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27 Commits

Author SHA1 Message Date
Einar Ryeng a1ab79024e Adding simple workflow named "default" with PCA, PLS and LPLS. Changed the program to
use this as the default workflow.
2011-03-06 15:27:16 +00:00
Einar Ryeng 256133275c * Changed build behaviour to suit newer Ubuntu releases (at least 9.10).
* Added -c option to generate intial configuration file and directories. This will create
  the file ~/.laydi and the directories ~/laydi/datasets and ~/laydi/workflows.
* Removed debug print statements.
2010-01-19 16:45:51 +00:00
Einar Ryeng 14de18c507 IMPORTANT: identifiers in the resulting csv file were not correct before this patch. 2009-02-28 15:38:29 +00:00
Einar Ryeng 0858fd00e5 ftsv2csv - script to convert ftsv files to comma/tab separated values. 2009-02-09 22:12:39 +00:00
Einar Ryeng 648817cf0e Removed debug print line. 2009-02-06 22:23:24 +00:00
Einar Ryeng 5cfa505ae2 Fixed critical bug in txt2ftsv that made output datasets incorrect if more than one list was used. 2009-02-06 22:21:19 +00:00
Einar Ryeng 6c20de11c9 Added options to txt2ftsv to chose between datasets and category datasets and whether or not to use sparse format. 2009-02-05 20:08:51 +00:00
Einar Ryeng b46c381c3e Added txt2ftsv, a script to build ftsv category datasets from lists of identifiers.
Usages is txt2ftsv [-d dimension] [-o output.ftsv] [-n dsname] [FILE1 [FILE2 ...]]
Input and output can be - for STDIN/STDOUT respectively. The script is primarily ment
as a hack to easily load selections. Data is only half sanitized.
2009-02-05 00:11:48 +00:00
Einar Ryeng 7e6bac20e1 FIXING STUFF!
Rename should be complete or almost so.
2008-12-05 22:07:56 +00:00
Einar Ryeng 1eabbc5c48 BREAKING STUFF!
Renaming fluents to laydi
2008-12-05 21:51:08 +00:00
Einar Ryeng 5739de0a61 Name change to Laydi. 2008-12-05 20:01:02 +00:00
Einar Ryeng 04b7cbb872 Lots of changes in structure to make it possible to package the program while
still allowing workflows to be placed in several locations in the file system.

The installation procedure is now ./configure && make install configure will
run m4 on fluents/paths.py.m4, Makefile.m4 and doc/Makefile.m4 so that the
installation system and the program will know where some important directories
are located.

The paths.py.m4 and consequently also pahts.py files are just listings of
directories configured during install.  I did this to separate these from all
other files so that as little as possible is touched by m4. It is still
necessary to do an install now to get the program to run in a clean checkout.

Workflows can now be placed anywhere in the system. This is done by setting the
workflowdir variable in the configuration file. All workflow directories,
separated by semicolons, are added to the python path.

The use of setup.py is now deprecated.
2008-12-05 00:12:49 +00:00
Einar Ryeng a380093afc Added workflowdir to configuration file. workflowdir is a semicolon separated
path of directories where workflows can be found.
2008-02-07 14:20:52 +00:00
Einar Ryeng ba7d8fc34f Changed the way workflows are handled. You now specify a workflow by naming the
containing python module. The module must be in python's path.
2007-12-14 11:48:21 +00:00
Einar Ryeng ca51a0b382 Added mat2ftsv to naïvely convert matlab matrices to ftsv files. Works in at
least one case, but does not try to guess anything sensible for identifiers.
2007-10-31 17:43:02 +00:00
Einar Ryeng a45743c31e Added main.py that now contains the One & Only Singleton instance of these classes:
- Navigator
 - Aplication
 - Workflow
 - Project
 - Options
Corresponding changes have been added in lots of other files to account for this, but
the access to these objects should now be a lot easier.
2007-07-26 12:35:59 +00:00
Einar Ryeng b637a5badc Changed /usr/bin/python2.4 to /usr/bin/python, and hope that 2.5 will not have
trouble running the app.
2007-06-28 21:42:18 +00:00
Einar Ryeng 7bdfdea23b Added -d option to get all identifiers along a single dimension. 2007-05-16 10:30:54 +00:00
Einar Ryeng 1ab558248c Piping information through dataset -i works. Added names of planned features
to the dataset script.
2007-05-09 21:52:59 +00:00
Einar Ryeng 7272eb63d2 Working on a script to query datasets without starting fluents. 2007-05-09 17:41:50 +00:00
Einar Ryeng f31795ac2a Corrected erroneous checkin. 2007-03-01 15:27:50 +00:00
Einar Ryeng ff070e5312 Preserves PYTHONPATH. 2007-03-01 15:26:38 +00:00
Einar Ryeng 934640ea62 Searches for /etc/fluentsrc and ~/.fluents configuration files. Adds the
home configuration variable.
2007-02-28 14:07:33 +00:00
Einar Ryeng bf1ad1be87 Removed old help function. 2007-02-27 16:25:48 +00:00
Einar Ryeng 1ba4bf5f82 Initial config parser support. 2007-02-27 16:08:22 +00:00
Einar Ryeng 375d45e0cc Updated import statements, and removed the workflows pca_workflow and
affy_workflow.
2006-10-17 14:42:27 +00:00
Einar Ryeng 610812f265 Started to rename "system" package to "fluents". Repository will be broken
until this is completed.
2006-10-17 14:28:35 +00:00