biolab / orange3-network

🍊 🕸 Network analysis add-on for Orange data mining suite.

Orange3 Network

Orange3-Network is an add-on for Orange data mining software package. It provides network visualization and network analysis tools.

Documentation is found at: http://orange3-network.rtfd.io

Installation

Install from Orange add-on installer through Options - Add-ons.

To install the add-on with pip use

pip install orange3-network

To install the add-on from source, run

python setup.py install

To register this add-on with Orange, but keep the code in the development directory (do not copy it to Python's site-packages directory), run

python setup.py develop

You can also run

pip install -e .

which is sometimes preferable as you can pip uninstall packages later.

Anaconda

If using Anaconda Python distribution, simply run

pip install orange3-network

Compiling on Windows

If you are not using Anaconda distribution, but building the add-on directly from the source code, Windows users need to compile the code. Download Microsoft Visual Studio compiler and run the command

python setup.py build_ext -i --compiler=msvc install

Usage

After the installation, the widgets from this add-on are registered with Orange. To run Orange from the terminal, use

orange-canvas

or

python3 -m Orange.canvas

New widgets are in the toolbox bar under Networks section.

orange3-network's Issues

Error in NetworkExplorer

Network version 1.4.2

Orange version 3.17.0

Expected behavior Use Netwkork Explorer

Actual behavior

Steps to reproduce the behavior I use clicked "Network Explorer" and the error pops up

Additional info (worksheets, data, screenshots, ...)

I'm a newbie in Orange3

Network File: prettify the I/O status bar

Status bar reports the same thing twice. Avoid this for clarity.
I'd go with 1239 nodes, 3963 edges, undirected network.

Wrong format of edges in Network Explorer

This report came from Sentry.

ValueError:  row, column, and data arrays must be 1-D
(2 additional frame(s) were not displayed)
...
  Module "orangecontrib.network.widgets.OWNxExplorer", in set_actual_edges
    self.edges = sp.coo_matrix((data, (row, col)))
  Module "scipy.sparse.coo", in __init__
    self._check()
  Module "scipy.sparse.coo", in _check
    if self.nnz > 0:
  Module "scipy.sparse.base", in nnz
    return self.getnnz()
  Module "scipy.sparse.coo", in getnnz
    raise ValueError('row, column, and data arrays must be 1-D')

The code that crashed is:

                edges = network.edges(data='weight')
                ...
                row, col, data = zip(*edges)
                if all(w is None for w in data):
                    data = np.ones((len(data), ), dtype=float)
                self.edges = sp.coo_matrix((data, (row, col)))

Hence network.edges (from networkx) returns something strange. @ajdapretnar what were you actually doing?

Network Analysis: additional settings

Network version

1.3.0 and older versions

Expected behavior

This below may be added:

"""
TODO: add
    average-degree_connectivity
    is_bipartite
    is_chordal
    katz_centrality
    katz_centrality_numpy
    communicability
    communicability_exp
    communicability_centrality
    communicability_centrality_exp
    communicability_betweenness_centrality
    average_node_connectivity
    is_directed_acyclic_graph
    center
    ??
"""


# additional attr needed
# ("attribute_assortativity_coefficient", False, "Attribute assortativity coefficient", GRAPHLEVEL, nx.attribute_assortativity_coefficient),
# ("numeric_assortativity_coefficient", False, "Numeric assortativity coefficient", GRAPHLEVEL, nx.numeric_assortativity_coefficient),

# TODO: input parameters
# ("max_flow", False, "Maximum flow", GRAPHLEVEL, nx.max_flow),
# ("min_cut", False, "Minimum cut", GRAPHLEVEL, nx.min_cut),
# ("ford_fulkerson", False, "Maximum single-commodity flow (Ford-Fulkerson)", GRAPHLEVEL, nx.ford_fulkerson),
# ("min_cost_flow_cost", False, "min_cost_flow_cost", GRAPHLEVEL, nx.min_cost_flow_cost),
# returns dict of dict
# ("shortest_path_length", False, "Shortest path length", GRAPHLEVEL, nx.shortest_path_length),

Network Explorer terribly slow

NE terribly slow on a network of 44 nodes and 10 edges (from grimm-tales-selected.tab - BoW - Network Distances).

Network from Distances: buggy visualization

Network version

1.3.2.

Orange version

3.12.dev

Expected behavior

Network from Distances displays plot on a white background.

Actual behavior

Network from Distances displays plot on a black background.

Steps to reproduce the behavior

Connect NfromD to any Distance Matrix.

Additional info (worksheets, data, screenshots, ...)

[BUG/ENH] No support for directed graphs

Network add-on doesn't really support directed graphs. When directed networks are loaded, they get turned into an undirected graph. Moreover, some widgets provide 'support' for directed graphs (e.g. Network Analysis), but the computation always results in an error since the networks gets turned into an undirected graph.

Either introduce support for directed graphs (arrows in Network Explorer, computations in Network Analysis) or remove redundant methods for directed graphs.

Add on does not install from within Orange

Network version

1.4.1

Orange version

3.18 on Mac 10.13.5

Expected behavior

Add-on installed when ticked and installed from menu

Actual behavior

Failure notice: "Command failed: python python -m pip install Orange3-Network exited with non zero status"

Steps to reproduce the behavior

Additional info (worksheets, data, screenshots, ...)

ollecting Orange3-Network
Using cached https://files.pythonhosted.org/packages/e9/86/78093ab58194619133289d1ffadc13a02ee3a61c479913b88fe8a7c2fa99/Orange3-Network-1.4.1.tar.gz
Requirement already satisfied: networkx>=2.0 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from Orange3-Network)
Requirement already satisfied: pyqtgraph>=0.9.10 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from Orange3-Network)
Requirement already satisfied: numpy>=1.8.0 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from Orange3-Network)
Requirement already satisfied: Orange3>=3.3.9 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from Orange3-Network)
Requirement already satisfied: decorator>=4.3.0 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from networkx>=2.0->Orange3-Network)
Requirement already satisfied: AnyQt>=0.0.8 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: bottleneck>=1.0.0 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: chardet>=3.0.2 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: docutils in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: fastTSNE>=0.2.12 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: joblib>=0.9.4 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: keyring in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: keyrings.alt in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: matplotlib>=2.0.0 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: pip>=9.0 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: python-louvain in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: requests in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: scikit-learn>=0.20.0 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: scipy>=0.16.1 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: serverfiles in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: setuptools>=36.3 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: xlrd>=0.9.2 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: numba>=0.38.1 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from fastTSNE>=0.2.12->Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: six in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from keyrings.alt->Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from matplotlib>=2.0.0->Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: python-dateutil>=2.1 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from matplotlib>=2.0.0->Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: kiwisolver>=1.0.1 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from matplotlib>=2.0.0->Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: cycler>=0.10 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from matplotlib>=2.0.0->Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: certifi>=2017.4.17 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from requests->Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: urllib3<1.25,>=1.21.1 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from requests->Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: idna<2.8,>=2.5 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from requests->Orange3>=3.3.9->Orange3-Network)
Requirement already satisfied: llvmlite>=0.25.0dev0 in /Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from numba>=0.38.1->fastTSNE>=0.2.12->Orange3>=3.3.9->Orange3-Network)
Building wheels for collected packages: Orange3-Network
Running setup.py bdist_wheel for Orange3-Network: started
Running setup.py bdist_wheel for Orange3-Network: finished with status 'error'
Complete output from command /Applications/Orange3.app/Contents/MacOS/PythonApp -u -c "import setuptools, tokenize;file='/private/var/folders/19/r1rztl3d0yd03qc37zpnjpg40000gn/T/pip-build-5vgmwts6/Orange3-Network/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" bdist_wheel -d /var/folders/19/r1rztl3d0yd03qc37zpnjpg40000gn/T/tmp7upzq8h5pip-wheel- --python-tag cp36:
running bdist_wheel
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "orangecontrib.network._fr_layout" sources
build_src: building npy-pkg config files
running build_py
creating build
creating build/lib.macosx-10.6-intel-3.6
creating build/lib.macosx-10.6-intel-3.6/orangecontrib
copying orangecontrib/init.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib
creating build/lib.macosx-10.6-intel-3.6/orangecontrib/network
copying orangecontrib/network/init.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network
copying orangecontrib/network/community.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network
copying orangecontrib/network/network.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network
copying orangecontrib/network/readwrite.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network
copying orangecontrib/network/setup.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network
creating build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets
copying orangecontrib/network/widgets/init.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets
copying orangecontrib/network/widgets/graphview.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets
copying orangecontrib/network/widgets/OWNxAnalysis.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets
copying orangecontrib/network/widgets/OWNxClustering.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets
copying orangecontrib/network/widgets/OWNxExplorer.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets
copying orangecontrib/network/widgets/OWNxFile.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets
copying orangecontrib/network/widgets/OWNxFromDistances.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets
copying orangecontrib/network/widgets/OWNxGenerator.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets
copying orangecontrib/network/widgets/OWNxSave.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets
creating build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/airtraffic.net -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/airtraffic_items.tab -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/dicty_publication.net -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/dicty_publication_edges.tab -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/dicty_publication_items.tab -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/lastfm.net -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/lastfm.tab -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/lastfm_all.tab -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/lastfm_tags.tab -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/leu_by_genesets.net -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/leu_by_genesets_items.tab -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/leu_by_pmid.net -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/leu_by_pmid_items.tab -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/leu_huttenhower_a.net -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/leu_huttenhower_a_items.tab -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/makeNetworkList.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/mips_c2_cp_leu.net -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/mips_c2_cp_leu_items.tab -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/network_info.tab -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
creating build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/button_autoscale.png -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/button_rect.png -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/Category-Network.svg -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/Dlg_clear.png -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/Dlg_HideSelection.png -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/Dlg_Mark2Sel.png -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/Dlg_Sel2Mark.png -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/Dlg_SelisMark.png -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/Dlg_UnselectedNodes.png -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/NetworkAnalysis.svg -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/NetworkClustering.svg -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/NetworkExplorer.svg -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/NetworkFile.svg -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/NetworkFromDistances.svg -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/NetworkGenerator.svg -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize UnixCCompiler

