...

developer_install_linux.sh

@@ -1,3 +1,14 @@
-sudo apt-get install python-qt4 python-numpy python-scipy python-pandas python-yapsy python-requests python-matplotlib python-scikits-learn python-pip ipython ipython-notebook ipython-notebook-common ipython-qtconsole python-pygments
-# sudo apt-get install python-pkg-resources python-setuptools --reinstall
-sudo pip install --upgrade pyqtconfig mplstyler
+# We're using a development version of IPython so for now we need to get it via git
+cwd=$(pwd)
+mkdir /tmp/pathomx-install
+cd /tmp/pathomx-install
+git clone --recursive https://github.com/ipython/ipython.git
+cd ipython
+sudo pip install --upgrade .
+rm -rf /tmp/pathomx-install
+cd $cwd
+
+# Now install all other dependencies via apt-get or pip
+sudo apt-get install python-qt4 python-numpy python-scipy python-yapsy python-requests python-matplotlib python-scikits-learn python-pip ipython ipython-notebook ipython-notebook-common ipython-qtconsole python-pygments
+sudo pip install --upgrade pandas dill pyqtconfig mplstyler mistune biocyc pydot jsonschema
+

developer_install_linux_python3.sh

@@ -1,4 +1,16 @@
-sudo apt-get install python3-pyqt4 python3-numpy python3-scipy python3-pandas python3-yapsy python3-matplotlib python3-requests python3-pip ipython3 ipython3-qtconsole ipython3-notebook
-sudo pip3 install --upgrade pyqtconfig mplstyler
+# We're using a development version of IPython so for now we need to get it via git
+cwd=$(pwd)
+mkdir /tmp/pathomx-install
+cd /tmp/pathomx-install
+git clone --recursive https://github.com/ipython/ipython.git
+cd ipython
+sudo pip3 install --upgrade .
+rm -rf /tmp/pathomx-install
+cd $cwd
+
+# Now install all other dependencies via apt-get or pip
+sudo apt-get install python3-pyqt4 python3-numpy python3-scipy python3-yapsy python3-matplotlib python3-requests python3-pip ipython3 ipython3-qtconsole ipython3-notebook
+sudo pip3 install --upgrade pandas dill pyqtconfig mplstyler mistune biocyc jsonschema
+
 # The following may error, but is not essential
-sudo pip3 scikits.learn 
+sudo pip3 install scikits.learn 

pathomx/Pathomx.py

@@ -393,6 +393,7 @@ def do_open_demo(f):
         #self.dbBrowser = self.dbtool.dbBrowser
 
         self.setWindowTitle(tr('Pathomx'))
+        self.setWindowIcon(QIcon(os.path.join(utils.scriptdir, 'static', 'icon.png')))
 
         self.kernelStatus = ui.KernelStatusWidget()
         self.statusBar().addPermanentWidget(self.kernelStatus)

pathomx/figures.py

@@ -111,7 +111,7 @@ def find_linear_scale(data):
     if type(data.columns) == pd.MultiIndex:
         for n, l in enumerate(data.columns.levels):
             if l.dtype == np.dtype('O'):  # Object; maybe str?
-                if len(l) > longest:
+                if longest is None or len(l) > longest:
                     longest = len(l)
 
             elif np.issubdtype(l.dtype, np.integer) or np.issubdtype(l.dtype, np.float):
@@ -246,7 +246,6 @@ def spectra(data, figure=None, ax=None, styles=None, regions=None):
         anno_y = data_max[idx]
 
         for x, y, l in zip(anno_scale, anno_y, anno_label):
-            print "*", x, y, l
             if y >= 0:
                 r = '60'
             else:

pathomx/globals.py

@@ -14,6 +14,11 @@
 import matplotlib as mpl
 from . import utils
 
+try:
+    unicode
+except:
+    unicode = str
+
 # Pathomx global variables
 current_tools = []
 current_tools_by_id = {}

pathomx/kernel_helpers.py

@@ -3,6 +3,7 @@
 import numpy as np
 import pandas as pd
 import re
+import io
 
 from matplotlib.figure import Figure, AxesStack
 from matplotlib.axes import Subplot
@@ -106,7 +107,7 @@ def progress(progress):
     print("____pathomx_execute_progress_%.2f____" % progress)
 
