Bumped to version 1.3.3
Added flag to skip uniprot_trembl processing
Trying to catch the cause of an exception
Added generation of graphics (PDF, SVG) from th...
Found and (hopefully) fixed ancient bug which a...
Written parser for HMMPfam and HMMScan, and fix...
Deprecating an unused function
Lots of code refactoring, so SIAM can work with...
Several fixes on AC and GAF parsers
Removing debug traces from code
After fixing so many incompatibilities between ...
Lots of fixes towards python 3.3 (but it still ...
Removing mod_file, and adding several additiona...
itemgetter/attrgetter fixes
map objects are iterable, but not subscriptable
Replacement of file() constructors (removed fro...
Popen returns binary objects which must be deco...
Fixed management of the decompression in Python 3
Better stacktrace reporting
Fixed exception chaining
Removed has_key usage on dict-like objects, as ...
HUGE commit containing the code refactoring nee...
Exceptions and lambda expressions fixes
Fixed tabs
Fixed exception creation, according to python3 ...
Fixed lambda expressions and exception raising,...
Fixed lambda expressions for python3
Fixed tabs and lambda according to python3 stan...
Really fixed lambda functions
Tab mangling
Lambda expressions don't use parentheses
Tabs
Python 3.3 does not understand '<>' operator
installer being prepared for a multi-python env...
Fixed inconsistent tabulator usage
Added pythonver infix to SIAM-WS.env file, so b...
Adding PYTHONVER to the generated variables file
Compatiblity with python 2.7 and python 3.3
Due all the compatibility changes applied, it i...
SIAM needs at least six 1.5.0 in order to have ...
Adding six compatibility layer for cPickle
Removed unused module
More code refactoring: urllib + urllib2 calls t...
Removing duplicated urllib loading
Removing more unneeded urllib calls
Removing unused urllib library
Second batch of changes, substituting print cal...
First steps towards having SIAM running both on...
Call pygraphviz instead of explicitly run "dot"
Small fixes on graph generation
Almost all the dependencies, but pygraphviz, ca...
Improved matrix drawing. It is not perfect, but...
Fixed obscure corner case related to lost GOA s...
Forgot insert sentences were stored in class va...
Python does not understand unary increment/decr...
Even more insertion improvements
More tweaks to increase the insertion performance
Trying to get a performance boost on UniProt in...
Removing last semi-colon, which was leading to ...
Fixed extraction of taxonomic identifiers, as i...
Queries optimized for SQLite
Optimizations (1 of 2)
Performance improvements due explicit index cre...
Typo in method name used to fill in uniprot object
Lambda functions in Python are not so smart as ...
Class variables are not reachable in this way f...
Forgot a parentheses
Optimization of offline UniProt queries
Issuing wrong query to the database
Replacing wrong uses of issubclass by right isi...
Some code reordering
[bugfix]Avoided an upstream bug in Python gzip ...
[feature]OBO parser did not know how to handle ...
Documenting the program only understands OBO 1.0
* As some old GOA files were double recompresse...
Latest versions of setuptools do not have Libra...
Added UniProxy concept, so we can switch betwee...
Reworked calls, due the changes in mod_db.SIAMDB
* Added ID alias table
Removing unused parameters being passed to the ...
We cannot discard obsolete terms because they c...
Documenting new parameter (to be implemented)
[bugfix] Forgot to store the ec2go_table in the...
[optimize] As EC list associated to a UniProt e...
[bugfix] SQLite3 executemany cannot be used wit...
[bugfix] There could be some corner cases where...
[bugfix] New code was not assigning the scores ...
[feature] As new evidence code scores are confi...
[bugfix] More cosmetic changes
[bugfix] Cosmetic fixes on the output
[bugfix] XML Schema was not in sync with genera...
[bugfix] Another "variable" moved to a class va...
[bugfix] Sequence_Table was being printed twice!
[feature] Evidence code scoring system has been...
[feature] Added new mod_db class, which manages...
[feature] Added future parameters and descripti...
[bugfix] On custom GOA gaf file, wrong initiali...
[bugfix] Make R less dependent on the configura...
[janitor] Labelling a couple of methods as depr...
[bugfix] KMlocalHybrid and KMlocalEZHybrid did ...