FIXING STUFF!

Rename should be complete or almost so.

workflows/demo.py

@@ -6,8 +6,8 @@ import cPickle
 import scipy
 import networkx as nx
 
-from fluents import logger,plots,workflow,dataset,main
-from fluents.lib import blmfuncs,nx_utils,cx_utils
+from laydi import logger,plots,workflow,dataset,main
+from laydi.lib import blmfuncs,nx_utils,cx_utils
 
 import gobrowser
 
@@ -363,7 +363,7 @@ class MapGene2GO(workflow.Function):
         workflow.Function.__init__(self, 'gene2go', 'gene->GO')
         # load data at init
         try:
-            fname = "/home/flatberg/fluents/data/gene2go.pcl"
+            fname = "/home/flatberg/laydi/data/gene2go.pcl"
             self._gene2go = cPickle.load(open(fname))
         except:
             logger.log("notice", "could not load mapping")
@@ -395,7 +395,7 @@ class MapGO2Gene(workflow.Function):
         workflow.Function.__init__(self, 'go2gene', 'GO->gene')
         # load data at init
         try:
-            fname = "/home/flatberg/fluents/data/go2gene.pcl"
+            fname = "/home/flatberg/laydi/data/go2gene.pcl"
             self._go2gene = cPickle.load(open(fname))
         except:
             logger.log("notice", "could not load mapping")

workflows/go_workflow.py

@@ -1,6 +1,6 @@
 import gtk
-from fluents import dataset, logger, plots, workflow, fluents, project
-from fluents.lib import blmfuncs
+from laydi import dataset, logger, plots, workflow, laydi, project
+from laydi.lib import blmfuncs
 import geneontology
 #import gostat
 from scipy import array, randn, log, ones, zeros
@@ -245,7 +245,7 @@ class LoadGOFunction(workflow.Function):
         browser = GeneOntologyTree(go)
         label = gtk.Label('_Gene Ontology')
         label.set_use_underline(True)
-        fluents.app['bottom_notebook'].append_page(browser, label)
+        laydi.app['bottom_notebook'].append_page(browser, label)
 
 
 class LoadTextDatasetFunction(workflow.Function):

workflows/gobrowser.py

@@ -1,6 +1,6 @@
 
 import gtk
-from fluents import dataset, logger, plots, workflow, fluents, project, view, main
+from laydi import dataset, logger, plots, workflow, laydi, project, view, main
 import geneontology
 from matplotlib.nxutils import points_inside_poly
 import matplotlib
@@ -243,7 +243,7 @@ class LoadGOFunction(workflow.Function):
         browser = GeneOntologyTree(go)
         label = gtk.Label('_Gene Ontology')
         label.set_use_underline(True)
-        fluents.app['bottom_notebook'].append_page(browser, label)
+        laydi.app['bottom_notebook'].append_page(browser, label)
 
 class LoadAnnotationsFunction(workflow.Function):
 
@@ -699,7 +699,7 @@ class DagPlot(plots.Plot):
     def is_mappable_with(self, obj):
         """Returns True if dataset/selection is mappable with this plot.
         """
-        if isinstance(obj, fluents.dataset.Dataset):
+        if isinstance(obj, laydi.dataset.Dataset):
             if self.current_dim in obj.get_dim_name():
                 return True
         return False
@@ -718,7 +718,7 @@ class DagPlot(plots.Plot):
         # is dataset a vector or matrix?
         if not n==1:
             # we have a category dataset
-            if isinstance(ds, fluents.dataset.CategoryDataset):
+            if isinstance(ds, laydi.dataset.CategoryDataset):
                 vec = dot(array, diag(arange(n))).sum(1)
             else:
                 vec = array.sum(1)

workflows/smokers.py

@@ -3,8 +3,8 @@ import os.path
 import webbrowser
 import cPickle
 
-from fluents import logger, plots,workflow,dataset,main
-from fluents.lib import blmfuncs,nx_utils,validation,engines,cx_stats,cx_utils
+from laydi import logger, plots,workflow,dataset,main
+from laydi.lib import blmfuncs,nx_utils,validation,engines,cx_stats,cx_utils
 import gobrowser, geneontology
 import scipy
 import networkx as nx
@@ -103,7 +103,7 @@ class DatasetLoadFunctionCYCLE(workflow.Function):
         workflow.Function.__init__(self, 'load_data', 'Cycle')
 
     def run(self):
-        filename='fluents/data/CYCLE'
+        filename='laydi/data/CYCLE'
         if filename:
             return dataset.from_file(filename)            
 
@@ -419,7 +419,7 @@ class MapGene2GO(workflow.Function):
         workflow.Function.__init__(self, 'gene2go', 'gene->GO')
         # load data at init
         try:
-            fname = "/home/flatberg/fluents/data/gene2go.pcl"
+            fname = "/home/flatberg/laydi/data/gene2go.pcl"
             self._gene2go = cPickle.load(open(fname))
         except:
             logger.log("notice", "could not load mapping")
@@ -451,7 +451,7 @@ class MapGO2Gene(workflow.Function):
         workflow.Function.__init__(self, 'go2gene', 'GO->gene')
         # load data at init
         try:
-            fname = "/home/flatberg/fluents/data/go2gene.pcl"
+            fname = "/home/flatberg/laydi/data/go2gene.pcl"
             self._go2gene = cPickle.load(open(fname))
         except:
             logger.log("notice", "could not load mapping")

workflows/test_workflow.py

@@ -1,5 +1,5 @@
 import gtk
-from fluents import dataset, logger, plots, workflow
+from laydi import dataset, logger, plots, workflow
 #import geneontology
 #import gostat
 from scipy import array, randn, log, ones