.gitignore

+*.py[cod]
+
+# C extensions
+*.so
+
+# Packages
+*.egg
+*.egg-info
+dist
+build
+eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+lib
+lib64
+
+# Installer logs
+pip-log.txt
+
+# Unit test / coverage reports
+.coverage
+.tox
+nosetests.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+
+#Latex
+*.aux
+*.glo
+*.idx
+*.log
+*.toc
+*.ist
+*.acn
+*.acr
+*.alg
+*.bbl
+*.blg
+*.dvi
+*.glg
+*.gls
+*.ilg
+*.ind
+*.lof
+*.lot
+*.maf
+*.mtc
+*.mtc1
+*.out
+*.synctex.gz
+*.pdf
+
+.env
+*.c
+_version_save.py
+
+htmlcov
+.eggs
+.cache
+.pytest_cache

ChangeLog.txt → CHANGELOG

+0.3.0
+ - Move from Python 2 to Python 3 (#12)
+ - Move to wxPython 4.0.1 (#12)
+ - Move from deprecated pyfits to astropy (#10)
+ - Support numpy 1.13
+ - Fix two spelling mistakes (#11)
+ - Cython code cleanup using flake8
+ - Bugfix: trailing photon events were not used (<1% of input data)
+ - Remove manual update checker
 0.2.3
  - New tool to create artificial .dat files for testing
  - A couple of minor bug fixes

LICENSE

+Copyright (C) 2011-2012  Paul Müller
+
+PyScanFCS 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 2 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.
+
+
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc., <http://fsf.org/>
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users.  This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it.  (Some other Free Software Foundation software is covered by
+the GNU Lesser General Public License instead.)  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
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+that everyone understands that there is no warranty for this free
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+want its recipients to know that what they have is not the original, so
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+   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
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+
+  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.  THE ENTIRE RISK AS
+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU.  SHOULD THE
+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+REPAIR OR CORRECTION.
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+  12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
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+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+                     END OF TERMS AND CONDITIONS

MANIFEST.in

-include doc/*.tex
-include doc/*.bib
-include doc/*.pdf
-include pyscanfcs/*.pyx
-include doc/Images/*
-include Readme.txt
-include ChangeLog.txt
+include CHANGELOG
+include LICENSE
+include README.rst
+recursive-include doc *.tex *.bib *.pdf *.md *.png *.svg
+recursive-include docs *.py *.md *.txt *.rst *.bib *.gif *.jpg *.png
+recursive-include tests *.py *.md *.dat
+prune docs/_build
+exclude docs/_version_save.py

README.md

-![PyScanFCS](https://raw.github.com/paulmueller/PyScanFCS/master/doc-src/Images/PyScanFCS_logo_dark.png)
-=========
-
-This repository contains the source code of PyScanFCS - a tool for data evaluation
-in perpendicular line scanning fluorescence correlation spectroscopy (FCS).
-
-When a membrane is scanned perpendicularly to its surface, the fluorescence signal
-originating from the membrane itself must be separated from the signal of the
-surrounding medium for an FCS analysis. PyScanFCS interactively extracts the
-fluctuating fluorescence signal from such measurements and applies a multiple-tau
-algorithm. The obtained correlation curves can be evaluated using
-[PyCorrFit](https://github.com/paulmueller/PyCorrFit).
-
-It is possible to create test-data containing exponentially correlated data with
-[MakeTestDat_SFCS.py](https://github.com/paulmueller/multipletau/blob/master/MakeTestDat_SFCS.py).
-The obtained correlation curves can be fitted with
-[PyCorrFit](https://github.com/paulmueller/PyCorrFit) using the
-[appropriate model function](https://github.com/paulmueller/multipletau/blob/master/ExampleFunc_Exp_correlated_noise.txt).
-
-For further information, please visit the PyScanFCS homepage at
-[http://pyscanfcs.craban.de](http://pyscanfcs.craban.de).
-
-- [Download the latest version](https://github.com/paulmueller/PyScanFCS/releases)
-- [Documentation](https://github.com/paulmueller/PyScanFCS/wiki/PyScanFCS_doc.pdf)
-- [Using Cython on Windows XP](https://github.com/paulmueller/PyScanFCS/wiki/Using-Cython-on-Windows-XP)

