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Earlier this year Sep 23, 2009 issue 34 (pebl throws exception when trying to save results to html) Status changed by abhikshah - Status: Verified Status: Verified Sep 11, 2009 issue 35 (missing resources) reported by barna.gergely - The generated html result page doesn't work, because all the files in the lib folder are empty. They are also empty in the downloadable .tar.gz releases(src\pebl\resources\htmlresult\lib\) and in the easy_installed pebl folder (win32, python 2.6). Would you please upload a fixed .tar.gz or the missing files? The generated html result page doesn't work, because all the files in the lib folder are empty. They are also empty in the downloadable .tar.gz releases(src\pebl\resources\htmlresult\lib\) and in the easy_installed pebl folder (win32, python 2.6). Would you please upload a fixed .tar.gz or the missing files? Sep 07, 2009 issue 34 (pebl throws exception when trying to save results to html) commented on by installe - I'm using graphviz version 2.24.0. r142 solves the problem for me. I'm using graphviz version 2.24.0. r142 solves the problem for me. Aug 31, 2009 issue 34 (pebl throws exception when trying to save results to html) Status changed by abhikshah - For some reason, graphviz is returning position as float instead of int. New version of graphviz? I now convert using int(float(x)) so it works in either case. Will wait for confirmation from original submitter before closing ticket. Fixed in r142. Status: Started For some reason, graphviz is returning position as float instead of int. New version of graphviz? I now convert using int(float(x)) so it works in either case. Will wait for confirmation from original submitter before closing ticket. Fixed in r142. Status: Started Aug 31, 2009 r142 (Fixing issue 34.) committed by abhikshah - Fixing issue 34 . Fixing issue 34 . Aug 28, 2009 issue 34 (pebl throws exception when trying to save results to html) reported by installe - What steps will reproduce the problem? 1. Save the attached data file as data.txt 2. Run the example code from the tutorial, i.e. >>> from pebl import data >>> from pebl.learner import greedy >>> dataset = data.fromfile("data.txt") >>> dataset.discretize() >>> learner = greedy.GreedyLearner(dataset) >>> result = learner.run() >>> result.tohtml("result") What is the expected output? What do you see instead? I expect pebl to save the html output in the "result" directory, as it does on "pebl-tutorial-data1.txt". Instead, it throws the following exception: Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/users/sista/ainstall/pkg/lib/python2.5/site-packages/pebl-1.01-py2.5-linux-x86_64.egg/pebl/result.py", line 150, in tohtml outdir or config.get('result.outdir') File "/users/sista/ainstall/pkg/lib/python2.5/site-packages/pebl-1.01-py2.5-linux-x86_64.egg/pebl/result.py", line 211, in htmlreport top.layout() File "/users/sista/ainstall/pkg/lib/python2.5/site-packages/pebl-1.01-py2.5-linux-x86_64.egg/pebl/network.py", line 289, in layout self.node_positions = [[int(i) for i in n.get_pos()[1:-1].split(',')] for n in nodes] ValueError: invalid literal for int() with base 10: '174.52' What version of the product are you using? On what operating system? Latest version from trunk. Please provide any additional information below. What steps will reproduce the problem? 1. Save the attached data file as data.txt 2. Run the example code from the tutorial, i.e. >>> from pebl import data >>> from pebl.learner import greedy >>> dataset = data.fromfile("data.txt") >>> dataset.discretize() >>> learner = greedy.GreedyLearner(dataset) >>> result = learner.run() >>> result.tohtml("result") What is the expected output? What do you see instead? I expect pebl to save the html output in the "result" directory, as it does on "pebl-tutorial-data1.txt". Instead, it throws the following exception: Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/users/sista/ainstall/pkg/lib/python2.5/site-packages/pebl-1.01-py2.5-linux-x86_64.egg/pebl/result.py", line 150, in tohtml outdir or config.get('result.outdir') File "/users/sista/ainstall/pkg/lib/python2.5/site-packages/pebl-1.01-py2.5-linux-x86_64.egg/pebl/result.py", line 211, in htmlreport top.layout() File "/users/sista/ainstall/pkg/lib/python2.5/site-packages/pebl-1.01-py2.5-linux-x86_64.egg/pebl/network.py", line 289, in layout self.node_positions = [[int(i) for i in n.get_pos()[1:-1].split(',')] for n in nodes] ValueError: invalid literal for int() with base 10: '174.52' What version of the product are you using? On what operating system? Latest version from trunk. Please provide any additional information below. May 19, 2009 issue 33 (result.merge should accept