lmfit-py (0.9.5+dfsg-2) unstable; urgency=medium

  * Standards-Verion bumped to 3.9.8 (nothing to do)
  * Removed ipython(3)-notebook dependency (Closes: #840521)
  * Removed matplotlib, tk, latex, pandas Build-Depends (useless)
  * Simplified d/rules

[dgit import unpatched lmfit-py 0.9.5+dfsg-2]

12 files changed, 394 insertions, 0 deletions

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..accd0c8
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,53 @@
+lmfit-py (0.9.5+dfsg-2) unstable; urgency=medium
+
+  * Standards-Verion bumped to 3.9.8 (nothing to do)
+  * Removed ipython(3)-notebook dependency (Closes: #840521)
+  * Removed matplotlib, tk, latex, pandas Build-Depends (useless)
+  * Simplified d/rules
+
+ -- Picca Frédéric-Emmanuel <picca@debian.org>  Sat, 15 Oct 2016 09:01:40 +0200
+
+lmfit-py (0.9.5+dfsg-1) unstable; urgency=medium
+
+  * Imported Upstream version 0.9.5+dfsg
+
+ -- Picca Frédéric-Emmanuel <picca@debian.org>  Wed, 17 Aug 2016 08:29:47 +0200
+
+lmfit-py (0.9.3+dfsg-1) unstable; urgency=medium
+
+  * Imported Upstream version 0.9.3+dfsg
+  * fix the autopkgtest scripts
+  * Use cme to update the package
+  * Standards-Verion bumped to 3.9.7 (nothing to do)
+
+ -- Picca Frédéric-Emmanuel <picca@debian.org>  Thu, 31 Mar 2016 18:46:36 +0200
+
+lmfit-py (0.9.2+dfsg-1) unstable; urgency=medium
+
+  * Imported Upstream version 0.9.2+dfsg (Closes: #802085)
+  * Use the pypi redirector
+
+ -- Picca Frédéric-Emmanuel <picca@debian.org>  Sat, 31 Oct 2015 08:20:22 +0100
+
+lmfit-py (0.8.3+dfsg.1-1~exp1) experimental; urgency=medium
+
+  * Imported Upstream version 0.8.3+dfsg.1
+  * Run the test suite during the build
+  * Standards-Version bumped to 3.9.6 (no other changes required)
+  * Add the autopkgtest test suite.
+
+ -- Picca Frédéric-Emmanuel <picca@debian.org>  Thu, 30 Dec 2014 14:18:53 +0100
+
+lmfit-py (0.8.0+dfsg.1-1) unstable; urgency=medium
+
+  * Imported Upstream version 0.8.0+dfsg.1
+  * Remove all patches (applyed upstream)
+  * Add the doc-base registration
+
+ -- Picca Frédéric-Emmanuel <picca@debian.org>  Sun, 31 Aug 2014 10:56:03 +0200
+
+lmfit-py (0.7.4+dfsg.2-1) unstable; urgency=low
+
+  * Initial release (Closes: #741078)
+
+ -- Picca Frédéric-Emmanuel <picca@debian.org>  Fri, 07 Mar 2014 09:05:26 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..968ab06
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,196 @@
+Source: lmfit-py
+Maintainer: Debian Science Maintainers <debian-science-maintainers@lists.alioth.debian.org>
+Uploaders: Picca Frédéric-Emmanuel <picca@debian.org>
+Section: science
+Testsuite: autopkgtest
+Priority: extra
+Build-Depends: debhelper (>= 9),
+               dh-python,
+               python-all,
+               python-nose,
+               python-numpy,
+               python-pandas,
+               python-scipy,
+               python-setuptools,
+               python-sphinx,
+               python3-all,
+               python3-nose,
+               python3-numpy,
+               python3-pandas,
+               python3-scipy,
+               python3-setuptools,
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-science/packages/lmfit-py.git
+Vcs-Git: https://anonscm.debian.org/git/debian-science/packages/lmfit-py.git
+Homepage: http://lmfit.github.io/lmfit-py/
+X-Python-Version: >= 2.6
+X-Python3-Version: >= 3.2
+
+Package: python-lmfit
+Architecture: all
+Section: python
+Depends: ${misc:Depends},
+         ${python:Depends},
+         python-scipy
+Suggests: python-lmfit-doc
+Description: Least-Squares Minimization with Constraints (Python 2)
+ The lmfit Python package provides a simple, flexible interface to
+ non-linear optimization or curve fitting problems. The package
+ extends the optimization capabilities of scipy.optimize by replacing
+ floating pointing values for the variables to be optimized with
+ Parameter objects. These Parameters can be fixed or varied, have
+ upper and/or lower bounds placed on its value, or written as an
+ algebraic expression of other Parameters.
