| age |
author |
description |
| Fri, 03 Jun 2011 15:29:47 +0400 |
Daniil Alexeyevsky |
allpy.fileio: use stdin/stdout when communicating with EMBOSS [closes #38] |
| Mon, 30 May 2011 20:38:58 +0400 |
Daniil Alexeyevsky |
allpy.fileio: wrapped some calls into try-finally; EmbossFile should now behave correctly if exceptions occur now |
| Wed, 25 May 2011 20:25:32 +0400 |
Daniil Alexeyevsky |
Added sectioning comments to allpy.processors |
| Wed, 25 May 2011 19:49:12 +0400 |
Daniil Alexeyevsky |
allpy.processors: cleaner reimplementation of remove_gaps option in Muscle |
| Wed, 25 May 2011 19:46:20 +0400 |
Daniil Alexeyevsky |
allpy.processors: code cleanup, added more docstrings |
| Tue, 24 May 2011 22:12:57 +0400 |
Daniil Alexeyevsky |
Implemented processor.FixOrder and processor.BypassEmpty as processors instead of hacky fix_order and fix_empty helper functions |
| Fri, 20 May 2011 13:35:09 +0400 |
Daniil Alexeyevsky |
Code cleanup allpy.processors: removed ExternalCommand.to_file; renamed no_gaps to remove_gaps in Muscle |
| Thu, 19 May 2011 22:32:38 +0400 |
Daniil Alexeyevsky |
NEWS entry about new Needle processor |
| Thu, 19 May 2011 22:29:38 +0400 |
Daniil Alexeyevsky |
Rewritten of test/usecase2 to make it work. It works, but is still hacky and ugly since it relies on markups, which are not sufficiently designed/implemented yet. |
| Thu, 19 May 2011 22:13:56 +0400 |
Daniil Alexeyevsky |
Implemented processors.Needle; hacky and dirty, just like the rest of the module |
| Wed, 18 May 2011 22:26:35 +0400 |
Daniil Alexeyevsky |
Fix fileio.EmbossFile: it was totally broken and serialized file objects to make arguments for seqret |
| Wed, 18 May 2011 22:25:40 +0400 |
Daniil Alexeyevsky |
Use more modern interfaces in test_base; document untested parts from code coverage test |
| Wed, 18 May 2011 21:38:17 +0400 |
Daniil Alexeyevsky |
Monomer.== now allows comparison with None |
| Mon, 16 May 2011 20:40:58 +0400 |
Daniil Alexeyevsky |
Added some docstrings to tests |
| Mon, 16 May 2011 20:32:39 +0400 |
Daniil Alexeyevsky |
Use python-coverage in nosetests |
| Mon, 16 May 2011 20:05:39 +0400 |
Daniil Alexeyevsky |
Ignore .coverage files from python-coverage |
| Wed, 04 May 2011 01:00:04 +0400 |
Daniil Alexeyevsky |
Added NEWS entry for the last change |
| Tue, 03 May 2011 21:06:36 +0400 |
Daniil Alexeyevsky |
Fixed import error for allpy.rna |
| Tue, 03 May 2011 21:04:29 +0400 |
Daniil Alexeyevsky |
Added base.Alignment.rows_as_strings |
| Tue, 03 May 2011 21:04:08 +0400 |
Daniil Alexeyevsky |
Added allpy.util.UserString, a clone of str with ability to add attributes |
| Fri, 29 Apr 2011 17:02:41 +0400 |
boris (kodomo) |
Merge with backout of 612:3a27920ff4ed and 613:71910cefe37a |
| Fri, 29 Apr 2011 17:01:29 +0400 |
boris (kodomo) |
Backout 612:3a27920ff4ed and 613:71910cefe37a |
| Fri, 29 Apr 2011 16:35:24 +0400 |
boris (kodomo) |
Automated merge with ssh://kodomo/allpy |
| Fri, 29 Apr 2011 16:21:23 +0400 |
boris (kodomo) |
pair_cores: add rasmol_output.py to generate rasmol script and superimposition |
| Fri, 29 Apr 2011 16:17:55 +0400 |
boris (kodomo) |
pair_score/score.py: fixes and inprovements |
| Fri, 29 Apr 2011 16:04:51 +0400 |
boris (kodomo) |
allpy/structure.py: move superimpose(+fix) and save_pdb to AlignmentMixin |
| Fri, 29 Apr 2011 15:43:42 +0400 |
boris (kodomo) |
allpy/config.py: change min_width=4 |
| Tue, 05 Apr 2011 23:37:39 +0400 |
