From p.j.a.cock at googlemail.com Sat Nov 2 10:22:58 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 2 Nov 2013 14:22:58 +0000 Subject: [Biopython-dev] ExPASy / UniProt API for searching and fetching Message-ID: Hello Biopythoneers, Would anyone like to look at updating/replacing the old web API functions in Bio.ExPASy to talk to UniProt.org instead? See: https://github.com/biopython/biopython/issues/253 Peter From p.j.a.cock at googlemail.com Sat Nov 2 10:39:20 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 2 Nov 2013 14:39:20 +0000 Subject: [Biopython-dev] Python 2 and 3 migration thoughts In-Reply-To: References: Message-ID: On Sat, Oct 26, 2013 at 7:44 PM, Peter Cock wrote: > > A new pull request for people to comment on, which eliminates > all but two important fixers. As a bonus this makes installation > under Python 3 much much quicker: > > https://github.com/biopython/biopython/pull/250 > I take it there are no objections to me merging this work? If not, I will try to do it tomorrow (Sunday) or early next week, and move on to the final issues before we can drop 2to3 (which I do not anticipate being problematic). Once we've dropped 2to3, I would like us to a do a beta release (by mid November?), and then bar any problems, ship that as Biopython 1.63 (hopefully by late November). (There are plenty of things pending which would be great to have in the next release, but these changes are so wide ranging that I would prefer we focus primarily on Python 3 for the next release.) Regards, Peter From p.j.a.cock at googlemail.com Sat Nov 2 13:51:10 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 2 Nov 2013 17:51:10 +0000 Subject: [Biopython-dev] Python 2 and 3 migration thoughts In-Reply-To: References: Message-ID: On Sat, Nov 2, 2013 at 2:39 PM, Peter Cock wrote: > On Sat, Oct 26, 2013 at 7:44 PM, Peter Cock wrote: >> >> A new pull request for people to comment on, which eliminates >> all but two important fixers. As a bonus this makes installation >> under Python 3 much much quicker: >> >> https://github.com/biopython/biopython/pull/250 https://github.com/peterjc/biopython/tree/py3fixes > I take it there are no objections to me merging this work? > If not, I will try to do it tomorrow (Sunday) or early next week, > and move on to the final issues before we can drop 2to3 > (which I do not anticipate being problematic). They are not troublesome, perhaps worth applying soon too? (Can anyone propose a more elegant solution to __nonzero__ versus __bool__ than to just define both?) This allows us to stop using 2to3 (something NumPy have also managed in their recent NumPy 1.8 release), making installation of Biopython from source under Python 3.3 faster and much simpler: https://github.com/peterjc/biopython/tree/py3more Regards, Peter From eric.talevich at gmail.com Sat Nov 2 14:23:31 2013 From: eric.talevich at gmail.com (Eric Talevich) Date: Sat, 2 Nov 2013 11:23:31 -0700 Subject: [Biopython-dev] Python 2 and 3 migration thoughts In-Reply-To: References: Message-ID: On Sat, Nov 2, 2013 at 10:51 AM, Peter Cock wrote: > On Sat, Nov 2, 2013 at 2:39 PM, Peter Cock wrote: > > On Sat, Oct 26, 2013 at 7:44 PM, Peter Cock wrote: > >> > >> A new pull request for people to comment on, which eliminates > >> all but two important fixers. As a bonus this makes installation > >> under Python 3 much much quicker: > >> > >> https://github.com/biopython/biopython/pull/250 > > https://github.com/peterjc/biopython/tree/py3fixes > > > I take it there are no objections to me merging this work? > > If not, I will try to do it tomorrow (Sunday) or early next week, > > and move on to the final issues before we can drop 2to3 > > (which I do not anticipate being problematic). > > They are not troublesome, perhaps worth applying soon too? > (Can anyone propose a more elegant solution to __nonzero__ > versus __bool__ than to just define both?) > > This allows us to stop using 2to3 (something NumPy have > also managed in their recent NumPy 1.8 release), making > installation of Biopython from source under Python 3.3 > faster and much simpler: > > https://github.com/peterjc/biopython/tree/py3more > > Regards, > > Peter > Cool, no objections here. Maybe after the next stable release we can look into finalizing and merging the new GSoC work? As far as I can tell the best way to handle __nonzero__ vs. __bool__ is what you indicated: class Foo(object): def __bool__(self): return True __nonzero__ = __bool__ And presumably the 2to3 converter would need to be disabled at the same time, or it might try to rename __nonzero__ to __bool__ and get confused. Cheers, Eric From p.j.a.cock at googlemail.com Sun Nov 3 09:03:51 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sun, 3 Nov 2013 14:03:51 +0000 Subject: [Biopython-dev] Python 2 and 3 migration thoughts In-Reply-To: References: Message-ID: On Sat, Nov 2, 2013 at 6:23 PM, Eric Talevich wrote: > On Sat, Nov 2, 2013 at 10:51 AM, Peter Cock wrote: >> On Sat, Nov 2, 2013 at 2:39 PM, Peter Cock wrote: >>> I take it there are no objections to me merging this work? >>> If not, I will try to do it tomorrow (Sunday) or early next week, Applied https://github.com/biopython/biopython/pull/250 plus a follow up fix for Python 3 on Windows, https://github.com/biopython/biopython/commit/9a265285e587f243814ffc05772b639051b31be1 (The buildbot server is earning its keep) >> > and move on to the final issues before we can drop 2to3 >> > (which I do not anticipate being problematic). >> >> They are not troublesome, perhaps worth applying soon too? >> (Can anyone propose a more elegant solution to __nonzero__ >> versus __bool__ than to just define both?) >> >> This allows us to stop using 2to3 (something NumPy have >> also managed in their recent NumPy 1.8 release), making >> installation of Biopython from source under Python 3.3 >> faster and much simpler: >> >> https://github.com/peterjc/biopython/tree/py3more > > Cool, no objections here. Maybe after the next stable release > we can look into finalizing and merging the new GSoC work? Yes please. > As far as I can tell the best way to handle __nonzero__ vs. __bool__ is what > you indicated: > > class Foo(object): > def __bool__(self): return True > __nonzero__ = __bool__ OK, I've updated my change to use that style rather than my initial version which literally defined it twice: class Foo(object): def __bool__(self): return True def __nonzero__(self): return True > And presumably the 2to3 converter would need to be disabled at the same > time, or it might try to rename __nonzero__ to __bool__ and get confused. Yes indeed. This is all done as one commit: https://github.com/biopython/biopython/commit/d6aa77c43bf9bab6302d880ad458b46f80e21c5e That leaves one remaining fixer, unicode, which is addressed here https://github.com/peterjc/biopython/tree/py3more in part by dropping Python 3.2 so that we can use unicode literals. We deliberately didn't claim to support Python 3.2 in order to allow us this option. Tiago or I will need to update the buildbot server to drop Python 3.2 before applying that change... Regards, Peter From tra at popgen.net Sun Nov 3 11:30:15 2013 From: tra at popgen.net (Tiago Antao) Date: Sun, 03 Nov 2013 16:30:15 +0000 Subject: [Biopython-dev] Python 2 and 3 migration thoughts In-Reply-To: References: Message-ID: <874n7t5tyg.wl%tra@popgen.net> At Sun, 3 Nov 2013 14:03:51 +0000, Peter Cock wrote: > Tiago or I will need to update the buildbot server to drop > Python 3.2 before applying that change... Ready to roll From p.j.a.cock at googlemail.com Sun Nov 3 14:28:05 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sun, 3 Nov 2013 19:28:05 +0000 Subject: [Biopython-dev] Python 2 and 3 migration thoughts In-Reply-To: <874n7t5tyg.wl%tra@popgen.net> References: <874n7t5tyg.wl%tra@popgen.net> Message-ID: On Sun, Nov 3, 2013 at 4:30 PM, Tiago Antao wrote: > At Sun, 3 Nov 2013 14:03:51 +0000, > Peter Cock wrote: >> Tiago or I will need to update the buildbot server to drop >> Python 3.2 before applying that change... > > Ready to roll Lovely, thank you :) Unicode changes pushed to master: https://github.com/biopython/biopython/commit/0f85dd5f5a0ffd2e8c1f0c45a890e43c4d689f49 At this point we're not using any 2to3 fixers, so we could remove the do2to3.py script etc - which is what the remaining fixes on this branch do: https://github.com/peterjc/biopython/tree/py3more However, before I do that, are there any pending commits which would still need 2to3 in the short term? Thanks, Peter From w.arindrarto at gmail.com Sun Nov 3 19:12:52 2013 From: w.arindrarto at gmail.com (Wibowo Arindrarto) Date: Mon, 4 Nov 2013 01:12:52 +0100 Subject: [Biopython-dev] ExPASy / UniProt API for searching and fetching In-Reply-To: References: Message-ID: Hello everyone, I'm trying a jab at this in this branch: https://github.com/bow/biopython/blob/dev_uniprot-api/Bio/UniProt/API.py. It's still quite bare bones at the moment, but the general approach shouldn't change much for the other functions. I'm still not sure about the namespace, though. Should it be Bio.UniProt.API, Bio.UniProt.api, or something else? As always, let me know what you think :). Cheers, Bow On Sat, Nov 2, 2013 at 3:22 PM, Peter Cock wrote: > Hello Biopythoneers, > > Would anyone like to look at updating/replacing the old web > API functions in Bio.ExPASy to talk to UniProt.org instead? > See: https://github.com/biopython/biopython/issues/253 > > Peter > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev From p.j.a.cock at googlemail.com Mon Nov 4 05:35:37 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 4 Nov 2013 10:35:37 +0000 Subject: [Biopython-dev] ExPASy / UniProt API for searching and fetching In-Reply-To: References: Message-ID: On Mon, Nov 4, 2013 at 12:12 AM, Wibowo Arindrarto wrote: > Hello everyone, > > I'm trying a jab at this in this branch: > https://github.com/bow/biopython/blob/dev_uniprot-api/Bio/UniProt/API.py. > > It's still quite bare bones at the moment, but the general approach > shouldn't change much for the other functions. I'm still not sure > about the namespace, though. Should it be Bio.UniProt.API, > Bio.UniProt.api, or something else? > > As always, let me know what you think :). > > Cheers, > Bow Rather than Bio.UniProt.API, we should try to use lowercase PEP8 module names (I think here .api would be better). However, API seems to vague - how about www to be more clear this is an online resource? (Unlike the NCBI Entrez Utilities, there isn't a clear branding for the UniProt web API is there?) Peter From w.arindrarto at gmail.com Mon Nov 4 05:48:21 2013 From: w.arindrarto at gmail.com (Wibowo Arindrarto) Date: Mon, 4 Nov 2013 11:48:21 +0100 Subject: [Biopython-dev] ExPASy / UniProt API for searching and fetching In-Reply-To: References: Message-ID: Hi Peter, everyone, On Mon, Nov 4, 2013 at 11:35 AM, Peter Cock wrote: > On Mon, Nov 4, 2013 at 12:12 AM, Wibowo Arindrarto > wrote: >> Hello everyone, >> >> I'm trying a jab at this in this branch: >> https://github.com/bow/biopython/blob/dev_uniprot-api/Bio/UniProt/API.py. >> >> It's still quite bare bones at the moment, but the general approach >> shouldn't change much for the other functions. I'm still not sure >> about the namespace, though. Should it be Bio.UniProt.API, >> Bio.UniProt.api, or something else? >> >> As always, let me know what you think :). >> >> Cheers, >> Bow > > Rather than Bio.UniProt.API, we should try to use lowercase > PEP8 module names (I think here .api would be better). > > However, API seems to vague - how about www to be more > clear this is an online resource? Bio.UniProt.www is fine with me, too (and somewhat in line with what we already have in Bio.Blast.NCBIWWW). > (Unlike the NCBI Entrez Utilities, there isn't a clear branding > for the UniProt web API is there?) It's not as comprehensively branded as Entrez. They do have similar functionalities, though. We can do query searches, retrieve records, do a BLAST search, and even map identifiers across databases. The BLAST search API doesn't seem to be very well-documented in the website, but there is a Java API that allows you to do so: http://www.ebi.ac.uk/uniprot/remotingAPI/. They even have their own formats of the BLAST results (e.g. http://www.uniprot.org/blast/uniprot/2013110441MHJHFYCR.