{5} Assigned, Active Tickets by Owner (Full Description) (38 matches)

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Ticket Summary Component Milestone Type Created
Description
#1189 On-line scripting reference should be cleaned up slightly documentation bug 05/28/12

I'm currently using Orange 2.5a4 but I've found a few problems with the documentation:

  • The online reference doesn't specify what version it applies to. I eventually found the PCA code I was looking for at Orange.projection.pca.Pca which is fine but confusing when the  docs point me to Orange.projection.linear.Pca. I presume this is due to version mismatch, but without a version noted anywhere (at least that I could find) in the online reference, it was difficult to know to even look out for this.
  • The  reference index is broken – all links point to 404s
  • The PyPi page links to  http://orange-bioinformatics.readthedocs.org which mostly unpopulated and therefore not very useful. It would be better to point to the documentation on the main site, or keep the reasdthedocs.org page updated

#754 reference documentation - Attribute types defined in Python documentation 2.6 task 05/03/11

#854 Orange.projection.correspondence documentation Future task 07/04/11

That was assigned to you, wasn't it?


#953 Debian package: convert embedded libraries to external dependencies library Future task 09/11/11

For inclusion of our Debian package into official repository we have to move embedded libraries to external dependencies. Those are (at the time of writing):

There are  libqhull-dev,  libblas-dev and  liblapack-dev, respectively.

And probably libSVM (at least we have it mentioned in licenses file).


ales (4 matches)

Ticket Summary Component Milestone Type Created
Description
#1205 TypeError in Select Attributes on Orange Canvas canvas bug 06/22/12

When using the the Select Attributes module on Orange Canvas, I got the following error:

There were problems importing the following widgets:
   OWLiftCurve: name 'AROCFromCDT' is not defined
   OWRScript: No module named rpy2.robjects
   OWModelMapQt: No module named orangeqt
   OWDiscretizeQt: No module named orangeqt
   OWDistributionsQt: No module named orangeqt
   OWLinProj3D: No module named orangeqt
   OWLinProjQt: No module named orangeqt
   OWMDSQt: No module named orangeqt
   OWNxExplorer3D: No module named OWNxExplorerQt
   OWParallelCoordinatesQt: No module named orangeqt
   OWPolyvizQt: No module named orangeqt
   OWRadvizQt: No module named orangeqt
   OWScatterPlot3D: No module named orangeqt
   OWScatterPlotQt: No module named orangeqt
   OWSphereviz3D: No module named orangeqt
The following widgets could not be imported and will not be available: OWSphereviz3D, OWLiftCurve, OWModelMapQt, OWParallelCoordinatesQt, OWLinProj3D, OWScatterPlotQt, OWNxExplorer3D, OWRadvizQt, OWMDSQt, OWLinProjQt, OWDistributionsQt, OWScatterPlot3D, OWDiscretizeQt, OWPolyvizQt.
The following prototype widgets could not be imported and will not be available: OWRScript.

Unhandled exception of type TypeError occured at 10:39:30:
Traceback:
  File: OWBaseWidget.py, line 678 in processSignals
  Code: handler(value)
    File: OWDataDomain.py, line 478 in set_data
    Code: self.used_attrs[:] = attributes
      File: OWItemModels.py, line 199 in __setslice__
      Code: self.__delslice__(i, j)
        File: OWItemModels.py, line 189 in __delslice__
        Code: self.beginRemoveRows(QModelIndex(), i, j - 1)
          TypeError: QAbstractListModel.beginRemoveRows(QModelIndex, int, int): argument 3 has unexpected type 'long' 

The error occurs to every operation related to the "Select Attributes" module. Explored other modules on the Canvas, no same problem found so far.

  • Hardware:
    • Lenovo ThinkCenter
    • Intel i7-2600
    • 16G mem
  • Software:
    • Windows 7 64bit
    • Python 2.7.3 64bit
    • Orange 2.5a4 was installed from "Unofficial Windows Binaries for Python Extension Packages ( http://www.lfd.uci.edu/~gohlke/pythonlibs/)". I cannot use the official download because I need 64bit Python and other related Python modules.
    • Numpy: numpy-MKL-1.6.2.win-amd64-py2.7
    • PyQt: PyQt-Py2.7-x64-gpl-4.8.6-1
    • PyQwt: PyQwt-5.2.0-py2.7-x64
    • PythonWin: pywin32-217.win-amd64-py2.7

I like Orange, which features and usability are very impressive!