boris (kodomo) |
pair_cores: change min core size from 10 to 5 |
| Tue, 05 Apr 2011 23:35:31 +0400 |
boris (kodomo) |
pair_cores.py: skip joining cores |
| Tue, 05 Apr 2011 23:14:06 +0400 |
boris (kodomo) |
paired_cores/score_all.py: improvement |
| Tue, 05 Apr 2011 23:11:41 +0400 |
boris (kodomo) |
paired_cores/score.py: change method of score evaluation |
| Fri, 15 Apr 2011 22:34:45 +0400 |
Daniil Alexeyevsky |
Renamed debian package geometrical-core -> geometrical-core2 |
| Fri, 15 Apr 2011 22:08:32 +0400 |
Daniil Alexeyevsky |
Fixed dependency information for geometrical-core |
| Fri, 15 Apr 2011 21:54:35 +0400 |
Daniil Alexeyevsky |
Fixed installation of geometrical-core since it requires some local modules imported |
| Fri, 15 Apr 2011 21:42:08 +0400 |
Daniil Alexeyevsky |
Updated debian changelog for version 1.3.0 |
| Fri, 15 Apr 2011 21:10:16 +0400 |
Daniil Alexeyevsky |
NEWS file grows upwards - not in README.devel |
| Fri, 15 Apr 2011 21:05:50 +0400 |
Daniil Alexeyevsky |
Added a few words about NEWS file to README.devel |
| Fri, 15 Apr 2011 20:57:33 +0400 |
Daniil Alexeyevsky |
Added tag 1.3.0 for changeset b730512ecae5 |
| Fri, 15 Apr 2011 20:57:27 +0400 |
Daniil Alexeyevsky |
Added NEWS file1.3.0 |
| Fri, 15 Apr 2011 20:46:05 +0400 |
Daniil Alexeyevsky |
Added tag 1.2.0 for changeset 364232e42888 |
| Fri, 15 Apr 2011 20:44:29 +0400 |
Daniil Alexeyevsky |
Added tag 1.1.0 for changeset 292b74612a42 |
| Sun, 03 Apr 2011 17:05:32 +0400 |
boris (kodomo) |
pair_cores_all.py: close openned files to avoid error |
| Sun, 03 Apr 2011 17:00:38 +0400 |
boris (kodomo) |
structure.py: add test argument to add_surrounded_columns() |
| Sun, 03 Apr 2011 16:58:39 +0400 |
boris (kodomo) |
structure.py: add test argument to add_surrounded_columns() |
| Sat, 02 Apr 2011 17:04:11 +0400 |
boris (kodomo) |
pair_cores: multiprocessing, no forking |
| Fri, 01 Apr 2011 17:14:26 +0400 |
boris (kodomo) |
pair_cores: improve score.py |
| Fri, 01 Apr 2011 17:05:13 +0400 |
boris (kodomo) |
structure.py: fix blocks_from_file() |
| Sat, 26 Mar 2011 10:48:11 +0300 |
boris (kodomo) |
add pair_cores program package |
| Sat, 26 Mar 2011 02:18:36 +0300 |
boris (kodomo) |
structure.py: fix set_pdb_chain() |
| Sat, 26 Mar 2011 02:16:01 +0300 |
boris (kodomo) |
fix default values of set_pdb_chain() parameters |
| Sat, 26 Mar 2011 01:24:21 +0300 |
boris (kodomo) |
structure.py: add join parameter to pair_cores_parts() |
| Sat, 26 Mar 2011 01:15:35 +0300 |
boris (kodomo) |
fix syntax error |
| Sat, 26 Mar 2011 01:13:56 +0300 |
boris (kodomo) |
structure.py: add min_core_size parameter to pair_core_parts() |
| Sat, 26 Mar 2011 01:09:05 +0300 |
boris (kodomo) |
structure.py: fix add_surrounded_columns() |
| Sat, 26 Mar 2011 00:42:07 +0300 |
Daniil Alexeyevsky |
Probably fixed fileio.EmbossFile.write_strings error in unlink |
| Sat, 26 Mar 2011 00:34:30 +0300 |
boris (kodomo) |
structure.py: improve set_pdb_chain() |
| Sat, 26 Mar 2011 00:18:15 +0300 |
Daniil Alexeyevsky |
Typo in allpy.fileio.write_strings |
| Sat, 26 Mar 2011 00:15:56 +0300 |
Daniil Alexeyevsky |
Fixed alignment output: don't use 'write_string', since in only works for fasta |
| Fri, 25 Mar 2011 23:12:21 +0300 |
boris (kodomo) |
structure.py: opportunity not to store entire pdb info, xyz only |
| Fri, 25 Mar 2011 23:09:58 +0300 |
boris (kodomo) |
Automated merge with ssh://kodomo/allpy |
