Description of problem: When performing scientific computing/calculations, the scipy package is inappropriately writing commentary text to screen. Scipy is supposed to suppress screen commentary when disp==0, nonetheless, scipy is writing a lot of garbage text commentary to screen, destroying on-screen content. This problem was fixed upstream in April. I reported it as a bug in F18 but it was never fixed. It remains unfixed in F20. Version-Release number of selected component (if applicable): python3-scipy.x86_64 How reproducible: Always Steps to Reproduce: 1. Use scipy to perform scientific computing 2. Expect suppressed screen output 3. Ovserve unsuppressed screen output. Actual results: Scipy writes inappropriate commentary to screen. Expected results: Screen commentary suppressed. Additional info: Fixed upstream back in April 2013: https://github.com/scipy/scipy/issues/2261
Ah, so this isn't fixed until 0.13. So do we update F20 to 0.13.2 or just patch this. Any issues going from 0.12.1 to 0.13.2?
Created attachment 849097 [details] sample screen output with erroneous print to screen The attached sample screen output demonstrates the difference between the desired screen output (with successfully suppressed commentary as in previous versions of scipy) and the current screen output, which fails to suppress unwanted commentary written to screen.
Just wondering if any decision has been made about updating F20 to 0.13.2, or patching the current version. It's been three months since I filed the second bug report, and one year since the problem was fixed upstream... but the upstream fixes still aren't being incorporated into Fedora. A year seems like an unreasonably long time to wait for a bug that's been fixed upstream to be incorporated into a cutting-edge linux distribution.
this bug persists in F20 even though it was fixed upstream in April 2013 -- 18 months ago. I see that the new post-fix package will be part of F21. Is there any chance it could be added to the F20 stable repository?
scipy-0.12.1-2.fc20 has been submitted as an update for Fedora 20. https://admin.fedoraproject.org/updates/scipy-0.12.1-2.fc20
Package scipy-0.12.1-2.fc20: * should fix your issue, * was pushed to the Fedora 20 testing repository, * should be available at your local mirror within two days. Update it with: # su -c 'yum update --enablerepo=updates-testing scipy-0.12.1-2.fc20' as soon as you are able to. Please go to the following url: https://admin.fedoraproject.org/updates/FEDORA-2014-13772/scipy-0.12.1-2.fc20 then log in and leave karma (feedback).
Works for me. :) I left feedback, but it doesn't seem to have increased the karma count.
Yeah, you need to be logged in to make karma count. Thanks for testing though.
Found another problem. For the most part, all of the comments have now been silenced, with the exception of one: "ascent direction in projection gd = ..." This results in the interruption of on-screen data presentation. For example, I have a status bar that is displayed as one of scipy's functions iterates, which produces output that should look like this: Find Solutions : [****************] With the inappropriate writing of comments to screen, the output looks like this: Find Solutions : [ ascent direction in projection gd = 3.4351693296130657E-007 **** ascent direction in projection gd = 3.3637004228124568E-009 ascent direction in projection gd = 6.3770073492238517E-007 ** ascent direction in projection gd = 2.4667536965736238E-007 ascent direction in projection gd = 7.5293195786678251E-006 * ascent direction in projection gd = 2.0071489327006647E-008 *** ascent direction in projection gd = 6.2247249962986455E-008 ******
(In reply to bob from comment #9) > Found another problem. For the most part, all of the comments have now been > silenced, with the exception of one: > > "ascent direction in projection gd = ..." This is actually a warning or even an error. From the sources: c the directional derivative >=0. c Line search is impossible. write(6,*)' ascent direction in projection gd = ', gd So one can argue, if this should be printed to stderr instead... Yet this wouldn't solve your interruption as you would still redefine sys.stderr and write anything to /dev/null instead to the screen.
I also am interested in this bug. I have solutions whose convergence in optimize.fmin_l_bfgs_b() is very sensitive to small changes in input data. I notice the code above is in Fortran, meaning it could be a mature dusty deck that is thoroughly debugged. If so, why are there now problems with display debug spew, and Comment 10 hints that some could be warnings or errors? What is exactly the revision history of optimize.fmin_l_bfgs_b(), and why are there problems now? What functional testing is done to ensure integrity of fmin_l_bfgs_b()? Thanks. James
(In reply to James from comment #11) > I also am interested in this bug. > I have solutions whose convergence in optimize.fmin_l_bfgs_b() is very > sensitive to small changes in input data. > I notice the code above is in Fortran, meaning it could be a mature dusty > deck that is thoroughly debugged. If so, why are there now problems with > display debug spew, and Comment 10 hints that some could be warnings or > errors? The comments in the code hint that line search was not possible. For implications you could consult the source code or ask the scipy developers what that means. > What is exactly the revision history of optimize.fmin_l_bfgs_b(), and why > are there problems now? What functional testing is done to ensure integrity > of fmin_l_bfgs_b()? You can find the tests at [1] and full history of lbfgs at [2]. It seems, in a later commit [3], the scipy developers remove this print too, so I'll push a new update soonish. [1] https://github.com/scipy/scipy/tree/master/scipy/optimize/tests [2] https://github.com/scipy/scipy/commits/master/scipy/optimize/lbfgsb/ [3] https://github.com/scipy/scipy/commit/ea96f8697deea203675c44b3d24e427e552c4de7
Package scipy-0.12.1-3.fc20: * should fix your issue, * was pushed to the Fedora 20 testing repository, * should be available at your local mirror within two days. Update it with: # su -c 'yum update --enablerepo=updates-testing scipy-0.12.1-3.fc20' as soon as you are able to. Please go to the following url: https://admin.fedoraproject.org/updates/FEDORA-2014-13772/scipy-0.12.1-3.fc20 then log in and leave karma (feedback).
scipy-0.12.1-3.fc20 has been pushed to the Fedora 20 stable repository. If problems still persist, please make note of it in this bug report.