  • It will be great if Orange can provide official 64bit Windows build (full packages with dependent libraries).
  • If the above is not possible due to license issue, it will be also good to provide standalone installation package on Windows, e.g. like the Orange Mac OSX dmg package, so it will install Python and other libraries in a separated location and not register Python in the system, which causing multiple Python in the system.
  • Where can I find a list of all Orange dependencies?

#1225 Only one decimal after feature constructor widget canvas bug 08/14/12

Attributes generated by the feature constructor widget are shown and output with only 1 decimal, which can be highly insufficient in many cases. The numbers are kept internally with higher precision, but there is no easy way in the canvas to override the formatting for display and file output.


#1285 Installer doeas not work - manual installation yields QT4 incompatibility library bug 02/15/13

The installationprocedure of Orange is ever since not working very well! Right now it requires manual installation of all components. Would you please mind to post a full list of requirements of _working_ software libraries of numpy,scypy etc.. Obviously the current QT4 version does not install and is not compatible. the plugins do not load all properly either.

Please TEST your software before relasing- otherwise it is a lot of wasted time to try to setup a running installation.

Greetings Lareo


#16 Load File: splosni bralnik library Future wish 05/02/07

Zanimivo bi bilo imeti branje iz poljubnega tekstovnega filea, kjer uporabnik sam dolo?i delimiterje ipd. Podobno kot v Excelu in Knimeu


anze (2 matches)

Ticket Summary Component Milestone Type Created
Description
#994 Fink install on Mac OS X Lion other 2.6 bug 10/28/11

Install script trunk/install-scripts/mac/fink-selfupdate-orange.sh does not work on Mac OS X Lion.


#865 Check how setup.py works other 2.6 check 07/23/11

Check how setup.py works on different platforms. Can we use it everywhere to install Orange and generate packages for Fink/Debian and bundle? Currently we are using there custom scripts.


blaz (6 matches)

Ticket Summary Component Milestone Type Created
Description
#867 Broken link in tutorial other Future bug 07/23/11

When following the "Beginning with orange" tutorial, the link to "assoc.py is broken.


#772 orngCI other Next 2.x task 05/03/11

#775 orngInteract, orngInteractions other Next 2.x task 05/03/11

#872 Follow data mining poll at KDnuggets other task 07/29/11

 KDnuggets has a  yearly Data Mining / Analytic Tools Used poll. It starts somewhere in the May. We should follow it and make sure we rank food.


#881 Check and maybe apply for Google Faculty Research Awards program other task 08/03/11

Google provides  university awards for research in fields in which people working on Orange also do research. So we could check and maybe try to apply for some funding and research collaboration with Google.

Deadline is April 15 2012.


#1179 Widget highlighting canvas 2.6 wish 04/19/12

Highlighting the compatible widgets to a particular widget when the mouse hovers over that widget in the schema, would be a fascinating and quite helpful experience in orange.

Hey , here's a suitable design to the patch : add 2 more line to widget popup menu : ( orangeCanvbas.pyc:line 497)

self.widgetPopup.addAction("Common signal inputs",self.input_types) self.widgetPopup.addAction("Common signaloutputs",self.output_types)

#now define the two methods :(line 523)

def input_types(self):

""" the code follows here """ return

def output_types(self):

""" the code follows here """ return

""" On right clicking the widget , the options to find common input/output widgets comes in the pop up menu""" """ The result of clicking this ,

will either highlight the widgets or popup a menu containing these widgets """


crt (1 match)

Ticket Summary Component Milestone Type Created
Description
#710 Change in orngText.py, Text addon canvas Future bug 03/25/11

I think there is a missing check in TextClassifier in line 1646: "if self.p_cond[c].has_key(w):".

Later I got snapshot of orange orange-source-snapshot-2010-06-30.zip and addons26.zip (attached). In that zip orngText has that check.


janez (4 matches)

Ticket Summary Component Milestone Type Created
Description
#1185 pick_class #RNGE bug library Future bug 05/08/12

Sometimes when working with multi-target data and using the pick_class function the remaining classes get corrupted with values outside their range, represented by #RNGE.

This is a sample of code that reproduces the error. In the first one the error is minor and only produces two #RNGEs, the second example that also changes the domain to include the picked class into the features shows the escalation of the problem.

d = Orange.data.Table('bridges.v2.nm') for i in [3,2,1,0]:

i = random.randrange(0,3) print d.domain.class_vars[i] d.pick_class(d.domain.class_vars[i]) for x in d:

print x

d = Orange.data.Table('bridges.v2.nm') for i in [3,2,1,0]:

print d.domain.class_vars[i] d.pick_class(d.domain.class_vars[i]) for x in d:

print x

d.change_domain(Orange.data.Domain(d.domain, False, \

class_vars=d.domain.class_vars))


#1230 Table.save() method missing from the documentation documentation bug 09/04/12

Table.save() method is missing from the documentation of Orange.data.table/


#618 Kaj se manjka v oknu Report canvas Future task 07/04/10

Gumb Clear in Print Tipka Delete, ko si v listboxu


#958 Replace allVariables with a multimap library 3.0 task 09/12/11

For variables to match, they must have the same varType and name. Since all variables are, in principle, constructed through TVariable::make, lookups take O(n2) when, say, loading a data file. This may be quite significant with 10000 variables.

