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dendik@1077
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1 1.4.3 (2012-05-25) |
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dendik@1076
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2 |
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3 This release collects a lot of changes that happened during half year. Most |
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4 notable are: |
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5 |
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6 * thorough testing of the core which discovered bugs in `realign` |
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7 (fixes were back-ported into 1.4.0 too), |
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8 * greatly improved markups support and markups IO |
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9 (but it is still somewhat not user-friendly enough yet), |
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10 * utils `markup_to_file` and `markup_to_html` |
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11 * file IO overrehaul, |
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12 * and a lot of work on `blocks3d` and `pair_cores` with many new features, |
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13 fixes, added web-interface for `pair_cores` (clone of the `blocks3d` |
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14 interface). |
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15 |
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16 Detailed: |
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17 |
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18 * change(!): removed a lot of dead / obsolete code: `allpy.markup` (not to be |
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19 confused with `allpy.markups`), sandbox, `pytale`, `sec_str` |
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20 * change: a lot of code cleanup |
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21 * change: replaced direct code inclusions from other projectd into allpy with |
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22 Makefiles to download the necessary code. |
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23 * new(!): `markup_to_file` util for converting `.markup` to e.g `.fasta` |
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24 (by adding pseudo sequences consisting of markup) |
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25 * new(!): `markup_to_html` util for visually displaying markups in HTML |
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26 * bugfix: `Muscle` processor became incompatible with newer muscle |
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27 |
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28 In allpy core (allpy.base, allpy.dna, allpy.protein, allpy.rna, fllpy.fileio): |
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29 |
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30 * change: Allow markup to be tagged as saved / not saved (closes #83) |
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31 * change(!): fileio overhaul; split one giant module into several; many bugfixes |
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32 * new: `fileio` added internal support for `FastQ` (the new Illumina one) |
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33 * new: method `dna.Sequence.reverse_complement()` |
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34 * bugfix(!): until this release `alignment.realign(...)` could lose monomers |
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35 * bugfix: dna module has seen some use, minimal bugfixes followed |
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36 |
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37 In module markups: |
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38 |
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39 * new: added `MarkupIOMixin` which simplifies defining savable markup classes |
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40 * new: added pre-defined generic markups for simple data types (int, char, |
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41 str, float, bool) |
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42 |
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43 In module structure: |
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44 |
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45 * change: geometrical cores produces less false negatives by ignoring cores |
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46 contained within a single secondary-structure unit |
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47 * change: structure.ChachedDownloadPdb: option to discard downloaded files |
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48 * change: improved command-line interface of pair_cores (display defaults) |
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49 * change: blocks3d builds high blocks using MonomerHomology |
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50 * change: blocks3d() allows to specify pre-computed pair cores as `parts` |
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51 * change: new method blocks_from_homology() |
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52 * new: draft feature for pymol superimposition |
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bnagaev@992
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53 * new: allow to load custom pdbs (allpy.structure) |
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54 * new: web interface for pair-cores (similar to the existing for blocks3d) |
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bnagaev@992
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55 |
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56 1.4.2 |
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57 |
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58 This release was internal. |
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59 Please refer to changes in the 1.4.3 release, since 1.4.2 never made public. |
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bnagaev@991
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60 |
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dendik@848
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61 1.4.1 |
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62 |
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63 This would have been a code cleanup release. |
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64 Please refer to changes in the 1.4.3 release, since 1.4.1 never made public. |
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65 |
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66 1.4.0 (2011-07-20) |
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dendik@624
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67 |
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dendik@697
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68 * new: Alignments, Sequences and Blocks now can have Markups, see the wiki |
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dendik@717
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69 * new: File format 'markup' for storing alignment with arbitrary markups |
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70 * new: processor `allpy.processors.Needle()` |
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71 * new: method `allpy.base.Alignment.rows_as_strings()` |
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72 * new: method `allpy.base.Alignment.row_as_list(sequence)` |
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73 * new: method `allpy.base.Alignment.row_as_string(sequence)` |
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74 * new: `columns_as_lists()` returns list of lists, each has `column` attribute |
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dendik@662
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75 * new: javascript viewer colors columns by conservedness |
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dendik@624
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76 |
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dendik@602
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77 1.3.0 (2011-04-15) |
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dendik@602
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78 |
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dendik@602
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79 * new: started NEWS file |
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dendik@602
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80 * new: started tracking version numbers |
