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allpy: f2a7332dbc09 NEWS

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view NEWS @ 1155:f2a7332dbc09

pair-cores/web: link from detailed description to section 'Geometrical core'
author Boris Nagaev <bnagaev@gmail.com>
date Tue, 15 Jan 2013 18:51:35 +0400
parents 452ac0c16295
children
line source
1 1.4.3 (2012-05-25)
3 This release collects a lot of changes that happened during half year. Most
4 notable are:
6 * thorough testing of the core which discovered bugs in `realign`
7 (fixes were back-ported into 1.4.0 too),
8 * greatly improved markups support and markups IO
9 (but it is still somewhat not user-friendly enough yet),
10 * utils `markup_to_file` and `markup_to_html`
11 * file IO overrehaul,
12 * and a lot of work on `blocks3d` and `pair_cores` with many new features,
13 fixes, added web-interface for `pair_cores` (clone of the `blocks3d`
14 interface).
16 Detailed:
18 * change(!): removed a lot of dead / obsolete code: `allpy.markup` (not to be
19 confused with `allpy.markups`), sandbox, `pytale`, `sec_str`
20 * change: a lot of code cleanup
21 * change: replaced direct code inclusions from other projectd into allpy with
22 Makefiles to download the necessary code.
23 * new(!): `markup_to_file` util for converting `.markup` to e.g `.fasta`
24 (by adding pseudo sequences consisting of markup)
25 * new(!): `markup_to_html` util for visually displaying markups in HTML
26 * bugfix: `Muscle` processor became incompatible with newer muscle
28 In allpy core (allpy.base, allpy.dna, allpy.protein, allpy.rna, fllpy.fileio):
30 * change: Allow markup to be tagged as saved / not saved (closes #83)
31 * change(!): fileio overhaul; split one giant module into several; many bugfixes
32 * new: `fileio` added internal support for `FastQ` (the new Illumina one)
33 * new: method `dna.Sequence.reverse_complement()`
34 * bugfix(!): until this release `alignment.realign(...)` could lose monomers
35 * bugfix: dna module has seen some use, minimal bugfixes followed
37 In module markups:
39 * new: added `MarkupIOMixin` which simplifies defining savable markup classes
40 * new: added pre-defined generic markups for simple data types (int, char,
41 str, float, bool)
43 In module structure:
45 * change: geometrical cores produces less false negatives by ignoring cores
46 contained within a single secondary-structure unit
47 * change: structure.ChachedDownloadPdb: option to discard downloaded files
48 * change: improved command-line interface of pair_cores (display defaults)
49 * change: blocks3d builds high blocks using MonomerHomology
50 * change: blocks3d() allows to specify pre-computed pair cores as `parts`
51 * change: new method blocks_from_homology()
52 * new: draft feature for pymol superimposition
53 * new: allow to load custom pdbs (allpy.structure)
54 * new: web interface for pair-cores (similar to the existing for blocks3d)
56 1.4.2
58 This release was internal.
59 Please refer to changes in the 1.4.3 release, since 1.4.2 never made public.
61 1.4.1
63 This would have been a code cleanup release.
64 Please refer to changes in the 1.4.3 release, since 1.4.1 never made public.
66 1.4.0 (2011-07-20)
68 * new: Alignments, Sequences and Blocks now can have Markups, see the wiki
69 * new: File format 'markup' for storing alignment with arbitrary markups
70 * new: processor `allpy.processors.Needle()`
71 * new: method `allpy.base.Alignment.rows_as_strings()`
72 * new: method `allpy.base.Alignment.row_as_list(sequence)`
73 * new: method `allpy.base.Alignment.row_as_string(sequence)`
74 * new: `columns_as_lists()` returns list of lists, each has `column` attribute
75 * new: javascript viewer colors columns by conservedness
77 1.3.0 (2011-04-15)
79 * new: started NEWS file
80 * new: started tracking version numbers