['/usr/bin/clang', '-fno-strict-aliasing', '-Wsign-compare', '-fno-common', '-dynamic', '-DNDEBUG', '-g', '-fwrapv', '-O3', '-Wall', '-Wstrict-prototypes', '-arch', 'i386', '-arch', 'x86_64', '-g']

customize UnixCCompiler using build_ext
building 'orangecontrib.network._fr_layout' extension
compiling C++ sources
C compiler: /usr/bin/clang++ -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch i386 -arch x86_64 -g

creating build/temp.macosx-10.6-intel-3.6/orangecontrib
creating build/temp.macosx-10.6-intel-3.6/orangecontrib/network
compile options: '-I/Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/numpy/core/include -I/Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/numpy/core/include -I/Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/include/python3.6m -c'
clang++: orangecontrib/network/_fr_layout.cpp
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: Command "/usr/bin/clang++ -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch i386 -arch x86_64 -g -I/Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/numpy/core/include -I/Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/numpy/core/include -I/Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/include/python3.6m -c orangecontrib/network/_fr_layout.cpp -o build/temp.macosx-10.6-intel-3.6/orangecontrib/network/_fr_layout.o -MMD -MF build/temp.macosx-10.6-intel-3.6/orangecontrib/network/_fr_layout.o.d" failed with exit status 1

---

Failed building wheel for Orange3-Network
Running setup.py clean for Orange3-Network
Failed to build Orange3-Network
Installing collected packages: Orange3-Network
Running setup.py install for Orange3-Network: started
Running setup.py install for Orange3-Network: finished with status 'error'
Complete output from command /Applications/Orange3.app/Contents/MacOS/PythonApp -u -c "import setuptools, tokenize;file='/private/var/folders/19/r1rztl3d0yd03qc37zpnjpg40000gn/T/pip-build-5vgmwts6/Orange3-Network/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /var/folders/19/r1rztl3d0yd03qc37zpnjpg40000gn/T/pip-lecl0oaz-record/install-record.txt --single-version-externally-managed --compile:
running install
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "orangecontrib.network._fr_layout" sources
build_src: building npy-pkg config files
running build_py
creating build
creating build/lib.macosx-10.6-intel-3.6
creating build/lib.macosx-10.6-intel-3.6/orangecontrib
copying orangecontrib/init.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib
creating build/lib.macosx-10.6-intel-3.6/orangecontrib/network
copying orangecontrib/network/init.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network
copying orangecontrib/network/community.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network
copying orangecontrib/network/network.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network
copying orangecontrib/network/readwrite.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network
copying orangecontrib/network/setup.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network
creating build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets
copying orangecontrib/network/widgets/init.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets
copying orangecontrib/network/widgets/graphview.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets
copying orangecontrib/network/widgets/OWNxAnalysis.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets
copying orangecontrib/network/widgets/OWNxClustering.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets
copying orangecontrib/network/widgets/OWNxExplorer.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets
copying orangecontrib/network/widgets/OWNxFile.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets
copying orangecontrib/network/widgets/OWNxFromDistances.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets
copying orangecontrib/network/widgets/OWNxGenerator.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets
copying orangecontrib/network/widgets/OWNxSave.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets
creating build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/airtraffic.net -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/airtraffic_items.tab -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/dicty_publication.net -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/dicty_publication_edges.tab -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/dicty_publication_items.tab -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/lastfm.net -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/lastfm.tab -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/lastfm_all.tab -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/lastfm_tags.tab -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/leu_by_genesets.net -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/leu_by_genesets_items.tab -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/leu_by_pmid.net -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/leu_by_pmid_items.tab -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/leu_huttenhower_a.net -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/leu_huttenhower_a_items.tab -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/makeNetworkList.py -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/mips_c2_cp_leu.net -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/mips_c2_cp_leu_items.tab -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
copying orangecontrib/network/networks/network_info.tab -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/networks
creating build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/button_autoscale.png -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/button_rect.png -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/Category-Network.svg -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/Dlg_clear.png -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/Dlg_HideSelection.png -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/Dlg_Mark2Sel.png -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/Dlg_Sel2Mark.png -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/Dlg_SelisMark.png -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/Dlg_UnselectedNodes.png -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/NetworkAnalysis.svg -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/NetworkClustering.svg -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/NetworkExplorer.svg -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/NetworkFile.svg -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/NetworkFromDistances.svg -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
copying orangecontrib/network/widgets/icons/NetworkGenerator.svg -> build/lib.macosx-10.6-intel-3.6/orangecontrib/network/widgets/icons
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize UnixCCompiler
#### ['/usr/bin/clang', '-fno-strict-aliasing', '-Wsign-compare', '-fno-common', '-dynamic', '-DNDEBUG', '-g', '-fwrapv', '-O3', '-Wall', '-Wstrict-prototypes', '-arch', 'i386', '-arch', 'x86_64', '-g'] #######
customize UnixCCompiler using build_ext
building 'orangecontrib.network._fr_layout' extension
compiling C++ sources
C compiler: /usr/bin/clang++ -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch i386 -arch x86_64 -g

creating build/temp.macosx-10.6-intel-3.6/orangecontrib
creating build/temp.macosx-10.6-intel-3.6/orangecontrib/network
compile options: '-I/Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/numpy/core/include -I/Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/numpy/core/include -I/Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/include/python3.6m -c'
clang++: orangecontrib/network/_fr_layout.cpp
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: Command "/usr/bin/clang++ -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch i386 -arch x86_64 -g -I/Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/numpy/core/include -I/Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/numpy/core/include -I/Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.6/include/python3.6m -c orangecontrib/network/_fr_layout.cpp -o build/temp.macosx-10.6-intel-3.6/orangecontrib/network/_fr_layout.o -MMD -MF build/temp.macosx-10.6-intel-3.6/orangecontrib/network/_fr_layout.o.d" failed with exit status 1

----------------------------------------

Command "/Applications/Orange3.app/Contents/MacOS/PythonApp -u -c "import setuptools, tokenize;file='/private/var/folders/19/r1rztl3d0yd03qc37zpnjpg40000gn/T/pip-build-5vgmwts6/Orange3-Network/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /var/folders/19/r1rztl3d0yd03qc37zpnjpg40000gn/T/pip-lecl0oaz-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/19/r1rztl3d0yd03qc37zpnjpg40000gn/T/pip-build-5vgmwts6/Orange3-Network/
You are using pip version 9.0.1, however version 18.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

Network from Distances crashes if the matrix is empty

Here:

IndexError:  list index out of range
  Module "Orange.canvas.scheme.widgetsscheme", in process_signals_for_widget

    handler(*args)
  Module "orangecontrib.network.widgets.OWNxFromDistances", in set_matrix

    low, upp = values[0], values[-1]

Importing graphs from networkx .net gives errors

Network version

1.4.2

Orange version

3.24

When importing graphs exported from Netwrokx 2.3 (python3) as .net an error occasionally occurs (in canvas there is no additional information, in Python it says that an index is out of bounds). This happens after pruning the graph (the saved nodes' labels in first row of .net are not from 1 to N). If graph is exported as .gml (nodes' indices are always starting with 0 and progressing without gaps) and then re-imported in python and exported as .net the error goes away. The error seems to be happening in vertices parsing function.