+ .
+ The principal advantage of using Parameters instead of simple
+ variables is that the objective function does not have to be
+ rewritten to reflect every change of what is varied in the fit, or
+ what relationships or constraints are placed on the Parameters. This
+ means a scientific programmer can write a general model that
+ encapsulates the phenomenon to be optimized, and then allow user of
+ that model to change what is varied and fixed, what range of values
+ is acceptable for Parameters, and what constraints are placed on the
+ model. The ease with which the model can be changed also allows one
+ to easily test the significance of certain Parameters in a fitting
+ model.
+ .
+ The lmfit package allows a choice of several optimization methods
+ available from scipy.optimize. The default, and by far best tested
+ optimization method used is the Levenberg-Marquardt algorithm from
+ from MINPACK-1 as implemented in scipy.optimize.leastsq. This method
+ is by far the most tested and best support method in lmfit, and much
+ of this document assumes this algorithm is used unless explicitly
+ stated. An important point for many scientific analysis is that this
+ is only method that automatically estimates uncertainties and
+ correlations between fitted variables from the covariance matrix
+ calculated during the fit.
+ .
+ A few other optimization routines are also supported, including
+ Nelder-Mead simplex downhill, Powell's method, COBYLA, Sequential
+ Least Squares methods as implemented in scipy.optimize.fmin, and
+ several others from scipy.optimize. In their native form, some of
+ these methods setting allow upper or lower bounds on parameter
+ variables, or adding constraints on fitted variables. By using
+ Parameter objects, lmfit allows bounds and constraints for all of
+ these methods, and makes it easy to swap between methods without
+ hanging the objective function or set of Parameters.
+ .
+ Finally, because the approach derived from MINPACK-1 usin the
+ covariance matrix to determine uncertainties is sometimes questioned
+ (and sometimes rightly so), lmfit supports methods to do a brute
+ force search of the confidence intervals and correlations for sets of
+ parameters.
+ .
+ This is the Python 2 version of the package.
+
+Package: python3-lmfit
+Architecture: all
+Section: python
+Depends: ${misc:Depends},
+         ${python3:Depends},
+         python3-scipy
+Suggests: python-lmfit-doc
+Description: Least-Squares Minimization with Constraints (Python 3)
+ The lmfit Python package provides a simple, flexible interface to
+ non-linear optimization or curve fitting problems. The package
+ extends the optimization capabilities of scipy.optimize by replacing
+ floating pointing values for the variables to be optimized with
+ Parameter objects. These Parameters can be fixed or varied, have
+ upper and/or lower bounds placed on its value, or written as an
+ algebraic expression of other Parameters.
+ .
+ The principal advantage of using Parameters instead of simple
+ variables is that the objective function does not have to be
+ rewritten to reflect every change of what is varied in the fit, or
+ what relationships or constraints are placed on the Parameters. This
+ means a scientific programmer can write a general model that
+ encapsulates the phenomenon to be optimized, and then allow user of
+ that model to change what is varied and fixed, what range of values
+ is acceptable for Parameters, and what constraints are placed on the
+ model. The ease with which the model can be changed also allows one
+ to easily test the significance of certain Parameters in a fitting
+ model.
+ .
+ The lmfit package allows a choice of several optimization methods
+ available from scipy.optimize. The default, and by far best tested
+ optimization method used is the Levenberg-Marquardt algorithm from
+ from MINPACK-1 as implemented in scipy.optimize.leastsq. This method
+ is by far the most tested and best support method in lmfit, and much
+ of this document assumes this algorithm is used unless explicitly
+ stated. An important point for many scientific analysis is that this
+ is only method that automatically estimates uncertainties and
+ correlations between fitted variables from the covariance matrix
+ calculated during the fit.
+ .
+ A few other optimization routines are also supported, including
+ Nelder-Mead simplex downhill, Powell's method, COBYLA, Sequential
+ Least Squares methods as implemented in scipy.optimize.fmin, and
+ several others from scipy.optimize. In their native form, some of
+ these methods setting allow upper or lower bounds on parameter
+ variables, or adding constraints on fitted variables. By using
+ Parameter objects, lmfit allows bounds and constraints for all of
+ these methods, and makes it easy to swap between methods without
+ hanging the objective function or set of Parameters.