We can replace allVariables, which is currently a list, with a multimap indexed by varType and name.

Alternatively (and perhaps better), we can have separate multimaps for each varType; multimaps key would then be a name.


MarinkaZitnik (1 match)

Ticket Summary Component Milestone Type Created
Description
#1284 NMF not working library bug 02/15/13

the NMF library does not install. Obvisously the dependency to NIMFA is missing. Can you fix thisn please.


marko (7 matches)

Ticket Summary Component Milestone Type Created
Description
#829 gsea orng_modules Future bug 06/27/11

Gsea widget: no warning if there are is no gene attribute or group attribute


#859 Mushroom dataset je falsh. documentation 2.6 bug 07/08/11

V zbirki datasetov je "mushroom.tab" pokvecen: target class je nastavljen na zadnji atribut, namesto na prvi, ki manjka - imena atributov so temu primero zamaknjena, pri cemer je zadnje ime sproducirano iz predzadnjega...skratka, za popravit je. Zadeva je precej ocitna, saj daje CA okrog 50% namesto okrog 99%, tako da kake hujse skode od tega (upam ;) ) doslej ni bilo.


#1001 debian packege: networkx to recommends other 2.6 bug 11/02/11

Please move networkx from dependencies to recommends.


#1032 netexplorer: zoom (when you click the zoom icon) does not work canvas Future bug 12/14/11

Zomming with control + mouse works, but the icon click does nothing. Also applies to Scatterplot (Qt) and possibly other Qt widgets.


#830 gsea: select whole columns orng_modules Future task 06/27/11

If there are no group specification, should we allow users to make groups of phenotypes themselves?


#1177 Orange Schema canvas wish 04/13/12

The current orange schema is far too sensible to dragging . Once all widgets are removed from the schema the schema does not come back to its original size. Also , it would nice to limit and autoresize the schema according to the placement of widgets .

The required patch :

go to => Orange/Orange/OrangeCanvas/orngView.py import time module and add to (mouseMoveEvent)line 279: time.sleep(0.01)

This will reduce the sensibility of dragging.


#1229 TreeClassifier to_networkx_tree() function library 2.6 wish 08/27/12

The TreeClassifier has a to_string() function that prints the decision tree in text format. Even though this function can be customized via formatting arguments, the output is still unstructured and the tree cannot be easily traversed and inspected.

Below, I propose to add a new function called to_netwrokx_tree() that converts the internal Orange tree structure to a Networkx directed graph, where internal nodes are features and leaves are decisions. Internal node labels are feature names and edges' labels are feature values on which the tree splits. The leaves' labels are the decisions along with their probabilities.

def to_networkx_tree(pnode, tree=None, level=0, local_index=0):
    '''Returns a networkx tree of the orange classification tree'''

    # create a new directed graph if this is the first call
    if not tree:
        tree = networkx.DiGraph()

    # reached null nodes
    if not pnode:
        return tree

    # if the node has children (not leaves), traverse
    if pnode.branch_selector:

        pnode_desc = pnode.branch_selector.class_var.name

        # create a root node only on first call
        if level == 0:
            pnode_id = str(pnode_desc) + '_%i' % len(tree)
            tree.add_node(pnode_id, shape='none', label=str(pnode_desc))
        else:
            pnode_id = str(pnode_desc) + '_%i' % (len(tree) - 1)

        # iterate through children and update branch
        for i in range(len(pnode.branches)):
            cnode = pnode.branches[i]

            # if the child is not a null node, update the tree
            if cnode:

                # if the child is a parent, update a branch
                if cnode.branch_selector:
                    # add child node
                    cnode_desc = cnode.branch_selector.class_var.name
                    cnode_id = str(cnode_desc) + '_%i' % len(tree)
                    tree.add_node(cnode_id, shape='none', label=str(cnode_desc))

                    # add edge between parent and child
                    edge_desc = str(pnode.branch_descriptions[i])
                    tree.add_edge(pnode_id, cnode_id, label=edge_desc)

