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dendik@1077: 1.4.3 (2012-05-25)
dendik@1076:
dendik@1076: This release collects a lot of changes that happened during half year. Most
dendik@1076: notable are:
dendik@1076:
dendik@1076: * thorough testing of the core which discovered bugs in `realign`
dendik@1076: (fixes were back-ported into 1.4.0 too),
dendik@1076: * greatly improved markups support and markups IO
dendik@1076: (but it is still somewhat not user-friendly enough yet),
dendik@1076: * utils `markup_to_file` and `markup_to_html`
dendik@1076: * file IO overrehaul,
dendik@1076: * and a lot of work on `blocks3d` and `pair_cores` with many new features,
dendik@1076: fixes, added web-interface for `pair_cores` (clone of the `blocks3d`
dendik@1076: interface).
dendik@1076:
dendik@1076: Detailed:
dendik@1076:
dendik@1076: * change(!): removed a lot of dead / obsolete code: `allpy.markup` (not to be
dendik@1076: confused with `allpy.markups`), sandbox, `pytale`, `sec_str`
dendik@1076: * change: a lot of code cleanup
dendik@1076: * change: replaced direct code inclusions from other projectd into allpy with
dendik@1076: Makefiles to download the necessary code.
dendik@1076: * new(!): `markup_to_file` util for converting `.markup` to e.g `.fasta`
dendik@1076: (by adding pseudo sequences consisting of markup)
dendik@1076: * new(!): `markup_to_html` util for visually displaying markups in HTML
dendik@1076: * bugfix: `Muscle` processor became incompatible with newer muscle
dendik@1076:
dendik@1076: In allpy core (allpy.base, allpy.dna, allpy.protein, allpy.rna, fllpy.fileio):
dendik@1076:
dendik@1076: * change: Allow markup to be tagged as saved / not saved (closes #83)
dendik@1076: * change(!): fileio overhaul; split one giant module into several; many bugfixes
dendik@1076: * new: `fileio` added internal support for `FastQ` (the new Illumina one)
dendik@1076: * new: method `dna.Sequence.reverse_complement()`
dendik@1076: * bugfix(!): until this release `alignment.realign(...)` could lose monomers
dendik@1076: * bugfix: dna module has seen some use, minimal bugfixes followed
dendik@1076:
dendik@1076: In module markups:
dendik@1076:
dendik@1076: * new: added `MarkupIOMixin` which simplifies defining savable markup classes
dendik@1076: * new: added pre-defined generic markups for simple data types (int, char,
dendik@1076: str, float, bool)
dendik@1076:
dendik@1076: In module structure:
dendik@1076:
dendik@1076: * change: geometrical cores produces less false negatives by ignoring cores
dendik@1076: contained within a single secondary-structure unit
dendik@1076: * change: structure.ChachedDownloadPdb: option to discard downloaded files
dendik@1076: * change: improved command-line interface of pair_cores (display defaults)
dendik@1076: * change: blocks3d builds high blocks using MonomerHomology
dendik@1076: * change: blocks3d() allows to specify pre-computed pair cores as `parts`
dendik@1076: * change: new method blocks_from_homology()
dendik@1076: * new: draft feature for pymol superimposition
bnagaev@992: * new: allow to load custom pdbs (allpy.structure)
dendik@1076: * new: web interface for pair-cores (similar to the existing for blocks3d)
bnagaev@992:
dendik@1076: 1.4.2
dendik@1076:
dendik@1076: This release was internal.
dendik@1076: Please refer to changes in the 1.4.3 release, since 1.4.2 never made public.
bnagaev@991:
dendik@848: 1.4.1
dendik@848:
dendik@1076: This would have been a code cleanup release.
dendik@1076: Please refer to changes in the 1.4.3 release, since 1.4.1 never made public.
dendik@848:
dendik@848: 1.4.0 (2011-07-20)
dendik@624:
dendik@697: * new: Alignments, Sequences and Blocks now can have Markups, see the wiki
dendik@717: * new: File format 'markup' for storing alignment with arbitrary markups
dendik@1076: * new: processor `allpy.processors.Needle()`
dendik@1076: * new: method `allpy.base.Alignment.rows_as_strings()`
dendik@1076: * new: method `allpy.base.Alignment.row_as_list(sequence)`
dendik@1076: * new: method `allpy.base.Alignment.row_as_string(sequence)`
dendik@1076: * new: `columns_as_lists()` returns list of lists, each has `column` attribute
dendik@662: * new: javascript viewer colors columns by conservedness
dendik@624:
dendik@602: 1.3.0 (2011-04-15)
dendik@602:
dendik@602: * new: started NEWS file
dendik@602: * new: started tracking version numbers