+ .
+ Finally, because the approach derived from MINPACK-1 usin the
+ covariance matrix to determine uncertainties is sometimes questioned
+ (and sometimes rightly so), lmfit supports methods to do a brute
+ force search of the confidence intervals and correlations for sets of
+ parameters.
+ .
+ This is the Python 3 version of the package.
+
+Package: python-lmfit-doc
+Architecture: all
+Section: doc
+Depends: ${misc:Depends},
+         ${sphinxdoc:Depends}
+Description: Least-Squares Minimization with Constraints (Documentation)
+ The lmfit Python package provides a simple, flexible interface to
+ non-linear optimization or curve fitting problems. The package
+ extends the optimization capabilities of scipy.optimize by replacing
+ floating pointing values for the variables to be optimized with
+ Parameter objects. These Parameters can be fixed or varied, have
+ upper and/or lower bounds placed on its value, or written as an
+ algebraic expression of other Parameters.
+ .
+ The principal advantage of using Parameters instead of simple
+ variables is that the objective function does not have to be
+ rewritten to reflect every change of what is varied in the fit, or
+ what relationships or constraints are placed on the Parameters. This
+ means a scientific programmer can write a general model that
+ encapsulates the phenomenon to be optimized, and then allow user of
+ that model to change what is varied and fixed, what range of values
+ is acceptable for Parameters, and what constraints are placed on the
+ model. The ease with which the model can be changed also allows one
+ to easily test the significance of certain Parameters in a fitting
+ model.
+ .
+ The lmfit package allows a choice of several optimization methods
+ available from scipy.optimize. The default, and by far best tested
+ optimization method used is the Levenberg-Marquardt algorithm from
+ from MINPACK-1 as implemented in scipy.optimize.leastsq. This method
+ is by far the most tested and best support method in lmfit, and much
+ of this document assumes this algorithm is used unless explicitly
+ stated. An important point for many scientific analysis is that this
+ is only method that automatically estimates uncertainties and
+ correlations between fitted variables from the covariance matrix
+ calculated during the fit.
+ .
+ A few other optimization routines are also supported, including
+ Nelder-Mead simplex downhill, Powell's method, COBYLA, Sequential
+ Least Squares methods as implemented in scipy.optimize.fmin, and
+ several others from scipy.optimize. In their native form, some of
+ these methods setting allow upper or lower bounds on parameter
+ variables, or adding constraints on fitted variables. By using
+ Parameter objects, lmfit allows bounds and constraints for all of
+ these methods, and makes it easy to swap between methods without
+ hanging the objective function or set of Parameters.
+ .
+ Finally, because the approach derived from MINPACK-1 usin the
+ covariance matrix to determine uncertainties is sometimes questioned
+ (and sometimes rightly so), lmfit supports methods to do a brute
+ force search of the confidence intervals and correlations for sets of
+ parameters.
+ .
+ This is the common documentation package.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..5276e16
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,73 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: LM-Fit Development Team
+Upstream-Contact: matt.newville@gmail.com
+Source: http://lmfit.github.io/lmfit-py/
+Files-Excluded: doc/sphinx/apigen.py doc/sphinx/github.py doc/sphinx/numpydoc
+
+Files: debian/*
+Copyright: © 2014, Picca Frédéric-Emmanuel <picca@debian.org>
+License: Expat
+
+Files: *
+Copyright: 2012-2014 Matthew Newville, The University of Chicago
+                     Till Stensitzki, Freie Universitat Berlin
+License: Expat
+
+Files: ./lmfit/ordereddict.py
+Copyright: 2009, Raymond Hettinger
+License: Expat
+
+Files: ./lmfit/uncertainties/*
+Copyright: 2010-2013, Eric O. LEBIGOT (EOL)
+License: BSD-3-clause
+
+License: BSD-3-clause
+ All rights reserved.
+ .
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ .
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+ .
+    * Redistributions in binary form must reproduce the above
+      copyright notice, this list of conditions and the following
+      disclaimer in the documentation and/or other materials provided
+      with the distribution.
+ .
