Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.fbb.msu.ru/hg/allpy/raw-rev/452ac0c16295 Дата изменения: Unknown Дата индексирования: Tue Oct 2 07:49:21 2012 Кодировка:

# HG changeset patch
# User Daniil Alexeyevsky
# Date 1337965156 -14400
# Node ID 452ac0c16295739364449fa3655c2437add719d9
# Parent 3c32489fcb3be88164612af0fe3892b7a945aa53
Documented the changes since 1.4.0 in NEWS

diff -r 3c32489fcb3b -r 452ac0c16295 NEWS
--- a/NEWS Fri May 25 20:53:18 2012 +0400
+++ b/NEWS Fri May 25 20:59:16 2012 +0400
@@ -1,29 +1,77 @@
- * new: add an argument not to save downloaded pdb (CachedDownloadPdb)
- * new: Geometrical core improvement: ignore cores, owned by one SS element
+1.4.3
+
+This release collects a lot of changes that happened during half year. Most
+notable are:
+
+ * thorough testing of the core which discovered bugs in `realign`
+ (fixes were back-ported into 1.4.0 too),
+ * greatly improved markups support and markups IO
+ (but it is still somewhat not user-friendly enough yet),
+ * utils `markup_to_file` and `markup_to_html`
+ * file IO overrehaul,
+ * and a lot of work on `blocks3d` and `pair_cores` with many new features,
+ fixes, added web-interface for `pair_cores` (clone of the `blocks3d`
+ interface).
+
+Detailed:
+
+ * change(!): removed a lot of dead / obsolete code: `allpy.markup` (not to be
+ confused with `allpy.markups`), sandbox, `pytale`, `sec_str`
+ * change: a lot of code cleanup
+ * change: replaced direct code inclusions from other projectd into allpy with
+ Makefiles to download the necessary code.
+ * new(!): `markup_to_file` util for converting `.markup` to e.g `.fasta`
+ (by adding pseudo sequences consisting of markup)
+ * new(!): `markup_to_html` util for visually displaying markups in HTML
+ * bugfix: `Muscle` processor became incompatible with newer muscle
+
+In allpy core (allpy.base, allpy.dna, allpy.protein, allpy.rna, fllpy.fileio):
+
+ * change: Allow markup to be tagged as saved / not saved (closes #83)
+ * change(!): fileio overhaul; split one giant module into several; many bugfixes
+ * new: `fileio` added internal support for `FastQ` (the new Illumina one)
+ * new: method `dna.Sequence.reverse_complement()`
+ * bugfix(!): until this release `alignment.realign(...)` could lose monomers
+ * bugfix: dna module has seen some use, minimal bugfixes followed
+
+In module markups:
+
+ * new: added `MarkupIOMixin` which simplifies defining savable markup classes
+ * new: added pre-defined generic markups for simple data types (int, char,
+ str, float, bool)
+
+In module structure:
+
+ * change: geometrical cores produces less false negatives by ignoring cores
+ contained within a single secondary-structure unit
+ * change: structure.ChachedDownloadPdb: option to discard downloaded files
+ * change: improved command-line interface of pair_cores (display defaults)
+ * change: blocks3d builds high blocks using MonomerHomology
+ * change: blocks3d() allows to specify pre-computed pair cores as `parts`
+ * change: new method blocks_from_homology()
+ * new: draft feature for pymol superimposition
* new: allow to load custom pdbs (allpy.structure)
- * new: add pymol superimposition feature draft (allpy.structure)
+ * new: web interface for pair-cores (similar to the existing for blocks3d)

- * new: add features of blocks3d.py to pair_cores.py
- * new: add ``parts'' argument to blocks3d() (allpy.structure)
- * new: add method blocks_from_homology() (allpy.structure)
- * new: add MonomerHomology-based high blocks building algo to pair-cores
- * new: print default values of command line args in help message (pair_cores)
- * new: add web interface for pair-cores
+1.4.2
+
+This release was internal.
+Please refer to changes in the 1.4.3 release, since 1.4.2 never made public.

1.4.1

-This is a code cleanup release.
-Nothing should change in the interface or behaviour at all.
+This would have been a code cleanup release.
+Please refer to changes in the 1.4.3 release, since 1.4.1 never made public.

1.4.0 (2011-07-20)

* new: Alignments, Sequences and Blocks now can have Markups, see the wiki
* new: File format 'markup' for storing alignment with arbitrary markups
- * new: processor allpy.processors.Needle()
- * new: method allpy.base.Alignment.rows_as_strings()
- * new: method allpy.base.Alignment.row_as_list(sequence)
- * new: method allpy.base.Alignment.row_as_string(sequence)
- * new: columns_as_lists() returns list of lists, each has 'column' attribute
+ * new: processor `allpy.processors.Needle()`
+ * new: method `allpy.base.Alignment.rows_as_strings()`
+ * new: method `allpy.base.Alignment.row_as_list(sequence)`
+ * new: method `allpy.base.Alignment.row_as_string(sequence)`
+ * new: `columns_as_lists()` returns list of lists, each has `column` attribute
* new: javascript viewer colors columns by conservedness

1.3.0 (2011-04-15)