@@ -17,7 +17,7 @@ % You will also need the pictures included in the document, some of % which are UMLish diagrams created by Dia % (http://www.lysator.liu.se/~alla/dia/dia.html). -% These diagrams are available from Biopython CVS in the original dia +% These diagrams are available from Biopython git in the original dia % format, which you can easily save as .png format using Dia itself. % They are also checked in as the png files, so if you make % modifications to the original dia files, the png files should also be @@ -207,6 +207,8 @@ and HTML formats \end{verbatim} If the ``\verb|import Bio|'' line fails, Biopython is not installed. If the second line fails, your version is very out of date. + If the version string ends with a plus, you don't have an official + release, but a snapshot of the in development code. \item \emph{Where is the latest version of this document?}\\ If you download a Biopython source code archive, it will include the @@ -281,6 +283,8 @@ and HTML formats \item \emph{I looked in a directory for code, but I couldn't find the code that does something. Where's it hidden?} \\ One thing to know is that we put code in \verb|__init__.py| files. If you are not used to looking for code in this file this can be confusing. The reason we do this is to make the imports easier for users. For instance, instead of having to do a ``repetitive'' import like \verb|from Bio.GenBank import GenBank|, you can just use \verb|from Bio import GenBank|. + \item \emph{Why does the code from CVS seem out of date?} \\ + In late September 2009, just after the release of Biopython 1.52, we switched from using CVS to git, a distributed version control system. The old CVS server will remain available as a static and read only backup, but if you want to grab the latest code, you'll need to use git instead. See our website for more details. \end{enumerate} \chapter{Quick Start -- What can you do with Biopython?} @@ -6840,8 +6844,8 @@ The medium term objective for the module is to support widely used data formats, applications and databases. This module is currently under intense development and support for new features should appear at a rather fast pace. Unfortunately this might also entail some instability on the API, especially -if you are using a CVS version. APIs that are made available on public -versions should be much stabler. +if you are using a development version. APIs that are made available on +our official public releases should be much more stable. \section{GenePop} Doc/Tutorial.tex @@ -40,6 +40,9 @@ efneighbor) whose Biopython wrappers are now obsolete. See also the DEPRECATED file, as several old deprecated modules have finally been removed (e.g. Bio.EUtils which had been replaced by Bio.Entrez). +On a technical note, this will be the last release using CVS for source code +control. Biopython is moving from CVS to git. + =================================================================== August 17, 2009: Biopython 1.51 released. NEWS @@ -1,3 +1,13 @@ +**NOTE ABOUT CVS** + +Until late September 2009, Biopython source code was hosted in CVS running +on the Open Bioinformatics Foundation (OBF) servers. We are now using git, +a distributed version control system. The CVS repositories at the OBF will +remain for a while as "read only" static backups of everything up to and +including Biopython 1.52 but will not be updated in future. See our website +for further details, http://www.biopython.org/ + + **Biopython README file** "The Biopython Project":http://www.biopython.org/ is an international @@ -102,16 +112,15 @@ data format has changed and broken the parsing code. (The BLAST and GenBank formats seem to be particularly fragile.) Thus, the parsing code in Biopython is sometimes updated faster than we can build Biopython releases. You can get the most recent parser by pulling the relevant -files (e.g. the ones in Bio.SeqIO or Bio.Blast) out of -"anonymous cvs":http://cvs.biopython.org/ or our git mirror on +files (e.g. the ones in Bio.SeqIO or Bio.Blast) out git mirror on "github":http://github.com/biopython/biopython/ . -However, be careful when doing this, because the code in CVS/github is +However, be careful when doing this, because the code in github is not as well-tested as released code, and may contain new dependencies. Finally, you can send a bug report to the bug database or biopython@biopython.org. In the bug report, please let us know 1) which operating system and hardware you are using, 2) Python version, -3) Biopython version (or CVS/git version/date), 4) traceback that occurs, +3) Biopython version (or git version/date), 4) traceback that occurs, 5) offending code, and 6) data file that causes the problem. README 2a3310b306eb983042099815865fe0592888127c peterc peterc http://github.com/etal/biopython/commit/d42ef908d0a997c9f285ca2ec0c2b395fa8f31d9 d42ef908d0a997c9f285ca2ec0c2b395fa8f31d9 2009-09-23T03:00:48-07:00 2009-09-23T03:00:48-07:00 Adding notes about CVS/git 7f70d98476b4a678ba45aa86a3f2e7c399c34e7c peterc peterc