Commit Graph

30 Commits

Author SHA1 Message Date
einarr ed486ddf2e Changed default directories for:
* Load dataset
 * Import annotations
 * Export annotations
to the correct directories in the current project.
2011-03-07 16:19:45 +00:00
einarr dc8da8823e Partial fix to #22. Laydi will require a project directory to run. If the
project directory does not exist, i.e. if a new project should be created, the
new -n switch is required. New syntax to run laydi is now
{{{
laydi [options] </path/to/project>
}}}
2011-03-06 23:08:09 +00:00
einarr b5d2e8e181 Changed the name of the current Project class to ProjectView, to make room for a new
non-GUI project class.
2011-03-06 22:33:51 +00:00
einarr 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
einarr 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
einarr 14de18c507 IMPORTANT: identifiers in the resulting csv file were not correct before this patch. 2009-02-28 15:38:29 +00:00
einarr 0858fd00e5 ftsv2csv - script to convert ftsv files to comma/tab separated values. 2009-02-09 22:12:39 +00:00
einarr 648817cf0e Removed debug print line. 2009-02-06 22:23:24 +00:00
einarr 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
einarr 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
einarr 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
einarr 7e6bac20e1 FIXING STUFF!
Rename should be complete or almost so.
2008-12-05 22:07:56 +00:00
einarr 1eabbc5c48 BREAKING STUFF!
Renaming fluents to laydi
2008-12-05 21:51:08 +00:00
einarr 5739de0a61 Name change to Laydi. 2008-12-05 20:01:02 +00:00
einarr 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
einarr 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
einarr 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
einarr 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
einarr 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
einarr 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
einarr 7bdfdea23b Added -d option to get all identifiers along a single dimension. 2007-05-16 10:30:54 +00:00
einarr 1ab558248c Piping information through dataset -i works. Added names of planned features
to the dataset script.
2007-05-09 21:52:59 +00:00
einarr 7272eb63d2 Working on a script to query datasets without starting fluents. 2007-05-09 17:41:50 +00:00
einarr f31795ac2a Corrected erroneous checkin. 2007-03-01 15:27:50 +00:00
einarr ff070e5312 Preserves PYTHONPATH. 2007-03-01 15:26:38 +00:00
einarr 934640ea62 Searches for /etc/fluentsrc and ~/.fluents configuration files. Adds the
home configuration variable.
2007-02-28 14:07:33 +00:00
einarr bf1ad1be87 Removed old help function. 2007-02-27 16:25:48 +00:00
einarr 1ba4bf5f82 Initial config parser support. 2007-02-27 16:08:22 +00:00
einarr 375d45e0cc Updated import statements, and removed the workflows pca_workflow and
affy_workflow.
2006-10-17 14:42:27 +00:00
einarr 610812f265 Started to rename "system" package to "fluents". Repository will be broken
until this is completed.
2006-10-17 14:28:35 +00:00