Steffen Möller pushed to branch master at Debian Med / nanoplot
Commits: d4514a62 by Steffen Moeller at 2020-07-05T22:29:53+02:00 Preparing for initial upload - - - - - 57b98e92 by Steffen Moeller at 2020-07-05T22:30:54+02:00 New upstream version 1.30.1 - - - - - a72e8e82 by Steffen Moeller at 2020-07-05T22:30:55+02:00 Update upstream source from tag 'upstream/1.30.1' Update to upstream version '1.30.1' with Debian dir 80dd594600b541882e3c5aad4a8973b2d599d7e5 - - - - - 10 changed files: - − NanoPlot.egg-info/SOURCES.txt - − NanoPlot.egg-info/requires.txt - debian/changelog - debian/control - debian/copyright - + debian/patches/DontInstallLicense.patch - − debian/patches/not-requiring-statsmodels.patch - debian/patches/series - debian/rules - debian/watch Changes: ===================================== NanoPlot.egg-info/SOURCES.txt deleted ===================================== @@ -1,26 +0,0 @@ -LICENSE -MANIFEST.in -README.md -README.rst -setup.py -NanoPlot.egg-info/PKG-INFO -NanoPlot.egg-info/SOURCES.txt -NanoPlot.egg-info/dependency_links.txt -NanoPlot.egg-info/entry_points.txt -NanoPlot.egg-info/requires.txt -NanoPlot.egg-info/top_level.txt -extra/color_options.txt -nanoplot/NanoPlot.py -nanoplot/__init__.py -nanoplot/filteroptions.py -nanoplot/utils.py -nanoplot/version.py -nanoplotter/__init__.py -nanoplotter/nanoplotter_main.py -nanoplotter/plot.py -nanoplotter/spatial_heatmap.py -nanoplotter/timeplots.py -scripts/add_barcodes_to_summary.py -scripts/sequencing_speed_only.py -scripts/split_summary_on_barcodes.py -scripts/test.sh \ No newline at end of file ===================================== NanoPlot.egg-info/requires.txt deleted ===================================== @@ -1,12 +0,0 @@ -biopython -pysam>0.10.0.0 -pandas>=0.22.0 -numpy -scipy -python-dateutil -seaborn>=0.10.1 -matplotlib>=3.1.3 -nanoget>=1.13.0 -nanomath>=0.23.1 -pauvre==0.2.0 -plotly>=4.1.0 ===================================== debian/changelog ===================================== @@ -1,9 +1,5 @@ nanoplot (1.30.1-1) UNRELEASED; urgency=medium - [ Andreas Tille ] - * Initial release (Closes: #<bug>) - - [ Steffen Moeller ] - * debhelper-compat 13 (routine-update) + * Initial release (Closes: #964345) -- Andreas Tille <ti...@debian.org> Wed, 22 Apr 2020 16:40:23 +0200 ===================================== debian/control ===================================== @@ -16,6 +16,7 @@ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/nanoplot Vcs-Git: https://salsa.debian.org/med-team/nanoplot.git Homepage: https://github.com/wdecoster/NanoPlot +Rules-Requires-Root: no Package: nanoplot Architecture: all ===================================== debian/copyright ===================================== @@ -1,6 +1,9 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: nanoplot Source: https://github.com/wdecoster/NanoPlot/releases +Files-Excluded: + NanoPlot.egg-info/SOURCES.txt + NanoPlot.egg-info/requires.txt Files: * Copyright: 2018 Wouter De Coster ===================================== debian/patches/DontInstallLicense.patch ===================================== @@ -0,0 +1,12 @@ +Index: nanoplot/setup.py +=================================================================== +--- nanoplot.orig/setup.py ++++ nanoplot/setup.py +@@ -50,6 +50,5 @@ setup( + 'console_scripts': [ + 'NanoPlot=nanoplot.NanoPlot:main', + ], +- }, +- data_files=[("", ["LICENSE"])] ++ } + ) ===================================== debian/patches/not-requiring-statsmodels.patch deleted ===================================== @@ -1,55 +0,0 @@ -Description: not requiring statsmodels - Statsmodel does not seem to handle well data coming from certain BAM files, - and upstream simply dropped requiring it. This solves the following as long - as python3-statsmodel is absent of the machine, but it reappears in case the - package is installed for whatever reason: - . - 2020-04-29 19:35:11,174 Selected KDE bandwidth is 0. Cannot estimate density. - 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/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. -Origin: upstream, https://github.com/wdecoster/NanoPlot/commit/da185a2e9d4f494987aedeb1eb15374cdbf99d7a -Bug: https://github.com/wdecoster/NanoPlot/issues/177 -Applied-Upstream: 1.29.1 -Last-Update: 2020-04-29 ---- -This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ ---- nanoplot.orig/setup.py -+++ nanoplot/setup.py -@@ -41,7 +41,7 @@ - 'nanoget>=1.9.0', - 'nanomath>=0.23.1', - "pauvre==0.1.86", -- "statsmodels==0.10.1", -+ #"statsmodels==0.10.1", - 'plotly>=4.1.0', - ], - package_data={'NanoPlot': []}, ===================================== debian/patches/series ===================================== @@ -1 +1 @@ -not-requiring-statsmodels.patch +DontInstallLicense.patch ===================================== debian/rules ===================================== @@ -23,3 +23,7 @@ override_dh_installexamples: find debian -name scripts -type d | xargs rm -rf dh_installexamples sed -i 's/^git clone/#&/' `find debian -name test.sh` + +override_dh_auto_clean: + dh_auto_clean + rm -f NanoPlot.egg-info/SOURCES.txt NanoPlot.egg-info/requires.txt ===================================== debian/watch ===================================== @@ -1,5 +1,6 @@ version=4 +opts="repack,compression=gz" \ https://pypi.python.org/simple/NanoPlot .*/NanoPlot-@ANY_VERSION@@ARCHIVE_EXT@#sha256=.* # Upstream does not tag releases properly :-( View it on GitLab: https://salsa.debian.org/med-team/nanoplot/-/compare/612411d72b7ea940566fc853bb5cd47b3f85e374...a72e8e822e0673c8e89db24bc48e3a38e45d172f -- View it on GitLab: https://salsa.debian.org/med-team/nanoplot/-/compare/612411d72b7ea940566fc853bb5cd47b3f85e374...a72e8e822e0673c8e89db24bc48e3a38e45d172f You're receiving this email because of your account on salsa.debian.org.
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