From biopython at maubp.freeserve.co.uk Thu Aug 19 11:43:56 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 19 Aug 2010 16:43:56 +0100 Subject: [Biopython-announce] Biopython 1.55 beta released Message-ID: Dear Biopythoneers, We?ve just released a beta of Biopython 1.55 for user testing, as announced on the news server (which has RSS and atom feeds) and on twitter: http://news.open-bio.org/news/2010/08/biopython-1-55-beta-released/ http://twitter.com/biopython Since Biopython 1.54 was released three months ago, we?ve made a good start on work for Python 3 support (via the 2to3 script), but as a side effect of this we?ve had to update quite a lot of the older parts of the library. Although the unit tests are all fine, there is a small but real chance that we?ve accidentally broken things ? which is why we?re doing this beta release. In terms of new features, the most noticeable highlight is that the command line tool application wrapper classes are now executable, which should make it much easier to call external tools. This is described in the updated documentation. http://biopython.org/DIST/docs/tutorial/Tutorial.html http://biopython.org/DIST/docs/tutorial/Tutorial.pdf Note we are phasing out support for Python 2.4. We will continue to support it for at least one further release (i.e. Biopython 1.56). This could be delayed given feedback from our users (e.g. if this proves to be a problem in combination with other libraries or a popular Linux distribution). (At least) 10 people have contributed to this release (so far), including 5 new people - thank you all: * Andres Colubri (first contribution) * Carlos Rios Vera (first contribution) * Claude Paroz (first contribution) * Eric Talevich * Frank Kauff * Joao Rodrigues (first contribution) * Konstantin Okonechnikov (first contribution) * Michiel de Hoon * Peter Cock * Tiago Antao Source distributions and Windows installers are available from the downloads page on the Biopython website: http://www.biopython.org/wiki/Download Feedback is welcome through the mailing lists (or bugzilla), especially if you find something that doesn't work. Thank you, Peter From biopython at maubp.freeserve.co.uk Thu Aug 26 06:57:27 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 26 Aug 2010 11:57:27 +0100 Subject: [Biopython-announce] Problem with biopython.org domain Message-ID: Hi all, We appear to have a temporary problem with our biopython.org domain, which I trust the OBF admin team will address shortly. As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page and http://biopython.open-bio.org/DIST/ for the downloads. Source code is hosted separately on github, http://github.com/biopython/biopython/ Apologies, Peter From dag at sonsorol.org Thu Aug 26 07:26:57 2010 From: dag at sonsorol.org (Chris Dagdigian) Date: Thu, 26 Aug 2010 07:26:57 -0400 Subject: [Biopython-announce] [Open-bio-l] Problem with biopython.org domain In-Reply-To: References: Message-ID: <4C764F81.1060100@sonsorol.org> I manage or am the admin/technical/billing account holder for 24 domains, among them most of the open-bio.org ones. Biopython.org is one that I do not own. Actually since NetSol is offering to let me change DNS maybe I'm the technical contact - have to wait and see on this. Normally for domains I control netsol starts email nagging me constantly - never got emails about this one. However, Networksolutions allows *anyone* with a payment method to renew any domain for any reason. I've renewed biopython.org for a 2-year term, paying out of pocket like I do for all OBF domains so our $$ stays in our bank account. > Order Confirmation > > Order Number: 375229424 > Today's Charges: $65.98 > Future Charges: $0.00 > Credit Card: xxxxxxxxxxx1002 The site should be back up soonish. I can't change the DNS entry that points the website to the expired splash page until netsol processes the renewal. Upcoming domain expiration dates: biomoby.org will expire Oct 1 bior.org will expire Nov 5 biosoap.org will expire Oct 9 -Chris Peter wrote: > Hi all, > > We appear to have a temporary problem with our biopython.org domain, > which I trust the OBF admin team will address shortly. > > As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page > and http://biopython.open-bio.org/DIST/ for the downloads. > > Source code is hosted separately on github, > http://github.com/biopython/biopython/ > > Apologies, > > Peter > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l From biopython at maubp.freeserve.co.uk Fri Aug 27 04:57:04 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 27 Aug 2010 