debian/0000755000000000000000000000000012071111270007156 5ustar debian/python-mzml-doc.70000644000000000000000000000337312071111270012315 0ustar .TH "PYTHON-MZML" "7" "October 2012" .SH "NAME" python\-mzml\-doc \- mzML mass spectrometric data parsing (documentation) .SH "DESCRIPTION" This manual page documents briefly the \fBpython\-mzml\-doc\fR package. This package contains the documentation for the \fBpython-mzml\fR software package. The documentation is provided in the form of source code (ReST files), in the form of HTML files and, finally, as a PDF\-formatted file. The files are located in \fI\%/usr/share/doc/python-mzml\-doc\fP. .SH "EXAMPLES" A number of useful examples are shipped within the \fBpython\-mzml\fR package and can be found at \fI\%/usr/share/doc/python-mzml/example_scripts\fP. A number of the examples make use of functions contained in get_example_file.py via an import of that file's contents. It is suggested to copy this directory to a temporary place and to run python from inside that new directory so as to gain access to the features contained in that get_example_file.py file through an import (which would not work otherwise). .PP .SH "BIBLIOGRAPHICAL REFERENCE TO BE CITED" Bald, T., Barth, J., Niehues, A., Specht, M., Hippler, M., and Fufezan, C. (2012) pymzML - Python module for high throughput bioinformatics on mass spectrometry data. \fIBioinformatics, UK\fP,28:1052-1053. doi:10.1093/bioinformatics/bts066. .SH "SEE ALSO" .BR python-mzml (7). .SH "AUTHOR" This manual page was written by Filippo Rusconi <\&lopippo@debian.org\&>\&. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 3 (GPL-3+), published by the Free Software Foundation. .PP On a Debian system the complete text of the GNU General Public License version 3 can be found in the file `\fI\%/usr/share/common-licenses/GPL\-3\fP'. debian/python-mzml-doc.install0000644000000000000000000000022112071111270013602 0ustar debian/doc/pymzml.pdf usr/share/doc/python-mzml-doc/ debian/doc/html/ usr/share/doc/python-mzml-doc/ README.txt usr/share/doc/python-mzml-doc/ debian/python-mzml-doc.doc-base0000644000000000000000000000071212071111270013616 0ustar Document: pymzml-documentation Title: python-mzml (pymzML) Documentation Author: Dr. Christian Fufezan and Colleagues Abstract: This documentation describes the uses and features of the Python extension module pymzML (Debian package python-mzml). Section: Science/Chemistry Format: PDF Files: /usr/share/doc/python-mzml-doc/pymzml.pdf Format: HTML Index: /usr/share/doc/python-mzml-doc/html/index.html Files: /usr/share/doc/python-mzml-doc/html/*.html debian/compat0000644000000000000000000000000212071111270010354 0ustar 7 debian/python-mzml.lintian-overrides0000644000000000000000000000011412071111270015030 0ustar python-mzml binary: no-upstream-changelog package-contains-empty-directory debian/python-mzml-doc.lintian-overrides0000644000000000000000000000006012071111270015573 0ustar python-mzml-doc binary: no-upstream-changelog debian/python-mzml.70000644000000000000000000000411412071111270011544 0ustar .TH "PYTHON-MZML" "7" "October 2012" .SH "NAME" python\-mzml \- mzML mass spectrometric data parsing .SH "DESCRIPTION" This manual page documents briefly the \fBpython\-mzml\fR package that packages the pymzML Python extension. .PP pymzML is an extension to Python that offers: .HP 4 \- easy access to mass spectrometry (MS) data that allows the rapid development of tools; .PP \- a very fast parser for mzML data, the standard in mass spectrometry data format; .PP \- a set of functions to compare or handle spectra. .PP pymzML requires Python2.6.5+ and is fully compatible with Python3. The module is freely available on pymzml.github.com or pypi, published under LGPL and requires no additional modules to be installed. .PP The documentation of this Python extension is packaged in the \fBpython\-mzml\-doc\fR package. .PP .SH "EXAMPLES" A number of useful examples are shipped within the \fBpython\-mzml\fR package and can be found at \fI\%/usr/share/doc/python-mzml/example_scripts\fP. A number of the examples make use of functions contained in get_example_file.py via