README.rst

+|PyScanFCS|
+===========
+
+|PyPI Version| |Build Status Win| |Build Status Travis| |Coverage Status| |Docs Status|
+
+A tool for data evaluation in perpendicular line scanning fluorescence correlation spectroscopy (FCS)
+
+When a membrane is scanned perpendicularly to its surface, the fluorescence signal
+originating from the membrane itself must be separated from the signal of the
+surrounding medium for an FCS analysis. PyScanFCS interactively extracts the
+fluctuating fluorescence signal from such measurements and applies a multiple-tau
+algorithm. The obtained correlation curves can be evaluated using
+`PyCorrFit <https://github.com/FCS-analysis/PyCorrFit>`__.
+
+Getting started
+===============
+
+Installation
+------------
+Installers for PyScanFCS are available at the `release page <https://github.com/FCS-analysis/PyScanFCS/releases>`__.
+
+Documentation
+-------------
+A detailed documentation including an explanation of the graphical user interface and available model
+functions is available as a `PDF file <https://github.com/FCS-analysis/PyScanFCS/wiki/PyScanFCS_doc.pdf>`__.
+
+
+
+.. |PyScanFCS| image:: https://raw.github.com/FCS-analysis/PyScanFCS/master/doc/Images/PyScanFCS_logo_dark.png
+.. |PyPI Version| image:: http://img.shields.io/pypi/v/PyScanFCS.svg
+   :target: https://pypi.python.org/pypi/pyscanfcs
+.. |Build Status Win| image:: https://img.shields.io/appveyor/ci/paulmueller/PyScanFCS/master.svg?label=win
+   :target: https://ci.appveyor.com/project/paulmueller/pyscanfcs
+.. |Build Status Travis| image:: https://img.shields.io/travis/FCS-analysis/PyScanFCS/master.svg?label=linux_osx
+   :target: https://travis-ci.org/FCS-analysis/PyScanFCS
+.. |Coverage Status| image:: https://img.shields.io/codecov/c/github/FCS-analysis/PyScanFCS/master.svg
+   :target: https://codecov.io/gh/FCS-analysis/PyScanFCS
+.. |Docs Status| image:: https://readthedocs.org/projects/pyscanfcs/badge/?version=latest
+   :target: https://readthedocs.org/projects/pyscanfcs/builds/

Readme.txt

-PyCorrFit can be used for analyzing data from perpendicular line
-scanning FCS.
-
-For a full list of features and supported file formats visit http://pyscanfcs.craban.de.
-There are also precompiled binaries for various systems.
-
-This package provides the Python module `pyscanfcs` and its graphical user interface. The 
-graphical user interface is written in wxPython.
-
-Installation and usage:
-
-    pip install pyscanfcs  
-    
-    python -m pyscanfcs

appveyor.yml

+clone_depth: 256
+build: off
+notifications:
+  - provider: Email
+    on_build_success: false
+    on_build_failure: false
+    on_build_status_changed: false
+environment:
+  matrix:
+    - PYTHON: "C:\\Miniconda36-x64"
+      PYTHON_VERSION: "3.6"
+      PYTHON_ARCH: "64"
+
+init:
+  - "ECHO %PYTHON% %PYTHON_VERSION% %PYTHON_ARCH%"
+
+install:
+  # Install InnoSetup and add to path
+  # Copied from
+  # https://github.com/Phonations/Joker/blob/master/appveyor.yml
+  - appveyor-retry choco install -y InnoSetup
+
+  # Prepend newly installed Python to the PATH of this build (this cannot be
+  # done from inside the powershell script as it would require to restart
+  # the parent CMD process).
+  - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
+
+  # CONDA installs
+  # Pinned versions are defined in .appveyor\pinned
+  - xcopy .appveyor\pinned %PYTHON%\conda-meta\ /Y
+  - "appveyor-retry conda install --yes --quiet matplotlib numpy pip scipy wxpython"
+  # Check that we have the expected version and architecture for Python
+  - "python --version"
+  - "pip install cython wheel"
+  - "pip install pyinstaller==3.3.1"
+  - "pip install -e ."
+  # Show the installed packages
+  - "pip freeze"
+
+test_script:
+  - "pip install coverage"
+  - "pip install codecov"
+  - "coverage run --source=pyscanfcs ./setup.py test"
+  - "coverage report -m"
+  - "codecov || exit 0"
+
+after_test:
+  # If tests are successful, create a whl package for the project.
+  - "python setup.py bdist_wheel"
+  - ps: "ls dist"
+  # Run pyinstaller
+  # This will create the "win7_innosetup.iss" file
+  - "pyinstaller -y --log-level=WARN .appveyor\\PyScanFCS_win7.spec"
+  # Create InnoSetup installers
+  # Set InnoSetup path here, because Cython complained about it.
+  - set PATH=%PATH%;"C:\\Program Files (x86)\\Inno Setup 5"
+  - iscc /Q win7_innosetup.iss
+
+artifacts:
+  # Archive the generated wheel package in the ci.appveyor.com build report.
+  - path: dist\*
+  # InnoSetup files
+  - path: Output\*
+
+deploy:
+  provider: GitHub
+  auth_token:
+    secure: TODO_not_set_yet
+  artifact: /.*\.exe/, /.*\.whl/
+  draft: true
+  prerelease: true
+  on:
+    branch: master                 # release from master branch only
+    appveyor_repo_tag: true        # deploy on tag push only

