<div dir="ltr">Excellent news, thank you Chris.<div><br></div><div>Two passes of LaTex is the norm when using labels and references, three passes if you use references to page numbers. The Makefile should do that. Hevea includes its own loop which is a littles easier to use.</div><div><br></div><div>As to the outstanding issues, the BLAST DB v5 test update seems easy enough - could you review this pull request Chris?</div><div><br></div><div><div><a href="https://github.com/biopython/biopython/issues/2863" target="_blank">https://github.com/biopython/biopython/issues/2863</a><br></div><div></div></div><div></div><div><a href="https://github.com/biopython/biopython/pull/2890" target="_blank">https://github.com/biopython/biopython/pull/2890</a><br></div><div><br></div><div>Updating the BLAST wrappers would be nice, but it seems we might just skip that (and silence the test warnings about the BLAST wrappers being out of date) if we're serious about dropping the Bio.Application framework:</div><div><br></div><div><a href="https://github.com/biopython/biopython/issues/2184">https://github.com/biopython/biopython/issues/2184</a><br></div><div><a href="https://github.com/biopython/biopython/issues/2877" target="_blank">https://github.com/biopython/biopython/issues/2877</a><br><div><br></div><div>Oh, and can we close the UniProt/SwissProt parser issue or not?:</div><div><br></div><div><a href="https://github.com/biopython/biopython/issues/2417" target="_blank">https://github.com/biopython/biopython/issues/2417</a><br></div><div><br></div><div>Other suggestions are <a href="https://github.com/biopython/biopython/pull/2399" target="_blank">https://github.com/biopython/biopython/pull/2399</a> which has some merge conflicts and needs a review.</div><div><br></div><div>Also if I can finish the documentation <a href="https://github.com/biopython/biopython/pull/2334">https://github.com/biopython/biopython/pull/2334</a> would be nice to include too.<br></div><div><br></div><div>Right now I still think only #2863/#2890 for the BLAST test, and #2417 for UniProt/SwissProt are blockers.</div><div><br></div><div>Peter</div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, May 14, 2020 at 8:16 AM 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">
<div dir="ltr">
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
I fetched the latest commits just now and ran the full tests, including the tar-ball and documentation and it all seems to be in order. I do a lot of Latex work, so pretty well set up in that area although I had to install Hevea from APT. The version in the
Ubuntu 18.04 repos is 2.30 which is pretty recent and seems to output the Tutorial nicely enough although it took two passes of the latex compiler.
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It looks all set from this end, barring the pull requests - are there any blocking issues or PRs?</div>
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Chris<br>
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<div id="gmail-m_-1798157624698031977gmail-m_5818143958217651218gmail-m_8132913268019563757appendonsend"></div>
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<div id="gmail-m_-1798157624698031977gmail-m_5818143958217651218gmail-m_8132913268019563757divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" 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> Tuesday, May 12, 2020 7:52 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">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.
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<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>
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<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>
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<div>Peter<br>
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<div dir="ltr">On Mon, May 11, 2020 at 3:20 PM Daley, Christopher <<a href="mailto:dalchr28@evergreen.edu" target="_blank">dalchr28@evergreen.edu</a>> wrote:<br>
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
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_-1798157624698031977gmail-m_5818143958217651218gmail-m_8132913268019563757x_gmail-m_-6416857139516828440appendonsend"></div>
<hr style="display:inline-block;width:98%">
<div id="gmail-m_-1798157624698031977gmail-m_5818143958217651218gmail-m_8132913268019563757x_gmail-m_-6416857139516828440divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><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>
<br>
Perhaps you will have some pull requests to update the Docker images?<br>
<br>
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%7C0f2d9d6e9164401aa66e08d7f684241d%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637248919720142489&sdata=Bxr5BeYAh7J8wj8VUy6bLwBcwz4Cne3j5nnkmGe0RwI%3D&reserved=0" id="gmail-m_-1798157624698031977gmail-m_5818143958217651218gmail-m_8132913268019563757x_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%7C0f2d9d6e9164401aa66e08d7f684241d%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637248919720142489&sdata=Is7cTyw%2BAieycEyj5VWm8cDoZaUziCrGG8OvYGfmTKg%3D&reserved=0" id="gmail-m_-1798157624698031977gmail-m_5818143958217651218gmail-m_8132913268019563757x_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%7C0f2d9d6e9164401aa66e08d7f684241d%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637248919720152483&sdata=%2BntvyTrH3Drw0DeZLhCksmBkRURRwcWWgqF7fz5%2BwyU%3D&reserved=0" id="gmail-m_-1798157624698031977gmail-m_5818143958217651218gmail-m_8132913268019563757x_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_-1798157624698031977gmail-m_5818143958217651218gmail-m_8132913268019563757x_gmail-m_-6416857139516828440x_gmail-m_6253262022126358377appendonsend">
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<div id="gmail-m_-1798157624698031977gmail-m_5818143958217651218gmail-m_8132913268019563757x_gmail-m_-6416857139516828440x_gmail-m_6253262022126358377divRplyFwdMsg" dir="ltr">
<font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><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>
<div> </div>
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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:
<div><br>
<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%7C0f2d9d6e9164401aa66e08d7f684241d%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637248919720162478&sdata=OwY6vorDjyNvrN3Lhm1OXe5ECBeqVfhEaiYugyREXcs%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%7C0f2d9d6e9164401aa66e08d7f684241d%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637248919720162478&sdata=stgShVLrb%2BuUsjXenxp2PQeFaWFQa4OKqX67Y6CzQQI%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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