[med-svn] [Git][med-team/nanoplot][master] 3 commits: Preparing for initial upload
Steffen Möller
gitlab at salsa.debian.org
Sun Jul 5 21:31:14 BST 2020
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 <tille at 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- at 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
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