Example files:
AX4_prunedSubNet110.zip

setup.py should fail if Python < 3.4

I tired both on OS X and CentOS to do the following commands:

$ pip install orange3-network
$ ipython -c "import Orange"

Same result both times:

/home/xapple/.local/lib/python2.7/site-packages/Orange/__init__.py:159: UserWarning: Importing add-on 'network' failed: cannot import name DiscreteVariable
  _import_addons()

Error while trying to replicate clustering example

Error while trying to replicate https://orange3-network.readthedocs.io/en/latest/widgets/networkclustering.html

Orange version

3.24, Network 1.4.2

Revise outdated documentation

I tired both on OS X and CentOS to do the following commands:

$ pip install orange-network
$ ipython -c "import Orange"

Same result both times:

/home/xapple/.local/lib/python2.7/site-packages/Orange/__init__.py:159: UserWarning: An exception occurred during the loading of 'network':
 AttributeError("'NoneType' object has no attribute 'replace'",)
   _import_addons()

Enable more edges+nodes on Netwrok Explorer

Could be Netwrok Explorer changed to enable display of more nodes+edges.
Many nodes+edges may result in crowded graph, but the display may still help in decisions about pruning (eg. display of intermediate steps).
The time it takes to lay out graph is reasonable even on larger graphs (much better than Cytsocape). However, it is necesary to click on re-layout multiple times - could a box be added where you could specify to perform multiple re-layouts with one click?
Example of a graph with 8232 nodes and 46618 edges - the number of edges may rise due to the use of multigraphs, despite them not being completely crowded (although I am not sure if they are even displayed).

Network explorer component selection

A double click on a node sometimes fails to select the connected component. E.g. in network leu_by_genesets the components {IDS, GNS} and {BLVRB, HMOX1, BLVRA} don't work, while most of the others do.

A triple click on a node, where selection works, causes an error.

Network Clustering doesn't cluster correctly

Network version

1.4.2

Orange version

3.23.dev

Expected behavior

Network Clustering clusters the data correctly, i.e. reported number of clusters found and the actual number of clusters in the data are the same.

Actual behavior

Regardless of the method chosen, the clustering is always the same. It doesn't match the reported number of clusters (widget says 162 clusters found, data reports 93). Also, the clustering doesn't change regardless of the method chosen.

Steps to reproduce the behavior

Network File (lastfm) - Network Clustering. Change the method a couple of times and observe the output. Cluster values are not correct.

Additional info (worksheets, data, screenshots, ...)

Network from Distances crashes if the graph has no edges

ValueError:  max() arg is an empty sequence
  Module "Orange.widgets.gui", in __call__

    self.func(**kwds)
  Module "orangecontrib.network.widgets.OWNxFromDistances", in generateGraph

    max_weight = max(d for u, v, d in edge_list)

Network explorer should allow selecting a connected component

... also as adding to a selection or as another group.

[ENH] Network Explorer improvements

1.) Network Explorer should display legend if coloring by attribute.
2.) Network Explorer should allow saving images (I thought this was working already??) and Report (while at it).
3.) Widget crashes when coloring by sparse attributes. NaN should probably be white and/or add warning.
4.) Widget's output should be compatible with Word Enrichment (wishlist, but so great for text analysis!). @nikicc

Prevent showing too many labels

When the network would show more that 2000 labels (nodes or edge weights), don't do it but display a warning instead.

Network explorer keeps selection after data is removed

The problem manifests like this:

TypeError:  object of type 'NoneType' has no len()
(7 additional frame(s) were not displayed)
...
  Module "Orange.widgets.gui", in unconditional_commit
    do_commit()
  Module "Orange.widgets.gui", in do_commit
    commit()
  Module "Orange.widgets.visualize.utils.widget", in commit
    self.send_data()
  Module "orangecontrib.network.widgets.OWNxExplorer", in send_data
    super().send_data()
  Module "Orange.widgets.visualize.utils.widget", in send_data
    group_sel = np.zeros(len(data), dtype=int)

The trace comes from sentry, hence no instructions to reproduce.

OWDataProjectionWidget expects that if graph.selection is not None, then self._get_projection_data() doesn't return None. Network explorer apparently violates this.

Options add-on not installing Network

Network installation fails.
Command "python setup.py egg_info" failed with error code 1 in C:\Users\numai\AppData\Local\Temp\pip-install-10b6qjwi\orange-network\

preceded by:
File "C:\Users\james\AppData\Local\Temp\pip-install-10b6qjwi\orange-network\distribute_setup.py", line 193, in download_setuptools
src = urlopen(url)
File "C:\Apps\nac\lib\urllib\request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "C:\Apps\nac\lib\urllib\request.py", line 531, in open
response = meth(req, response)
File "C:\Apps\nac\lib\urllib\request.py", line 641, in http_response
'http', request, response, code, msg, hdrs)
File "C:\Apps\nac\lib\urllib\request.py", line 569, in error
return self._call_chain(*args)
File "C:\Apps\nac\lib\urllib\request.py", line 503, in _call_chain
result = func(*args)
File "C:\Apps\nac\lib\urllib\request.py", line 649, in http_error_default
raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 403: SSL is required

Orange version

Single mode doesn't handle missing values

This happens when data is converted to int to be used as indices: column = data.get_column_view(self.variable)[0].astype(int). A mask has to be applied first.

[ENH] Save Network

Idea

Implement support for saving network files. As far as I understand, networks are currently NetworkX objects that cannot be stored simply. How could we go about this? I think this should be implemented in Save Data in core Orange.

Network Explorer: warning on too many labels

Network version

1.4.3-dev

Expected behavior

Labels appear in Network Explorer.

Actual behavior

Widget reports an error.
AttributeError: 'Warning' object has no attribute 'too_many_labels'

Steps to reproduce the behavior

Network File (last.fm) - Network Explorer. Try to set the label.

[Question] Is it possible to create network from adjacency matrix?

Hi, maybe such feature already exists within the package and i just haven't find it yet.
For instance i have such table (adjacency matrix), and would like to visualise it into the network.
Such table is not hard to create with Cooccurrence widget in Textable package, which also allows to transform data to Orange table, but is there away to proceed further from this?

Network Explorer: fails on conditional selection.

Network version

1.4.3-dev

Expected behavior

Labeling in Network Explorer works.

Actual behavior

Network Explorer reports an error:
AttributeError: 'UndirectedEdges' object has no attribute 'data'

Steps to reproduce the behavior

Network File (last.fm) - Network Explorer. Use 'Mark nodes reachable from selected'.

Single mode bipartiteness check

The Single mode widget crashes on non-bipartite networks.

It should check and offer only attributes that result in bipartite networks.

Error when connecting Network File to Explorer

Data is successfully loaded, but an error appears when trying to connect it to the Network Explorer widget. Error can be ignored, and the graph is plotted, but is very persistent even after.