* or http://www.uniprot.org/blast/uniprot/2013110441MHJHFYCR.xml) There are still some things left in Bio.ExPASy that UniProt doesn't seem to cover, though, such as the Prosite search. I was thinking maybe we could reorganize the existing Bio.UniProt code base like this: Bio.UniProt | |-- parsers | | | |-- GOA, etc. |-- www (or api, or remote) |-- __init__.py containing main functions Best, Bow From p.j.a.cock at googlemail.com Mon Nov 4 06:04:03 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 4 Nov 2013 11:04:03 +0000 Subject: [Biopython-dev] ExPASy / UniProt API for searching and fetching In-Reply-To: References: Message-ID: On Mon, Nov 4, 2013 at 10:48 AM, Wibowo Arindrarto wrote: > Hi Peter, everyone, > > On Mon, Nov 4, 2013 at 11:35 AM, Peter Cock wrote: >> On Mon, Nov 4, 2013 at 12:12 AM, Wibowo Arindrarto >> wrote: >>> Hello everyone, >>> >>> I'm trying a jab at this in this branch: >>> https://github.com/bow/biopython/blob/dev_uniprot-api/Bio/UniProt/API.py. >>> >>> It's still quite bare bones at the moment, but the general approach >>> shouldn't change much for the other functions. I'm still not sure >>> about the namespace, though. Should it be Bio.UniProt.API, >>> Bio.UniProt.api, or something else? >>> >>> As always, let me know what you think :). >>> >>> Cheers, >>> Bow >> >> Rather than Bio.UniProt.API, we should try to use lowercase >> PEP8 module names (I think here .api would be better). >> >> However, API seems to vague - how about www to be more >> clear this is an online resource? > > Bio.UniProt.www is fine with me, too (and somewhat in line with what > we already have in Bio.Blast.NCBIWWW). > >> (Unlike the NCBI Entrez Utilities, there isn't a clear branding >> for the UniProt web API is there?) > > It's not as comprehensively branded as Entrez. They do have similar > functionalities, though. We can do query searches, retrieve records, > do a BLAST search, and even map identifiers across databases. The > BLAST search API doesn't seem to be very well-documented in the > website, but there is a Java API that allows you to do so: > http://www.ebi.ac.uk/uniprot/remotingAPI/. See: http://www.ebi.ac.uk/Tools/webservices/services/sss/ncbi_blast_rest > They even have their own > formats of the BLAST results (e.g. > http://www.uniprot.org/blast/uniprot/2013110441MHJHFYCR.* or > http://www.uniprot.org/blast/uniprot/2013110441MHJHFYCR.xml) Hmm, another XML variant. Maybe ignore that for now. > There are still some things left in Bio.ExPASy that UniProt doesn't > seem to cover, though, such as the Prosite search. Anyone know? > I was thinking maybe we could reorganize the existing Bio.UniProt code > base like this: > > Bio.UniProt > | > |-- parsers > | | > | |-- GOA, etc. > |-- www (or api, or remote) > |-- __init__.py containing main functions > Bio.UniProt.GOA was only introduced in the last release, moving it under Bio.UniProt.parsers.GOA doesn't seem ideal. CC'ing Iddo for comment. Peter From tra at popgen.net Tue Nov 5 08:25:39 2013 From: tra at popgen.net (Tiago Antao) Date: Tue, 05 Nov 2013 13:25:39 +0000 Subject: [Biopython-dev] Biopython 1.63 release Message-ID: <87eh6v7zfw.wl%tra@popgen.net> Dear all, Unless somebody else wants to step forward, I am thinking in volunteering to handle the release of 1.63. This would be a first and therefore I hope you would all have some patience with my inexperience doing this. The upside of it is that, having inexperienced hands will allow for a review of the release procedure (if something is missing, an inexperienced release manager will be more prone to detect it than an experienced one). I no one steps forward, I will start the ball rolling later today here on the list. Regards, Tiago From p.j.a.cock at googlemail.com Tue Nov 5 08:36:24 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 5 Nov 2013 13:36:24 +0000 Subject: [Biopython-dev] Biopython 1.63 release In-Reply-To: <87eh6v7zfw.wl%tra@popgen.net> References: <87eh6v7zfw.wl%tra@popgen.net> Message-ID: On Tuesday, November 5, 2013, Tiago Antao wrote: > Dear all, > > Unless somebody else wants to step forward, I am thinking in > volunteering to handle the release of 1.63. > > This would be a first and therefore I hope you would all have some > patience with my inexperience doing this. The upside of it is that, > having inexperienced hands will allow for a review of the release > procedure (if something is missing, an inexperienced release manager > will be more prone to detect it than an experienced one). > > I no one steps forward, I will start the ball rolling later today here > on the list. > > Regards, > Tiago > Thanks Tiago - I think this a great idea. As per the 2to3 thread, I'd like us to do a beta release first - as an unusually large number of files have been changed since the last release (as part of getting the code to run on both Python 2 and 3 without conversion by 2to3 first). Regards, Peter From p.j.a.cock at googlemail.com Tue Nov 5 15:58:12 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 5 Nov 2013 20:58:12 +0000 Subject: [Biopython-dev] Python 2 and 3 migration thoughts In-Reply-To: References: <874n7t5tyg.wl%tra@popgen.net> Message-ID: On Sun, Nov 3, 2013 at 7:28 PM, Peter Cock wrote: > > At this point we're not using any 2to3 fixers, so we could > remove the do2to3.py script etc - which is what the remaining > fixes on this branch do: > > https://github.com/peterjc/biopython/tree/py3more > > However, before I do that, are there any pending commits > which would still need 2to3 in the short term? Pushed to master, Biopython now runs on Python 2 and Python 3 natively without using the 2to3 converter :) https://github.com/biopython/biopython/commit/6b24a509b13e9df3c41fc211646d24382685e050 https://github.com/biopython/biopython/commit/a9cb8c10f68fe6d8bdccf34d8217838cc9d4db7f Now let's focus on Biopython 1.63 (beta), which Tiago has kindly offered to managed :) http://lists.open-bio.org/pipermail/biopython-dev/2013-November/010955.html Peter From arklenna at gmail.com Tue Nov 5 16:08:19 2013 From: arklenna at gmail.com (Lenna Peterson) Date: Tue, 5 Nov 2013 16:08:19 -0500 Subject: [Biopython-dev] Biopython 1.63 release In-Reply-To: References: <87eh6v7zfw.wl%tra@popgen.net> Message-ID: On Tue, Nov 5, 2013 at 8:36 AM, Peter Cock wrote: > On Tuesday, November 5, 2013, Tiago Antao wrote: > > > Dear all, > > > > Unless somebody else wants to step forward, I am thinking in > > volunteering to handle the release of 1.63. > > > > This would be a first and therefore I hope you would all have some > > patience with my inexperience doing this. The upside of it is that, > > having inexperienced hands will allow for a review of the release > > procedure (if something is missing, an inexperienced release manager > > will be more prone to detect it than an experienced one). > > > > I no one steps forward, I will start the ball rolling later today here > > on the list. > > > > Regards, > > Tiago > > > > Thanks Tiago - I think this a great idea. > > As per the 2to3 thread, I'd like us to do a beta release first - > as an unusually large number of files have been changed > since the last release (as part of getting the code to run on > both Python 2 and 3 without conversion by 2to3 first). > > Regards, > > Peter > > Is the `open()` to `with open()` conversion a priority for this release? If so, I can carve out some hours to punch that out. Big whitespace changes to lots of files. Cheers, Lenna From tra at popgen.net Tue Nov 5 16:22:04 2013 From: tra at popgen.net (Tiago Antao) Date: Tue, 05 Nov 2013 21:22:04 +0000 Subject: [Biopython-dev] Biopython 1.63 beta - preparations Message-ID: <874n7qilxf.wl%tra@popgen.net> Dear all, As previously discussed I would like to start preparing the beta version of 1.63. I would like to try to have a beta build somewhere between Sunday and Tuesday (this variation is mostly dependent on the availability of a suitable Windows machine), unless someone finds this timing not ideal. If anyone is thinking on committing new functionality (other than bug corrections, that is), please do inform the mailing list in advance. Correct me if I am wrong, but this is the first version NOT supporting Python 2.5. Therefore no attempts will be made of building on 2.5. If such is the case, I will also amend the Wiki page http://biopython.org/wiki/Building_a_release Thus Python versions supported will be 2.6, 2.7 and 3.3. I will follow all the steps on the wiki page above, that will mean that I will bump (during the process) the version numbers and documentation to 1.63 beta. Feel free to correct me or add any pertinent information. This concludes this message for your newbie 1.63 release manager, Tiago From tra at popgen.net Tue Nov 5 16:38:14 2013 From: tra at popgen.net (Tiago Antao) Date: Tue, 05 Nov 2013 21:38:14 +0000 Subject: [Biopython-dev] Biopython 1.63 release In-Reply-To: References: <87eh6v7zfw.wl%tra@popgen.net> Message-ID: <87ob5yy1fd.wl%tra@popgen.net> At Tue, 5 Nov 2013 16:08:19 -0500, Lenna Peterson wrote: > Is the `open()` to `with open()` conversion a priority for this release? If so, I can carve out some > hours to punch that out. Big whitespace changes to lots of files. >From my side, anything that is done before the weekend should be OK (regarding the issue of being a priority or not, I have no opinion). I would just ask that, during the weekend, only minor bug corrections are done. I will probably do everything this next Sunday (unless here there is here an opinion against, or my Windows setup becomes problematic) Tiago From p.j.a.cock at googlemail.com Wed Nov 6 04:11:21 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 6 Nov 2013 09:11:21 +0000 Subject: [Biopython-dev] Biopython 1.63 beta - preparations In-Reply-To: <874n7qilxf.wl%tra@popgen.net> References: <874n7qilxf.wl%tra@popgen.net> Message-ID: On Tue, Nov 5, 2013 at 9:22 PM, Tiago Antao wrote: > Dear all, > > As previously discussed I would like to start preparing the beta > version of 1.63. > > I would like to try to have a beta build somewhere between Sunday and > Tuesday (this variation is mostly dependent on the availability of a > suitable Windows machine), unless someone finds this timing not ideal. > > If anyone is thinking on committing new functionality (other than bug > corrections, that is), please do inform the mailing list in advance. > > Correct me if I am wrong, but this is the first version NOT supporting > Python 2.5. Therefore no attempts will be made of building on 2.5. If > such is the case, I will also amend the Wiki page > http://biopython.org/wiki/Building_a_release > > Thus Python versions supported will be 2.6, 2.7 and 3.3. Yes (since 3.4 is still only in alpha). Also this line will change now we don't call 2to3, copy build\py3.3\dist\biopython-1.62.win32-py3.3.exe dist to just: copy dist\biopython-1.63.win32-py3.3.exe dist Something else I think I should have done to the wiki page is move epydoc nearer the start - it has often found issues needing fixing. Regards, Peter From tra at popgen.net Sat Nov 9 14:45:25 2013 From: tra at popgen.net (Tiago Antao) Date: Sat, 09 Nov 2013 19:45:25 +0000 Subject: [Biopython-dev] Biopython 1.63 beta - preparations In-Reply-To: <874n7qilxf.wl%tra@popgen.net> References: <874n7qilxf.wl%tra@popgen.net> Message-ID: <87wqkh7416.wl%tra@popgen.net> Dear all, At Tue, 05 Nov 2013 21:22:04 +0000, > As previously discussed I would like to start preparing the beta > version of 1.63. This seems on track (a dry-run worked including compiling on an Windows 8 machine) and I would like to do the whole procedure tomorrow morning (Western European Time). I will be able to go up to step 18 of the build instructions (i.e. I will alter the repository and tag biopython-163b). Regards, Tiago From p.j.a.cock at googlemail.com Sat Nov 9 18:33:47 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 9 Nov 2013 23:33:47 +0000 Subject: [Biopython-dev] Biopython 1.63 beta - preparations In-Reply-To: <87wqkh7416.wl%tra@popgen.net> References: <874n7qilxf.wl%tra@popgen.net> <87wqkh7416.wl%tra@popgen.net> Message-ID: On Saturday, November 9, 2013, Tiago Antao wrote: > Dear all, > > At Tue, 05 Nov 2013 21:22:04 +0000, > > As previously discussed I would like to start preparing the beta > > version of 1.63. > > This seems on track (a dry-run worked including compiling on an > Windows 8 machine) and I would like to do the whole procedure > tomorrow morning (Western European Time). I will be able to go up to > step 18 of the build instructions (i.e. I will alter the repository > and tag biopython-163b). > > Regards, > Tiago > Excellent - we wouldn't push a beta to PyPI anyway which is one of