<div dir="ltr">Excellent - Markus said on GitHub that the NCBI tests did complete recently but sometimes took up to 2 hours. This is something we will probably have to reduce as that is not practical.<div><br></div><div>If you haven't already, I suggest you next try building the tar-ball and wheels locally, installing them, and running the tests from an unzipped tar-ball. The reason we do this is to catch problems with the manifest (e.g. new test files not being included in the tar-ball).</div><div><br></div><div>Also are you setup to build the Tutorial? Latex is easy to install (just a large download), but Hevea can be a pain. I did spend some effort trying to get that into conda, but didn't succeed.</div><div><br></div><div>Peter<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, May 11, 2020 at 3:20 PM Daley, Christopher <<a href="mailto:dalchr28@evergreen.edu">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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I've stood up a Docker container with all of the dependencies and successfully run the full online test suite with the exception of the NCBI_qblast test which seems to be timing out.</div>
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I'll make a pull request to update the Docker images once I test them a bit more locally.
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Chris<br>
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<div id="gmail-m_-6416857139516828440divRplyFwdMsg" 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> Saturday, May 9, 2020 10:47 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">Good news I guess: Bio.PopGen.FDist was deprecated in Release 1.68, removed in Release 1.70. So we don't need to worry about fdist2 anymore.<br>
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Perhaps you will have some pull requests to update the Docker images?<br>
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Peter<br>
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<div dir="ltr">On Sat, May 9, 2020 at 6:40 PM Daley, Christopher <<a href="mailto:dalchr28@evergreen.edu" target="_blank">dalchr28@evergreen.edu</a>> wrote:<br>
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Glad it was a simple fix.</div>
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I started building a Docker container to run the full tests locally based on the <a href="https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbiopython%2Fbiopython_docker&data=02%7C01%7Cdalchr28%40evergreen.edu%7Ce9972947678043a59dc508d7f44110dc%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637246432609609976&sdata=bel4oJcIXDukRJ04lh7xRDtCEV4q%2FLP7yJrhktf6ZSI%3D&reserved=0" id="gmail-m_-6416857139516828440x_gmail-m_6253262022126358377LPNoLP702564" target="_blank">
https://github.com/biopython/biopython_docker</a> repo, updated to Ubuntu 18.04 and Python 3.6. In doing so, I discovered that the download link for fdist2 is dead and there doesn't seem to be any other source for it online. Checking the other links it also
seems like <a href="https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fxxmotif.genzentrum.lmu.de%2Findex.php&data=02%7C01%7Cdalchr28%40evergreen.edu%7Ce9972947678043a59dc508d7f44110dc%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637246432609619967&sdata=anfoX9KQBQf99Vbhle%2BonIg1Uvw4T6nZol5joL2UW%2BI%3D&reserved=0" id="gmail-m_-6416857139516828440x_gmail-m_6253262022126358377LPlnk110296" target="_blank">
http://xxmotif.genzentrum.lmu.de</a> is down as well. The Bioconda package points to this github repo:
<a href="https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsoedinglab%2Fxxmotif&data=02%7C01%7Cdalchr28%40evergreen.edu%7Ce9972947678043a59dc508d7f44110dc%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637246432609619967&sdata=346MRRlAdxdd6P7ko%2Fl2zC%2BkoA2W%2BftxhDwCb7bSLHg%3D&reserved=0" id="gmail-m_-6416857139516828440x_gmail-m_6253262022126358377LPNoLP853185" target="_blank">
https://github.com/soedinglab/xxmotif</a></div>
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Any thoughts on how to proceed? <br>
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Chris<br>
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<div id="gmail-m_-6416857139516828440x_gmail-m_6253262022126358377appendonsend"></div>
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<div id="gmail-m_-6416857139516828440x_gmail-m_6253262022126358377divRplyFwdMsg" 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> Friday, May 8, 2020 1:34 PM<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">Good work on this documentation fix Chris - something I was hoping we'd fixed for the next release:
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<div><a href="https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbiopython%2Fbiopython%2Fissues%2F2502&data=02%7C01%7Cdalchr28%40evergreen.edu%7Ce9972947678043a59dc508d7f44110dc%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637246432609629962&sdata=wYDatOGqtGI3SXjMluMw1hXBcG2C5mrPs3314QwjMZM%3D&reserved=0" target="_blank">https://github.com/biopython/biopython/issues/2502</a><br>
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<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>
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<div><a href="https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbiopython.org%2Fwiki%2FBuilding_a_release&data=02%7C01%7Cdalchr28%40evergreen.edu%7Ce9972947678043a59dc508d7f44110dc%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637246432609639958&sdata=huVRxUELB%2Br7P%2FxMjtSGfm0Aoqg9%2BOdmXMaWCU2DCTw%3D&reserved=0" target="_blank">https://biopython.org/wiki/Building_a_release</a><br>
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<div>Peter</div>
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