---

Exception:
IndexError: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices
Module:
Orange.data.table:452
Widget Name:
Network Explorer
Widget Module:
orangecontrib.network.widgets.OWNxExplorer:237
Widget Scheme:
C:\Users\vodopma2\AppData\Local\Temp\ows-kwpl4ho6.ows.xml
Version:
3.8.0
Environment:
Python 3.6.3 on Windows 7 6.1.7601 x86
Installed Packages:
AnyQt==0.0.8, Bottleneck==1.2.1, CommonMark==0.7.4, Orange3-Network==1.3.0, Orange3==3.8.0, PySocks==1.6.7, asn1crypto==0.23.0, certifi==2017.11.5, cffi==1.11.2, chardet==3.0.4, cryptography==2.1.4, decorator==4.1.2, dill==0.2.7.1, docutils==0.14, future==0.16.0, idna==2.6, joblib==0.11, keyring==9.0, keyrings.alt==2.3, networkx==2.0, numpy==1.13.3, pip==9.0.1, pyOpenSSL==17.5.0, pycparser==2.18, pyqtgraph==0.10.0, pyreadline==2.1, pywin32==221, requests==2.18.4, scikit-learn==0.19.1, scipy==0.19.1, serverfiles==0.2.1, setuptools==36.5.0.post20170922, six==1.11.0, urllib3==1.22, wheel==0.30.0, win-inet-pton==1.0.1, wincertstore==0.2, xlrd==1.1.0
Machine ID:
118796715501792
Stack Trace:
Traceback (most recent call last):
  File "C:\Users\vodopma2\AppData\Local\Orange_3-8\lib\site-packages\orangecontrib\network\widgets\OWNxExplorer.py", line 237, in on_selection_change
    self.commit()
  File "C:\Users\vodopma2\AppData\Local\Orange_3-8\lib\site-packages\Orange\widgets\gui.py", line 2001, in unconditional_commit
    do_commit()
  File "C:\Users\vodopma2\AppData\Local\Orange_3-8\lib\site-packages\Orange\widgets\gui.py", line 2009, in do_commit
    commit()
  File "C:\Users\vodopma2\AppData\Local\Orange_3-8\lib\site-packages\orangecontrib\network\widgets\OWNxExplorer.py", line 276, in commit
    self.send_data()
  File "C:\Users\vodopma2\AppData\Local\Orange_3-8\lib\site-packages\orangecontrib\network\widgets\OWNxExplorer.py", line 412, in send_data
    self.send(Output.REMAINING, items[remaining, :] if remaining else None)
  File "C:\Users\vodopma2\AppData\Local\Orange_3-8\lib\site-packages\Orange\data\table.py", line 743, in __getitem__
    return self.from_table(domain, self, row_idx)
  File "C:\Users\vodopma2\AppData\Local\Orange_3-8\lib\site-packages\Orange\data\table.py", line 361, in from_table
    table = cls.from_table_rows(source, row_indices)
  File "C:\Users\vodopma2\AppData\Local\Orange_3-8\lib\site-packages\Orange\data\table.py", line 452, in from_table_rows
    self.X = source.X[row_indices]
IndexError: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Error: Changed NetworkX API

hi guys,

Network explorer, throws an error (messages attached), in whichever way i am trying to connect it (based on distance file, generated network, or network file). I 'm using Mac OSx and Orange is standalone application, not withing Anaconda. Tried on Orange 3.6 and 3.7 versions. Network library is 1.2.0

Cannot Install Orange3-Network on Windows

Hi, here's the error I get:

Collecting Orange3-Network
  Using cached Orange3-Network-1.2.0.tar.gz
Requirement already satisfied (use --upgrade to upgrade): networkx>=1.10 in c:\python34\lib\site-packages (from Orange3-Network)
Requirement already satisfied (use --upgrade to upgrade): pyqtgraph>=0.9.10 in c:\python34\lib\site-packages (from Orange3-Network)
Requirement already satisfied (use --upgrade to upgrade): decorator>=3.4.0 in c:\python34\lib\site-packages (from networkx>=1.10->Orange3-Network)
Requirement already satisfied (use --upgrade to upgrade): numpy in c:\python34\lib\site-packages (from pyqtgraph>=0.9.10->Orange3-Network)
Installing collected packages: Orange3-Network
  Running setup.py install for Orange3-Network: started
    Running setup.py install for Orange3-Network: finished with status 'error'
    Complete output from command C:\Python34\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\iagovar\\AppData\\Local\\Temp\\pip-build-btitb11u\\Orange3-Network\\setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record C:\Users\iagovar\AppData\Local\Temp\pip-19lq6ns1-record\install-record.txt --single-version-externally-managed --compile:
    running install
    running build
    running config_cc
    unifing config_cc, config, build_clib, build_ext, build commands --compiler options
    running config_fc
    unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
    running build_src
    build_src
    building extension "orangecontrib.network._fr_layout" sources
    build_src: building npy-pkg config files
    running build_py
    creating build
    creating build\lib.win32-3.4
    creating build\lib.win32-3.4\orangecontrib
    copying orangecontrib\__init__.py -> build\lib.win32-3.4\orangecontrib
    creating build\lib.win32-3.4\orangecontrib\network
    copying orangecontrib\network\community.py -> build\lib.win32-3.4\orangecontrib\network
    copying orangecontrib\network\network.py -> build\lib.win32-3.4\orangecontrib\network
    copying orangecontrib\network\readwrite.py -> build\lib.win32-3.4\orangecontrib\network
    copying orangecontrib\network\setup.py -> build\lib.win32-3.4\orangecontrib\network
    copying orangecontrib\network\__init__.py -> build\lib.win32-3.4\orangecontrib\network
    creating build\lib.win32-3.4\orangecontrib\network\widgets
    copying orangecontrib\network\widgets\graphview.py -> build\lib.win32-3.4\orangecontrib\network\widgets
    copying orangecontrib\network\widgets\OWNxAnalysis.py -> build\lib.win32-3.4\orangecontrib\network\widgets
    copying orangecontrib\network\widgets\OWNxClustering.py -> build\lib.win32-3.4\orangecontrib\network\widgets
    copying orangecontrib\network\widgets\OWNxExplorer.py -> build\lib.win32-3.4\orangecontrib\network\widgets
    copying orangecontrib\network\widgets\OWNxFile.py -> build\lib.win32-3.4\orangecontrib\network\widgets
    copying orangecontrib\network\widgets\OWNxFromDistances.py -> build\lib.win32-3.4\orangecontrib\network\widgets
    copying orangecontrib\network\widgets\OWNxGenerator.py -> build\lib.win32-3.4\orangecontrib\network\widgets
    copying orangecontrib\network\widgets\__init__.py -> build\lib.win32-3.4\orangecontrib\network\widgets
    creating build\lib.win32-3.4\orangecontrib\network\networks
    copying orangecontrib\network\networks\airtraffic.net -> build\lib.win32-3.4\orangecontrib\network\networks
    copying orangecontrib\network\networks\airtraffic_items.tab -> build\lib.win32-3.4\orangecontrib\network\networks
    copying orangecontrib\network\networks\dicty_publication.net -> build\lib.win32-3.4\orangecontrib\network\networks
    copying orangecontrib\network\networks\dicty_publication_edges.tab -> build\lib.win32-3.4\orangecontrib\network\networks
    copying orangecontrib\network\networks\dicty_publication_items.tab -> build\lib.win32-3.4\orangecontrib\network\networks
    copying orangecontrib\network\networks\lastfm.net -> build\lib.win32-3.4\orangecontrib\network\networks
    copying orangecontrib\network\networks\lastfm.tab -> build\lib.win32-3.4\orangecontrib\network\networks
    copying orangecontrib\network\networks\lastfm_all.tab -> build\lib.win32-3.4\orangecontrib\network\networks
    copying orangecontrib\network\networks\lastfm_tags.tab -> build\lib.win32-3.4\orangecontrib\network\networks
    copying orangecontrib\network\networks\leu_by_genesets.net -> build\lib.win32-3.4\orangecontrib\network\networks
    copying orangecontrib\network\networks\leu_by_genesets_items.tab -> build\lib.win32-3.4\orangecontrib\network\networks
    copying orangecontrib\network\networks\leu_by_pmid.net -> build\lib.win32-3.4\orangecontrib\network\networks
    copying orangecontrib\network\networks\leu_by_pmid_items.tab -> build\lib.win32-3.4\orangecontrib\network\networks
    copying orangecontrib\network\networks\leu_huttenhower_a.net -> build\lib.win32-3.4\orangecontrib\network\networks
    copying orangecontrib\network\networks\leu_huttenhower_a_items.tab -> build\lib.win32-3.4\orangecontrib\network\networks
    copying orangecontrib\network\networks\makeNetworkList.py -> build\lib.win32-3.4\orangecontrib\network\networks
    copying orangecontrib\network\networks\mips_c2_cp_leu.net -> build\lib.win32-3.4\orangecontrib\network\networks
    copying orangecontrib\network\networks\mips_c2_cp_leu_items.tab -> build\lib.win32-3.4\orangecontrib\network\networks
    copying orangecontrib\network\networks\network_info.tab -> build\lib.win32-3.4\orangecontrib\network\networks
    creating build\lib.win32-3.4\orangecontrib\network\widgets\icons
    copying orangecontrib\network\widgets\icons\button_autoscale.png -> build\lib.win32-3.4\orangecontrib\network\widgets\icons
    copying orangecontrib\network\widgets\icons\button_rect.png -> build\lib.win32-3.4\orangecontrib\network\widgets\icons
    copying orangecontrib\network\widgets\icons\Category-Network.svg -> build\lib.win32-3.4\orangecontrib\network\widgets\icons
    copying orangecontrib\network\widgets\icons\Dlg_clear.png -> build\lib.win32-3.4\orangecontrib\network\widgets\icons
    copying orangecontrib\network\widgets\icons\Dlg_HideSelection.png -> build\lib.win32-3.4\orangecontrib\network\widgets\icons
    copying orangecontrib\network\widgets\icons\Dlg_Mark2Sel.png -> build\lib.win32-3.4\orangecontrib\network\widgets\icons
    copying orangecontrib\network\widgets\icons\Dlg_Sel2Mark.png -> build\lib.win32-3.4\orangecontrib\network\widgets\icons
    copying orangecontrib\network\widgets\icons\Dlg_SelisMark.png -> build\lib.win32-3.4\orangecontrib\network\widgets\icons
    copying orangecontrib\network\widgets\icons\Dlg_UnselectedNodes.png -> build\lib.win32-3.4\orangecontrib\network\widgets\icons
    copying orangecontrib\network\widgets\icons\NetworkAnalysis.svg -> build\lib.win32-3.4\orangecontrib\network\widgets\icons
    copying orangecontrib\network\widgets\icons\NetworkClustering.svg -> build\lib.win32-3.4\orangecontrib\network\widgets\icons
    copying orangecontrib\network\widgets\icons\NetworkExplorer.svg -> build\lib.win32-3.4\orangecontrib\network\widgets\icons
    copying orangecontrib\network\widgets\icons\NetworkFile.svg -> build\lib.win32-3.4\orangecontrib\network\widgets\icons
    copying orangecontrib\network\widgets\icons\NetworkFromDistances.svg -> build\lib.win32-3.4\orangecontrib\network\widgets\icons
    copying orangecontrib\network\widgets\icons\NetworkGenerator.svg -> build\lib.win32-3.4\orangecontrib\network\widgets\icons
    running build_ext
    customize MSVCCompiler
    customize MSVCCompiler using build_ext
    customize MSVCCompiler
    Missing compiler_cxx fix for MSVCCompiler
    customize MSVCCompiler using build_ext
    building 'orangecontrib.network._fr_layout' extension
    compiling C sources
    error: Microsoft Visual C++ 10.0 is required (Unable to find vcvarsall.bat).
    