generator) reported by abhikshah - result.merge should check if it has been passed a generator and list() it since people often pass in generators instead of lists.. result.merge should check if it has been passed a generator and list() it since people often pass in generators instead of lists.. May 13, 2009 issue 32 (Discretizing with missing values) reported by abhikshah - When discretizing data with missing values, Pebl should ignore the missing values when selecting bins for each data point. When discretizing data with missing values, Pebl should ignore the missing values when selecting bins for each data point. May 13, 2009 issue 31 (Learners don't handle missing data) Status changed by abhikshah - Status: Fixed Status: Fixed Apr 23, 2009 r141 (Added testdata13.txt) committed by abhikshah - Added testdata13.txt Added testdata13.txt Apr 21, 2009 issue 31 (Learners don't handle missing data) commented on by abhikshah - Fixed in revision 140. Will close issue once original bug submitter is ok with the changes. Fixed in revision 140. Will close issue once original bug submitter is ok with the changes. Apr 21, 2009 r140 (Fix for issue #31 (learners fail with missing data)) committed by abhikshah - Fix for issue #31 (learners fail with missing data) Fix for issue #31 (learners fail with missing data) Apr 20, 2009 issue 31 (Learners don't handle missing data) Status changed by abhikshah - This was a planned feature that unfortunately seems to be in a half-complete state. Currently, the gibbs sampler can be used successfully but only with custom learners (that don't use the SmartNetworkEvaluator interface). The fix is quite simple, however, and will be ready in a day or so. Status: Accepted This was a planned feature that unfortunately seems to be in a half-complete state. Currently, the gibbs sampler can be used successfully but only with custom learners (that don't use the SmartNetworkEvaluator interface). The fix is quite simple, however, and will be ready in a day or so. Status: Accepted Apr 20, 2009 issue 31 (Learners don't handle missing data) reported by abhikshah - This is based on email from user. The greedy and simanneal learners use the SmartNetworkEvaluator interface which isn't available for datasets with missing values. Thus, trying to use these learners with missing data fails. This is based on email from user. The greedy and simanneal learners use the SmartNetworkEvaluator interface which isn't available for datasets with missing values. Thus, trying to use these learners with missing data fails. Apr 20, 2009 issue 17 (Reading data fully into memory) Status changed by abhikshah - Status: WontFix Status: WontFix Apr 20, 2009 issue 4 (Better scorer for networks with missing values) Status changed by abhikshah - Status: WontFix Status: WontFix Apr 20, 2009 issue 16 (Pebl's tutorial is uninformative) Status changed by abhikshah - Status: Fixed Status: Fixed Mar 04, 2009 r139 (Updated config param documentation.) committed by abhikshah - Updated config param documentation. Updated config param documentation. Mar 04, 2009 PeblDependencies (Links to download dependencies for Pebl.) Wiki page edited by abhikshah Mar 04, 2009 PeblDependencies (Links to download dependencies for Pebl.) Wiki page added by abhikshah Mar 04, 2009 pebl-1.0.1.tar.gz (PEBL 1.0.1 (same as previous version but fixed filename)) file uploaded by abhikshah Jan 14, 2009 issue 30 (AttributeError) commented on by xuhanf - I added do.ext to the system path. and this problem was solved. but I got another error: Traceback (most recent call last): File "C:\111.py", line 8, in <module> ex1result.tohtml("example1-result") File "C:\Python25\lib\site-packages\pebl-1.01-py2.5-win32.egg\pebl\result.py", line 150, in tohtml outdir or config.get('result.outdir') File "C:\Python25\lib\site-packages\pebl-1.01-py2.5-win32.egg\pebl\result.py", line 217, in htmlreport top.node_positions File "C:\Python25\lib\site-packages\pebl-1.01-py2.5-win32.egg\pebl\result.py", line 249, in network_image os.remove(fname) WindowsError: [Error 32] : 'c:\\docume~1\\admini~1\\locals~1\\temp\\tmpt2ru3x' what's wrong? I added do.ext to the system path. and this problem was solved. but I got another error: Traceback (most recent call last): File "C:\111.py", line 8, in <module> ex1result.tohtml("example1-result") File "C:\Python25\lib\site-packages\pebl-1.01-py2.5-win32.egg\pebl\result.py", line 150, in tohtml outdir or config.get('result.outdir') File "C:\Python25\lib\site-packages\pebl-1.01-py2.5-win32.egg\pebl\result.py", line 217, in htmlreport top.node_positions File "C:\Python25\lib\site-packages\pebl-1.01-py2.5-win32.egg\pebl\result.py", line 249, in network_image os.remove(fname) WindowsError: [Error 32] : 