the final tasks. Thank you :) Peter From tra at popgen.net Sat Nov 9 18:37:34 2013 From: tra at popgen.net (Tiago Antao) Date: Sat, 09 Nov 2013 23:37:34 +0000 Subject: [Biopython-dev] online tests Message-ID: <87d2m9ywn5.wl%tra@popgen.net> Hi, Some of the online tests are failing: These are: test_Entrez_online.py test_SeqIO_online.py test_TogoWS.py I would not be shocked that in some cases the services are just down for now, but there is one error that seems worrying: tra at UX32A:~/Dropbox/bp-release/prepare/biopython$ python Tests/test_TogoWS.py Traceback (most recent call last): File "Tests/test_TogoWS.py", line 12, in from Bio._py3k import StringIO ImportError: cannot import name StringIO (same happens with the SeqIO test) Tiago From tra at popgen.net Sun Nov 10 07:49:39 2013 From: tra at popgen.net (Tiago Antao) Date: Sun, 10 Nov 2013 12:49:39 +0000 Subject: [Biopython-dev] 1.63 beta Message-ID: <87r4ao5sm4.wl%tra@popgen.net> Dear all, I do not have access to the deployment machines, so I have put everything on: http://popgen.net/bp This includes: The API The source (tar and zip) Windows binaries (2.6, 2.7, 3.3) I think it is better this way as this will allow some testing before going live. I suspect the biggest change from previous versions is that I used MinGW instead of MS compilers to do the binaries. Tiago From p.j.a.cock at googlemail.com Sun Nov 10 08:05:02 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sun, 10 Nov 2013 13:05:02 +0000 Subject: [Biopython-dev] 1.63 beta In-Reply-To: <87r4ao5sm4.wl%tra@popgen.net> References: <87r4ao5sm4.wl%tra@popgen.net> Message-ID: On Sunday, November 10, 2013, Tiago Antao wrote: > Dear all, > > I do not have access to the deployment machines, so I have put > everything on: > > http://popgen.net/bp > > This includes: > The API > The source (tar and zip) > Windows binaries (2.6, 2.7, 3.3) > > I think it is better this way as this will allow some testing before > going live. Yeah, a few test installs first would be great before publisicing this - I can try the Windows installers tomorrow. Tiago you probably have got SSH key access to the biopython.org website, I'll email you off list... > I suspect the biggest change from previous versions is that I used > MinGW instead of MS compilers to do the binaries. > > Tiago > > I think the win32 installers I have been making are a mix of mingw and the MS compilers (depending on the Python version). Can you work on a draft release announcement (for the blog & email)? If you don't have an account on the OBF Wordpress I can arrange that... Thanks, Peter From tra at popgen.net Sun Nov 10 14:15:35 2013 From: tra at popgen.net (Tiago Antao) Date: Sun, 10 Nov 2013 19:15:35 +0000 Subject: [Biopython-dev] 1.63 beta In-Reply-To: References: <87r4ao5sm4.wl%tra@popgen.net> Message-ID: <8761s05aqw.wl%tra@popgen.net> At Sun, 10 Nov 2013 13:05:02 +0000, Peter Cock wrote: > Can you work on a draft release announcement (for the > blog & email)? If you don't have an account on the OBF > Wordpress I can arrange that... I have cooked up a draft announcement (plagiarised from the NEWS) here: http://popgen.net/bp/ann.html I am travelling back to the UK tomorrow and will be able to release this in the evening assuming that: 1. People are OK with the sources and binaries generated 2. People are OK with the announcement 3. I have access to the servers 4. I will _not_ try to deploy to pypi, as this is a beta Tiago From p.j.a.cock at googlemail.com Mon Nov 11 05:23:48 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 11 Nov 2013 10:23:48 +0000 Subject: [Biopython-dev] 1.63 beta In-Reply-To: References: <87r4ao5sm4.wl%tra@popgen.net> Message-ID: On Sun, Nov 10, 2013 at 1:05 PM, Peter Cock wrote: > > On Sunday, November 10, 2013, Tiago Antao wrote: >> >> Dear all, >> >> I do not have access to the deployment machines, so I have put >> everything on: >> >> http://popgen.net/bp >> >> This includes: >> The API >> The source (tar and zip) >> Windows binaries (2.6, 2.7, 3.3) >> >> I think it is better this way as this will allow some testing before >> going live. > > > Yeah, a few test installs first would be great before publisicing > this - I can try the Windows installers tomorrow. The Windows installers seemed fine (they worked on my Windows XP machine). Can you try copying them (and the epydoc folder) over to biopython.org or do I need to update your SSH key? Thanks, Peter From tra at popgen.net Mon Nov 11 17:45:51 2013 From: tra at popgen.net (Tiago Antao) Date: Mon, 11 Nov 2013 22:45:51 +0000 Subject: [Biopython-dev] bugzilla on new releases?? Message-ID: <87vbzy1rs0.wl%tra@popgen.net> Hi, The release instructions refer updating bugzilla. Isn't that deprecated??? Tiago From p.j.a.cock at googlemail.com Mon Nov 11 19:13:44 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 12 Nov 2013 00:13:44 +0000 Subject: [Biopython-dev] bugzilla on new releases?? In-Reply-To: <87vbzy1rs0.wl%tra@popgen.net> References: <87vbzy1rs0.wl%tra@popgen.net> Message-ID: On Mon, Nov 11, 2013 at 10:45 PM, Tiago Antao wrote: > Hi, > > The release instructions refer updating bugzilla. Isn't that > deprecated??? > > Tiago Yeah, but it is still accepting new issues (if anyone can work out how to stop that let us know) so perhaps we might as well add the release tags to it? Peter From p.j.a.cock at googlemail.com Tue Nov 12 11:57:53 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 12 Nov 2013 16:57:53 +0000 Subject: [Biopython-dev] [Biopython] Biopython 1.63 beta release In-Reply-To: <87vbzx37m9.wl%tra@popgen.net> References: <87vbzx37m9.wl%tra@popgen.net> Message-ID: Thank you Tiago, on behalf of us all, for handling the Biopython 1.63 beta release. Hopefully other than accounts (for the webserver & blog etc) things went smoothly, and I see you've already updated some little details on the wiki so make it easier for the next person :) http://biopython.org/wiki/Building_a_release Regards, Peter On Tue, Nov 12, 2013 at 4:30 PM, Tiago Antao wrote: > Dear Biopythoneers, > > A beta release for Biopython 1.63 is now available for download and > testing. > > This is a beta release for testing purposes, the main reason for a > beta version is the large amount of changes imposed by the removal of > the 2to3 library previously required for the support of Python 3.X. > This was made possible by dropping Python 2.5 (and Jython 2.5). > > This release of Biopython supports Python 2.6 and 2.7, and also Python > 3.3. > > The Biopython Tutorial & Cookbook, and the docstring examples in the > source code, now use the Python 3 style print function in place of the > Python 2 style print statement. This language feature is available > under Python 2.6 and 2.7 via: > > from __future__ import print_function > > Similarly we now use the Python 3 style built-in next function in > place of the Python 2 style iterators' .next() method. This language > feature is also available under Python 2.6 and 2.7. > > > Many thanks to the Biopython developers and community for making this > release possible, especially the following contributors: > > Chris Mitchell (first contribution) > Christian Brueffer > Eric Talevich > Josha Inglis (first contribution) > Konstantin Tretyakov (first contribution) > Lenna Peterson > Martin Mokrejs > Nigel Delaney (first contribution) > Peter Cock > Sergei Lebedev (first contribution) > Tiago Antao > Wayne Decatur (first contribution) > Wibowo 'Bow' Arindrarto > > > Regards, > Tiago > _______________________________________________ > Biopython mailing list - Biopython at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython From zruan1991 at gmail.com Thu Nov 14 21:57:03 2013 From: zruan1991 at gmail.com (Zheng Ruan) Date: Thu, 14 Nov 2013 21:57:03 -0500 Subject: [Biopython-dev] Pull Request for Codon Alignment GSoC project Message-ID: Hi all, Since a beta version of biopython has been released, it might be safe to merge my GSoC work. I just made a pull request and there seems to be some problems when running the code in different platforms. In python2.7 and python3.3, the error message complains they cannot find CodonAlign module. I'm not sure why this happens. The dependency of Scipy and Numpy might also introduce some problems for the testing. Thanks! Best, Zheng Ruan From p.j.a.cock at googlemail.com Fri Nov 15 06:08:31 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 15 Nov 2013 11:08:31 +0000 Subject: [Biopython-dev] [Biopython] I've written a library for executing fuzzy searches... In-Reply-To: References: Message-ID: On Tue, Nov 12, 2013 at 5:59 PM, Tal Einat wrote: > Hi everyone, > > (I'm not on this list, so please make sure to reply to me as well as the > list.) > > In response to a stackoverflow > question, > I've written a Python library for fuzzy searches called > 'fuzzysearch'. > Currently, it allows searching for a string inside a longer string, > returning the best sub-string which match up to a given maximum Levenshtein > distance. This is done quite efficiently, and there is more optimization to > be done, as needed. > > Is there any interest in this library and its further development? One > thing which I think might be useful is support for BioPython Sequence types. > > This is open-source with a very liberal license (the MIT license). > > I'd be happy to collaborate on this! > > - Tal Einat Hi Tal, This does sounds interesting, yes. It might fit nicely into Biopython as Bio/SeqUtils/fizzysearch.py? I agree it would be good to ensure that your code will accept Biopython's (string like) Seq objects as well as plain strings. In terms of the license, I presume you'd be happy to accept the Biopython licence (or the 3-clause BSD licence which we are looking at switching to), which are both quite similar to the MIT licence? In terms of dependencies, you are using namedtuple which is fine (it wasn't in Python 2.5 but we've dropped that now). Also I see you are already supporting Python 2.6, 2.7 and 3.2, 3.3 with a single code base - which is good and perfect for integration into Biopython (we've recently dropped 2to3 which we used to use). In terms of unit tests, it is great to see you've done this already - although using unittest2 where we're still using unittest (v1) that shouldn't be a problem Peter From p.j.a.cock at googlemail.com Fri Nov 15 06:16:10 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 15 Nov 2013 11:16:10 +0000 Subject: [Biopython-dev] Pull Request for Codon Alignment GSoC project In-Reply-To: References: Message-ID: On Fri, Nov 15, 2013 at 2:57 AM, Zheng Ruan wrote: > Hi all, > > Since a beta version of biopython has been released, it might be safe to > merge my GSoC work. We'll normally only do minor bug fixes and documentation improvements between a beta and final release, but this is perfect timing for getting your work merged immediately after Biopython 1.63 is out. (So far there have been no problems reported with the beta, and we've fixed some newline issues when testing under Windows) > I just made a pull request and there seems to be some > problems when running the code in different platforms. In > python2.7 and python3.3, the error message complains they > cannot find CodonAlign module. I'm not sure why this happens. Some discussion is on the pull request itself: https://github.com/biopython/biopython/pull/259 > The dependency of Scipy and Numpy might also > introduce some problems for the testing. Thanks! We've got a mechanism for skipping tests when a dependency is missing - the MissingExternalDependencyError and MissingPythonDependencyError exceptions. You need to use this in test_CodonAlign.py, see test_PDB.py etc. Related to this we would need to install new dependencies on some of the buildbot slaves and perhaps TravisCI. Regards, Peter From anaryin at gmail.com Sat Nov 16 17:28:26 2013 From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=) Date: Sat, 16 Nov 2013 23:28:26 +0100 Subject: [Biopython-dev] Possible Bug in psi-blast via web? Message-ID: Someone posted this problem in Reddit. Anyone with some more expertise can probably give a better answer. http://www.reddit.com/r/bioinformatics/comments/1qmpbm/problems_with_psiblast_results_from_biopython/ From p.j.a.cock at googlemail.com Mon Nov 18 05:07:12 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 18 Nov 2013 10:07:12 +0000 Subject: [Biopython-dev] Possible Bug in psi-blast via web? In-Reply-To: References: Message-ID: On Sat, Nov 16, 2013 at 10:28 PM, Jo?o Rodrigues wrote: > Someone