| age |
author |
description |
| Thu, 21 Jul 2011 18:34:27 +0400 |
Daniil Alexeyevsky |
'make tests' now also searches for doctests and runs them. |
| Thu, 21 Jul 2011 18:29:42 +0400 |
Daniil Alexeyevsky |
Added allpy.util.open(), a wrapper around open(), which allows "-" as a filename to signify stdin or stdout |
| Thu, 21 Jul 2011 16:41:08 +0400 |
Daniil Alexeyevsky |
Removed pair_cores/html.htm and blocks3d/html.htm, whcih were autogenerated files. Looks like this closes #93. |
| Thu, 21 Jul 2011 16:25:15 +0400 |
Daniil Alexeyevsky |
Removed pytale, sandbox, sec_str, since they are not working, there is no work on them going on and it is not likely that they will fork in any near future (see #99) |
| Thu, 21 Jul 2011 16:01:37 +0400 |
Daniil Alexeyevsky |
Added ignore rules for files removed in several preceeding commits (see #93) |
| Thu, 21 Jul 2011 15:18:42 +0400 |
Daniil Alexeyevsky |
Removed downloaded PDB-files from test/, they were not used anywhere too (see #93) |
| Thu, 21 Jul 2011 14:50:20 +0400 |
Daniil Alexeyevsky |
Removed some downloaded files from blocks3d/www (see #93) |
| Thu, 21 Jul 2011 14:23:12 +0400 |
Daniil Alexeyevsky |
Removed some of downloaded files fomr blocks3d/wt (see #93) |
| Thu, 21 Jul 2011 13:51:01 +0400 |
Daniil Alexeyevsky |
Extracted part for updating allpy.data.codes from top-level Makefile. (code cleanup) |
| Thu, 21 Jul 2011 13:47:49 +0400 |
Daniil Alexeyevsky |
Updated docs sources for the recent additions |
| Thu, 21 Jul 2011 13:12:54 +0400 |
Daniil Alexeyevsky |
Allow markup to be tagged as saved / not saved (closes #83) |
| Wed, 20 Jul 2011 20:44:59 +0400 |
Daniil Alexeyevsky |
Added allpy.markups.MarkupIOMixin to simplify new saveable markups creation. Switched existing saveable makrups to using it. Tested. (closes #82) |
| Wed, 20 Jul 2011 19:17:03 +0400 |
Daniil Alexeyevsky |
Added call to blocks3d-www makefile target to debian package building rules (see #62) |
| Wed, 20 Jul 2011 19:09:31 +0400 |
Daniil Alexeyevsky |
Added blocks3d javascript builder target to the global Makefile (closes #62) |
| Wed, 20 Jul 2011 18:36:15 +0400 |
Daniil Alexeyevsky |
Removed allpy.data.codes from repository, since it is automatically generated anyway. (see #93) |
| Wed, 20 Jul 2011 18:29:18 +0400 |
Daniil Alexeyevsky |
Fixed versions in NEWS; added comment for 1.4.1 |
| Wed, 20 Jul 2011 17:41:14 +0400 |
Daniil Alexeyevsky |
Released 1.4.0. [closes #53] |
| Wed, 20 Jul 2011 17:40:45 +0400 |
Daniil Alexeyevsky |
Marked release date for 1.4.0 in debian/changelog and NEWS |
| Wed, 20 Jul 2011 03:05:06 +0200 |
boris |
blocks3d/wt: fix possible races in try_to_run() method of Blocks3DWidget |
| Wed, 20 Jul 2011 02:46:23 +0200 |
boris |
blocks3d/wt: fix a typo in variable name |
| Wed, 20 Jul 2011 02:42:04 +0200 |
boris |
blocks3d/wt: use vector instead of list as container for tasks |
| Wed, 20 Jul 2011 02:38:59 +0400 |
boris (kodomo) |
blocks3d/wt: suggest better filenames for downloading |
| Wed, 20 Jul 2011 02:02:50 +0400 |
boris (kodomo) |
pair_cores_all: do not break all workers if error occured in one worker |
| Tue, 19 Jul 2011 20:04:22 +0400 |
Daniil Alexeyevsky |
allpy.util.lazy_import: the returned value after first query should also be a usable value |
| Tue, 19 Jul 2011 20:01:36 +0400 |
Daniil Alexeyevsky |
allpy.base.default_gaps is now list instead of set, with first item being the preferred output gap symbol |
| Tue, 19 Jul 2011 19:57:34 +0400 |
Daniil Alexeyevsky |
allpy.util.lazy_import: added all the arguments that __import__ has |
| Tue, 19 Jul 2011 19:39:59 +0400 |
Daniil Alexeyevsky |
Added allpy.utils.lazy_import: a helper to break import loops less pervasively |
| Tue, 19 Jul 2011 14:40:22 +0400 |
Daniil Alexeyevsky |
Added deprecation warnings to the deprecated functions. |
| Mon, 18 Jul 2011 19:53:06 +0400 |
Daniil Alexeyevsky |
convert_homology: mapping of column numbers was totally wrong; fixed |
| Mon, 18 Jul 2011 19:26:21 +0400 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