bin/pyscanfcs

-#!/bin/bash
-# go to this directory to prevent execution of a git checkout
-cd "$(dirname "$0")"
-python -m pyscanfcs

debian/changelog

+pyscanfcs (0.3.0+dfsg-1) UNRELEASED; urgency=medium
+
+  [ Steffen Möller ]
+  * Added new d/u/metadata file
+
+  [ Alexandre Mestiashvili ]
+  * Bump policy 4.1.4, update VCS-* fields to salsa
+  * Update Files-Excluded list in d/copyright
+  * New upstream version 0.3.0+dfsg
+  * Drop patches applied by upstream
+  * Update build-deps, use python3 modules, apply wrap-and-sort
+  * Bump compat to level 11
+  * Update d/rules to use python3, cleanup dh_install target
+  * Update d/pyscanfcs.docs
+  * Update d/source/options, ignore pyscanfcs/_version_save.py
+  * Update d/rules
+  * Update tests control file, use python3
+
+ -- Alexandre Mestiashvili <mestia@debian.org>  Thu, 31 May 2018 16:07:07 +0200
+
 pyscanfcs (0.2.3+dfsg-1) unstable; urgency=medium
 
   * Team upload.

debian/compat

-10
+11

debian/control

@@ -3,35 +3,35 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
 Section: python
 Priority: optional
-Build-Depends: python-setuptools,
-               python-all-dev,
+Build-Depends: cython3,
+               debhelper (>= 11),
                dh-python,
                faketime,
-               debhelper (>= 10),
-               cython,
-               python-matplotlib,
-               python-multipletau,
-               python-numpy,
-               python-astropy,
-               python-scipy,
-               python-wxgtk3.0,
                imagemagick,
                librsvg2-bin,
-               texlive-science,
+               python3-all-dev,
+               python3-astropy,
+               python3-matplotlib,
+               python3-multipletau,
+               python3-numpy,
+               python3-pytest-runner,
+               python3-scipy,
+               python3-setuptools,
+               python3-skimage,
+               python3-wxgtk4.0,
+               texlive-bibtex-extra,
+               texlive-fonts-recommended,
                texlive-latex-extra,
                texlive-latex-recommended,
-               texlive-fonts-recommended,
-               texlive-bibtex-extra
-Standards-Version: 4.1.1
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/pyscanfcs.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/pyscanfcs.git
+               texlive-science
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/pyscanfcs
+Vcs-Git: https://salsa.debian.org/med-team/pyscanfcs.git
 Homepage: https://fcs-analysis.github.io/PyScanFCS/
 
 Package: pyscanfcs
 Architecture: any
-Depends: ${misc:Depends},
-         ${python:Depends},
-         ${shlibs:Depends}
+Depends: ${misc:Depends}, ${python3:Depends}, ${shlibs:Depends}
 Description: scientific tool for perpendicular line scanning FCS
  When a membrane is scanned perpendicularly to its surface,
  the fluorescence signal originating from the membrane itself

debian/copyright

@@ -2,9 +2,11 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: PyScanFCS
 Source: https://github.com/FCS-analysis/PyScanFCS
 Files-Excluded:
- .gitignore
- .gitmodules
- freeze_pyinstaller
+ .appveyor/
+ .travis/
+ .appveyor.yml
+ .travis.yml
+ .readthedocs.yml
 