posted this problem in Reddit. Anyone with some more expertise can > probably give a better answer. > > http://www.reddit.com/r/bioinformatics/comments/1qmpbm/problems_with_psiblast_results_from_biopython/ I would presume this is not supported by the NCBI (or it wasn't 5 years ago anyway): http://lists.open-bio.org/pipermail/biopython/2008-May/004231.html ... http://lists.open-bio.org/pipermail/biopython/2008-May/004234.html http://bugzilla.open-bio.org/show_bug.cgi?id=2496 Peter From p.j.a.cock at googlemail.com Thu Nov 21 12:19:55 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 21 Nov 2013 17:19:55 +0000 Subject: [Biopython-dev] Import problems when testing under PyPy 2.2 Message-ID: Hello all, TravisCI is being updated to target PyPy 2.2 any day now, http://about.travis-ci.org/blog/2013-11-18-upcoming-build-environment-updates/ Meanwhile in local testing on Mac OS X, Biopython looks fine under PyPy 2.2. However, I'm seeing some oddities with imports failing under PyPy 2.2 via run_tests.py on Windows 32 bit & Linux 64 though - can anyone reproduce this? e.g. C:\repositories\biopython\Tests>c:\pypy-2.2\pypy test_Nexus.py test_NexusTest1 (__main__.NexusTest1) Test Nexus module ... ok test_TreeTest1 (__main__.NexusTest1) Test Tree module. ... ok test_WriteToFileName (__main__.NexusTest1) Test writing to a given filename. ... ok test_internal_node_labels (__main__.NexusTest1) Handle text labels on internal nodes. ... ok ---------------------------------------------------------------------- Ran 4 tests in 0.125s OK i.e. Here test_Nexus.py works fine using the installed Biopython. However, via run_tests.py which tries to mess with the Python path to use the local not-yet installed Biopython: C:\repositories\biopython\Tests>c:\pypy-2.2\pypy run_tests.py test_Nexus.py Python version: 2.7.3 (2cec7296d7fb, Nov 12 2013, 13:24:40) [PyPy 2.2.0 with MSC v.1500 32 bit] Operating system: nt win32 test_Nexus ... ERROR ====================================================================== ERROR: test_Nexus ---------------------------------------------------------------------- Traceback (most recent call last): File "run_tests.py", line 407, in runTest suite = unittest.TestLoader().loadTestsFromName(name) File "c:\pypy-2.2\lib-python\2.7\unittest\loader.py", line 91, in loadTestsFro mName module = __import__('.'.join(parts_copy)) File "C:\repositories\biopython\Tests\test_Nexus.py", line 13, in from Bio._py3k import StringIO ImportError: cannot import name 'StringIO' ---------------------------------------------------------------------- Ran 1 test in 0.016 seconds FAILED (failures = 1) Note: C:\repositories\biopython\Tests> C:\repositories\biopython\Tests>c:\pypy-2.2\pypy Python 2.7.3 (2cec7296d7fb, Nov 12 2013, 13:24:40) [PyPy 2.2.0 with MSC v.1500 32 bit] on win32 Type "help", "copyright", "credits" or "license" for more information. And now for something completely different: ``do you know about a toaster with 8KB of RAM and 64KB of ROM?'' >>>> from Bio._py3k import StringIO >>>> quit() This seems rather odd... Thanks, Peter From gokcen.eraslan at gmail.com Sun Nov 24 19:23:15 2013 From: gokcen.eraslan at gmail.com (=?ISO-8859-1?Q?G=F6kcen_Eraslan?=) Date: Mon, 25 Nov 2013 02:23:15 +0200 Subject: [Biopython-dev] [PATCH] Various NACCESS fixes and unit tests Message-ID: <52929873.9020504@gmail.com> Hello, I am developing a machine learning project which is using some command line tools such as NACCESS, STRIDE, netsurfp. I have decided to use BioPython and started digging NACCESS and DSSP codes in Bio/PDB to learn more about how to write parsers for BioPython. I have made some minor changes to NACCESS code and prepared some unit test files. Patch is attached. It would be nice to push this to master branch. I am also writing parsers for STRIDE and netsurfp tools and I would like to send those when I finish writing. Regards. -- Gokcen Eraslan -------------- next part -------------- A non-text attachment was scrubbed... Name: 0001-Bio-PDB-NACCESS-Various-NACCESS-fixes-and-unit-tests.patch Type: text/x-patch Size: 96937 bytes Desc: not available URL: From p.j.a.cock at googlemail.com Mon Nov 25 05:15:08 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 25 Nov 2013 10:15:08 +0000 Subject: [Biopython-dev] [PATCH] Various NACCESS fixes and unit tests In-Reply-To: <52929873.9020504@gmail.com> References: <52929873.9020504@gmail.com> Message-ID: Hi Gokcen, This looks very promising - would you be happy to submit this patch as a pull request on GitHub? Thanks, Peter P.S. Thanks for this report & fix: https://github.com/biopython/biopython/pull/261 On Mon, Nov 25, 2013 at 12:23 AM, G?kcen Eraslan wrote: > Hello, > > I am developing a machine learning project which is using some command line > tools such as NACCESS, STRIDE, netsurfp. I have decided to use BioPython and > started digging NACCESS and DSSP codes in Bio/PDB to learn more about how to > write parsers for BioPython. > > I have made some minor changes to NACCESS code and prepared some unit test > files. Patch is attached. It would be nice to push this to master branch. > > I am also writing parsers for STRIDE and netsurfp tools and I would like to > send those when I finish writing. > > Regards. > > -- > Gokcen Eraslan > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev > From gokcen.eraslan at gmail.com Mon Nov 25 06:37:59 2013 From: gokcen.eraslan at gmail.com (=?ISO-8859-1?Q?G=F6kcen_Eraslan?=) Date: Mon, 25 Nov 2013 13:37:59 +0200 Subject: [Biopython-dev] [PATCH] Various NACCESS fixes and unit tests In-Reply-To: References: <52929873.9020504@gmail.com> Message-ID: <52933697.3010301@gmail.com> On 2013-11-25 12:15, Peter Cock wrote: > Hi Gokcen, > Hello, > This looks very promising - would you be happy to submit this patch > as a pull request on GitHub? > Done. > Thanks, > > Peter > > P.S. Thanks for this report & fix: > https://github.com/biopython/biopython/pull/261 > > > On Mon, Nov 25, 2013 at 12:23 AM, G?kcen Eraslan > wrote: >> Hello, >> >> I am developing a machine learning project which is using some command line >> tools such as NACCESS, STRIDE, netsurfp. I have decided to use BioPython and >> started digging NACCESS and DSSP codes in Bio/PDB to learn more about how to >> write parsers for BioPython. >> >> I have made some minor changes to NACCESS code and prepared some unit test >> files. Patch is attached. It would be nice to push this to master branch. >> >> I am also writing parsers for STRIDE and netsurfp tools and I would like to >> send those when I finish writing. >> >> Regards. >> >> -- >> Gokcen Eraslan >> >> _______________________________________________ >> Biopython-dev mailing list >> Biopython-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biopython-dev >> -- G?k?en Eraslan From p.j.a.cock at googlemail.com Mon Nov 25 06:41:58 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 25 Nov 2013 11:41:58 +0000 Subject: [Biopython-dev] [PATCH] Various NACCESS fixes and unit tests In-Reply-To: <52933697.3010301@gmail.com> References: <52929873.9020504@gmail.com> <52933697.3010301@gmail.com> Message-ID: On Mon, Nov 25, 2013 at 11:37 AM, G?kcen Eraslan wrote: > On 2013-11-25 12:15, Peter Cock wrote: >> >> Hi Gokcen, >> > > Hello, > >> This looks very promising - would you be happy to submit this patch >> as a pull request on GitHub? >> > > Done. Thanks, https://github.com/biopython/biopython/pull/262 I'm made a couple of comments on GitHub. Peter From p.j.a.cock at googlemail.com Tue Nov 26 12:20:24 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 26 Nov 2013 17:20:24 +0000 Subject: [Biopython-dev] Import problems when testing under PyPy 2.2 In-Reply-To: References: Message-ID: On Thu, Nov 21, 2013 at 5:19 PM, Peter Cock wrote: > Hello all, > TravisCI is being updated to target PyPy 2.2 any day now, > http://about.travis-ci.org/blog/2013-11-18-upcoming-build-environment-updates/ > > Meanwhile in local testing on Mac OS X, Biopython looks fine > under PyPy 2.2. > > However, I'm seeing some oddities with imports failing under > PyPy 2.2 via run_tests.py on Windows 32 bit & Linux 64 though - > can anyone reproduce this? e.g. > > > C:\repositories\biopython\Tests>c:\pypy-2.2\pypy test_Nexus.py > test_NexusTest1 (__main__.NexusTest1) > Test Nexus module ... ok > test_TreeTest1 (__main__.NexusTest1) > Test Tree module. ... ok > test_WriteToFileName (__main__.NexusTest1) > Test writing to a given filename. ... ok > test_internal_node_labels (__main__.NexusTest1) > Handle text labels on internal nodes. ... ok > > ---------------------------------------------------------------------- > Ran 4 tests in 0.125s > > OK > > i.e. Here test_Nexus.py works fine using the installed Biopython. > However, via run_tests.py which tries to mess with the Python path > to use the local not-yet installed Biopython: > > C:\repositories\biopython\Tests>c:\pypy-2.2\pypy run_tests.py test_Nexus.py > Python version: 2.7.3 (2cec7296d7fb, Nov 12 2013, 13:24:40) > [PyPy 2.2.0 with MSC v.1500 32 bit] > Operating system: nt win32 > test_Nexus ... ERROR > ====================================================================== > ERROR: test_Nexus > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "run_tests.py", line 407, in runTest > suite = unittest.TestLoader().loadTestsFromName(name) > File "c:\pypy-2.2\lib-python\2.7\unittest\loader.py", line 91, in loadTestsFro > mName > module = __import__('.'.join(parts_copy)) > File "C:\repositories\biopython\Tests\test_Nexus.py", line 13, in > from Bio._py3k import StringIO > ImportError: cannot import name 'StringIO' > ---------------------------------------------------------------------- > Ran 1 test in 0.016 seconds > > FAILED (failures = 1) > > > Note: > > C:\repositories\biopython\Tests> > C:\repositories\biopython\Tests>c:\pypy-2.2\pypy > Python 2.7.3 (2cec7296d7fb, Nov 12 2013, 13:24:40) > [PyPy 2.2.0 with MSC v.1500 32 bit] on win32 > Type "help", "copyright", "credits" or "license" for more information. > And now for something completely different: ``do you know about a toaster with > 8KB of RAM and 64KB of ROM?'' >>>>> from Bio._py3k import StringIO >>>>> quit() > > > This seems rather odd... Solved - I think. There was something in the old build directory which was causing this, removing that and reinstalling Biopython under PyPy made it work. Not yet quite sure what this was though... perhaps stale compiled Python files from an older PyPy version? Peter From p.j.a.cock at googlemail.com Thu Nov 28 06:33:05 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 28 Nov 2013 11:33:05 +0000 Subject: [Biopython-dev] [Biopython] Biopython 1.63 beta release In-Reply-To: References: <87vbzx37m9.wl%tra@popgen.net> Message-ID: Dear Biopythoneers, On Tue, Nov 12, 2013 at 4:57 PM, Peter Cock wrote: > Thank you Tiago, on behalf of us all, for handling the Biopython 1.63 > beta release. Thank you to everyone who has tried the beta release - from the lack of new issues reported, it seems no new problems in the beta were uncovered which need to be fixed urgently? If so, then over on the biopython-dev list, I think we should let Tiago propose a convenient day to do the Biopython 1.63 release Thanks all, Peter From p.j.a.cock at googlemail.com Thu Nov 28 08:21:45 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 28 Nov 2013 13:21:45 +0000 Subject: [Biopython-dev] [Biopython] Biopython 1.63 beta release In-Reply-To: References: <87vbzx37m9.wl%tra@popgen.net> Message-ID: On Thu, Nov 28, 2013 at 1:17 PM, Tiago Ant?o wrote: > Dear all, > > On 28 November 2013 11:33, Peter Cock wrote: >> >> If so, then over on the biopython-dev list, I think we should let Tiago >> propose a convenient day to do the Biopython 1.63 release > > I would like to propose next Wednesday. But any day next week would be fine. Wednesday 4 December? Sounds fine to me :) Thanks, Peter From mjldehoon at yahoo.com Sat Nov 30 22:28:45 2013 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Sat, 30 Nov 2013 19:28:45 -0800 (PST) Subject: [Biopython-dev] [biopython] Missing DTD files (#260) In-Reply-To: Message-ID: <1385868525.19183.YahooMailBasic@web164002.mail.gq1.yahoo.com> How would people feel about Biopython always downloading DTD files on the fly instead of distributing them with Biopython? After downloading and parsing a DTD file, we can keep it in memory so we won't need to parse the same DTD file over and over again. So the impact on speed will be minimal. If we do so, we'll never run into the problem of missing