    ----------------------------------------
Command "C:\Python34\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\iagovar\\AppData\\Local\\Temp\\pip-build-btitb11u\\Orange3-Network\\setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record C:\Users\iagovar\AppData\Local\Temp\pip-19lq6ns1-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in C:\Users\iagovar\AppData\Local\Temp\pip-build-btitb11u\Orange3-Network\
You are using pip version 8.1.2, however version 9.0.1 is available.
You should consider upgrading via the 'python -m pip install --upgrade pip' command.

I tried with pip in the command line for python3, but I'm not a programmer and did achieve nothing :(

Network File crashed when I pull it into canvas

Stack Trace:

Traceback (most recent call last):  File "D:\ProgramData\Anaconda3\envs\orange\lib\site-packages\Orange\canvas\scheme\widgetsscheme.py", line 580, in create_widget_instance    widget.init()  File "D:\ProgramData\Anaconda3\envs\orange\lib\site-packages\orangecontrib\network\widgets\OWNxFile.py", line 85, in init    self.reload()  File "D:\ProgramData\Anaconda3\envs\orange\lib\site-packages\orangecontrib\network\widgets\OWNxFile.py", line 89, in reload    self.selectNetFile()  File "D:\ProgramData\Anaconda3\envs\orange\lib\site-packages\orangecontrib\network\widgets\OWNxFile.py", line 117, in selectNetFile    self.openNetFile(self.recentFiles[0])  File "D:\ProgramData\Anaconda3\envs\orange\lib\site-packages\orangecontrib\network\widgets\OWNxFile.py", line 140, in openNetFile    G = network.readwrite.read(filename, auto_table=self.auto_table)  File "D:\ProgramData\Anaconda3\envs\orange\lib\site-packages\orangecontrib\network\readwrite.py", line 137, in read    return read_edgelist(path, auto_table)  File "D:\ProgramData\Anaconda3\envs\orange\lib\site-packages\orangecontrib\network\readwrite.py", line 185, in read_edgelist    G.set_items(graph_to_table(G))  File "D:\ProgramData\Anaconda3\envs\orange\lib\site-packages\orangecontrib\network\readwrite.py", line 114, in graph_to_table    return tableUnboundLocalError: local variable 'table' referenced before assignment

Additional info (worksheets, data, screenshots, ...)

[BUG] OWNetworkExplorer: Change highlight when input changes

When highlighting nodes by subset ID, highlights don't change when the input changes.

Try lastfm.net and select a subset with Data Table. Highlight the nodes by ID. Now change the selecting in a Data Table. Highlight doesn't change as it should.

Implement support for .gml files

Continuation of biolab/orange3#3608.

Network version

1.4.2

Orange version

3.21.dev

Expected behavior

Network add-on reads and processes .gml files.

Actual behavior

Even simple .gml fail.

Steps to reproduce the behavior

Load an example data set from https://gephi.org/users/supported-graph-formats/gml-format/.

Additional info (worksheets, data, screenshots, ...)

Either discontinue support for .gml (because now it seems as if .gml files are supported) or fix issues with reading .gml files.

OWNXGroups does not test computation of weights

... and it won't until we decide what kinds of weights we actually want.

This issue is here as reminder that tests need to be written some day.

[Feature Request] Enable removing nodes from network

Nodes can be moved around, but cannot be deleted. For ego networks, this would be highly desirable. Removing the largest node better shows connections among the rest of the network.

Problem installing on Windos

The error message say I need to install MS C++ 10.0 which I already have installed on my system. If you try the installation through anaconda prompt with pip install orange3-network everything works fine except the add-ons isn't showing up in orange3.

