+++ /dev/null
-#### THIS IS A REDUCED DESTRIBUTION OF BIOPYTHON ####
-
-**Biopython README file**
-
- "The Biopython Project":http://www.biopython.org/ is an
-international association of developers of freely available Python
-tools for computational molecular biology.
-
-biopython.org provides an online resource for modules, scripts, and
-web links for developers of Python-based software for life science
-research. Thanks to bioperl, we can also provide web, FTP and CVS
-space for individuals and organizations wishing to distribute or
-otherwise make available standalone scripts & code.
-
-This Biopython package is made available under generous terms. Please
-see the LICENSE file for further details.
-
-
-**For the impatient**
-
-To build and install Biopython, download and unzip the source code,
-go to this directory at the command line, and type:
-
-python setup.py build
-python setup.py test
-python setup.py install
-
-**System Requirements**
-
-o "Python 2.3, 2.4, 2.5 or 2.6":http://www.python.org/
- Note that Biopython 1.50 is expected to the our final release to support
- Python 2.3. Given that Python 2.6 is still very new, it would be prudent
- to opt for Python 2.5 or 2.4 at this time.
-
-o "NumPy":http://numpy.scipy.org/ (optional, but strongly recommended)
- This package is only used in the computationally-oriented modules.
- It is required for Bio.Cluster, Bio.PDB and a few other modules. If you
- think you might need these modules, then please install NumPy first BEFORE
- installing Biopython. The older Numeric library is no longer supported in
- Biopython.
-
-o "ReportLab":http://www.reportlab.org/downloads.html (optional)
- This package is only used in Bio.Graphics, so if you do not need this
- functionality, you will not need to install this package. You can install
- it later if needed.
-
-o "psycopg":http://initd.org/software/psycopg/ (optional) or
- "pgdb":http://www.druid.net/pygresql/ (optional)
- These packages are used by BioSQL to access a PostgreSQL database.
-
-o "MySQLdb":http://sourceforge.net/projects/mysql-python (optional)
- This package is used by BioSQL or Bio.GFF to access a MySQL database.
-
-o "mxTextTools":http://www.egenix.com/files/python/mxTextTools.html (unlikely)
- You probably won't need mxTextTools. This was used in some of Biopython's
- older parsers, and Martel/Mindy, but these have all been deprecated now.
-
-In addition there are a number of useful third party tools you may wish to
-install such as standalone NCBI BLAST or ClustalW.
-
-
-**Installation**
-
-*** Make sure that Python is installed correctly ***
-
-Installation should be as simple as going to the biopython source code
-directory, and typing:
-
- 'python setup.py build'
- 'python setup.py test'
- 'sudo python setup.py install'
-
-If you need to do additional configuration, e.g. changing the base
-directory, please type 'python setup.py', or see the documentation for
-Distutils.
-
-
-**Testing**
-
-Biopython includes a suite of regression tests to check if everything is
-running correctly. To do the tests, go to the biopython source code directory
-and type:
-
- 'python setup.py test'
-
-Do not panic if you see messages warning of skipped tests:
- test_DocSQL ... skipping. Install MySQLdb if you want to use Bio.DocSQL.
-
-This most likely means that a package is not installed. You can
-ignore this if it occurs in the tests for a module that you were not
-planning on using. If you did want to use that module, please install
-the required dependency and re-run the tests.
-
-
-**Bugs**
-
-While we try to ship a robust package, bugs inevitably pop up. If you
-are having problems that might be caused by a bug in Biopython, it is
-possible that it has already been identified. Search the
-"bug database":http://bugzilla.open-bio.org/ and mailing lists
-to see if it has already been reported (and hopefully fixed).
-
-If you suspect the problem lies within a parser, it is likely that the
-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/ .
-However, be careful when doing this, because the code in CVS 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 version/date), 4) traceback that occurs,
-5) offending code, and 6) data file that causes the problem.
-
-
-
-**Contributing, Bug Reports**
-
-Biopython is run by volunteers from all over the world, with many
-types of backgrounds. We are always looking for people interested in
-helping with code development, web-site management, documentation
-writing, technical administration, and whatever else comes up.
-
-If you wish to contribute, please visit the
-"web site":http://www.biopython.org
-and join our "mailing list":http://biopython.org/wiki/Mailing_lists
-
-
-
-**Distribution Structure**
-
-README -- This file.
-
-NEWS -- Release notes and news
-
-LICENSE -- What you can do with the code.
-
-CONTRIB -- An (incomplete) list of people who helped Biopython in
- one way or another.
-
-DEPRECATED -- Contains information about modules in Biopython that are
- removed or no longer recommended for use, and how to update
- code that uses those modules.
-
-MANIFEST.in -- Tells distutils what files to distribute
-
-setup.py -- Installation file.
-
-Bio/ -- The main code base code.
-
-Martel/ -- Code for the Martel parsing system, once used in many
- Biopython parsers but now deprecated.
-
-BioSQL/ -- Code for using Biopython with BioSQL databases.
-
-Doc/ -- Documentation.
-
-Scripts/ -- Miscellaneous, possibly useful, standalone scripts
-
-Tests/ -- Regression testing code
git://source.jalview.org / jabaws.git / blobdiff