allpy
view README.devel @ 1091:afed1fd8920c
Added backreferences to `Seqeunce`s from `Monomer`s (closes #49)
WARNING! Please note that `Sequence` API almost changed entirely!
WARNING! This commit immediately obsoletes classmethods `Monomer.from_code*`,
`Monomer.from_name` and `Sequence.from_monomers`.
Turns out, python can not pickle sets/dicts which have keys, which inderecly
reference the set/dict itself: http://bugs.python.org/issue9269 -- which is
excatly what we have in abundance after this change.
To allow pickling added `__getstate__` to `Monomer` to return all attributes,
except `sequence` and `__setstate__` to `Sequence`, which runs through all
monomers and returns the `sequence` attribute back to where it belongs.
WARNING! This MAY result in unexpected behaviour in some cases. (Which should
be rare enough).
| author | Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru> |
|---|---|
| date | Sat, 02 Jun 2012 19:33:42 +0400 |
| parents | b87eb91bd929 |
| children |
line source
1 Using library in-place
2 ======================
4 To use the library in-place, without installing, you have to add it's
5 directory to PYTHONPATH.
7 e.g, type this in your shell::
9 export PYTHONPATH=`pwd`
11 alternatively, you can type::
13 . ./SETPATH
15 which adds the right path to PYTHONPATH and also adds 'utils' directory
16 to PATH.
18 NEWS file
19 =========
21 NEWS file contains news that are important to the library users, not to the
22 devels. It must contain a word abot every change in any interfaces. It may
23 contain a word about bugfix, if that bugfix was important and could cause users
24 some grief. It must not contain anything else.
26 The file grows upwards (like blog, so that all the most important things are at
27 the top, like)
29 Example file format::
31 1.3.1 (2011-05-01)
32 * bugfix: the Moon was going to fall
34 1.3.0 (2011-04-15)
36 * new: new feature description
37 * new: new feature description
38 * change(!): critical library interface change
39 * change: change in the library interface
40 * bugfix: short bug summary, see #ticket
41 * bugfix: important bug that could destroy the Earth but did not hit trac