You are using pip version 6.0.8, however version 8.0.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Collecting Orange3-Network
  Using cached Orange3-Network-1.1.2.tar.gz
    build_src
    building extension "orangecontrib.network._fr_layout" sources
    build_src: building npy-pkg config files
Requirement already satisfied (use --upgrade to upgrade): networkx>=1.10 in c:\python34\lib\site-packages (from Orange3-Network)
Requirement already satisfied (use --upgrade to upgrade): pyqtgraph>=0.9.10 in c:\python34\lib\site-packages (from Orange3-Network)
Requirement already satisfied (use --upgrade to upgrade): decorator>=3.4.0 in c:\python34\lib\site-packages (from networkx>=1.10->Orange3-Network)
Requirement already satisfied (use --upgrade to upgrade): numpy in c:\python34\lib\site-packages (from pyqtgraph>=0.9.10->Orange3-Network)
Installing collected packages: Orange3-Network
  Running setup.py install for Orange3-Network
    unifing config_cc, config, build_clib, build_ext, build commands --compiler options
    unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
    build_src
    building extension "orangecontrib.network._fr_layout" sources
    build_src: building npy-pkg config files
    No module named 'numpy.distutils.msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
    customize MSVCCompiler using build_ext
    No module named 'numpy.distutils.msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
    Missing compiler_cxx fix for MSVCCompiler
    customize MSVCCompiler using build_ext
    building 'orangecontrib.network._fr_layout' extension
    compiling C sources
    error: Microsoft Visual C++ 10.0 is required (Unable to find vcvarsall.bat).
    Complete output from command C:\Python34\python.exe -c "import setuptools, tokenize;__file__='C:\\Users\\chovanec\\AppData\\Local\\Temp\\pip-build-gqjgc8_8\\Orange3-Network\\setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record C:\Users\chovanec\AppData\Local\Temp\pip-39qph15q-record\install-record.txt --single-version-externally-managed --compile:
    running install

    running build

    running config_cc

    unifing config_cc, config, build_clib, build_ext, build commands --compiler options

    running config_fc

    unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options

    running build_src

    build_src

    building extension "orangecontrib.network._fr_layout" sources

    build_src: building npy-pkg config files

    running build_py

    creating build

    creating build\lib.win32-3.4

    creating build\lib.win32-3.4\orangecontrib

    copying orangecontrib\__init__.py -> build\lib.win32-3.4\orangecontrib

    creating build\lib.win32-3.4\orangecontrib\network

    copying orangecontrib\network\community.py -> build\lib.win32-3.4\orangecontrib\network

    copying orangecontrib\network\network.py -> build\lib.win32-3.4\orangecontrib\network

    copying orangecontrib\network\readwrite.py -> build\lib.win32-3.4\orangecontrib\network

    copying orangecontrib\network\setup.py -> build\lib.win32-3.4\orangecontrib\network

    copying orangecontrib\network\snap.py -> build\lib.win32-3.4\orangecontrib\network

    copying orangecontrib\network\__init__.py -> build\lib.win32-3.4\orangecontrib\network

    creating build\lib.win32-3.4\orangecontrib\network\widgets

    copying orangecontrib\network\widgets\graphview.py -> build\lib.win32-3.4\orangecontrib\network\widgets

    copying orangecontrib\network\widgets\OWNxAnalysis.py -> build\lib.win32-3.4\orangecontrib\network\widgets

    copying orangecontrib\network\widgets\OWNxClustering.py -> build\lib.win32-3.4\orangecontrib\network\widgets

    copying orangecontrib\network\widgets\OWNxExplorer.py -> build\lib.win32-3.4\orangecontrib\network\widgets

    copying orangecontrib\network\widgets\OWNxFile.py -> build\lib.win32-3.4\orangecontrib\network\widgets

    copying orangecontrib\network\widgets\OWNxFromDistances.py -> build\lib.win32-3.4\orangecontrib\network\widgets

    copying orangecontrib\network\widgets\OWNxGenerator.py -> build\lib.win32-3.4\orangecontrib\network\widgets

    copying orangecontrib\network\widgets\OWNxInsideView.py -> build\lib.win32-3.4\orangecontrib\network\widgets

    copying orangecontrib\network\widgets\OWNxSNAP.py -> build\lib.win32-3.4\orangecontrib\network\widgets

    copying orangecontrib\network\widgets\__init__.py -> build\lib.win32-3.4\orangecontrib\network\widgets

    creating build\lib.win32-3.4\orangecontrib\network\networks

    copying orangecontrib\network\networks\airtraffic.net -> build\lib.win32-3.4\orangecontrib\network\networks

    copying orangecontrib\network\networks\airtraffic_items.tab -> build\lib.win32-3.4\orangecontrib\network\networks

    copying orangecontrib\network\networks\dicty_publication.net -> build\lib.win32-3.4\orangecontrib\network\networks

    copying orangecontrib\network\networks\dicty_publication_edges.tab -> build\lib.win32-3.4\orangecontrib\network\networks

    copying orangecontrib\network\networks\dicty_publication_items.tab -> build\lib.win32-3.4\orangecontrib\network\networks

    copying orangecontrib\network\networks\lastfm.net -> build\lib.win32-3.4\orangecontrib\network\networks

    copying orangecontrib\network\networks\lastfm.tab -> build\lib.win32-3.4\orangecontrib\network\networks

    copying orangecontrib\network\networks\lastfm_all.tab -> build\lib.win32-3.4\orangecontrib\network\networks

    copying orangecontrib\network\networks\lastfm_tags.tab -> build\lib.win32-3.4\orangecontrib\network\networks

    copying orangecontrib\network\networks\leu_by_genesets.net -> build\lib.win32-3.4\orangecontrib\network\networks

    copying orangecontrib\network\networks\leu_by_genesets_items.tab -> build\lib.win32-3.4\orangecontrib\network\networks

    copying orangecontrib\network\networks\leu_by_pmid.net -> build\lib.win32-3.4\orangecontrib\network\networks

    copying orangecontrib\network\networks\leu_by_pmid_items.tab -> build\lib.win32-3.4\orangecontrib\network\networks

    copying orangecontrib\network\networks\leu_huttenhower_a.net -> build\lib.win32-3.4\orangecontrib\network\networks

    copying orangecontrib\network\networks\leu_huttenhower_a_items.tab -> build\lib.win32-3.4\orangecontrib\network\networks

    copying orangecontrib\network\networks\makeNetworkList.py -> build\lib.win32-3.4\orangecontrib\network\networks

    copying orangecontrib\network\networks\mips_c2_cp_leu.net -> build\lib.win32-3.4\orangecontrib\network\networks

    copying orangecontrib\network\networks\mips_c2_cp_leu_items.tab -> build\lib.win32-3.4\orangecontrib\network\networks

    copying orangecontrib\network\networks\network_info.tab -> build\lib.win32-3.4\orangecontrib\network\networks

    creating build\lib.win32-3.4\orangecontrib\network\widgets\icons

    copying orangecontrib\network\widgets\icons\button_autoscale.png -> build\lib.win32-3.4\orangecontrib\network\widgets\icons

    copying orangecontrib\network\widgets\icons\button_rect.png -> build\lib.win32-3.4\orangecontrib\network\widgets\icons

    copying orangecontrib\network\widgets\icons\Category-Network.svg -> build\lib.win32-3.4\orangecontrib\network\widgets\icons

    copying orangecontrib\network\widgets\icons\Dlg_clear.png -> build\lib.win32-3.4\orangecontrib\network\widgets\icons

    copying orangecontrib\network\widgets\icons\Dlg_HideSelection.png -> build\lib.win32-3.4\orangecontrib\network\widgets\icons

    copying orangecontrib\network\widgets\icons\Dlg_Mark2Sel.png -> build\lib.win32-3.4\orangecontrib\network\widgets\icons

    copying orangecontrib\network\widgets\icons\Dlg_Sel2Mark.png -> build\lib.win32-3.4\orangecontrib\network\widgets\icons

    copying orangecontrib\network\widgets\icons\Dlg_SelisMark.png -> build\lib.win32-3.4\orangecontrib\network\widgets\icons

    copying orangecontrib\network\widgets\icons\Dlg_UnselectedNodes.png -> build\lib.win32-3.4\orangecontrib\network\widgets\icons

    copying orangecontrib\network\widgets\icons\NetworkAnalysis.svg -> build\lib.win32-3.4\orangecontrib\network\widgets\icons

    copying orangecontrib\network\widgets\icons\NetworkClustering.svg -> build\lib.win32-3.4\orangecontrib\network\widgets\icons

    copying orangecontrib\network\widgets\icons\NetworkExplorer.svg -> build\lib.win32-3.4\orangecontrib\network\widgets\icons

    copying orangecontrib\network\widgets\icons\NetworkFile.svg -> build\lib.win32-3.4\orangecontrib\network\widgets\icons

    copying orangecontrib\network\widgets\icons\NetworkFromDistances.svg -> build\lib.win32-3.4\orangecontrib\network\widgets\icons

    copying orangecontrib\network\widgets\icons\NetworkGenerator.svg -> build\lib.win32-3.4\orangecontrib\network\widgets\icons

    copying orangecontrib\network\widgets\icons\NetworkInsideView.svg -> build\lib.win32-3.4\orangecontrib\network\widgets\icons

    copying orangecontrib\network\widgets\icons\SNAP.svg -> build\lib.win32-3.4\orangecontrib\network\widgets\icons

    copying orangecontrib\network\widgets\icons\snap_logo.png -> build\lib.win32-3.4\orangecontrib\network\widgets\icons

    running build_ext

    No module named 'numpy.distutils.msvccompiler' in numpy.distutils; trying from distutils

    customize MSVCCompiler

    customize MSVCCompiler using build_ext

    No module named 'numpy.distutils.msvccompiler' in numpy.distutils; trying from distutils

    customize MSVCCompiler

    Missing compiler_cxx fix for MSVCCompiler

    customize MSVCCompiler using build_ext

    building 'orangecontrib.network._fr_layout' extension

    compiling C sources

    error: Microsoft Visual C++ 10.0 is required (Unable to find vcvarsall.bat).