'c:\\docume~1\\admini~1\\locals~1\\temp\\tmpt2ru3x' what's wrong? Jan 14, 2009 issue 30 (AttributeError) reported by xuhanf - Error while trying to run example >>> from pebl import data >>> from pebl.learner import greedy >>> dataset = data.fromfile("pebl-tutorial-data1.txt") >>> dataset.discretize() >>> learner = greedy.GreedyLearner(dataset) >>> ex1result = learner.run() >>> ex1result.tohtml("example1-result") I got the message: Traceback (most recent call last): File "C:\111.py", line 8, in <module> ex1result.tohtml("example1-result") File "c:\python25\lib\site-packages\pebl-1.01-py2.5- win32.egg\pebl\result.py", line 150, in tohtml outdir or config.get('result.outdir') File "c:\python25\lib\site-packages\pebl-1.01-py2.5- win32.egg\pebl\result.py", line 211, in htmlreport top.layout() File "c:\python25\lib\site-packages\pebl-1.01-py2.5- win32.egg\pebl\network.py", line 288, in layout nodes = (n for n in dotgraph.get_node_list() if n.get_pos()) AttributeError: 'NoneType' object has no attribute 'get_node_list' Error while trying to run example >>> from pebl import data >>> from pebl.learner import greedy >>> dataset = data.fromfile("pebl-tutorial-data1.txt") >>> dataset.discretize() >>> learner = greedy.GreedyLearner(dataset) >>> ex1result = learner.run() >>> ex1result.tohtml("example1-result") I got the message: Traceback (most recent call last): File "C:\111.py", line 8, in <module> ex1result.tohtml("example1-result") File "c:\python25\lib\site-packages\pebl-1.01-py2.5- win32.egg\pebl\result.py", line 150, in tohtml outdir or config.get('result.outdir') File "c:\python25\lib\site-packages\pebl-1.01-py2.5- win32.egg\pebl\result.py", line 211, in htmlreport top.layout() File "c:\python25\lib\site-packages\pebl-1.01-py2.5- win32.egg\pebl\network.py", line 288, in layout nodes = (n for n in dotgraph.get_node_list() if n.get_pos()) AttributeError: 'NoneType' object has no attribute 'get_node_list' Older Nov 25, 2008 pebl-1.01.tar.gz (PEBL version 1.0.1 (a small bugfix)) file uploaded by abhikshah Nov 25, 2008 issue 29 (taskcontrollers are no longer optional) Status changed by abhikshah - Fixed in r136, pebl version 1.01 Status: Fixed Fixed in r136, pebl version 1.01 Status: Fixed Nov 25, 2008 r136 (Fixing issue 29. Incrementing to version 1.01) committed by abhikshah - Fixing issue 29 . Incrementing to version 1.01 Fixing issue 29 . Incrementing to version 1.01 Nov 25, 2008 issue 29 (taskcontrollers are no longer optional) reported by abhikshah - taskcontroller subpackage should be optional because it requires additional dependencies.. but due to a review comment, I had imported all submodules in pebl/src/__init__.py.. That should be removed. taskcontroller subpackage should be optional because it requires additional dependencies.. but due to a review comment, I had imported all submodules in pebl/src/__init__.py.. That should be removed. Oct 28, 2008 r135 (Updated description in setup.py) committed by abhikshah - Updated description in setup.py Updated description in setup.py Oct 11, 2008 r134 (forgot to upgrade the version listed in the documentation) committed by abhikshah - forgot to upgrade the version listed in the documentation forgot to upgrade the version listed in the documentation Oct 11, 2008 r133 (Updating documentation, adding one manual test and increment...) committed by abhikshah - Updating documentation, adding one manual test and incrementing version to 1.0 before publication Updating documentation, adding one manual test and incrementing version to 1.0 before publication Sep 23, 2008 r132 (Making test.manual/test_scale.py easier to use) committed by abhikshah - Making test.manual/test_scale.py easier to use Making test.manual/test_scale.py easier to use Sep 22, 2008 r131 (Fixing the max_entropy discretizer (should update variable's...) committed by abhikshah - Fixing the max_entropy discretizer (should update variable's arity) Fixing the max_entropy discretizer (should update variable's arity) Sep 22, 2008 r130 (One more change to fix failing tests) committed by abhikshah - One more change to fix failing tests One more change to fix failing tests Sep 22, 2008 r129 (Making suggested changes before final submission to JMLR) committed by abhikshah - Making suggested changes before final submission to JMLR Making suggested changes before final submission to JMLR Sep 22, 2008 issue 28 (XGrid Controller prints lots of debug messages to stdout) reported by abhikshah - Also cleanup other modules. FIX: remove print statements. BETTER FIX: replace with logging statements (ticket for this already exists and this is a bigger task) Also cleanup other modules. FIX: remove print statements. BETTER FIX: replace with logging statements (ticket for this already exists