FIXING STUFF!

Rename should be complete or almost so.

scripts/README

@@ -1,6 +1,6 @@
 
 This directory and its subdirectories are intended for small scripts that are
-not considered parts of fluents proper. They are included because they do
+not considered parts of laydi proper. They are included because they do
 useful tings in preprocessing data, often for a specific use (e.g. microarray
 analysis with gene ontology background information).
 

scripts/geneontology/entrez-go-mapping

@@ -52,7 +52,7 @@ def parse_options():
                   help="Output annotations in the cellular component tree.",
                   action="store_true", default=False)
     op.add_option('-d', '--output-dataset',
-                  help="Export as ftsv (Fluents dataset) file.")
+                  help="Export as ftsv (Laydi dataset) file.")
     op.add_option('-m', '--molecular-function', dest="mf",
                   help="Output annotations in the molecular function tree.",
                   action="store_true", default=False)

scripts/geneontology/go-gene-matrix

@@ -3,7 +3,7 @@
 import os, sys
 import getopt
 sys.path.append('../..')
-from fluents import dataset
+from laydi import dataset
 import numpy
 
 max_val = numpy.inf

scripts/lpls/lpls.py

@@ -4,7 +4,7 @@ import matplotlib
 from scipy import *
 from scipy.linalg import inv,norm
 
-sys.path.append("../../fluents/lib")
+sys.path.append("../../laydi/lib")
 import select_generators
 
 def nipals_lpls(X, Y, Z, a_max, alpha=.7, mean_ctr=[2, 0, 1], scale='scores', verbose=True):

scripts/lpls/run_smoker.py

@@ -6,9 +6,9 @@ from scipy.linalg import norm
 from lpls import correlation_loadings
 
 import rpy_go
-sys.path.append("../../fluents") # home of dataset
-sys.path.append("../../fluents/lib") # home of cx_stats
-sys.path.append("/home/flatberg/fluents/scripts/lpls")
+sys.path.append("../../laydi") # home of dataset
+sys.path.append("../../laydi/lib") # home of cx_stats
+sys.path.append("/home/flatberg/laydi/scripts/lpls")
 sys.path.append("/home/flatberg/pyblm/")
 import dataset
 import cx_stats