Merge pull request #165 from FCS-analysis/develop

version 0.9.9

Author: Paul Müller

.travis.yml

@@ -30,42 +30,57 @@ before_install:
 # a lot of cool formulae for scientific tools
 #- brew tap homebrew/science
 # numpy, scipy, matplotlib, ...
-- brew tap homebrew/python
-- brew tap homebrew/dupes
-- brew update
+#- brew tap homebrew/python
+#- brew tap homebrew/dupes
+#- brew update
 #- brew update && brew upgrade
-- brew install python --universal --framework
+#- brew install python --universal --framework
 #- brew install wget
-- which python
-- python --version
-- export VERSIONER_PYTHON_PREFER_32_BIT=no
-- defaults write com.apple.versioner.python Prefer-32-Bit -bool no
+#- which python
+#- python --version
+#- export VERSIONER_PYTHON_PREFER_32_BIT=no
+#- defaults write com.apple.versioner.python Prefer-32-Bit -bool no
 
 install:
-- brew unlink gcc
-- brew install gcc --universal
-- brew install freetype --universal
-#- brew install numpy --universal
-#- brew install scipy --universal
-#- brew install matplotlib --universal
-
-# https://github.com/Homebrew/homebrew/issues/34470
-#- brew install wxpython --universal
-#- brew install openblas
-#- brew install gfortran
-
-- pip install pyinstaller==3.0.0
+- wget https://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh
+- bash Miniconda2-latest-MacOSX-x86_64.sh -b -p $HOME/miniconda
+- export PATH=$HOME/miniconda/bin:$PATH
+- which python
+- conda search numpy
+- conda search scipy
+- conda search wxpython
+# https://github.com/ContinuumIO/anaconda-issues/issues/565
+- conda install --yes numpy==1.8.2 scipy wxpython
+
+#- brew unlink gcc
+#- brew install gcc --universal
+#- brew install freetype --universal
+##- brew install numpy --universal
+##- brew install scipy --universal
+##- brew install matplotlib --universal
+#
+## https://github.com/Homebrew/homebrew/issues/34470
+##- brew install wxpython --universal
+##- brew install openblas
+##- brew install gfortran
+
+# fixes (matplotlib backend)
+- ./freeze_travis/fixes.sh
+
+- pip install pyinstaller==3.2.0
 # final pip installs
 - pip install -r ./freeze_travis/requirements.txt
 
-# wxPython
-- wget http://downloads.sourceforge.net/wxpython/wxPython3.0-osx-3.0.2.0-cocoa-py2.7.dmg
+## wxPython
+#- wget http://downloads.sourceforge.net/wxpython/wxPython3.0-osx-3.0.2.0-cocoa-py2.7.dmg
+
 - sudo ./freeze_travis/install_dmg.sh
+
 # Patch wx.lib.plot
 # http://trac.wxwidgets.org/ticket/16767#no1
 - python -c "import wx; print wx.__version__"
 - python -c "import wx; import wx.lib; import wx.lib.plot; print wx.lib.plot.__file__"
-- patch /usr/local/lib/wxPython-3.0.2.0/lib/python2.7/site-packages/wx-3.0-osx_cocoa/wx/lib/plot.py ./freeze_travis/wxPython-3.0.2.0-plot.patch
+#- patch /usr/local/lib/wxPython-3.0.2.0/lib/python2.7/site-packages/wx-3.0-osx_cocoa/wx/lib/plot.py ./freeze_travis/wxPython-3.0.2.0-plot.patch
 # wxPython is only available in 64bit version with homebrew
 #- brew install wxpython
 
@@ -76,7 +91,11 @@ install:
 
 script:
 # Run tests
-- python setup.py test
+- travis_retry pip install coverage
+- travis_retry pip install coveralls
+- coverage run --source=pycorrfit ./setup.py test
+- coverage report -m
+- coveralls
 # Create wheel pacakge
 - python setup.py bdist_wheel
 # Create source pacakge
@@ -107,7 +126,8 @@ deploy:
   file_glob: true
   file: 
     - "${RELEASE_PKG_FILEC}"
-    - "${RELEASE_PKG_FILEB}"
+    # Mac OSx build is broken (issue #147)
+    #- "${RELEASE_PKG_FILEB}"
     - "${RELEASE_PKG_FILEA}"
   on:
     tags: true

ChangeLog.txt

@@ -1,3 +1,9 @@
+0.9.9
+- Remove admin-requirement during install (Windows)
+- Support newer correlator.com .sin file format (experimental, #135)
+- Add smart progress dialog for fitting (#155)
+- Statistics: check "filename/title" by default (#151)
+- Documentation: fix bad LaTeX commands (#163)
 0.9.8
 - Bugfixes:
   - Indexing error when saving sessions (#154)
@@ -68,7 +74,7 @@
   - Computation of average intensity did not work
     correctly for unequally spaced traces
 - Update .pt3 reader to version 8399ff7401
-- Import traces of .pt3 files (#118)
+- Import traces of .pt3 files (experimental, #118)
   Warning: Absolute values for intensity might be wrong
 0.9.1
 - Tool 'Overlay curves': improve UI (#117)