and this is a bigger task) Sep 22, 2008 issue 27 ("Import pebl" should import all sub-modules) reported by abhikshah - This would make it possible to use tab-completion in Ipython so that users can introspect pebl easier. FIX: added imports in __init__.py This would make it possible to use tab-completion in Ipython so that users can introspect pebl easier. FIX: added imports in __init__.py Sep 22, 2008 issue 26 (network.is_acyclic fails on Windows) reported by abhikshah - If _network.c isn't compiled, there are no error reports and network.is_acyclic() fails Error reported by reviewer of pebl paper. FIX: use the python version of is_acyclic when "import _network" fails. The same solution is used with cpd.py and _cpd.c If _network.c isn't compiled, there are no error reports and network.is_acyclic() fails Error reported by reviewer of pebl paper. FIX: use the python version of is_acyclic when "import _network" fails. The same solution is used with cpd.py and _cpd.c Sep 21, 2008 issue 24 (Mermory Error for Large Network) Status changed by abhikshah - Fixed. configuration parameter localscore_cache.maxsize can be used to limit memory usage. Default (-1) means unlimited size and is appropriate for most uses. Status: Fixed Fixed. configuration parameter localscore_cache.maxsize can be used to limit memory usage. Default (-1) means unlimited size and is appropriate for most uses. Status: Fixed Jul 25, 2008 issue 25 (Pebl needs to use Logging (or have better output management)) reported by abhikshah - Use python's logging module (or something similar) to manage output. Currently, pebl is too silent and it's not obvious if it's working as expected or has failed until the process is finished. Use python's logging module (or something similar) to manage output. Currently, pebl is too silent and it's not obvious if it's working as expected or has failed until the process is finished.

issue 34 (pebl throws exception when trying to save results to html) reported by installe - What steps will reproduce the problem? 1. Save the attached data file as data.txt 2. Run the example code from the tutorial, i.e. >>> from pebl import data >>> from pebl.learner import greedy >>> dataset = data.fromfile("data.txt") >>> dataset.discretize() >>> learner = greedy.GreedyLearner(dataset) >>> result = learner.run() >>> result.tohtml("result") What is the expected output? What do you see instead? I expect pebl to save the html output in the "result" directory, as it does on "pebl-tutorial-data1.txt". Instead, it throws the following exception: Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/users/sista/ainstall/pkg/lib/python2.5/site-packages/pebl-1.01-py2.5-linux-x86_64.egg/pebl/result.py", line 150, in tohtml outdir or config.get('result.outdir') File "/users/sista/ainstall/pkg/lib/python2.5/site-packages/pebl-1.01-py2.5-linux-x86_64.egg/pebl/result.py", line 211, in htmlreport top.layout() File "/users/sista/ainstall/pkg/lib/python2.5/site-packages/pebl-1.01-py2.5-linux-x86_64.egg/pebl/network.py", line 289, in layout self.node_positions = [[int(i) for i in n.get_pos()[1:-1].split(',')] for n in nodes] ValueError: invalid literal for int() with base 10: '174.52' What version of the product are you using? On what operating system? Latest version from trunk. Please provide any additional information below.

What steps will reproduce the problem? 1. Save the attached data file as data.txt 2. Run the example code from the tutorial, i.e. >>> from pebl import data >>> from pebl.learner import greedy >>> dataset = data.fromfile("data.txt") >>> dataset.discretize() >>> learner = greedy.GreedyLearner(dataset) >>> result = learner.run() >>> result.tohtml("result") What is the expected output? What do you see instead? I expect pebl to save the html output in the "result" directory, as it does on "pebl-tutorial-data1.txt". Instead, it throws the following exception: Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/users/sista/ainstall/pkg/lib/python2.5/site-packages/pebl-1.01-py2.5-linux-x86_64.egg/pebl/result.py", line 150, in tohtml outdir or config.get('result.outdir') File "/users/sista/ainstall/pkg/lib/python2.5/site-packages/pebl-1.01-py2.5-linux-x86_64.egg/pebl/result.py", line 211, in htmlreport top.layout() File "/users/sista/ainstall/pkg/lib/python2.5/site-packages/pebl-1.01-py2.5-linux-x86_64.egg/pebl/network.py", line 289, in layout self.node_positions = [[int(i) for i in n.get_pos()[1:-1].split(',')] for n in nodes] ValueError: invalid literal for int() with base 10: '174.52' What version of the product are you using? On what operating system? Latest version from trunk. Please provide any additional information below.

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