an import of that file's contents. It is suggested to copy this directory to a temporary place and to run python from inside that new directory so as to gain access to the features contained in that get_example_file.py file through an import (which would not work otherwise). .PP .SH "BIBLIOGRAPHICAL REFERENCE TO BE CITED" Bald, T., Barth, J., Niehues, A., Specht, M., Hippler, M., and Fufezan, C. (2012) pymzML - Python module for high throughput bioinformatics on mass spectrometry data. \fIBioinformatics, UK\fP,28:1052-1053. doi:10.1093/bioinformatics/bts066. .SH "SEE ALSO" .BR python-mzml-doc (7). .SH "AUTHOR" This manual page was written by Filippo Rusconi <\&lopippo@debian.org\&>\&. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 3 (GPL-3+), published by the Free Software Foundation. .PP On a Debian system the complete text of the GNU General Public License version 3 can be found in the file `\fI\%/usr/share/common-licenses/GPL\-3\fP'. debian/rules0000755000000000000000000000210712071111270010236 0ustar #!/usr/bin/make -f TMPDIR="debian/tmp" DOCDIR="debian/doc" SRCDIR=$(CURDIR) %: dh $@ --with python2 --buildsystem=python_distutils # dh_compress insists on compressing that file: override_dh_compress: dh_compress -X get_example_file.py -X pymzml.pdf override_dh_install: dh_install -iv -O--buildsystem=python_distutils ls -lR debian/python-mzml/usr/share/doc/python-mzml/example_scripts/ # Remove the symbolic link. rm debian/python-mzml/usr/share/doc/python-mzml/example_scripts/pymzml # Remove the license file rm -f debian/python-mzml/usr/share/doc/python-mzml/COPYING.txt rm -f debian/python-mzml-doc/usr/share/doc/python-mzml-doc/COPYING.txt override_dh_auto_build-indep: cp -prf Documentation_src Documentation_src-bkp && \ rm -rf Documentation_src/build/* && \ cd Documentation_src && \ make html latexpdf && \ cd $(SRCDIR) && \ mkdir -p $(DOCDIR) && \ rm -rf $(DOCDIR)/* && \ cp -rpvf Documentation_src/build/html $(DOCDIR) && \ cp -v Documentation_src/build/latex/pymzml.pdf $(DOCDIR) && \ rm -rf Documentation_src && \ mv Documentation_src-bkp Documentation_src debian/python-mzml-doc.manpages0000644000000000000000000000003112071111270013726 0ustar debian/python-mzml-doc.7 debian/upstream0000644000000000000000000000105412071111270010741 0ustar Reference: Author: Bald, T., Barth, J., Niehues, A., Specht, M., Hippler, M., and Fufezan, C. Title: pymzML - Python module for high throughput bioinformatics on mass spectrometry data Journal: Bioinformatics, UK Year: 2012 Volume: 28 Number: 7 Pages: 1052-1053 DOI: 10.1093/bioinformatics/bts066 PMID: 22302572 URL: http://bioinformatics.oxfordjournals.org/content/25/20/2741.long eprint: http://bioinformatics.oxfordjournals.org/content/early/2012/02/02/bioinformatics.bts066.full.pdf Repository : https://github.com/pymzml/pymzML debian/python-mzml.install0000644000000000000000000000017112071111270013043 0ustar usr/lib/python2.*/dist-packages/pymzml README.txt usr/share/doc/python-mzml example_scripts usr/share/doc/python-mzml/ debian/python-mzml-doc.links0000644000000000000000000000031112071111270013254 0ustar /usr/share/javascript/underscore/underscore.js /usr/share/doc/python-mzml-doc/html/_static/underscore.js /usr/share/javascript/jquery/jquery.js /usr/share/doc/python-mzml-doc/html/_static/jquery.js debian/control0000644000000000000000000000360112071111270010561 0ustar Source: python-mzml Maintainer: The Debichem Group Uploaders: Filippo Rusconi Section: python Priority: optional Build-Depends: python-all (>= 2.6.6-3), debhelper (>= 7.0.50~), dpkg-dev (>= 1.16.1~), python-sphinx (>= 1.1.3) Build-Depends-Indep: doxygen (>= 1.8.1.2), texlive-extra-utils, texlive-latex-extra, latex-xcolor, texlive-font-utils, ghostscript, texlive-fonts-recommended Standards-Version: 3.9.3 Homepage: http://pymzml.github.com/ Vcs-Git: git://git.debian.org/git/debichem/packages/python-mzml.git Vcs-Browser: http://git.debian.org/?p=debichem/packages/python-mzml.git Package: python-mzml Architecture: all Depends: ${misc:Depends}, ${python:Depends} Suggests: python-mzml-doc Description: mzML mass spectrometric data parsing python-mzml is an extension to Python