    ----------------------------------------
    Command "C:\Python34\python.exe -c "import setuptools, tokenize;__file__='C:\\Users\\chovanec\\AppData\\Local\\Temp\\pip-build-gqjgc8_8\\Orange3-Network\\setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record C:\Users\chovanec\AppData\Local\Temp\pip-39qph15q-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in C:\Users\chovanec\AppData\Local\Temp\pip-build-gqjgc8_8\Orange3-Network

chemoinformatics add on is empty

Network version

Orange version

Expected behavior

Actual behavior

Steps to reproduce the behavior

Additional info (worksheets, data, screenshots, ...)

[BUG] Network File not working when re-opening an .ows

Orange version: 3.3.9.
Orange Network: last commit 9f15272

1. Open a .net file using the Network File widget.
2. Save .ows schema.
3. Delete .net file.
4. Re-open schema. The Network File widget fails and does not allow to change path to file, because the whole traceback is dispalyed in an errorbar.

[BUG] Network Explorer fails with SNAP datasets

Orange version: 3.3.9.
Orange Network: last commit 9f15272

SNAP -> Network Clustering -> Network Explorer

SNAP datasets are too large to visualize with Network Explorer.

Network Clustering is however successfully computed. If connected to Network Explorer, an Index Out of Bounds Exception occurs. This doesn't happen with Networks that are small enough to visualise.

Network File improvements

1.) Remove main area.
2.) Align buttons and make them all the same.

Error when trying to open Vertices data file

If I open the system dialog for loading a Vertices data file (...) in Network File and then close it without choosing a file (..I do this for example if I want to check what data formats are supported), I get an error and Networks stops functioning.

workaround: reset widget settings and restart Orange

---

Exception:
TypeError: expected str, bytes or os.PathLike object, not tuple
Module:
ntpath:204
Widget Name:
Network File
Widget Module:
orangecontrib.network.widgets.OWNxFile:267
Widget Scheme:
C:\Users\vodopma2\AppData\Local\Temp\ows-x6bs9p57.ows.xml
Version:
3.8.0
Environment:
Python 3.6.3 on Windows 7 6.1.7601 x86
Installed Packages:
AnyQt==0.0.8, Bottleneck==1.2.1, CommonMark==0.7.4, Orange3-Network==1.3.0, Orange3==3.8.0, PySocks==1.6.7, asn1crypto==0.23.0, certifi==2017.11.5, cffi==1.11.2, chardet==3.0.4, cryptography==2.1.4, decorator==4.1.2, dill==0.2.7.1, docutils==0.14, future==0.16.0, idna==2.6, joblib==0.11, keyring==9.0, keyrings.alt==2.3, networkx==2.0, numpy==1.13.3, pip==9.0.1, pyOpenSSL==17.5.0, pycparser==2.18, pyqtgraph==0.10.0, pyreadline==2.1, pywin32==221, requests==2.18.4, scikit-learn==0.19.1, scipy==0.19.1, serverfiles==0.2.1, setuptools==36.5.0.post20170922, six==1.11.0, urllib3==1.22, wheel==0.30.0, win-inet-pton==1.0.1, wincertstore==0.2, xlrd==1.1.0
Machine ID:
118796715501792
Stack Trace:
Traceback (most recent call last):
  File "C:\Users\vodopma2\AppData\Local\Orange_3-8\lib\site-packages\orangecontrib\network\widgets\OWNxFile.py", line 267, in browseDataFile
    self.populate_comboboxes()
  File "C:\Users\vodopma2\AppData\Local\Orange_3-8\lib\site-packages\orangecontrib\network\widgets\OWNxFile.py", line 102, in populate_comboboxes
    self.datacombo.addItem(path.basename(file))
  File "C:\Users\vodopma2\AppData\Local\Orange_3-8\lib\ntpath.py", line 235, in basename
    return split(p)[1]
  File "C:\Users\vodopma2\AppData\Local\Orange_3-8\lib\ntpath.py", line 204, in split
    p = os.fspath(p)
TypeError: expected str, bytes or os.PathLike object, not tuple

Local Variables:
OrderedDict([('p', ('', ''))])

Create graph by connecting points that share the same value of one of the selected set of attributes

Toy example: Connect metro stations by lines.
metro-stations.txt

Suggestion: automatically show subset on Network Explorer

When importing data and subset data into Network Explorer it is required to select an option to label subset before subset is labeled on graph. Could Network Explorer be changed to automatically select this option when the subset is first feed in the Network Explorer and when a new subset is chosen.

[BUG] Some SNAP Networks are not found.

Orange version: 3.3.9.
Orange Network: last commit 9f15272

Automatically refresh SNAP Network list. Some, such as Facebook ego Network are not found (404 HTTP Error).

While at it, make sure the currently selected SNAP network remains highlighted when re-opening the widget.

NetworkExplorer/graphview issues

Based on NetworkX package, I would expect to be able to (https://networkx.github.io/documentation/networkx-1.10/tutorial/tutorial.html#nodes)

1. use different labels (strings and ints in the same graph)
2. use another graph as a node

NetworkExplorer throws error for both. If this is not supported intentionally, it'd be nice to at least see that somewhere in the documentation or the code

error encounted in NetworkExplorer, Exception: AttributeError: 'GraphView' object has no attribute 'step_resizing'

Network version

orange-Network_1.4.3

Orange version

Orange3.19.0

Expected behavior

Actual behavior

Steps to reproduce the behavior

Additional info (worksheets, data, screenshots, ...)