DTD files. The downside of course is that we will need internet access to parse any XML file through Bio.Entrez. But maybe in today's world that is acceptable. Best, -Michiel. -------------------------------------------- On Thu, 11/28/13, Karol M. Langner wrote: Subject: Re: [biopython] Missing DTD files (#260) To: "biopython/biopython" Date: Thursday, November 28, 2013, 9:46 AM It's true, and I didn't bother to look at the newer version. Thanks for the explanation. On the plus side, biopython still downloads the missing DTD, so I don't critically need to install a newer local version. ? Reply to this email directly or view it on GitHub. From p.j.a.cock at googlemail.com Sat Nov 2 14:22:58 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 2 Nov 2013 14:22:58 +0000 Subject: [Biopython-dev] ExPASy / UniProt API for searching and fetching Message-ID: Hello Biopythoneers, Would anyone like to look at updating/replacing the old web API functions in Bio.ExPASy to talk to UniProt.org instead? See: https://github.com/biopython/biopython/issues/253 Peter From p.j.a.cock at googlemail.com Sat Nov 2 14:39:20 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 2 Nov 2013 14:39:20 +0000 Subject: [Biopython-dev] Python 2 and 3 migration thoughts In-Reply-To: References: Message-ID: On Sat, Oct 26, 2013 at 7:44 PM, Peter Cock wrote: > > A new pull request for people to comment on, which eliminates > all but two important fixers. As a bonus this makes installation > under Python 3 much much quicker: > > https://github.com/biopython/biopython/pull/250 > I take it there are no objections to me merging this work? If not, I will try to do it tomorrow (Sunday) or early next week, and move on to the final issues before we can drop 2to3 (which I do not anticipate being problematic). Once we've dropped 2to3, I would like us to a do a beta release (by mid November?), and then bar any problems, ship that as Biopython 1.63 (hopefully by late November). (There are plenty of things pending which would be great to have in the next release, but these changes are so wide ranging that I would prefer we focus primarily on Python 3 for the next release.) Regards, Peter From p.j.a.cock at googlemail.com Sat Nov 2 17:51:10 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 2 Nov 2013 17:51:10 +0000 Subject: [Biopython-dev] Python 2 and 3 migration thoughts In-Reply-To: References: Message-ID: On Sat, Nov 2, 2013 at 2:39 PM, Peter Cock wrote: > On Sat, Oct 26, 2013 at 7:44 PM, Peter Cock wrote: >> >> A new pull request for people to comment on, which eliminates >> all but two important fixers. As a bonus this makes installation >> under Python 3 much much quicker: >> >> https://github.com/biopython/biopython/pull/250 https://github.com/peterjc/biopython/tree/py3fixes > I take it there are no objections to me merging this work? > If not, I will try to do it tomorrow (Sunday) or early next week, > and move on to the final issues before we can drop 2to3 > (which I do not anticipate being problematic). They are not troublesome, perhaps worth applying soon too? (Can anyone propose a more elegant solution to __nonzero__ versus __bool__ than to just define both?) This allows us to stop using 2to3 (something NumPy have also managed in their recent NumPy 1.8 release), making installation of Biopython from source under Python 3.3 faster and much simpler: https://github.com/peterjc/biopython/tree/py3more Regards, Peter From eric.talevich at gmail.com Sat Nov 2 18:23:31 2013 From: eric.talevich at gmail.com (Eric Talevich) Date: Sat, 2 Nov 2013 11:23:31 -0700 Subject: [Biopython-dev] Python 2 and 3 migration thoughts In-Reply-To: References: Message-ID: On Sat, Nov 2, 2013 at 10:51 AM, Peter Cock wrote: > On Sat, Nov 2, 2013 at 2:39 PM, Peter Cock wrote: > > On Sat, Oct 26, 2013 at 7:44 PM, Peter Cock wrote: > >> > >> A new pull request for people to comment on, which eliminates > >> all but two important fixers. As a bonus this makes installation > >> under Python 3 much much quicker: > >> > >> https://github.com/biopython/biopython/pull/250 > > https://github.com/peterjc/biopython/tree/py3fixes > > > I take it there are no objections to me merging this work? > > If not, I will try to do it tomorrow (Sunday) or early next week, > > and move on to the final issues before we can drop 2to3 > > (which I do not anticipate being problematic). > > They are not troublesome, perhaps worth applying soon too? > (Can anyone propose a more elegant solution to __nonzero__ > versus __bool__ than to just define both?) > > This allows us to stop using 2to3 (something NumPy have > also managed in their recent NumPy 1.8 release), making > installation of Biopython from source under Python 3.3 > faster and much simpler: > > https://github.com/peterjc/biopython/tree/py3more > > Regards, > > Peter > Cool, no objections here. Maybe after the next stable release we can look into finalizing and merging the new GSoC work? As far as I can tell the best way to handle __nonzero__ vs. __bool__ is what you indicated: class Foo(object): def __bool__(self): return True __nonzero__ = __bool__ And presumably the 2to3 converter would need to be disabled at the same time, or it might try to rename __nonzero__ to __bool__ and get confused. Cheers, Eric From p.j.a.cock at googlemail.com Sun Nov 3 14:03:51 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sun, 3 Nov 2013 14:03:51 +0000 Subject: [Biopython-dev] Python 2 and 3 migration thoughts In-Reply-To: References: Message-ID: On Sat, Nov 2, 2013 at 6:23 PM, Eric Talevich wrote: > On Sat, Nov 2, 2013 at 10:51 AM, Peter Cock wrote: >> On Sat, Nov 2, 2013 at 2:39 PM, Peter Cock wrote: >>> I take it there are no objections to me merging this work? >>> If not, I will try to do it tomorrow (Sunday) or early next week, Applied https://github.com/biopython/biopython/pull/250 plus a follow up fix for Python 3 on Windows, https://github.com/biopython/biopython/commit/9a265285e587f243814ffc05772b639051b31be1 (The buildbot server is earning its keep) >> > and move on to the final issues before we can drop 2to3 >> > (which I do not anticipate being problematic). >> >> They are not troublesome, perhaps worth applying soon too? >> (Can anyone propose a more elegant solution to __nonzero__ >> versus __bool__ than to just define both?) >> >> This allows us to stop using 2to3 (something NumPy have >> also managed in their recent NumPy 1.8 release), making >> installation of Biopython from source under Python 3.3 >> faster and much simpler: >> >> https://github.com/peterjc/biopython/tree/py3more > > Cool, no objections here. Maybe after the next stable release > we can look into finalizing and merging the new GSoC work? Yes please. > As far as I can tell the best way to handle __nonzero__ vs. __bool__ is what > you indicated: > > class Foo(object): > def __bool__(self): return True > __nonzero__ = __bool__ OK, I've updated my change to use that style rather than my initial version which literally defined it twice: class Foo(object): def __bool__(self): return True def __nonzero__(self): return True > And presumably the 2to3 converter would need to be disabled at the same > time, or it might try to rename __nonzero__ to __bool__ and get confused. Yes indeed. This is all done as one commit: https://github.com/biopython/biopython/commit/d6aa77c43bf9bab6302d880ad458b46f80e21c5e That leaves one remaining fixer, unicode, which is addressed here https://github.com/peterjc/biopython/tree/py3more in part by dropping Python 3.2 so that we can use unicode literals. We deliberately didn't claim to support Python 3.2 in order to allow us this option. Tiago or I will need to update the buildbot server to drop Python 3.2 before applying that change... Regards, Peter From tra at popgen.net Sun Nov 3 16:30:15 2013 From: tra at popgen.net (Tiago Antao) Date: Sun, 03 Nov 2013 16:30:15 +0000 Subject: [Biopython-dev] Python 2 and 3 migration thoughts In-Reply-To: References: Message-ID: <874n7t5tyg.wl%tra@popgen.net> At Sun, 3 Nov 2013 14:03:51 +0000, Peter Cock wrote: > Tiago or I will need to update the buildbot server to drop > Python 3.2 before applying that change... Ready to roll From p.j.a.cock at googlemail.com Sun Nov 3 19:28:05 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sun, 3 Nov 2013 19:28:05 +0000 Subject: [Biopython-dev] Python 2 and 3 migration thoughts In-Reply-To: <874n7t5tyg.wl%tra@popgen.net> References: <874n7t5tyg.wl%tra@popgen.net> Message-ID: On Sun, Nov 3, 2013 at 4:30 PM, Tiago Antao wrote: > At Sun, 3 Nov 2013 14:03:51 +0000, > Peter Cock wrote: >> Tiago or I will need to update the buildbot server to drop >> Python 3.2 before applying that change... > > Ready to roll Lovely, thank you :) Unicode changes pushed to master: https://github.com/biopython/biopython/commit/0f85dd5f5a0ffd2e8c1f0c45a890e43c4d689f49 At this point we're not using any 2to3 fixers, so we could remove the do2to3.py script etc - which is what the remaining fixes on this branch do: https://github.com/peterjc/biopython/tree/py3more However, before I do that, are there any pending commits which would still need 2to3 in the short term? Thanks, Peter From w.arindrarto at gmail.com Mon Nov 4 00:12:52 2013 From: w.arindrarto at gmail.com (Wibowo Arindrarto) Date: Mon, 4 Nov 2013 01:12:52 +0100 Subject: [Biopython-dev] ExPASy / UniProt API for searching and fetching In-Reply-To: References: Message-ID: Hello everyone, I'm trying a jab at this in this branch: https://github.com/bow/biopython/blob/dev_uniprot-api/Bio/UniProt/API.py. It's still quite bare bones at the moment, but the general approach shouldn't change much for the other functions. I'm still not sure about the namespace, though. Should it be Bio.UniProt.API, Bio.UniProt.api, or something else? As always, let me know what you think :). Cheers, Bow On Sat, Nov 2, 2013 at 3:22 PM, Peter Cock wrote: > Hello Biopythoneers, > > Would anyone like to look at updating/replacing the old web > API functions in Bio.ExPASy to talk to UniProt.org instead? > See: https://github.com/biopython/biopython/issues/253 > > Peter > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev From p.j.a.cock at googlemail.com Mon Nov 4 10:35:37 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 4 Nov 2013 10:35:37 +0000 Subject: [Biopython-dev] ExPASy / UniProt API for searching and fetching In-Reply-To: References: Message-ID: On Mon, Nov 4, 2013 at 12:12 AM, Wibowo Arindrarto wrote: > Hello everyone, > > I'm trying a jab at this in this branch: > https://github.com/bow/biopython/blob/dev_uniprot-api/Bio/UniProt/API.py. > > It's still quite bare bones at the moment, but the general approach > shouldn't change much for the other functions. I'm still not sure > about the namespace, though. Should it be Bio.UniProt.API, > Bio.UniProt.api, or something else? > > As always, let me know what you think :). > > Cheers, > Bow Rather than Bio.UniProt.API, we should try to use lowercase PEP8 module names (I think here .api would be better). However, API seems to vague - how about www to be more clear this is an online resource? (Unlike the NCBI Entrez Utilities, there isn't a clear branding for the UniProt web API is there?) Peter From w.arindrarto at gmail.com Mon Nov 4 10:48:21 2013 From: w.arindrarto at gmail.com (Wibowo Arindrarto) Date: Mon, 4 Nov 2013 11:48:21 +0100 Subject: [Biopython-dev] ExPASy / UniProt API for searching and fetching In-Reply-To: References: Message-ID: Hi Peter, everyone, On Mon, Nov 4, 2013 at 11:35 AM, Peter Cock wrote: > On Mon, Nov 4, 2013 at 12:12 AM, Wibowo Arindrarto > wrote: >> Hello everyone, >> >> I'm trying a jab at this in this branch: >> https://github.com/bow/biopython/blob/dev_uniprot-api/Bio/UniProt/API.py. >> >> It's still quite bare bones at the moment, but the general approach >> shouldn't change much for the other functions. I'm still not sure >> about the namespace, though. Should it be Bio.UniProt.API, >> Bio.UniProt.api, or something else? >> >> As always, let me know what you think :). >> >> Cheers, >> Bow > > Rather than Bio.UniProt.API, we should try to use lowercase > PEP8 module names (I think here .api would be better). > > However, API seems to vague - how about www to be more > clear this is an online resource? Bio.UniProt.www is fine with me, too (and somewhat in line with what we already have in Bio.Blast.NCBIWWW). > (Unlike the NCBI Entrez Utilities, there isn't a clear branding > for the UniProt web API is there?) It's not as comprehensively branded as Entrez. They do have similar functionalities, though. We can do query searches, retrieve records, do a BLAST search, and even map identifiers across databases. The BLAST search API doesn't seem to be very well-documented in the website, but there is a Java API that allows you to do so: http://www.ebi.ac.uk/uniprot/remotingAPI/. They even have their own formats of the BLAST results (e.g. http://www.uniprot.org/blast/uniprot/2013110441MHJHFYCR.