Your message dated Sat, 02 May 2020 08:36:19 +0000 with message-id <[email protected]> and subject line Bug#959366: fixed in seaborn 0.10.1-1 has caused the Debian Bug report #959366, regarding python3-seaborn: Allow fallback to scipy when statsmodels is present and issues runtime errors to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 959366: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=959366 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: python3-seaborn Version: 0.10.0-1 Severity: important Tags: patch upstream Dear Maintainers, With certain datasets having a particular distribution, the seaborn library crashes with a runtime error, issued first by the python3-statsmodels library. statsmodels seems to expect the caller to trap the error and adapt its logic, but seaborn as available currently in Sid does not do so. There is a patch upstream that fixes this issue, available at the following location: https://github.com/mwaskom/seaborn/commit/09fef026ad89a299e13db44fa5b92885fb5b2823 This patch is part of seaborn 0.10.1, so getting this fix brought to Sid will just be a matter of upgrading to that version or later, hopefuly. This issue is preventing the autopkgtest base of NanoPlot, which is currently being packaged by the Debian Med Team, to run properly, hence the severity set to "important": https://salsa.debian.org/med-team/nanoplot The issue can be reproduced with building the nanoplot package, building the package python3-nanoget-examples which stores the test data, installing both on the system, and running the test. Here is the relevant part of the test output for reference: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/statsmodels/nonparametric/kde.py", line 451, in kdensityfft bw = float(bw) ValueError: could not convert string to float: 'scott' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/bin/NanoPlot", line 11, in <module> load_entry_point('NanoPlot==1.29.0', 'console_scripts', 'NanoPlot')() File "/usr/lib/python3/dist-packages/nanoplot/NanoPlot.py", line 96, in main plots = make_plots(datadf, settings) File "/usr/lib/python3/dist-packages/nanoplot/NanoPlot.py", line 227, in make_plots nanoplotter.scatter( File "/usr/lib/python3/dist-packages/nanoplotter/nanoplotter_main.py", line 193, in scatter plot = sns.jointplot( File "/usr/lib/python3/dist-packages/seaborn/axisgrid.py", line 2338, in jointplot grid.plot_marginals(kdeplot, **marginal_kws) File "/usr/lib/python3/dist-packages/seaborn/axisgrid.py", line 1823, in plot_marginals func(self.x, **kwargs) File "/usr/lib/python3/dist-packages/seaborn/distributions.py", line 703, in kdeplot ax = _univariate_kdeplot(data, shade, vertical, kernel, bw, File "/usr/lib/python3/dist-packages/seaborn/distributions.py", line 293, in _univariate_kdeplot x, y = _statsmodels_univariate_kde(data, kernel, bw, File "/usr/lib/python3/dist-packages/seaborn/distributions.py", line 367, in _statsmodels_univariate_kde kde.fit(kernel, bw, fft, gridsize=gridsize, cut=cut, clip=clip) File "/usr/lib/python3/dist-packages/statsmodels/nonparametric/kde.py", line 138, in fit density, grid, bw = kdensityfft(endog, kernel=kernel, bw=bw, File "/usr/lib/python3/dist-packages/statsmodels/nonparametric/kde.py", line 453, in kdensityfft bw = bandwidths.select_bandwidth(X, bw, kern) # will cross-val fit this pattern? File "/usr/lib/python3/dist-packages/statsmodels/nonparametric/bandwidths.py", line 174, in select_bandwidth raise RuntimeError(err) RuntimeError: Selected KDE bandwidth is 0. Cannot estimate density. Manually patching the file seaborn/distributions.py with upstream's approach to solving the problem allowed me to go through the autopkgtest suite of NanoPlot. Kind Regards, Étienne. -- System Information: Debian Release: bullseye/sid APT prefers unstable APT policy: (500, 'unstable'), (1, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386, riscv64 Kernel: Linux 5.5.6 (SMP w/4 CPU cores; PREEMPT) Locale: LANG=C.UTF-8, LC_CTYPE=C.UTF-8 (charmap=UTF-8), LANGUAGE=C.