Exception:
AttributeError: 'GraphView' object has no attribute 'step_resizing'
Module:
orangecontrib.network.widgets.graphview:129
Widget Name:
Network Explorer
Widget Module:
orangecontrib.network.widgets.OWNxExplorer:78
Widget Scheme:
C:\Users\tlcb\AppData\Local\Temp\ows-0mflg6zt.ows.xml
Version:
3.19.0
Environment:
Python 3.7.1 on Windows 7 6.1.7601 AMD64
Installed Packages:
AnyQt==0.0.10, Babel==2.6.0, Bottleneck==1.2.1, Click==7.0, Cython==0.29.2, Flask-Cors==3.0.7, Flask==1.0.2, Jinja2==2.10, Keras-Applications==1.0.7, Keras-Preprocessing==1.0.9, Markdown==3.0.1, MarkupSafe==1.1.0, Orange3-Network==1.4.2, Orange3==3.19.0, Pillow==5.3.0, PyOpenGL==3.1.1a1, PySocks==1.6.8, PyWavelets==1.0.1, PyYAML==3.13, Pygments==2.3.1, QtAwesome==0.5.3, QtPy==1.5.2, SQLAlchemy==1.2.15, Send2Trash==1.5.0, Sphinx==1.8.2, Werkzeug==0.14.1, XlsxWriter==1.1.2, absl-py==0.7.0, alabaster==0.7.12, anaconda-client==1.7.2, anaconda-navigator==1.9.6, anaconda-project==0.8.2, asn1crypto==0.24.0, astor==0.7.1, astroid==2.1.0, astropy==3.1, atomicwrites==1.2.1, attrs==18.2.0, backcall==0.1.0, backports.os==0.1.1, backports.shutil-get-terminal-size==1.0.0, beautifulsoup4==4.6.3, bitarray==0.8.3, bkcharts==0.2, blaze==0.11.3, bleach==3.0.2, bokeh==1.0.2, boto==2.49.0, certifi==2018.11.29, cffi==1.11.5, chardet==3.0.4, cloudpickle==0.6.1, clyent==1.2.2, colorama==0.4.1, comtypes==1.1.7, conda-build==3.17.6, conda-verify==3.1.1, conda==4.6.8, contextlib2==0.5.5, cryptography==2.4.2, cycler==0.10.0, cytoolz==0.9.0.1, dask==1.0.0, datashape==0.5.4, decorator==4.3.0, defusedxml==0.5.0, dill==0.2.8.2, distributed==1.25.1, docutils==0.14, entrypoints==0.2.3, et-xmlfile==1.0.1, fast-histogram==0.5, fastTSNE==0.2.13, fastcache==1.0.2, filelock==3.0.10, future==0.17.1, gast==0.2.2, gevent==1.3.7, glob2==0.6, glue-core==0.14.1, glue-vispy-viewers==0.11, greenlet==0.4.15, grpcio==1.16.1, h5py==2.8.0, heapdict==1.0.0, html5lib==1.0.1, idna==2.8, imageio==2.4.1, imagesize==1.1.0, importlib-metadata==0.6, ipykernel==5.1.0, ipython-genutils==0.2.0, ipython==7.2.0, ipywidgets==7.4.2, isort==4.3.4, itsdangerous==1.1.0, jdcal==1.4, jedi==0.13.2, joblib==0.13.1, jsonschema==2.6.0, jupyter-client==5.2.4, jupyter-console==6.0.0, jupyter-core==4.4.0, jupyter==1.0.0, jupyterlab-server==0.2.0, jupyterlab==0.35.3, keyring==17.0.0, keyrings.alt==3.1.1, kiwisolver==1.0.1, lazy-object-proxy==1.3.1, libarchive-c==2.8, llvmlite==0.26.0, locket==0.2.0, lxml==4.2.5, matplotlib==3.0.2, mccabe==0.6.1, menuinst==1.4.14, mistune==0.8.4, mkl-fft==1.0.6, mkl-random==1.0.2, mock==2.0.0, more-itertools==4.3.0, mpl-scatter-density==0.4, mpmath==1.1.0, msgpack==0.5.6, multipledispatch==0.6.0, navigator-updater==0.2.1, nbconvert==5.4.0, nbformat==4.4.0, networkx==2.2, nltk==3.4, nose==1.3.7, notebook==5.7.4, numba==0.41.0, numexpr==2.6.8, numpy==1.15.4, numpydoc==0.8.0, odo==0.5.1, olefile==0.46, openpyxl==2.5.12, opentsne==0.3.2, packaging==18.0, pandas==0.23.4, pandocfilters==1.4.2, parso==0.3.1, partd==0.3.9, path.py==11.5.0, pathlib2==2.3.3, patsy==0.5.1, pbr==5.1.3, pep8==1.7.1, pickleshare==0.7.5, pip==18.1, pkginfo==1.4.2, plotly==3.5.0, pluggy==0.8.0, ply==3.11, prometheus-client==0.5.0, prompt-toolkit==2.0.7, protobuf==3.6.1, psutil==5.4.8, py==1.7.0, pyOpenSSL==18.0.0, pycodestyle==2.4.0, pycosat==0.6.3, pycparser==2.19, pycrypto==2.6.1, pycurl==7.43.0.2, pyflakes==2.0.0, pylint==2.2.2, pyodbc==4.0.25, pyparsing==2.3.0, pyqtgraph==0.10.0, pyreadline==2.1, pytest-arraydiff==0.3, pytest-astropy==0.5.0, pytest-doctestplus==0.2.0, pytest-openfiles==0.3.1, pytest-remotedata==0.3.1, pytest==4.0.2, python-dateutil==2.7.5, python-louvain==0.11, pytz==2018.7, pywin32==223, pywinpty==0.5.5, pyzmq==17.1.2, qtconsole==4.4.3, requests==2.21.0, retrying==1.3.3, rope==0.11.0, ruamel-yaml==0.15.46, scikit-image==0.14.1, scikit-learn==0.20.1, scipy==1.1.0, seaborn==0.9.0, serverfiles==0.3.0, setuptools==40.6.3, simplegeneric==0.8.1, singledispatch==3.4.0.3, six==1.12.0, snowballstemmer==1.2.1, sortedcollections==1.0.1, sortedcontainers==2.1.0, sphinxcontrib-websupport==1.1.0, spyder-kernels==0.3.0, spyder==3.3.2, statsmodels==0.9.0, sympy==1.3, tables==3.4.4, tblib==1.3.2, tensorboard==1.13.1, tensorflow-estimator==1.13.0, tensorflow==1.13.1, termcolor==1.1.0, terminado==0.8.1, testpath==0.4.2, toolz==0.9.0, tornado==5.1.1, tqdm==4.28.1, traitlets==4.3.2, unicodecsv==0.14.1, urllib3==1.24.1, wcwidth==0.1.7, webencodings==0.5.1, wheel==0.32.3, widgetsnbextension==3.4.2, win-inet-pton==1.0.1, win-unicode-console==0.5, wincertstore==0.2, wrapt==1.10.11, xlrd==1.2.0, xlwings==0.15.1, xlwt==1.3.0, zict==0.1.3
Machine ID:
24062491136
Stack Trace:
Traceback (most recent call last):
File "D:\Anaconda3\lib\site-packages\Orange\canvas\scheme\widgetsscheme.py", line 579, in create_widget_instance
widget.init()
File "D:\Anaconda3\pkgs\orange3-network\orangecontrib\network\widgets\OWNxExplorer.py", line 78, in init
super().init()
File "D:\Anaconda3\lib\site-packages\Orange\widgets\visualize\utils\widget.py", line 378, in init
self.setup_gui()
File "D:\Anaconda3\lib\site-packages\Orange\widgets\visualize\utils\widget.py", line 382, in setup_gui
self._add_graph()
File "D:\Anaconda3\lib\site-packages\Orange\widgets\visualize\utils\widget.py", line 387, in _add_graph
self.graph = self.GRAPH_CLASS(self, box)
File "D:\Anaconda3\pkgs\orange3-network\orangecontrib\network\widgets\graphview.py", line 129, in init
self.step_resizing.connect(self.update_edges)
AttributeError: 'GraphView' object has no attribute 'step_resizing'

Local Variables:
OrderedDict([('class',
<class 'orangecontrib.network.widgets.graphview.GraphView'>),
('master',
<orangecontrib.network.widgets.OWNxExplorer.OWNxExplorer object at 0x000000001B65D3A8>),
('parent',
<PyQt5.QtWidgets.QGroupBox object at 0x000000000AF74558>),
('self',
<orangecontrib.network.widgets.graphview.GraphView object at 0x000000000C90E588>)])

Network Explorer: cannot select a subset

Network version

1.4.2

Orange version

3.21.dev

Expected behavior

Selected subset network can be shown in Network Explorer.

Actual behavior

While nodes seem to be selected, there is nothing on the output.

Steps to reproduce the behavior

Network Generator (or load a simple network) - Network Explorer (select a couple of nodes) - Network Explorer (2).

Additional info (worksheets, data, screenshots, ...)

[BUG] Computing Node-level indices when Network is constructed from columns

Orange version: 3.3.9.
Orange Network: last commit 9f15272

Fails when computing Node-level indices for columns.

1. Construct a Network from distances where distances are computed between columns
2. Run Network analysis, and select e.g. Node-level indices > Degree

How to visualize separate Nodes File and Edges File as CSV

I am trying to visualize a network by adding the nodes.csv and edges.csv into File and then connecting to Network explorer. Its not working.

It would be great if you could provide an example at http://orange3-network.readthedocs.io/