already?
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<div><a href="https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fchebizarro&data=02%7C01%7Cdalchr28%40evergreen.edu%7C19fff98a94fd48ec146808d7f1d3c80e%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637243764213082843&sdata=l4wghnNFxk03ZR6a9MgIJXhPEINA0rC%2BEI8Cj5aX634%3D&reserved=0" target="_blank">https://github.com/chebizarro</a></div>
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<div><a href="https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbiopython%2Fbiopython%2Fpull%2F2349&data=02%7C01%7Cdalchr28%40evergreen.edu%7C19fff98a94fd48ec146808d7f1d3c80e%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637243764213082843&sdata=T%2BRqIl7u6RJE0mOyBt38tv0Xz67A2L0y0DsbqK%2BQrLM%3D&reserved=0" target="_blank">https://github.com/biopython/biopython/pull/2349</a><br>
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<div>Some of the release steps need accounts or write permissions, but we could do most of it via pull requests so that doesn't stop you taking a very active role.</div>
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<div>First is working out what if any blocking issues remain to be addressed before calling a commit freeze and doing the release. Do you have any thoughts on this? Even additional eyes on the open issues and pull requests would be helpful there.</div>
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<div>Thank you, </div>
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<div>Peter</div>
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<div dir="ltr">On Wed, May 6, 2020 at 3:37 PM Daley, Christopher <<a href="mailto:dalchr28@evergreen.edu" target="_blank">dalchr28@evergreen.edu</a>> wrote:<br>
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<div dir="auto" style="direction:ltr;margin:0px;padding:0px;font-family:sans-serif;font-size:11pt;color:black">
I missed the original message due to aggressive spam filtering by our IT dept.<br>
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I'd be very much interested in managing a release, especially now the mid quarter rush is over. I've looked at the process and can pretty much get started straight away.<br>
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<div dir="auto" style="direction:ltr;margin:0px;padding:0px;font-family:sans-serif;font-size:11pt;color:black">
Chris Daley <br>
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<span id="gmail-m_5634063817524550212gmail-m_4745488177747252685gmail-m_7377791612198749394x_gmail-m_198720815412801420gmail-m_-5680398779240223709OutlookSignature">
<div dir="auto" style="direction:ltr;margin:0px;padding:0px;font-family:sans-serif;font-size:11pt;color:black">
Sent from my Verizon, Samsung Galaxy smartphone</div>
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<div id="gmail-m_5634063817524550212gmail-m_4745488177747252685gmail-m_7377791612198749394x_gmail-m_198720815412801420gmail-m_-5680398779240223709divRplyFwdMsg" dir="ltr">
<font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Biopython <biopython-bounces+dalchr28=<a href="mailto:evergreen.edu@mailman.open-bio.org" target="_blank">evergreen.edu@mailman.open-bio.org</a>> on behalf of Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>><br>
<b>Sent:</b> Wednesday, May 6, 2020 7:11:32 AM<br>
<b>To:</b> Michiel de Hoon <<a href="mailto:mjldehoon@yahoo.com" target="_blank">mjldehoon@yahoo.com</a>><br>
<b>Cc:</b> <a href="mailto:biopython@biopython.org" target="_blank">biopython@biopython.org</a> <<a href="mailto:biopython@biopython.org" target="_blank">biopython@biopython.org</a>><br>
<b>Subject:</b> Re: [Biopython] Volunteers for making Biopython release 1.77</font>
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<div dir="ltr">Perhaps I will have to do it again? Anyway - are there any open issues you all think need to be fixed before the release? My initial thoughts are just these two:
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<div>NCBI BLAST v2.10.0 updates with arguments and DB changes:</div>
<div><a href="https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbiopython%2Fbiopython%2Fissues%2F2863&data=02%7C01%7Cdalchr28%40evergreen.edu%7C19fff98a94fd48ec146808d7f1d3c80e%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637243764213092841&sdata=lQfFkK9F9P%2B2k%2Bb89gahILSNx7guZXqU6kBHghsXZjs%3D&reserved=0" target="_blank">https://github.com/biopython/biopython/issues/2863</a><br>
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<div>UniProt release 2019_11 changes FT and CC lines<br>
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<div><a href="https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbiopython%2Fbiopython%2Fissues%2F2417&data=02%7C01%7Cdalchr28%40evergreen.edu%7C19fff98a94fd48ec146808d7f1d3c80e%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637243764213092841&sdata=aVj2i5yONk%2B3NX2b48X3GPJFktnkEtSbYwb0q%2BEa%2BEg%3D&reserved=0" target="_blank">https://github.com/biopython/biopython/issues/2417</a><br>
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<div>(might be resolved already, need triage)</div>
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<div>Peter</div>
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