+    * The names of its contributors may not be used to endorse or
+      promote products derived from this software without specific
+      prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+ INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+ BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
+ OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED
+ AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY
+ WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ POSSIBILITY OF SUCH DAMAGE.
+
+License: Expat
+ Permission to use and redistribute the source code or binary forms of
+ this software and its documentation, with or without modification is
+ hereby granted provided that the above notice of copyright, these
+ terms of use, and the disclaimer of warranty below appear in the
+ source code and documentation, and that none of the names of above
+ institutions or authors appear in advertising or endorsement of works
+ derived from this software without specific prior written permission
+ from all parties.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THIS
+ SOFTWARE.
diff --git a/debian/python-lmfit-doc.doc-base b/debian/python-lmfit-doc.doc-base
new file mode 100644
index 0000000..8e6dcb1
--- /dev/null
+++ b/debian/python-lmfit-doc.doc-base
@@ -0,0 +1,9 @@
+Document: lmfit-py-manual
+Title: lmfit-py documentation manual
+Author: Matthew Newville <newville@cars.uchicago.edu>
+Abstract: Simple Least Squares Minimization, with flexible Parameter settings, based on scipy.optimize.leastsq
+Section: Text
+
+Format: HTML
+Index: /usr/share/doc/python-lmfit-doc/html/index.html
+Files: /usr/share/doc/python-lmfit-doc/html/*
diff --git a/debian/python-lmfit-doc.docs b/debian/python-lmfit-doc.docs
new file mode 100644
index 0000000..b2dbf19
--- /dev/null
+++ b/debian/python-lmfit-doc.docs
@@ -0,0 +1 @@
+build/html
\ No newline at end of file
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..e280670
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,30 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+## Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+#export NOSE_VERBOSE=2
+
+export PYBUILD_NAME=lmfit
+
+## This might have been used, but doctest should be optional
+## https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=749506
+#export PYBUILD_TEST_NOSE=1
+
+# copy the tests to the build dir to be able to pass nose
+export PYBUILD_AFTER_BUILD=cp -r NIST_STRD {build_dir}
+export PYBUILD_BEFORE_INSTALL=rm -fr {build_dir}/NIST_STRD
+export PYBUILD_AFTER_INSTALL_python2=dh_numpy
+export PYBUILD_AFTER_INSTALL_python3=dh_numpy3
+
+%:
+	dh $@ --with python2,python3,sphinxdoc --buildsystem=pybuild
+
+override_dh_clean:
+	rm -rf doc/_static/conf_interval2.png
+	rm -rf doc/_static/conf_interval.png
+	dh_clean
+
+override_dh_auto_build:
+	dh_auto_build
+	PYTHONPATH=. http_proxy='localhost' sphinx-build -N -bhtml doc/ build/html  # HTML generator
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..5583f53
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,5 @@
+Tests: python2
+Depends: python-lmfit, python-all, python-tk, python-nose, python-matplotlib, python-pandas, python-scipy
+
+Tests: python3
+Depends: python3-lmfit, python3-all, python3-tk, python3-nose, python3-matplotlib, python3-pandas, python3-scipy
diff --git a/debian/tests/python2 b/debian/tests/python2
new file mode 100755
index 0000000..186b763
--- /dev/null
+++ b/debian/tests/python2
@@ -0,0 +1,10 @@
+#!/bin/sh
+set -e -u
+
+cp -a  NIST_STRD/ "$ADTTMP"
+cd "$ADTTMP/NIST_STRD"
+
+for python in $(pyversions -i); do
+        PYTHONWARNINGS=d $python /usr/bin/nosetests -v 2>&1
+done
+
diff --git a/debian/tests/python3 b/debian/tests/python3
new file mode 100755
index 0000000..41b20e0
--- /dev/null
+++ b/debian/tests/python3
@@ -0,0 +1,10 @@
+#!/bin/sh
+set -e -u
+
+cp -a  NIST_STRD/ "$ADTTMP"
+cd "$ADTTMP/NIST_STRD"
+
+for python in $(py3versions -i); do
+        PYTHONWARNINGS=d $python /usr/bin/nosetests3 -v 2>&1
+done
+
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..ed7610b
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,5 @@
+version=3
+opts=repacksuffix=+dfsg,\
+dversionmangle=s/.dfsg//,\
+uversionmangle=s/(rc|a|b|c)/~$1/ \
+http://pypi.debian.net/lmfit/lmfit-(.+)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))