* or http://www.uniprot.org/blast/uniprot/2013110441MHJHFYCR.xml) There are still some things left in Bio.ExPASy that UniProt doesn't seem to cover, though, such as the Prosite search. I was thinking maybe we could reorganize the existing Bio.UniProt code base like this: Bio.UniProt | |-- parsers | | | |-- GOA, etc. |-- www (or api, or remote) |-- __init__.py containing main functions Best, Bow From p.j.a.cock at googlemail.com Mon Nov 4 11:04:03 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 4 Nov 2013 11:04:03 +0000 Subject: [Biopython-dev] ExPASy / UniProt API for searching and fetching In-Reply-To: References: Message-ID: On Mon, Nov 4, 2013 at 10:48 AM, Wibowo Arindrarto wrote: > Hi Peter, everyone, > > On Mon, Nov 4, 2013 at 11:35 AM, Peter Cock wrote: >> On Mon, Nov 4, 2013 at 12:12 AM, Wibowo Arindrarto >> wrote: >>> Hello everyone, >>> >>> I'm trying a jab at this in this branch: >>> https://github.com/bow/biopython/blob/dev_uniprot-api/Bio/UniProt/API.py. >>> >>> It's still quite bare bones at the moment, but the general approach >>> shouldn't change much for the other functions. I'm still not sure >>> about the namespace, though. Should it be Bio.UniProt.API, >>> Bio.UniProt.api, or something else? >>> >>> As always, let me know what you think :). >>> >>> Cheers, >>> Bow >> >> Rather than Bio.UniProt.API, we should try to use lowercase >> PEP8 module names (I think here .api would be better). >> >> However, API seems to vague - how about www to be more >> clear this is an online resource? > > Bio.UniProt.www is fine with me, too (and somewhat in line with what > we already have in Bio.Blast.NCBIWWW). > >> (Unlike the NCBI Entrez Utilities, there isn't a clear branding >> for the UniProt web API is there?) > > It's not as comprehensively branded as Entrez. They do have similar > functionalities, though. We can do query searches, retrieve records, > do a BLAST search, and even map identifiers across databases. The > BLAST search API doesn't seem to be very well-documented in the > website, but there is a Java API that allows you to do so: > http://www.ebi.ac.uk/uniprot/remotingAPI/. See: http://www.ebi.ac.uk/Tools/webservices/services/sss/ncbi_blast_rest > They even have their own > formats of the BLAST results (e.g. > http://www.uniprot.org/blast/uniprot/2013110441MHJHFYCR.* or > http://www.uniprot.org/blast/uniprot/2013110441MHJHFYCR.xml) Hmm, another XML variant. Maybe ignore that for now. > There are still some things left in Bio.ExPASy that UniProt doesn't > seem to cover, though, such as the Prosite search. Anyone know? > I was thinking maybe we could reorganize the existing Bio.UniProt code > base like this: > > Bio.UniProt > | > |-- parsers > | | > | |-- GOA, etc. > |-- www (or api, or remote) > |-- __init__.py containing main functions > Bio.UniProt.GOA was only introduced in the last release, moving it under Bio.UniProt.parsers.GOA doesn't seem ideal. CC'ing Iddo for comment. Peter From tra at popgen.net Tue Nov 5 13:25:39 2013 From: tra at popgen.net (Tiago Antao) Date: Tue, 05 Nov 2013 13:25:39 +0000 Subject: [Biopython-dev] Biopython 1.63 release Message-ID: <87eh6v7zfw.wl%tra@popgen.net> Dear all, Unless somebody else wants to step forward, I am thinking in volunteering to handle the release of 1.63. This would be a first and therefore I hope you would all have some patience with my inexperience doing this. The upside of it is that, having inexperienced hands will allow for a review of the release procedure (if something is missing, an inexperienced release manager will be more prone to detect it than an experienced one). I no one steps forward, I will start the ball rolling later today here on the list. Regards, Tiago From p.j.a.cock at googlemail.com Tue Nov 5 13:36:24 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 5 Nov 2013 13:36:24 +0000 Subject: [Biopython-dev] Biopython 1.63 release In-Reply-To: <87eh6v7zfw.wl%tra@popgen.net> References: <87eh6v7zfw.wl%tra@popgen.net> Message-ID: On Tuesday, November 5, 2013, Tiago Antao wrote: > Dear all, > > Unless somebody else wants to step forward, I am thinking in > volunteering to handle the release of 1.63. > > This would be a first and therefore I hope you would all have some > patience with my inexperience doing this. The upside of it is that, > having inexperienced hands will allow for a review of the release > procedure (if something is missing, an inexperienced release manager > will be more prone to detect it than an experienced one). > > I no one steps forward, I will start the ball rolling later today here > on the list. > > Regards, > Tiago > Thanks Tiago - I think this a great idea. As per the 2to3 thread, I'd like us to do a beta release first - as an unusually large number of files have been changed since the last release (as part of getting the code to run on both Python 2 and 3 without conversion by 2to3 first). Regards, Peter From p.j.a.cock at googlemail.com Tue Nov 5 20:58:12 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 5 Nov 2013 20:58:12 +0000 Subject: [Biopython-dev] Python 2 and 3 migration thoughts In-Reply-To: References: <874n7t5tyg.wl%tra@popgen.net> Message-ID: On Sun, Nov 3, 2013 at 7:28 PM, Peter Cock wrote: > > At this point we're not using any 2to3 fixers, so we could > remove the do2to3.py script etc - which is what the remaining > fixes on this branch do: > > https://github.com/peterjc/biopython/tree/py3more > > However, before I do that, are there any pending commits > which would still need 2to3 in the short term? Pushed to master, Biopython now runs on Python 2 and Python 3 natively without using the 2to3 converter :) https://github.com/biopython/biopython/commit/6b24a509b13e9df3c41fc211646d24382685e050 https://github.com/biopython/biopython/commit/a9cb8c10f68fe6d8bdccf34d8217838cc9d4db7f Now let's focus on Biopython 1.63 (beta), which Tiago has kindly offered to managed :) http://lists.open-bio.org/pipermail/biopython-dev/2013-November/010955.html Peter From arklenna at gmail.com Tue Nov 5 21:08:19 2013 From: arklenna at gmail.com (Lenna Peterson) Date: Tue, 5 Nov 2013 16:08:19 -0500 Subject: [Biopython-dev] Biopython 1.63 release In-Reply-To: References: <87eh6v7zfw.wl%tra@popgen.net> Message-ID: On Tue, Nov 5, 2013 at 8:36 AM, Peter Cock wrote: > On Tuesday, November 5, 2013, Tiago Antao wrote: > > > Dear all, > > > > Unless somebody else wants to step forward, I am thinking in > > volunteering to handle the release of 1.63. > > > > This would be a first and therefore I hope you would all have some > > patience with my inexperience doing this. The upside of it is that, > > having inexperienced hands will allow for a review of the release > > procedure (if something is missing, an inexperienced release manager > > will be more prone to detect it than an experienced one). > > > > I no one steps forward, I will start the ball rolling later today here > > on the list. > > > > Regards, > > Tiago > > > > Thanks Tiago - I think this a great idea. > > As per the 2to3 thread, I'd like us to do a beta release first - > as an unusually large number of files have been changed > since the last release (as part of getting the code to run on > both Python 2 and 3 without conversion by 2to3 first). > > Regards, > > Peter > > Is the `open()` to `with open()` conversion a priority for this release? If so, I can carve out some hours to punch that out. Big whitespace changes to lots of files. Cheers, Lenna From tra at popgen.net Tue Nov 5 21:22:04 2013 From: tra at popgen.net (Tiago Antao) Date: Tue, 05 Nov 2013 21:22:04 +0000 Subject: [Biopython-dev] Biopython 1.63 beta - preparations Message-ID: <874n7qilxf.wl%tra@popgen.net> Dear all, As previously discussed I would like to start preparing the beta version of 1.63. I would like to try to have a beta build somewhere between Sunday and Tuesday (this variation is mostly dependent on the availability of a suitable Windows machine), unless someone finds this timing not ideal. If anyone is thinking on committing new functionality (other than bug corrections, that is), please do inform the mailing list in advance. Correct me if I am wrong, but this is the first version NOT supporting Python 2.5. Therefore no attempts will be made of building on 2.5. If such is the case, I will also amend the Wiki page http://biopython.org/wiki/Building_a_release Thus Python versions supported will be 2.6, 2.7 and 3.3. I will follow all the steps on the wiki page above, that will mean that I will bump (during the process) the version numbers and documentation to 1.63 beta. Feel free to correct me or add any pertinent information. This concludes this message for your newbie 1.63 release manager, Tiago From tra at popgen.net Tue Nov 5 21:38:14 2013 From: tra at popgen.net (Tiago Antao) Date: Tue, 05 Nov 2013 21:38:14 +0000 Subject: [Biopython-dev] Biopython 1.63 release In-Reply-To: References: <87eh6v7zfw.wl%tra@popgen.net> Message-ID: <87ob5yy1fd.wl%tra@popgen.net> At Tue, 5 Nov 2013 16:08:19 -0500, Lenna Peterson wrote: > Is the `open()` to `with open()` conversion a priority for this release? If so, I can carve out some > hours to punch that out. Big whitespace changes to lots of files. >From my side, anything that is done before the weekend should be OK (regarding the issue of being a priority or not, I have no opinion). I would just ask that, during the weekend, only minor bug corrections are done. I will probably do everything this next Sunday (unless here there is here an opinion against, or my Windows setup becomes problematic) Tiago From p.j.a.cock at googlemail.com Wed Nov 6 09:11:21 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 6 Nov 2013 09:11:21 +0000 Subject: [Biopython-dev] Biopython 1.63 beta - preparations In-Reply-To: <874n7qilxf.wl%tra@popgen.net> References: <874n7qilxf.wl%tra@popgen.net> Message-ID: On Tue, Nov 5, 2013 at 9:22 PM, Tiago Antao wrote: > Dear all, > > As previously discussed I would like to start preparing the beta > version of 1.63. > > I would like to try to have a beta build somewhere between Sunday and > Tuesday (this variation is mostly dependent on the availability of a > suitable Windows machine), unless someone finds this timing not ideal. > > If anyone is thinking on committing new functionality (other than bug > corrections, that is), please do inform the mailing list in advance. > > Correct me if I am wrong, but this is the first version NOT supporting > Python 2.5. Therefore no attempts will be made of building on 2.5. If > such is the case, I will also amend the Wiki page > http://biopython.org/wiki/Building_a_release > > Thus Python versions supported will be 2.6, 2.7 and 3.3. Yes (since 3.4 is still only in alpha). Also this line will change now we don't call 2to3, copy build\py3.3\dist\biopython-1.62.win32-py3.3.exe dist to just: copy dist\biopython-1.63.win32-py3.3.exe dist Something else I think I should have done to the wiki page is move epydoc nearer the start - it has often found issues needing fixing. Regards, Peter From tra at popgen.net Sat Nov 9 19:45:25 2013 From: tra at popgen.net (Tiago Antao) Date: Sat, 09 Nov 2013 19:45:25 +0000 Subject: [Biopython-dev] Biopython 1.63 beta - preparations In-Reply-To: <874n7qilxf.wl%tra@popgen.net> References: <874n7qilxf.wl%tra@popgen.net> Message-ID: <87wqkh7416.wl%tra@popgen.net> Dear all, At Tue, 05 Nov 2013 21:22:04 +0000, > As previously discussed I would like to start preparing the beta > version of 1.63. This seems on track (a dry-run worked including compiling on an Windows 8 machine) and I would like to do the whole procedure tomorrow morning (Western European Time). I will be able to go up to step 18 of the build instructions (i.e. I will alter the repository and tag biopython-163b). Regards, Tiago From p.j.a.cock at googlemail.com Sat Nov 9 23:33:47 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 9 Nov 2013 23:33:47 +0000 Subject: [Biopython-dev] Biopython 1.63 beta - preparations In-Reply-To: <87wqkh7416.wl%tra@popgen.net> References: <874n7qilxf.wl%tra@popgen.net> <87wqkh7416.wl%tra@popgen.net> Message-ID: On Saturday, November 9, 2013, Tiago Antao wrote: > Dear all, > > At Tue, 05 Nov 2013 21:22:04 +0000, > > As previously discussed I would like to start preparing the beta > > version of 1.63. > > This seems on track (a dry-run worked including compiling on an > Windows 8 machine) and I would like to do the whole procedure > tomorrow morning (Western European Time). I will be able to go up to > step 18 of the build instructions (i.e. I will alter the repository > and tag biopython-163b). > > Regards, > Tiago > Excellent - we wouldn't push a beta to PyPI anyway which is one of the final tasks. Thank you :) Peter From tra at popgen.net Sat Nov 9 23:37:34 2013 From: tra at popgen.net (Tiago Antao) Date: Sat, 09 Nov 2013 23:37:34 +0000 Subject: [Biopython-dev] online tests Message-ID: <87d2m9ywn5.wl%tra@popgen.net> Hi, Some of the online tests are failing: These are: test_Entrez_online.py test_SeqIO_online.py test_TogoWS.py I would not be shocked that in some cases the services are just down for now, but there is one error that seems worrying: tra at UX32A:~/Dropbox/bp-release/prepare/biopython$ python Tests/test_TogoWS.py Traceback (most recent call last): File "Tests/test_TogoWS.py", line 12, in from Bio._py3k import StringIO ImportError: cannot import name StringIO (same happens with the SeqIO test) Tiago From tra at popgen.net Sun Nov 10 12:49:39 2013 From: tra at popgen.net (Tiago Antao) Date: Sun, 10 Nov 2013 12:49:39 +0000 Subject: [Biopython-dev] 1.63 beta Message-ID: <87r4ao5sm4.wl%tra@popgen.net> Dear all, I do not have access to the deployment machines, so I have put everything on: http://popgen.net/bp This includes: The API The source (tar and zip) Windows binaries (2.6, 2.7, 3.3) I think it is better this way as this will allow some testing before going live. I suspect the biggest change from previous versions is that I used MinGW instead of MS compilers to do the binaries. Tiago From p.j.a.cock at googlemail.com Sun Nov 10 13:05:02 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sun, 10 Nov 2013 13:05:02 +0000 Subject: [Biopython-dev] 1.63 beta In-Reply-To: <87r4ao5sm4.wl%tra@popgen.net> References: <87r4ao5sm4.wl%tra@popgen.net> Message-ID: On Sunday, November 10, 2013, Tiago Antao wrote: > Dear all, > > I do not have access to the deployment machines, so I have put > everything on: > > http://popgen.net/bp > > This includes: > The API > The source (tar and zip) > Windows binaries (2.6, 2.7, 3.3) > > I think it is better this way as this will allow some testing before > going live. Yeah, a few test installs first would be great before publisicing this - I can try the Windows installers tomorrow. Tiago you probably have got SSH key access to the biopython.org website, I'll email you off list... > I suspect the biggest change from previous versions is that I used > MinGW instead of MS compilers to do the binaries. > > Tiago > > I think the win32 installers I have been making are a mix of mingw and the MS compilers (depending on the Python version). Can you work on a draft release announcement (for the blog & email)? If you don't have an account on the OBF Wordpress I can arrange that... Thanks, Peter From tra at popgen.net Sun Nov 10 19:15:35 2013 From: tra at popgen.net (Tiago Antao) Date: Sun, 10 Nov 2013 19:15:35 +0000 Subject: [Biopython-dev] 1.63 beta In-Reply-To: References: <87r4ao5sm4.wl%tra@popgen.net> Message-ID: <8761s05aqw.wl%tra@popgen.net> At Sun, 10 Nov 2013 13:05:02 +0000, Peter Cock wrote: > Can you work on a draft release announcement (for the > blog & email)? If you don't have an account on the OBF > Wordpress I can arrange that... I have cooked up a draft announcement (plagiarised from the NEWS) here: http://popgen.net/bp/ann.html I am travelling back to the UK tomorrow and will be able to release this in the evening assuming that: 1. People are OK with the sources and binaries generated 2. People are OK with the announcement 3. I have access to the servers 4. I will _not_ try to deploy to pypi, as this is a beta Tiago From p.j.a.cock at googlemail.com Mon Nov 11 10:23:48 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 11 Nov 2013 10:23:48 +0000 Subject: [Biopython-dev] 1.63 beta In-Reply-To: References: <87r4ao5sm4.wl%tra@popgen.net> Message-ID: On Sun, Nov 10, 2013 at 1:05 PM, Peter Cock wrote: > > On Sunday, November 10, 2013, Tiago Antao wrote: >> >> Dear all, >> >> I do not have access to the deployment machines, so I have put >> everything on: >> >> http://popgen.net/bp >> >> This includes: >> The API >> The source (tar and zip) >> Windows binaries (2.6, 2.7, 3.3) >> >> I think it is better this way as this will allow some testing before >> going live. > > > Yeah, a few test installs first would be great before publisicing > this - I can try the Windows installers tomorrow. The Windows installers seemed fine (they worked on my Windows XP machine). Can you try copying them (and the epydoc folder) over to biopython.org or do I need to update your SSH key? Thanks, Peter From tra at popgen.net Mon Nov 11 22:45:51 2013 From: tra at popgen.net (Tiago Antao) Date: Mon, 11 Nov 2013 22:45:51 +0000 Subject: [Biopython-dev] bugzilla on new releases?? Message-ID: <87vbzy1rs0.wl%tra@popgen.net> Hi, The release instructions refer updating bugzilla. Isn't that deprecated??? Tiago From p.j.a.cock at googlemail.com Tue Nov 12 00:13:44 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 12 Nov 2013 00:13:44 +0000 Subject: [Biopython-dev] bugzilla on new releases?? In-Reply-To: <87vbzy1rs0.wl%tra@popgen.net> References: <87vbzy1rs0.wl%tra@popgen.net> Message-ID: On Mon, Nov 11, 2013 at 10:45 PM, Tiago Antao wrote: > Hi, > > The release instructions refer updating bugzilla. Isn't that > deprecated??? > > Tiago Yeah, but it is still accepting new issues (if anyone can work out how to stop that let us know) so perhaps we might as well add the release tags to it? Peter From p.j.a.cock at googlemail.com Tue Nov 12 16:57:53 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 12 Nov 2013 16:57:53 +0000 Subject: [Biopython-dev] [Biopython] Biopython 1.63 beta release In-Reply-To: <87vbzx37m9.wl%tra@popgen.net> References: <87vbzx37m9.wl%tra@popgen.net> Message-ID: Thank you Tiago, on behalf of us all, for handling the Biopython 1.63 beta release. Hopefully other than accounts (for the webserver & blog etc) things went smoothly, and I see you've already updated some little details on the wiki so make it easier for the next person :) http://biopython.org/wiki/Building_a_release Regards, Peter On Tue, Nov 12, 2013 at 4:30 PM, Tiago Antao wrote: > Dear Biopythoneers, > > A beta release for Biopython 1.63 is now available for download and > testing. > > This is a beta release for testing purposes, the main reason for a > beta version is the large amount of changes imposed by the removal of > the 2to3 library previously required for the support of Python 3.X. > This was made possible by dropping Python 2.5 (and Jython 2.5). > > This release of Biopython supports Python 2.6 and 2.7, and also Python > 3.3. > > The Biopython Tutorial & Cookbook, and the docstring examples in the > source code, now use the Python 3 style print function in place of the > Python 2 style print statement. This language feature is available > under Python 2.6 and 2.7 via: > > from __future__ import print_function > > Similarly we now use the Python 3 style built-in next function in > place of the Python 2 style iterators' .next() method. This language > feature is also available under Python 2.6 and 2.7. > > > Many thanks to the Biopython developers and community for making this > release possible, especially the following contributors: > > Chris Mitchell (first contribution) > Christian Brueffer > Eric Talevich > Josha Inglis (first contribution) > Konstantin Tretyakov (first contribution) > Lenna Peterson > Martin Mokrejs > Nigel Delaney (first contribution) > Peter Cock > Sergei Lebedev (first contribution) > Tiago Antao > Wayne Decatur (first contribution) > Wibowo 'Bow' Arindrarto > > > Regards, > Tiago > _______________________________________________ > Biopython mailing list - Biopython at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython From zruan1991 at gmail.com Fri Nov 15 02:57:03 2013 From: zruan1991 at gmail.com (Zheng Ruan) Date: Thu, 14 Nov 2013 21:57:03 -0500 Subject: [Biopython-dev] Pull Request for Codon Alignment GSoC project Message-ID: Hi all, Since a beta version of biopython has been released, it might be safe to merge my GSoC work. I just made a pull request and there seems to be some problems when running the code in different platforms. In python2.7 and python3.3, the error message complains they cannot find CodonAlign module. I'm not sure why this happens. The dependency of Scipy and Numpy might also introduce some problems for the testing. Thanks! Best, Zheng Ruan From p.j.a.cock at googlemail.com Fri Nov 15 11:08:31 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 15 Nov 2013 11:08:31 +0000 Subject: [Biopython-dev] [Biopython] I've written a library for executing fuzzy searches... In-Reply-To: References: Message-ID: On Tue, Nov 12, 2013 at 5:59 PM, Tal Einat wrote: > Hi everyone, > > (I'm not on this list, so please make sure to reply to me as well as the > list.) > > In response to a stackoverflow > question, > I've written a Python library for fuzzy searches called > 'fuzzysearch'. > Currently, it allows searching for a string inside a longer string, > returning the best sub-string which match up to a given maximum Levenshtein > distance. This is done quite efficiently, and there is more optimization to > be done, as needed. > > Is there any interest in this library and its further development? One > thing which I think might be useful is support for BioPython Sequence types. > > This is open-source with a very liberal license (the MIT license). > > I'd be happy to collaborate on this! > > - Tal Einat Hi Tal, This does sounds interesting, yes. It might fit nicely into Biopython as Bio/SeqUtils/fizzysearch.py? I agree it would be good to ensure that your code will accept Biopython's (string like) Seq objects as well as plain strings. In terms of the license, I presume you'd be happy to accept the Biopython licence (or the 3-clause BSD licence which we are looking at switching to), which are both quite similar to the MIT licence? In terms of dependencies, you are using namedtuple which is fine (it wasn't in Python 2.5 but we've dropped that now). Also I see you are already supporting Python 2.6, 2.7 and 3.2, 3.3 with a single code base - which is good and perfect for integration into Biopython (we've recently dropped 2to3 which we used to use). In terms of unit tests, it is great to see you've done this already - although using unittest2 where we're still using unittest (v1) that shouldn't be a problem Peter From p.j.a.cock at googlemail.com Fri Nov 15 11:16:10 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 15 Nov 2013 11:16:10 +0000 Subject: [Biopython-dev] Pull Request for Codon Alignment GSoC project In-Reply-To: References: Message-ID: On Fri, Nov 15, 2013 at 2:57 AM, Zheng Ruan wrote: > Hi all, > > Since a beta version of biopython has been released, it might be safe to > merge my GSoC work. We'll normally only do minor bug fixes and documentation improvements between a beta and final release, but this is perfect timing for getting your work merged immediately after Biopython 1.63 is out. (So far there have been no problems reported with the beta, and we've fixed some newline issues when testing under Windows) > I just made a pull request and there seems to be some > problems when running the code in different platforms. In > python2.7 and python3.3, the error message complains they > cannot find CodonAlign module. I'm not sure why this happens. Some discussion is on the pull request itself: https://github.com/biopython/biopython/pull/259 > The dependency of Scipy and Numpy might also > introduce some problems for the testing. Thanks! We've got a mechanism for skipping tests when a dependency is missing - the MissingExternalDependencyError and MissingPythonDependencyError exceptions. You need to use this in test_CodonAlign.py, see test_PDB.py etc. Related to this we would need to install new dependencies on some of the buildbot slaves and perhaps TravisCI. Regards, Peter From anaryin at gmail.com Sat Nov 16 22:28:26 2013 