1.1 --- a/NEWS	Fri May 25 20:53:18 2012 +0400
     1.2 +++ b/NEWS	Fri May 25 20:59:16 2012 +0400
     1.3 @@ -1,29 +1,77 @@
     1.4 -  * new: add an argument not to save downloaded pdb (CachedDownloadPdb)
     1.5 -  * new: Geometrical core improvement: ignore cores, owned by one SS element
     1.6 +1.4.3
     1.7 +
     1.8 +This release collects a lot of changes that happened during half year. Most
     1.9 +notable are:
    1.10 +
    1.11 +  * thorough testing of the core which discovered bugs in `realign`
    1.12 +    (fixes were back-ported into 1.4.0 too),
    1.13 +  * greatly improved markups support and markups IO
    1.14 +    (but it is still somewhat not user-friendly enough yet),
    1.15 +  * utils `markup_to_file` and `markup_to_html`
    1.16 +  * file IO overrehaul,
    1.17 +  * and a lot of work on `blocks3d` and `pair_cores` with many new features,
    1.18 +    fixes, added web-interface for `pair_cores` (clone of the `blocks3d`
    1.19 +    interface).
    1.20 +
    1.21 +Detailed:
    1.22 +
    1.23 +  * change(!): removed a lot of dead / obsolete code: `allpy.markup` (not to be
    1.24 +    confused with `allpy.markups`), sandbox, `pytale`, `sec_str`
    1.25 +  * change: a lot of code cleanup
    1.26 +  * change: replaced direct code inclusions from other projectd into allpy with
    1.27 +    Makefiles to download the necessary code.
    1.28 +  * new(!): `markup_to_file` util for converting `.markup` to e.g `.fasta`
    1.29 +    (by adding pseudo sequences consisting of markup)
    1.30 +  * new(!): `markup_to_html` util for visually displaying markups in HTML
    1.31 +  * bugfix: `Muscle` processor became incompatible with newer muscle
    1.32 +
    1.33 +In allpy core (allpy.base, allpy.dna, allpy.protein, allpy.rna, fllpy.fileio):
    1.34 +
    1.35 +  * change: Allow markup to be tagged as saved / not saved (closes #83)
    1.36 +  * change(!): fileio overhaul; split one giant module into several; many bugfixes
    1.37 +  * new: `fileio` added internal support for `FastQ` (the new Illumina one)
    1.38 +  * new: method `dna.Sequence.reverse_complement()`
    1.39 +  * bugfix(!): until this release `alignment.realign(...)` could lose monomers
    1.40 +  * bugfix: dna module has seen some use, minimal bugfixes followed
    1.41 +
    1.42 +In module markups:
    1.43 +
    1.44 +  * new: added `MarkupIOMixin` which simplifies defining savable markup classes
    1.45 +  * new: added pre-defined generic markups for simple data types (int, char,
    1.46 +    str, float, bool)
    1.47 +
    1.48 +In module structure:
    1.49 +
    1.50 +  * change: geometrical cores produces less false negatives by ignoring cores
    1.51 +    contained within a single secondary-structure unit
    1.52 +  * change: structure.ChachedDownloadPdb: option to discard downloaded files
    1.53 +  * change: improved command-line interface of pair_cores (display defaults)
    1.54 +  * change: blocks3d builds high blocks using MonomerHomology
    1.55 +  * change: blocks3d() allows to specify pre-computed pair cores as `parts`
    1.56 +  * change: new method blocks_from_homology()
    1.57 +  * new: draft feature for pymol superimposition
    1.58    * new: allow to load custom pdbs (allpy.structure)
    1.59 -  * new: add pymol superimposition feature draft (allpy.structure)
    1.60 +  * new: web interface for pair-cores (similar to the existing for blocks3d)
    1.61  
    1.62 -  * new: add features of blocks3d.py to pair_cores.py
    1.63 -  * new: add ``parts'' argument to blocks3d() (allpy.structure)
    1.64 -  * new: add method blocks_from_homology() (allpy.structure)
    1.65 -  * new: add MonomerHomology-based high blocks building algo to pair-cores
    1.66 -  * new: print default values of command line args in help message (pair_cores)
    1.67 -  * new: add web interface for pair-cores
    1.68 +1.4.2
    1.69 +
    1.70 +This release was internal.
    1.71 +Please refer to changes in the 1.4.3 release, since 1.4.2 never made public.
    1.72  
    1.73  1.4.1
    1.74  
    1.75 -This is a code cleanup release.
    1.76 -Nothing should change in the interface or behaviour at all.
    1.77 +This would have been a code cleanup release.
    1.78 +Please refer to changes in the 1.4.3 release, since 1.4.1 never made public.
    1.79  
    1.80  1.4.0 (2011-07-20)
    1.81  
    1.82    * new: Alignments, Sequences and Blocks now can have Markups, see the wiki
    1.83    * new: File format 'markup' for storing alignment with arbitrary markups
    1.84 -  * new: processor allpy.processors.Needle()
    1.85 -  * new: method allpy.base.Alignment.rows_as_strings()
    1.86 -  * new: method allpy.base.Alignment.row_as_list(sequence)
    1.87 -  * new: method allpy.base.Alignment.row_as_string(sequence)
    1.88 -  * new: columns_as_lists() returns list of lists, each has 'column' attribute
    1.89 +  * new: processor `allpy.processors.Needle()`
    1.90 +  * new: method `allpy.base.Alignment.rows_as_strings()`
    1.91 +  * new: method `allpy.base.Alignment.row_as_list(sequence)`
    1.92 +  * new: method `allpy.base.Alignment.row_as_string(sequence)`
    1.93 +  * new: `columns_as_lists()` returns list of lists, each has `column` attribute
    1.94    * new: javascript viewer colors columns by conservedness
    1.95  
    1.96  1.3.0 (2011-04-15)