that offers: - easy access to mass spectrometry (MS) data that allows the rapid development of tools; - a very fast parser for mzML data, the standard in mass spectrometry data format; - a set of functions to compare or handle spectra. Package: python-mzml-doc Section: doc Architecture: all Depends: libjs-jquery, libjs-underscore, ${shlibs:Depends}, ${misc:Depends} Description: mzML mass spectrometric data parsing - documentation python-mzml is an extension to Python that offers: - easy access to mass spectrometry (MS) data that allows the rapid development of tools; - a very fast parser for mzML data, the standard in mass spectrometry data format; - a set of functions to compare or handle spectra. . This package contains the documentation in PDF and HTML format, along with the text sources (process with sphinx). debian/changelog0000644000000000000000000000135112071111270011030 0ustar python-mzml (0.7.4-dfsg-2) unstable; urgency=low * python-mzml.install: change the usr/lib/python2.[67]/dist-packages install directories to the degenerate form usr/lib/python2.*/dist-packages/pymzml. The package will still build and install fine when 2.6 is removed. Thanks to Dmitry Shachnev for suggesting the fix. Closes: #697189. -- Filippo Rusconi Wed, 02 Jan 2013 20:38:47 +0100 python-mzml (0.7.4-dfsg-1) unstable; urgency=low * Initial packaging of the pymzML software with COPYING file shipped for the first time within the source code tree after request to upstream. Closes: #690177. -- Filippo Rusconi Tue, 09 Oct 2012 22:38:41 +0200 debian/source/0000755000000000000000000000000012071111270010456 5ustar debian/source/format0000644000000000000000000000001412071111270011664 0ustar 3.0 (quilt) debian/source/include-binaries0000644000000000000000000000222112071111270013613 0ustar debian/python-pymzml-doc/usr/share/doc/python-mzml-doc/pymzml.pdf debian/python-pymzml-doc/usr/share/doc/python-mzml-doc/html/html/objects.inv debian/python-pymzml-doc/usr/share/doc/python-mzml-doc/html/html/_images/plot.png debian/python-pymzml-doc/usr/share/doc/python-mzml-doc/html/html/_static/up.png debian/python-pymzml-doc/usr/share/doc/python-mzml-doc/html/html/_static/up-pressed.png debian/python-pymzml-doc/usr/share/doc/python-mzml-doc/html/html/_static/ajax-loader.gif debian/python-pymzml-doc/usr/share/doc/python-mzml-doc/html/html/_static/comment-bright.png debian/python-pymzml-doc/usr/share/doc/python-mzml-doc/html/html/_static/comment-close.png debian/python-pymzml-doc/usr/share/doc/python-mzml-doc/html/html/_static/down-pressed.png debian/python-pymzml-doc/usr/share/doc/python-mzml-doc/html/html/_static/comment.png debian/python-pymzml-doc/usr/share/doc/python-mzml-doc/html/html/_static/minus.png debian/python-pymzml-doc/usr/share/doc/python-mzml-doc/html/html/_static/plus.png debian/python-pymzml-doc/usr/share/doc/python-mzml-doc/html/html/_static/file.png debian/python-pymzml-doc/usr/share/doc/python-mzml-doc/html/html/_static/down.png debian/copyright0000644000000000000000000000405112071111270011111 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: pymzML Upstream-Contact: Dr. Christian Fufezan (christian@fufezan.net) Source: http://pymzml.github.com/dist/pymzml.tar.bz2 Files: * Copyright: 2010-2011 T. Bald 2010-2011 J. Barth 2010-2011 A. Niehues 2010-2011 M. Specht 2010-2011 M. Hippler 2010-2011 C. Fufezan (christian@fufezan.net) License: LGPL This program is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU Lesser General Public License along with this program. If not, see . . On Debian systems, the full text of the GNU General Public License version 3 can be found in the file `/usr/share/common-licenses/LGPL-3'. Files: debian/* Copyright: 2012 Filippo Rusconi (lopippo@debian.org) License: GPL-3+ This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . . On Debian systems, the full text of the GNU General Public License version 2 can be found in the file `/usr/share/common-licenses/GPL-3'. debian/python-mzml.manpages0000644000000000000000000000002512071111270013166 0ustar debian/python-mzml.7 debian/python-mzml-doc.dirs0000644000000000000000000000001612071111270013077 0ustar usr/share/doc