README.rst

@@ -1,7 +1,7 @@
 |PyCorrFit|
 ===========
 
-|PyPI Version| |Build Status Win| |Build Status Mac|
+|PyPI Version| |Build Status Win| |Build Status Mac| |Coverage Status|
 
 A graphical fitting tool for fluorescence correlation spectroscopy (FCS) that comes with support for several file formats, can be applied to a large variety of problems, and attempts to be as user-friendly as possible. Some of the features are
 
@@ -97,3 +97,5 @@ the running time of the build). From there you can download the Windows installe
    :target: https://ci.appveyor.com/project/paulmueller/pycorrfit
 .. |Build Status Mac| image:: https://img.shields.io/travis/FCS-analysis/PyCorrFit/master.svg?label=build_mac
    :target: https://travis-ci.org/FCS-analysis/PyCorrFit
+.. |Coverage Status| image:: https://img.shields.io/coveralls/FCS-analysis/PyCorrFit.svg
+   :target: https://coveralls.io/r/FCS-analysis/PyCorrFit

appveyor.yml

@@ -26,13 +26,14 @@ environment:
     GH_READ_API_TOKEN:
       secure: GvXoZj2gfC/Zjpe5k3BLTNKTNLWPFK9hB97npxEDM5rUxcrESItbUhrPwXCaAt8s
 
+  # https://github.com/appveyor/ci/issues/359
   matrix:
-    - PYTHON: "C:\\Python27-conda32"
+    - PYTHON: "C:\\Miniconda"
       PYTHON_VERSION: "2.7"
       PYTHON_ARCH: "32"
       PYWIN_DL: "https://downloads.sourceforge.net/project/pywin32/pywin32/Build%20219/pywin32-219.win32-py2.7.exe"
 
-    - PYTHON: "C:\\Python27-conda64"
+    - PYTHON: "C:\\Miniconda-x64"
       PYTHON_VERSION: "2.7"
       PYTHON_ARCH: "64"
       PYWIN_DL: "https://downloads.sourceforge.net/project/pywin32/pywin32/Build%20219/pywin32-219.win-amd64-py2.7.exe"
@@ -45,9 +46,6 @@ install:
   # Copied from
   # https://github.com/Phonations/Joker/blob/master/appveyor.yml
   - choco install -y InnoSetup
-  # Install Python (from the official .msi of http://python.org) and pip when
-  # not already installed.
-  - "powershell freeze_appveyor\\install.ps1"
 
   # Determine platform
   - '%PYTHON%/python -c "import platform; print platform.uname()"'
@@ -75,12 +73,9 @@ install:
   - "pip install matplotlib==1.4.3"
   - "pip install sympy"
   - "pip install lmfit"
-  # Install pyinstaller
-  - 'ECHO Downloading %PYWIN_DL%'
-  - ps: (new-object net.webclient).DownloadFile("$env:PYWIN_DL", 'C:/pywin_inst.exe')
-  - "%PYTHON%/Scripts/easy_install.exe C:/pywin_inst.exe"
+  # Install pyinstaller (includes dependency for pywin32)
+  - "%WITH_COMPILER% pip install pypiwin32"
   - "%WITH_COMPILER% pip install git+git://github.com/pyinstaller/pyinstaller.git@779d07b236a943a4bf9d2b1a0ae3e0ebcc914798"
-  #- "%WITH_COMPILER% pip install pyinstaller==3.0.0"
 
   # Run develop (installs yet missing packages and runs cython)
   - "%WITH_COMPILER% %PYTHON%/python setup.py develop"
@@ -93,9 +88,13 @@ shallow_clone: true
 build: off
 
 test_script:
-#  - "pip freeze"
-# Disable pytest, because appveyor has problems with relative imports ??!
-  - "%WITH_COMPILER% %PYTHON%/python setup.py test"
+  - 'python -c "import pycorrfit; print pycorrfit.__version__"'
+  - "pip install coverage"
+  - "pip install coveralls"
+  - "coverage run --source=pycorrfit ./setup.py test"
+  - "coverage report -m"
+# https://github.com/lemurheavy/coveralls-public/issues/429
+#  - "coveralls --verbose"
 
 after_test:
   # If tests are successful, create a whl package for the project.

doc/PyCorrFit_doc.tex

@@ -20,7 +20,7 @@
 
 %Für englische Schriften:
 \usepackage[english]{babel}
-\usepackage{sistyle}
+\usepackage{siunitx}
 
 
 \usepackage[top = 2cm, left = 2.5cm, right = 2cm, bottom = 2.5cm]{geometry}