Obf-Projects

Biopython 1.84 has been released and is available from our website and PyPI. This contains about 5 months worth of updates, so the change-log in the news file is longer than usual. There have also been a few deprecations, most noteworthy this may be our last release with Python 3.9 support. Many thanks to the Biopython developers and community for making this release possible, especially the following contributors: Anil Tuncel (first contribution) David Cain Fabio Zanini (first contribution) Joao Rodrigues Judith Bernett (first contribution) Luca Monari (first contribution) Meridia Jane Bryant (first contribution) Manuel Lera-Ramirez Michael M. [Read More]

Dear Biopythoneers, Our first release of 2024 is now out, sooner than planned as this is purely to revert the removal of the .strand, .ref, and .ref_db attributes of the SeqFeature which was done in Biopython 1.82 without a deprecation period. They are again aliases for .location.strand etc, but now trigger deprecation warnings. See our deprecation policy. We apologize for any inconvenience, and thank you to those reporting this. This release of Biopython supports Python 3. [Read More]

We’re sharing some important news with you regarding our mailing lists. From early on, we’ve maintained a self-hosted Mailman server for any OBF project that needs a mailing list, including our member roster list. After careful consideration, we have decided we need a solution that keeps track more reliably with current and emerging spam-fighting technologies and standards, and that simultaneously requires much less administration time and know-how. Specifically, we are planning to migrate the lists to paid hosting, possibly Mailchimp. [Read More]

Biopython 1.79 has been released and is available from our website and PyPI. This is the final release supporting Python version 3.6. It also supports Python versions 3.7, 3.8, and 3.9, as well as PyPy 3.6.1 v7.1.1. The major changes in this version are listed below: - The Seq and MutableSeq classes in Bio.Seq now inherit from the same base class, ensuring their mutual consistency. In addition, both classes now store sequence data as bytes and bytearray objects, respectively. [Read More]

The OBF is committed to providing a harassment-free and respectful environment for all members of our community. To ensure that we are clearly describing norms, rules, and recommended practices for all our participants and members, we have provided a first draft of the OBF Code of Conduct and shared it recently in our newsletter. You can find the draft together with our request for comments on this pull request (see a preview here). [Read More]

The OBF has two sets of domain names available for adoption by a non-profit or open source project: biows.org, biows.com, biows.net and biocpp.org, biocpp.com, biocpp.net These domains were registered and donated to us with bio-web-services (biows) and bio-c-plus-plus (BioC++ or BioCPP) in mind, but we’ve failed to find a good home for them. Please note that this is like adopting a free puppy - we’ll transfer them at no cost, but domain names come with annual renewal charges which the recipient organisation would be responsible for paying. [Read More]

Biopython 1.78 has been released and is available from our website and PyPI. The main change is that Bio.Alphabet is no longer used. In some cases you will now have to specify expected letters, molecule type (DNA, RNA, protein), or gap character explicitly. Please consult the updated Tutorial and API documentation for guidance. This simplification has sped up many Seq object methods. See https://biopython.org/wiki/Alphabet for more information. Bio.SeqIO.parse() is faster with “fastq” format due to small improvements in the Bio. [Read More]

Biopython 1.77 has been released and is available from our website and PyPI. This is the first release since we dropped support for Python 2.7 and 3.5. Focusing on Python 3.6 or later will let us take advantage of new functionality and syntax, and simplify our code base and testing. This release of Biopython supports Python 3.6, 3.7 and 3.8 It has also been tested on PyPy3.6.1 v7.1.1. pairwise2 now allows the input of parameters with keywords and returns the alignments as a list of namedtuples. [Read More]

Biopython 1.76 has been released and is available from our website and PyPI. Coming relatively soon after our last release, the timing is linked to the official end of life for Python 2, and a focus hereafter on Python 3. We intend this to be our final release supporting Python 2.7 and 3.5. Focusing on Python 3.6 or later will let us take advantage of new functionality and syntax, and simplify our code base and testing. [Read More]

Dear Biopythoneers, Biopython 1.75 has been released and is available from our website and PyPI. This release of Biopython supports Python 2.7, 3.5, 3.6, 3.7 and is expected to work on the soon to be released Python 3.8. It has also been tested on PyPy2.7.13 v7.1.1 and PyPy3.6.1 v7.1.1-beta0. Note we intend to drop Python 2.7 support in early 2020. The restriction enzyme list in Bio.Restriction has been updated to the August 2019 release of REBASE. [Read More]