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages python3-seaborn depends on: ii python3 3.8.2-3 ii python3-matplotlib 3.2.1-1+b1 ii python3-numpy 1:1.18.3-1 ii python3-pandas 0.25.3+dfsg-9 ii python3-scipy 1.4.1-2 ii python3-tk 3.8.2-2 Versions of packages python3-seaborn recommends: ii python3-bs4 4.9.0-2 ii python3-patsy 0.5.1-1 python3-seaborn suggests no packages. Edited to add the package affecting the behavior of python3-seaborn, while not being referenced in its metadata: ii python3-statsmodels 0.11.1-2 -- no debconf information
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--- Begin Message ---Source: seaborn Source-Version: 0.10.1-1 Done: Andreas Tille <[email protected]> We believe that the bug you reported is fixed in the latest version of seaborn, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <[email protected]> (supplier of updated seaborn package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sat, 02 May 2020 10:00:57 +0200 Source: seaborn Architecture: source Version: 0.10.1-1 Distribution: unstable Urgency: medium Maintainer: Debian Science Maintainers <[email protected]> Changed-By: Andreas Tille <[email protected]> Closes: 959366 Changes: seaborn (0.10.1-1) unstable; urgency=medium . * Team upload. * New upstream version Closes: #959366 * Add salsa-ci file (routine-update) Checksums-Sha1: 503251f64ab220763aa7e74b5c3db139ccda8749 2227 seaborn_0.10.1-1.dsc f4ba035b1bd81d4b00c921cdde504d21ca849716 284553 seaborn_0.10.1.orig.tar.gz 9e8aaac647fab0dba1a514d408ca8165360b842a 5508 seaborn_0.10.1-1.debian.tar.xz fb5177811861a04603e215aaed87cd2fa59659ef 8948 seaborn_0.10.1-1_amd64.buildinfo Checksums-Sha256: 9ff6dce4a436770bce01c2d4b55ed112cf127060150d198c998575b208b4da0f 2227 seaborn_0.10.1-1.dsc 25bb4cd6d7d8cd2869354f6d61ce4b64cb60b10a84830ad0565cb35d87a537f0 284553 seaborn_0.10.1.orig.tar.gz 5e169329c1986abd6b32956e61896dc192fda385ff8e272d6a2ad5ebbddede56 5508 seaborn_0.10.1-1.debian.tar.xz e6ba2741fc6f68efb16648909e468bfb97b0f5859cca292958b56b12f10139cf 8948 seaborn_0.10.1-1_amd64.buildinfo Files: 6de6abc22c1ab2cbd160480a902e2b3a 2227 python optional seaborn_0.10.1-1.dsc 125586d58ef64fb47199d4eae71cbd69 284553 python optional seaborn_0.10.1.orig.tar.gz 1c0f874e9d184d6138f10a7a7a06914c 5508 python optional seaborn_0.10.1-1.debian.tar.xz 9e4ce71692f45809dc1d4d1612fd3049 8948 python optional seaborn_0.10.1-1_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl6tKusRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHNjQ//corZg30IW+tvCChhWdks5wVCeakw6Upc xaeUuujlDlFIWl+zNhVs2sv91iNA03QgfHUEys8jyOLzn+5Rd5LjEW4x833KL5I6 8RG1F9X7WFhWiehMtZs602EoeZT5b5ywcBs+CiYiK//SroKpl1os7FgbR6vBEeex zKejLKLqbl0yKX1AJugC4tJGbpx2tD+iTOJTReJUAPNzY4Py88JkBAR8Lzq0K9lT Lcd4qGzQSm4dL4PW+HAsF+i8xVmmpDiNjHrxSvo9nxkz4gQg3SRUyTuRCNkHrav8 C9CU/ozh58OpOyHaggEaAlhsUXdoWWmVBpQHkpwZ+DJ7TDCwhw6kfH0l9u/hvHKn P9Zn5IjKclMZNVaXkN9toEfOlscou0YsUm0CCK1i89fsgYZ0lVVuq4deTHJfiK2V Eq3qKmo5ApMRbjehnU6UO8EvFADMgbi3Sbj+GFyKO9WZbpS+Mhjz5IfRBJ7vAaEO cqfO8tHtr54yYSxykvSLki/pYMEuio7ffae2gewJVq/byoRlSObUsllkcBX+iPHN k9gENilhBRfAY6OrZng1OtUAH5HmNfrO+Bg1SdCHweFBPcX2TyPIUVtbE5zadiRJ unu6LH68X1RBO3ufoA01uC0rFaksPHIXxw1CA3UDYvI8M7SaAfAhiIlbCknc1hHu hRldCZK3tC4= =jDwR -----END PGP SIGNATURE-----
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