 
-class open_with_progress(file):
+class open_with_progress(io.IOBase):
 
     def __init__(self, f, *args, **kwargs):
         super(open_with_progress, self).__init__(f, *args, **kwargs)

pathomx/plugins/import_text/import_text.py

@@ -8,7 +8,9 @@
         dialect = csv.Sniffer().sniff(f.read(1024))
         f.close()
     except:
-        pass
+        dialect = None
+        format_dict = dict()
+
     else:
         format_dict = dict()
 else:
@@ -23,14 +25,14 @@
 if config['column_headers'] == 1:
     column_headers = 0
 elif config['column_headers'] > 1:
-    column_headers = range(config['column_headers'])
+    column_headers = list( range(config['column_headers']) )
 else:
     column_headers = None
 
 if config['row_headers'] == 0:
     row_headers = None
 else:
-    row_headers = range(config['row_headers'])
+    row_headers = list(range(config['row_headers']) )
 
 
 with open(config['filename'], 'rU') as f:
@@ -54,13 +56,13 @@
 # Check if we've got a singluar index (not multiindex) and convert
 if not isinstance(output_data.index, pd.MultiIndex):
     output_data.index = pd.MultiIndex.from_tuples(
-        zip(output_data.index.values, range(1, len(output_data.index.values) + 1)),
+        list( zip(output_data.index.values, range(1, len(output_data.index.values) + 1)) ),
         names=['Sample'])
 
 
 if not isinstance(output_data.columns, pd.MultiIndex):
     output_data.columns = pd.MultiIndex.from_tuples(
-        zip(output_data.columns.values, range(1, len(output_data.columns.values) + 1)),
+        list( zip(output_data.columns.values, range(1, len(output_data.columns.values) + 1)) ),
         names=['Label', 'Measurement'])
 
 
@@ -83,3 +85,4 @@
 
 Spectra = spectra(output_data, styles=styles)
 Heatmap = heatmap(output_data)
+

pathomx/runqueue.py

@@ -97,6 +97,7 @@ def run(self, tool, varsi, progress_callback=None, result_callback=None):
 
         # Check metadata to see if this kernel has the outputs for the previous tool
         self.e.execute('%reset_selective -f [^_]')
+        print(varsi)
         self.e.push({'varsi': varsi})
         self.e.execute(r'''from pathomx.kernel_helpers import pathomx_notebook_start, pathomx_notebook_stop, progress, open_with_progress
 pathomx_notebook_start(varsi, vars());''')
@@ -565,7 +566,7 @@ def run(self):
 
         if hasattr(tool, 'data'):
             # We can run code without an associated tool (e.g. for central-setup)
-            varsi['_pathomx_expected_output_vars'] = tool.data.o.keys()
+            varsi['_pathomx_expected_output_vars'] = list( tool.data.o.keys() )
 
             # Build the IO magic
             # - if the source did not run on the current runner we'll need to push the data over

pathomx/ui.py

@@ -49,6 +49,11 @@
 except:
     Qutepart = None
 
+try:
+    unicode
+except:
+    unicode = str
+
 PX_INIT_SHOT = 50
 PX_RENDER_SHOT = 500
 
@@ -1374,8 +1379,9 @@ def __init__(self, parent, name=None, code="", position=None, auto_focus=True, a
 
         self.logger.debug('Setup config manager...')
         self.config = ConfigManager()  # Configuration manager object; handle all get/setting, defaults etc.
+
         # Add hooks for custom widgets
-        self.config.hooks = dict(self.config.hooks.items() + custom_pyqtconfig_hooks.items())
+        self.config.hooks.update( custom_pyqtconfig_hooks.items() )
 
         self.logger.debug('Create editor icon...')
         self.editorItem = self.parent().editor.addApp(self, position=position)
@@ -1475,11 +1481,11 @@ def reload(self):
         self.load_source()
 
     def load_notes(self):
-        with open(os.path.join(self.plugin.path, "%s.md" % self.shortname), 'rU') as f:
+        with open(os.path.join(self.plugin.path, "%s.md" % self.shortname), 'rb') as f:
             self.notes = f.read().decode('utf-8')
 
     def load_source(self):
-        with open(os.path.join(self.plugin.path, "%s.py" % self.shortname), 'rU') as f:
+        with open(os.path.join(self.plugin.path, "%s.py" % self.shortname), 'rb') as f:
             self.default_code = f.read().decode('utf-8')
 
         if self.code == "":