                    # recursively update this branch of the tree
                    tree = get_tree(cnode, tree, level+1, i)

                # if the child is a leaf, then add class info
                else:
                    leaf_dist = cnode.node_classifier.default_distribution
                    leaf_prob = leaf_dist[int(cnode.node_classifier.default_val)]
                    leaf_class = cnode.node_classifier.default_value
                    leaf_id = str(leaf_class) + '_%i' % len(tree)
                    leaf_label = str(leaf_class) + ' (%.2f%%)' % (leaf_prob*100)
                    tree.add_node(leaf_id, shape='box', label=leaf_label)

                    # add edge between parent and child
                    edge_desc = str(pnode.branch_descriptions[i])
                    tree.add_edge(pnode_id, leaf_id, label=edge_desc)

            # null node reached
            else:
                pass

        # once done with children for this parent, return tree
        return tree

    # if it's a leaf and it's a root, update the node with class info
    else:
        if level == 0:
            leaf_dist = pnode.node_classifier.default_distribution
            leaf_prob = leaf_dist[int(pnode.node_classifier.default_val)]
            leaf_class = pnode.node_classifier.default_value
            leaf_id = str(leaf_class) + '_%i' % len(tree)
            leaf_label = str(leaf_class) + ' (%.2f%%)' % (leaf_prob*100)
            tree.add_node(leaf_id, shape='box', label=leaf_label)
        return tree

Here's how the code could be used and tested:

import orange, Orange
import networkx
import networkx.algorithms as nx_algorithms

# use voting dataset to train a decision tree
data = orange.ExampleTable('voting')
tree_classifier = orange.TreeLearner(data)

# convert the orange tree to networkx tree
networkx_tree = to_networkx_tree(tree_classifier.tree)

# assert that both trees have the same order, have one connected components, and is a DAG 
assert len(networkx_tree) == tree_classifier.tree.tree_size()
assert nx_algo.number_connected_components(networkx_tree.to_undirected()) == 1
assert nx_algo.is_directed_acyclic_graph(networkx_tree) == True

# convert the tree to AGraph and save it as a Graphviz DOT file
agraph = networkx.to_agraph(networkx_tree)
agraph.write('networkx_tree.dot')

miha (8 matches)

Ticket Summary Component Milestone Type Created
Description
#557 Podpora za lokacijo ikonic widgetov drugje kot v site-packages canvas 2.6 bug 02/21/10

Podpora za lokacijo ikonic widgetov drugje kot v site-packages, saj ni po Linux standardu, da bi te bile med Python kodo:

According to the Filesystem Hierarchy Standard, architecture-independent files need to be placed within /usr/share instead.

Lahko bi se naredilo podobno kot smo naredili za dokumentacijo, da se ob izgradnji paketa v orngConfiguration.py zapiše recimo iconsPath spremenljivka. (Trenutno imamo tako datasetsPath.)


#980 We should probably depend on python-qt4-gl on Debiana and Ubuntu systems other Future bug 10/07/11

VisualizeQt widgets don't work on Ubuntu 11.10, unless the python-qt4-gl package is installed. I believe this is also necessary (and exists) on older Ubuntu and Debian systems, but I haven't checked it. We should probably add a dependency, because there was already a  complaint on the forum because of this.


#1193 Sesutje ob uporabi net file-a library bug 06/05/12

aplikacija se pa je sesula ko sem v kliknil na Net File, al pa ce v netfile-u ko ze imam nalozen net file hocem izbrati drugega (tud ce je tisti, ki pride skup z orangom)

crashlog v prilozeni datoteki


#783 orngMosaic other Next 2.x task 05/03/11

#842 Start using orangerc.cfg instead of orngConfiguration.py other 2.6 task 07/01/11

Start using orangerc.cfg instead of orngConfiguration.py in building packages (Fink and Debian) to configure where example datasets (and icons) are.


#925 Build orangeqt in VM library 2.6 task 08/22/11

Check if orangeqt compiles in VMs and if it is included in Mac OS X package.


#1027 Add Python Qt OpenQL to requirements. other Future task 12/09/11

#1049 download links that are stable other Future task 12/23/11

Our download links include dates and revisions, like  http://orange.biolab.si/download/orange-source-snapshot-2011-12-21.zip.

This is very good, but we also need some stable download links, that would always return the newest version. Something like  http://orange.biolab.si/download/orange-source-snapshot.zip.


Noughmad (1 match)

Ticket Summary Component Milestone Type Created
Description
#1047 orangeqt - make installation possible with setup.py other 2.6 task 12/23/11

We are trying to make orange installable with setup.py, but as for now it does not support orangeqt.

Ales hinted, that we will probably need to make a new setup.py for orangeqt.


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