| Mon, 18 Jul 2011 19:26:03 +0400 |
Daniil Alexeyevsky |
Added script utils/convert_homology.py to convert homology files for similar alignments. |
| Mon, 18 Jul 2011 18:12:03 +0400 |
Daniil Alexeyevsky |
allpy.base.MarkupContainerMixin: fix add_markup to always return the newly created markup |
| Sat, 16 Jul 2011 19:59:16 +0400 |
boris (kodomo) |
apply changes of rasmol_output to rasmol_homology |
| Sat, 16 Jul 2011 17:07:19 +0400 |
Andrei |
Minor changes of output rasmol script |
| Fri, 15 Jul 2011 19:06:47 +0400 |
Daniil Alexeyevsky |
Enhanced allpy.base.Markup.sorted_values: it now accepts `map` and `default` arugments. Somewhat tested. (closes #67) |
| Fri, 15 Jul 2011 18:45:04 +0400 |
Andrei |
Automated merge with ssh://kodomo.fbb.msu.ru/allpy |
| Fri, 15 Jul 2011 18:29:55 +0400 |
Andrei |
Minor revision of rasmol output script |
| Fri, 15 Jul 2011 18:38:01 +0400 |
Daniil Alexeyevsky |
Bug: alignment IO recorded incorrect value to sequence's source attribute -- fixed |
| Fri, 15 Jul 2011 18:01:31 +0400 |
Daniil Alexeyevsky |
allpy.fileio. markup filetype now allows either - or _ to be used in headers interchangeably [closes #89] |
| Fri, 15 Jul 2011 17:13:01 +0400 |
Daniil Alexeyevsky |
Updated markup creation (and removal) in all scripts in the repository. There may still be some uses outside the repository, so watch out! [closes #95] |
| Fri, 15 Jul 2011 17:02:09 +0400 |
Daniil Alexeyevsky |
allpy.base: added parameter use_existing to *.add_markup() to allow same markup to be added multiple times explicitly [see #95] |
| Fri, 15 Jul 2011 16:43:03 +0400 |
Daniil Alexeyevsky |
Implemented & tested new markup API. See #95 |
| Fri, 15 Jul 2011 13:57:56 +0400 |
Daniil Alexeyevsky |
Added markups.by_name dictionary and markups.update() function to fill it. |
| Fri, 15 Jul 2011 12:27:21 +0400 |
boris (kodomo) |
pair_cores: more information in exceptions when reading input and loading pdb |
| Fri, 15 Jul 2011 12:23:35 +0400 |
Daniil Alexeyevsky |
Removed references to extract_pfam from utils/make_homolog* |
| Fri, 15 Jul 2011 12:03:46 +0400 |
Daniil Alexeyevsky |
Added utils/case_to_fasta for converting markup file with case markup to fasta file with letter case significant |
| Fri, 15 Jul 2011 02:23:27 +0400 |
boris (kodomo) |
optimization of rasmol_homology: keep structure loaded of two sequences only |
| Fri, 15 Jul 2011 02:06:23 +0400 |
boris (kodomo) |
structure: create method superimpose of SequenceMixin |
| Fri, 15 Jul 2011 03:03:39 +0400 |
boris (kodomo) |
structure: fix model saving (workaround) |
| Fri, 15 Jul 2011 02:56:28 +0400 |
boris (kodomo) |
structure: fix filtering by model in save_pdb method of SequenceMixin |
| Thu, 14 Jul 2011 18:15:45 +0400 |
Daniil Alexeyevsky |
utils/rasmol_homology: added options -d and -w for removing too thin / too narrow blocks |
| Thu, 14 Jul 2011 18:03:55 +0400 |
Daniil Alexeyevsky |
Added utils/rasmol_homology.py |
| Thu, 14 Jul 2011 17:30:18 +0400 |
Daniil Alexeyevsky |
Removed some dead code from pair_cores/rasmol_output (there is more dead code left) |
| Thu, 14 Jul 2011 17:07:07 +0400 |
Daniil Alexeyevsky |
pair_cores: no need to import extract_pfam for SequencePdbRsiMarkup anymore |
| Thu, 14 Jul 2011 16:19:07 +0400 |
Daniil Alexeyevsky |
Added option --pdb-cache to extract_pfam.py |
| Thu, 14 Jul 2011 16:15:21 +0400 |
Daniil Alexeyevsky |
Moved SequencePdbResiMarkup to allpy.markups, since it is used frequently |
| Thu, 14 Jul 2011 14:44:58 +0400 |
Daniil Alexeyevsky |
utils/make_homologies: added option -g to give input files as a glob expression |
| Thu, 14 Jul 2011 14:28:32 +0400 |
Daniil Alexeyevsky |
WARNING! Changed EOL formatting to UNIX everywhere! WARNING! |
| Thu, 14 Jul 2011 14:05:39 +0400 |
Daniil Alexeyevsky |
Removed executable permission from allpy.data modules with actual data tables (there is no sense in executing them and they do not have hash-bang header) |
| Thu, 14 Jul 2011 14:04:39 +0400 |
Daniil Alexeyevsky |
Added hash-bang to executable python files in utils/ |