 Files: *
 Copyright: 2013 Paul Mueller <paul.mueller@biotec.tu-dresden.de>

debian/patches/Use-Astropy-in-place-of-Pyfits.patch

-From: Ole Streicher <olebole@debian.org>
-Date: Sat, 12 Nov 2016 11:14:23 +0100
-Subject: Use Astropy in place of Pyfits
-Forwarded: https://github.com/FCS-analysis/PyScanFCS/issues/10
-
-Pyfits is obsolete and will not get any upstream updates anymore. It is
-replaced by Astropy which provides a drop-in-replacement as astropy.io.fits.
----
- freeze_pyinstaller/debian_ubuntu_bundle_script.sh | 2 +-
- pyscanfcs/doc.py                                  | 4 ++--
- pyscanfcs/main.py                                 | 2 +-
- setup.py                                          | 2 +-
- 4 files changed, 5 insertions(+), 5 deletions(-)
-
---- a/pyscanfcs/doc.py
-+++ b/pyscanfcs/doc.py
-@@ -25,7 +25,7 @@ import multipletau
- import numpy
- import os
- import platform
--import pyfits
-+import astropy
- import scipy
- import sys
- 
-@@ -143,7 +143,7 @@ def SoftwareUsed():
-            "\n - matplotlib "+matplotlib.__version__+\
-            "\n - multipletau "+multipletau.__version__+\
-            "\n - NumPy "+numpy.__version__+\
--           "\n - PyFITS "+pyfits.__version__+\
-+           "\n - Astropy "+astropy.__version__+\
-            "\n - SciPy "+scipy.__version__+\
-            "\n - uilayer "+uilayer.__version__+\
-            "\n - wxPython "+wx.__version__
---- a/pyscanfcs/main.py
-+++ b/pyscanfcs/main.py
-@@ -57,7 +57,7 @@ import matplotlib.pyplot as plt
- import multipletau
- 
- import numpy as np                            # NumPy
--import pyfits
-+import astropy.io.fits as pyfits
- from scipy.fftpack import fft
- from scipy.fftpack import fftfreq
- # SFCSnumeric needs scipy.optimize
---- a/setup.py
-+++ b/setup.py
-@@ -65,7 +65,7 @@ setup(
-         "matplotlib >= 1.1.0",
-         "multipletau >= 0.1.4",
-         "NumPy >= 1.5.1",
--        "pyfits",
-+        "astropy",
-         "SciPy >= 0.8.0",
-         "wxPython >= 2.8.10.1"
-         ],

debian/patches/series

-Use-Astropy-in-place-of-Pyfits.patch

debian/pyscanfcs.docs

 doc/PyScanFCS_doc.pdf
-ChangeLog.txt
+README.rst

debian/rules

@@ -15,7 +15,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 pkg := pyscanfcs
 
 %:
-	dh $@ --with python2 --buildsystem=pybuild
+	dh $@ --with python3 --buildsystem=pybuild
 
 override_dh_auto_clean:
 	touch doc/PyScanFCS_doc.pdf
@@ -38,14 +38,10 @@ override_dh_install:
 	mv debian/pyscanfcs.xpm \
 		debian/$(pkg)/usr/share/pixmaps
 	chmod -R 644 debian/$(pkg)/usr/share/doc/$(pkg)/examples/misc
-	rm -f debian/$(pkg)/usr/lib/python2.7/dist-packages/pyscanfcs_doc/ChangeLog.txt
-	rm -f debian/$(pkg)/usr/lib/python2.7/dist-packages/pyscanfcs_doc/$(PDF)
-	ln -s /usr/share/doc/pyscanfcs/ChangeLog.txt debian/$(pkg)/usr/lib/python2.7/dist-packages/pyscanfcs_doc/ChangeLog.txt
-	ln -s /usr/share/doc/pyscanfcs/$(PDF) debian/$(pkg)/usr/lib/python2.7/dist-packages/pyscanfcs_doc/$(PDF)
 
 override_dh_fixperms:
 	dh_fixperms
-	chmod 644 debian/$(pkg)/usr/lib/python2.7/dist-packages/pyscanfcs/SFCSnumeric.pyx
+	chmod 644 debian/$(pkg)/usr/lib/python3/dist-packages/pyscanfcs/sfcs_alg.pyx
 
 override_dh_compress:
 	dh_compress -X$(PDF)

debian/source/options

-extend-diff-ignore="\.egg-info"
\ No newline at end of file
+extend-diff-ignore="\.egg-info|pyscanfcs/_version_save.py"

debian/tests/control

-Test-Command: set -e ; for py in $(pyversions -r 2>/dev/null) ; do cd "$ADTTMP" ; echo "Testing with $py:" ; $py -c "import pyscanfcs; print pyscanfcs" ; done
-Depends: python-all, pyscanfcs
+Test-Command: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$ADTTMP" ; echo "Testing with $py:" ; $py -c "import pyscanfcs; print pyscanfcs" ; done
+Depends: python3-all, pyscanfcs
 Restrictions: allow-stderr