09:57:04 +0100 Subject: [Biopython-announce] [Biopython] [Open-bio-l] Problem with biopython.org domain In-Reply-To: <4C764F81.1060100@sonsorol.org> References: <4C764F81.1060100@sonsorol.org> Message-ID: On Thu, Aug 26, 2010 at 12:26 PM, Chris Dagdigian wrote: > > I manage or am the admin/technical/billing account holder for 24 > domains, among them most of the open-bio.org ones. ... I've > renewed biopython.org for a 2-year term, ... The site should be > back up soonish. Thanks for the speedy response Chris - www.biopython.org is back up now. If anyone is still having trouble, please allow another day or so for DNS servers to update. As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page and http://biopython.open-bio.org/DIST/ for the downloads. Source code is hosted separately on github, http://github.com/biopython/biopython/ Peter From p.j.a.cock at googlemail.com Tue Aug 31 19:00:37 2010 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 1 Sep 2010 00:00:37 +0100 Subject: [Biopython-announce] Biopython 1.55 released Message-ID: Dear Biopythoneers, After the beta earlier this month (thank you to everyone who helped test this), we?ve just released Biopython 1.55 . For full details see: http://news.open-bio.org/news/2010/08/biopython-1-55-released/ Note we are phasing out support for Python 2.4. We will continue to support it for at least one further release (i.e. Biopython 1.56). This could be delayed given feedback from our users (e.g. if this proves to be a problem in combination with other libraries or a popular Linux distribution). (At least) 12 people have contributed to this release, including 6 new people ? thank you all: * Andres Colubri (first contribution) * Carlos Rios Vera (first contribution) * Claude Paroz (first contribution) * Cymon Cox * Eric Talevich * Frank Kauff * Joao Rodrigues (first contribution) * Konstantin Okonechnikov (first contribution) * Michiel de Hoon * Nathan Edwards (first contribution) * Peter Cock * Tiago Antao Source distributions and Windows installers are available from the downloads page on the Biopython website: http://www.biopython.org/wiki/Download As usual, feedback is most welcome on the mailing lists (or bugzilla). Regards, Peter P.S. You can follow Biopython on Twitter, http://twitter.com/biopython From biopython at maubp.freeserve.co.uk Thu Aug 19 15:43:56 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 19 Aug 2010 16:43:56 +0100 Subject: [Biopython-announce] Biopython 1.55 beta released Message-ID: Dear Biopythoneers, We?ve just released a beta of Biopython 1.55 for user testing, as announced on the news server (which has RSS and atom feeds) and on twitter: http://news.open-bio.org/news/2010/08/biopython-1-55-beta-released/ http://twitter.com/biopython Since Biopython 1.54 was released three months ago, we?ve made a good start on work for Python 3 support (via the 2to3 script), but as a side effect of this we?ve had to update quite a lot of the older parts of the library. Although the unit tests are all fine, there is a small but real chance that we?ve accidentally broken things ? which is why we?re doing this beta release. In terms of new features, the most noticeable highlight is that the command line tool application wrapper classes are now executable, which should make it much easier to call external tools. This is described in the updated documentation. http://biopython.org/DIST/docs/tutorial/Tutorial.html http://biopython.org/DIST/docs/tutorial/Tutorial.pdf Note we are phasing out support for Python 2.4. We will continue to support it for at least one further release (i.e. Biopython 1.56). This could be delayed given feedback from our users (e.g. if this proves to be a problem in combination with other libraries or a popular Linux distribution). (At least) 10 people have contributed to this release (so far), including 5 new people - thank you all: * Andres Colubri (first contribution) * Carlos Rios Vera (first contribution) * Claude Paroz (first contribution) * Eric Talevich * Frank Kauff * Joao Rodrigues (first contribution) * Konstantin Okonechnikov (first contribution) * Michiel de Hoon * Peter Cock * Tiago Antao Source distributions and Windows installers are available from the downloads page on the Biopython website: http://www.biopython.org/wiki/Download Feedback is welcome through the mailing lists (or bugzilla), especially if you find something that doesn't work. Thank you, Peter From biopython at maubp.freeserve.co.uk Thu Aug 26 10:57:27 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 26 Aug 2010 11:57:27 +0100 Subject: [Biopython-announce] Problem with biopython.org domain Message-ID: Hi all, We appear to have a temporary problem with our biopython.org domain, which I trust the OBF admin team will address shortly. As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page and http://biopython.open-bio.org/DIST/ for the downloads. Source code is hosted separately on github, http://github.com/biopython/biopython/ Apologies, Peter From dag at sonsorol.org Thu Aug 26 11:26:57 2010 From: dag at sonsorol.org (Chris Dagdigian) Date: Thu, 26 Aug 2010 07:26:57 -0400 Subject: [Biopython-announce] [Open-bio-l] Problem with biopython.org domain In-Reply-To: References: Message-ID: <4C764F81.1060100@sonsorol.org> I manage or am the admin/technical/billing account holder for 24 domains, among them most of the open-bio.org ones. Biopython.org is one that I do not own. Actually since NetSol is offering to let me change DNS maybe I'm the technical contact - have to wait and see on this. Normally for domains I control netsol starts email nagging me constantly - never got emails about this one. However, Networksolutions allows *anyone* with a payment method to renew any domain for any reason. I've renewed biopython.org for a 2-year term, paying out of pocket like I do for all OBF domains so our $$ stays in our bank account. > Order Confirmation > > Order Number: 375229424 > Today's Charges: $65.98 > Future Charges: $0.00 > Credit Card: xxxxxxxxxxx1002 The site should be back up soonish. I can't change the DNS entry that points the website to the expired splash page until netsol processes the renewal. Upcoming domain expiration dates: biomoby.org will expire Oct 1 bior.org will expire Nov 5 biosoap.org will expire Oct 9 -Chris Peter wrote: > Hi all, > > We appear to have a temporary problem with our biopython.org domain, > which I trust the OBF admin team will address shortly. > > As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page > and http://biopython.open-bio.org/DIST/ for the downloads. > > Source code is hosted separately on github, > http://github.com/biopython/biopython/ > > Apologies, > > Peter > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l From biopython at maubp.freeserve.co.uk Fri Aug 27 08:57:04 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 27 Aug 2010 09:57:04 +0100 Subject: [Biopython-announce] [Biopython] [Open-bio-l] Problem with biopython.org domain In-Reply-To: <4C764F81.1060100@sonsorol.org> References: <4C764F81.1060100@sonsorol.org> Message-ID: On Thu, Aug 26, 2010 at 12:26 PM, Chris Dagdigian wrote: > > I manage or am the admin/technical/billing account holder for 24 > domains, among them most of the open-bio.org ones. ... I've > renewed biopython.org for a 2-year term, ... The site should be > back up soonish. Thanks for the speedy response Chris - www.biopython.org is back up now. If anyone is still having trouble, please allow another day or so for DNS servers to update. As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page and http://biopython.open-bio.org/DIST/ for the downloads. Source code is hosted separately on github, http://github.com/biopython/biopython/ Peter From p.j.a.cock at googlemail.com Tue Aug 31 23:00:37 2010 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 1 Sep 2010 00:00:37 +0100 Subject: [Biopython-announce] Biopython 1.55 released Message-ID: Dear Biopythoneers, After the beta earlier this month (thank you to everyone who helped test this), we?ve just released Biopython 1.55 . For full details see: http://news.open-bio.org/news/2010/08/biopython-1-55-released/ Note we are phasing out support for Python 2.4. We will continue to support it for at least one further release (i.e. Biopython 1.56). This could be delayed given feedback from our users (e.g. if this proves to be a problem in combination with other libraries or a popular Linux distribution). (At least) 12 people have contributed to this release, including 6 new people ? thank you all: * Andres Colubri (first contribution) * Carlos Rios Vera (first contribution) * Claude Paroz (first contribution) * Cymon Cox * Eric Talevich * Frank Kauff * Joao Rodrigues (first contribution) * Konstantin Okonechnikov (first contribution) * Michiel de Hoon * Nathan Edwards (first contribution) * Peter Cock * Tiago Antao Source distributions and Windows installers are available from the downloads page on the Biopython website: http://www.biopython.org/wiki/Download As usual, feedback is most welcome on the mailing lists (or bugzilla). Regards, Peter P.S. You can follow Biopython on Twitter, http://twitter.com/biopython