From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=) Date: Sat, 16 Nov 2013 23:28:26 +0100 Subject: [Biopython-dev] Possible Bug in psi-blast via web? Message-ID: Someone posted this problem in Reddit. Anyone with some more expertise can probably give a better answer. http://www.reddit.com/r/bioinformatics/comments/1qmpbm/problems_with_psiblast_results_from_biopython/ From p.j.a.cock at googlemail.com Mon Nov 18 10:07:12 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 18 Nov 2013 10:07:12 +0000 Subject: [Biopython-dev] Possible Bug in psi-blast via web? In-Reply-To: References: Message-ID: On Sat, Nov 16, 2013 at 10:28 PM, Jo?o Rodrigues wrote: > Someone posted this problem in Reddit. Anyone with some more expertise can > probably give a better answer. > > http://www.reddit.com/r/bioinformatics/comments/1qmpbm/problems_with_psiblast_results_from_biopython/ I would presume this is not supported by the NCBI (or it wasn't 5 years ago anyway): http://lists.open-bio.org/pipermail/biopython/2008-May/004231.html ... http://lists.open-bio.org/pipermail/biopython/2008-May/004234.html http://bugzilla.open-bio.org/show_bug.cgi?id=2496 Peter From p.j.a.cock at googlemail.com Thu Nov 21 17:19:55 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 21 Nov 2013 17:19:55 +0000 Subject: [Biopython-dev] Import problems when testing under PyPy 2.2 Message-ID: Hello all, TravisCI is being updated to target PyPy 2.2 any day now, http://about.travis-ci.org/blog/2013-11-18-upcoming-build-environment-updates/ Meanwhile in local testing on Mac OS X, Biopython looks fine under PyPy 2.2. However, I'm seeing some oddities with imports failing under PyPy 2.2 via run_tests.py on Windows 32 bit & Linux 64 though - can anyone reproduce this? e.g. C:\repositories\biopython\Tests>c:\pypy-2.2\pypy test_Nexus.py test_NexusTest1 (__main__.NexusTest1) Test Nexus module ... ok test_TreeTest1 (__main__.NexusTest1) Test Tree module. ... ok test_WriteToFileName (__main__.NexusTest1) Test writing to a given filename. ... ok test_internal_node_labels (__main__.NexusTest1) Handle text labels on internal nodes. ... ok ---------------------------------------------------------------------- Ran 4 tests in 0.125s OK i.e. Here test_Nexus.py works fine using the installed Biopython. However, via run_tests.py which tries to mess with the Python path to use the local not-yet installed Biopython: C:\repositories\biopython\Tests>c:\pypy-2.2\pypy run_tests.py test_Nexus.py Python version: 2.7.3 (2cec7296d7fb, Nov 12 2013, 13:24:40) [PyPy 2.2.0 with MSC v.1500 32 bit] Operating system: nt win32 test_Nexus ... ERROR ====================================================================== ERROR: test_Nexus ---------------------------------------------------------------------- Traceback (most recent call last): File "run_tests.py", line 407, in runTest suite = unittest.TestLoader().loadTestsFromName(name) File "c:\pypy-2.2\lib-python\2.7\unittest\loader.py", line 91, in loadTestsFro mName module = __import__('.'.join(parts_copy)) File "C:\repositories\biopython\Tests\test_Nexus.py", line 13, in from Bio._py3k import StringIO ImportError: cannot import name 'StringIO' ---------------------------------------------------------------------- Ran 1 test in 0.016 seconds FAILED (failures = 1) Note: C:\repositories\biopython\Tests> C:\repositories\biopython\Tests>c:\pypy-2.2\pypy Python 2.7.3 (2cec7296d7fb, Nov 12 2013, 13:24:40) [PyPy 2.2.0 with MSC v.1500 32 bit] on win32 Type "help", "copyright", "credits" or "license" for more information. And now for something completely different: ``do you know about a toaster with 8KB of RAM and 64KB of ROM?'' >>>> from Bio._py3k import StringIO >>>> quit() This seems rather odd... Thanks, Peter From gokcen.eraslan at gmail.com Mon Nov 25 00:23:15 2013 From: gokcen.eraslan at gmail.com (=?ISO-8859-1?Q?G=F6kcen_Eraslan?=) Date: Mon, 25 Nov 2013 02:23:15 +0200 Subject: [Biopython-dev] [PATCH] Various NACCESS fixes and unit tests Message-ID: <52929873.9020504@gmail.com> Hello, I am developing a machine learning project which is using some command line tools such as NACCESS, STRIDE, netsurfp. I have decided to use BioPython and started digging NACCESS and DSSP codes in Bio/PDB to learn more about how to write parsers for BioPython. I have made some minor changes to NACCESS code and prepared some unit test files. Patch is attached. It would be nice to push this to master branch. I am also writing parsers for STRIDE and netsurfp tools and I would like to send those when I finish writing. Regards. -- Gokcen Eraslan -------------- next part -------------- A non-text attachment was scrubbed... Name: 0001-Bio-PDB-NACCESS-Various-NACCESS-fixes-and-unit-tests.patch Type: text/x-patch Size: 96937 bytes Desc: not available URL: From p.j.a.cock at googlemail.com Mon Nov 25 10:15:08 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 25 Nov 2013 10:15:08 +0000 Subject: [Biopython-dev] [PATCH] Various NACCESS fixes and unit tests In-Reply-To: <52929873.9020504@gmail.com> References: <52929873.9020504@gmail.com> Message-ID: Hi Gokcen, This looks very promising - would you be happy to submit this patch as a pull request on GitHub? Thanks, Peter P.S. Thanks for this report & fix: https://github.com/biopython/biopython/pull/261 On Mon, Nov 25, 2013 at 12:23 AM, G?kcen Eraslan wrote: > Hello, > > I am developing a machine learning project which is using some command line > tools such as NACCESS, STRIDE, netsurfp. I have decided to use BioPython and > started digging NACCESS and DSSP codes in Bio/PDB to learn more about how to > write parsers for BioPython. > > I have made some minor changes to NACCESS code and prepared some unit test > files. Patch is attached. It would be nice to push this to master branch. > > I am also writing parsers for STRIDE and netsurfp tools and I would like to > send those when I finish writing. > > Regards. > > -- > Gokcen Eraslan > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev > From gokcen.eraslan at gmail.com Mon Nov 25 11:37:59 2013 From: gokcen.eraslan at gmail.com (=?ISO-8859-1?Q?G=F6kcen_Eraslan?=) Date: Mon, 25 Nov 2013 13:37:59 +0200 Subject: [Biopython-dev] [PATCH] Various NACCESS fixes and unit tests In-Reply-To: References: <52929873.9020504@gmail.com> Message-ID: <52933697.3010301@gmail.com> On 2013-11-25 12:15, Peter Cock wrote: > Hi Gokcen, > Hello, > This looks very promising - would you be happy to submit this patch > as a pull request on GitHub? > Done. > Thanks, > > Peter > > P.S. Thanks for this report & fix: > https://github.com/biopython/biopython/pull/261 > > > On Mon, Nov 25, 2013 at 12:23 AM, G?kcen Eraslan > wrote: >> Hello, >> >> I am developing a machine learning project which is using some command line >> tools such as NACCESS, STRIDE, netsurfp. I have decided to use BioPython and >> started digging NACCESS and DSSP codes in Bio/PDB to learn more about how to >> write parsers for BioPython. >> >> I have made some minor changes to NACCESS code and prepared some unit test >> files. Patch is attached. It would be nice to push this to master branch. >> >> I am also writing parsers for STRIDE and netsurfp tools and I would like to >> send those when I finish writing. >> >> Regards. >> >> -- >> Gokcen Eraslan >> >> _______________________________________________ >> Biopython-dev mailing list >> Biopython-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biopython-dev >> -- G?k?en Eraslan From p.j.a.cock at googlemail.com Mon Nov 25 11:41:58 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 25 Nov 2013 11:41:58 +0000 Subject: [Biopython-dev] [PATCH] Various NACCESS fixes and unit tests In-Reply-To: <52933697.3010301@gmail.com> References: <52929873.9020504@gmail.com> <52933697.3010301@gmail.com> Message-ID: On Mon, Nov 25, 2013 at 11:37 AM, G?kcen Eraslan wrote: > On 2013-11-25 12:15, Peter Cock wrote: >> >> Hi Gokcen, >> > > Hello, > >> This looks very promising - would you be happy to submit this patch >> as a pull request on GitHub? >> > > Done. Thanks, https://github.com/biopython/biopython/pull/262 I'm made a couple of comments on GitHub. Peter From p.j.a.cock at googlemail.com Tue Nov 26 17:20:24 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 26 Nov 2013 17:20:24 +0000 Subject: [Biopython-dev] Import problems when testing under PyPy 2.2 In-Reply-To: References: Message-ID: On Thu, Nov 21, 2013 at 5:19 PM, Peter Cock wrote: > Hello all, > TravisCI is being updated to target PyPy 2.2 any day now, > http://about.travis-ci.org/blog/2013-11-18-upcoming-build-environment-updates/ > > Meanwhile in local testing on Mac OS X, Biopython looks fine > under PyPy 2.2. > > However, I'm seeing some oddities with imports failing under > PyPy 2.2 via run_tests.py on Windows 32 bit & Linux 64 though - > can anyone reproduce this? e.g. > > > C:\repositories\biopython\Tests>c:\pypy-2.2\pypy test_Nexus.py > test_NexusTest1 (__main__.NexusTest1) > Test Nexus module ... ok > test_TreeTest1 (__main__.NexusTest1) > Test Tree module. ... ok > test_WriteToFileName (__main__.NexusTest1) > Test writing to a given filename. ... ok > test_internal_node_labels (__main__.NexusTest1) > Handle text labels on internal nodes. ... ok > > ---------------------------------------------------------------------- > Ran 4 tests in 0.125s > > OK > > i.e. Here test_Nexus.py works fine using the installed Biopython. > However, via run_tests.py which tries to mess with the Python path > to use the local not-yet installed Biopython: > > C:\repositories\biopython\Tests>c:\pypy-2.2\pypy run_tests.py test_Nexus.py > Python version: 2.7.3 (2cec7296d7fb, Nov 12 2013, 13:24:40) > [PyPy 2.2.0 with MSC v.1500 32 bit] > Operating system: nt win32 > test_Nexus ... ERROR > ====================================================================== > ERROR: test_Nexus > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "run_tests.py", line 407, in runTest > suite = unittest.TestLoader().loadTestsFromName(name) > File "c:\pypy-2.2\lib-python\2.7\unittest\loader.py", line 91, in loadTestsFro > mName > module = __import__('.'.join(parts_copy)) > File "C:\repositories\biopython\Tests\test_Nexus.py", line 13, in > from Bio._py3k import StringIO > ImportError: cannot import name 'StringIO' > ---------------------------------------------------------------------- > Ran 1 test in 0.016 seconds > > FAILED (failures = 1) > > > Note: > > C:\repositories\biopython\Tests> > C:\repositories\biopython\Tests>c:\pypy-2.2\pypy > Python 2.7.3 (2cec7296d7fb, Nov 12 2013, 13:24:40) > [PyPy 2.2.0 with MSC v.1500 32 bit] on win32 > Type "help", "copyright", "credits" or "license" for more information. > And now for something completely different: ``do you know about a toaster with > 8KB of RAM and 64KB of ROM?'' >>>>> from Bio._py3k import StringIO >>>>> quit() > > > This seems rather odd... Solved - I think. There was something in the old build directory which was causing this, removing that and reinstalling Biopython under PyPy made it work. Not yet quite sure what this was though... perhaps stale compiled Python files from an older PyPy version? Peter From p.j.a.cock at googlemail.com Thu Nov 28 11:33:05 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 28 Nov 2013 11:33:05 +0000 Subject: [Biopython-dev] [Biopython] Biopython 1.63 beta release In-Reply-To: References: <87vbzx37m9.wl%tra@popgen.net> Message-ID: Dear Biopythoneers, On Tue, Nov 12, 2013 at 4:57 PM, Peter Cock wrote: > Thank you Tiago, on behalf of us all, for handling the Biopython 1.63 > beta release. Thank you to everyone who has tried the beta release - from the lack of new issues reported, it seems no new problems in the beta were uncovered which need to be fixed urgently? If so, then over on the biopython-dev list, I think we should let Tiago propose a convenient day to do the Biopython 1.63 release Thanks all, Peter From p.j.a.cock at googlemail.com Thu Nov 28 13:21:45 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 28 Nov 2013 13:21:45 +0000 Subject: [Biopython-dev] [Biopython] Biopython 1.63 beta release In-Reply-To: References: <87vbzx37m9.wl%tra@popgen.net> Message-ID: On Thu, Nov 28, 2013 at 1:17 PM, Tiago Ant?o wrote: > Dear all, > > On 28 November 2013 11:33, Peter Cock wrote: >> >> If so, then over on the biopython-dev list, I think we should let Tiago >> propose a convenient day to do the Biopython 1.63 release > > I would like to propose next Wednesday. But any day next week would be fine. Wednesday 4 December? Sounds fine to me :) Thanks, Peter