Merge branch 'release-v1.3': kafe release 1.3.0

.travis.yml

@@ -1,16 +1,17 @@
 sudo: false
 
+# only one TRAVIS_PYTHON_VERSION
 language: python
 python:
   - 2.7
 
-# use cache for pip (especially for scipy)
-cache:
-    pip: true
-    custom_install: true
-
-virtualenv:
-    system_site_packages: true
+# matrix of several CONDA_PYTHON_VERSIONs
+env:
+  matrix:
+    - CONDA_PYTHON_VERSION=2.7.9
+    - CONDA_PYTHON_VERSION=2.7.12
+    - CONDA_PYTHON_VERSION=3.5
+    - CONDA_PYTHON_VERSION=3.4
 
 addons:
   apt:
@@ -22,32 +23,41 @@ addons:
     #- texlive-extra-utils
     #- texlive-latex-extra
     - dvipng
-    #- libfreetype6
-    - python-qt4
     #don't install ROOT yet
     #- root-system
 
 before_install:
-  # create cache directory if none exists
-  - mkdir -p $HOME/.cache/pip/wheels
-  # upgrade pip to latest version
+  # get miniconda
+  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
+      wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O $HOME/miniconda.sh;
+    else
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O $HOME/miniconda.sh;
+    fi
+  # install miniconda in batch mode and add to PATH
+  - bash $HOME/miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+
+  # configure conda for batch mode
+  - conda config --set always_yes yes --set changeps1 no
+  # update conda and show package/environment information
+  - conda update -q conda
+  - conda info -a
+
+  # install some dependencies with conda and activate environment
+  - conda create -q -n kafe_env python=$CONDA_PYTHON_VERSION numpy scipy tk matplotlib
+  - source activate kafe_env
+
+  # upgrade pip to latest version and install iminuit with pip
   - pip install --upgrade pip
-  # get and build scipy, if not already cached
-  - travis_wait pip wheel --find-links=$HOME/.cache/pip/wheels --use-wheel --wheel-dir=$HOME/.cache/pip/wheels scipy
-  # install from cache
-  - pip install --no-index --find-links=$HOME/.cache/pip/wheels scipy
-  # install other dependencies
-  - pip install pytest
-  - pip install numpy
-  - pip install matplotlib
   - pip install --upgrade iminuit
-  # check success
-  - python -c "import numpy"
-  - python -c "import scipy"
-  - python -c "import matplotlib"
+
+  # output python version to log
+  - python --version
 
 install:
+  # install kafe from current directory using pip
   - pip install -e .
 
 script:
+  # run unittests with setup.py
   - python setup.py test

CHANGELOG

@@ -1,12 +1,28 @@
-master
+v1.3.0
 ======
-    %  [TODO] add unit test for input file parser
 
-v1.3.0
+    %  [NEW] make code compatible with both Python 2 and 3
+    %  [NEW] add support for fits with correlated constraints
+             (example 11 added)
+    %  [NEW] add support for multi-model fits with shared parameters
+             (example 13 added)
+    %  [NEW] matplotlib 2.0 is now supported
+
+    %  [REQ] require numpy version 1.11.2
+    %  [REQ] require scipy version 0.17.0
+    %  [REQ] require iminuit version 1.2
+    %  [REQ] drop requirement for Qt (difficulty with conda):
+             make Tk the default backend
+
+    %  [BUG] fixed bugs related to output stream redirection
+    %  [FIX] running kafe in Jupyter Notebooks should now work
+    %  [DOC] update documentation of examples
+
+v1.2.0
 ======
 
-    %  [FIX] make code Python 3 compatible. 
-       Imports solved with try: Python2 variant; except ImportError: Python3 variant
+    %  [NEW] add support for fits with correlated constraints
+    %  several bugfixes
 
 v1.1.0
 ======

README.rst

@@ -36,26 +36,26 @@ or on `ReadTheDocs <http://kafe.readthedocs.org/en/latest/>`_.
 Requirements
 ============
 
-*kafe* needs some additional Python packages. The recommended versions of these are
+*kafe* runs under both Python 2 (`>=2.7.9`) and Python 3 (tested with `3.5.2`).
+
+Some additional Python packages are required. The recommended versions of these are
 as follows. Please note that more recent versions of these packages should work
 as well:
 
-* `SciPy <http://www.scipy.org>`_ >= 0.12.0
-* `NumPy <http://www.numpy.org>`_ >= 1.6.1
+* `SciPy <http://www.scipy.org>`_ >= 0.17.0
+* `NumPy <http://www.numpy.org>`_ >= 1.11.2
 * `matplotlib <http://matplotlib.org>`_ >= 1.5.0
 
 
 Additionally, a function minimizer is needed. *kafe* implements interfaces to two
 function minimizers and requires at least one of them to be installed:
 
 * *MINUIT*, which is included in *CERN*'s data analysis package `ROOT <http://root.cern.ch>`_ (>= 5.34), or
-* `iminuit <https://github.com/iminuit/iminuit>`_ (>= 1.1.1), which is independent of ROOT
+* `iminuit <https://github.com/iminuit/iminuit>`_ (>= 1.2), which is independent of ROOT
 
 
 Finally, *kafe* requires a number of external programs:
 
-* Qt4 (>= 4.8.5) and the Python bindings PyQt4 (>= 3.18.1) are needed because *Qt* is the supported
-  interactive frontend for matplotlib. Other frontends are not supported and may cause unexpected behavior.
 * A *LaTeX* distribution (tested with `TeX Live <https://www.tug.org/texlive/>`_), since *LaTeX* is
   used by matplotlib for typesetting labels and mathematical expressions.
 * `dvipng <http://www.nongnu.org/dvipng/>`_ for converting DVI files to PNG graphics
@@ -94,6 +94,13 @@ In Fedora/RHEL/CentOS:
 Install *ROOT*
 --------------
 
+**Note**: This section is written with ROOT version 5.34 in mind.
+When using this version, take care that the Python bindings (PyROOT)
+are compiled for the version of Python you intend to use (either 2.x or 3.x),
+as it is not possible to use both. For newer versions of ROOT (i.e. 6 and
+above), this should no longer be an issue.
+
+
 ROOT and its Python bindings can be obtained via the package manager in
 Ubuntu/Mint/Debian:
 
@@ -110,7 +117,7 @@ Or, in Fedora/RHEL/CentOS:
 
 This setup is usually sufficient. However, you may decide to build ROOT yourself. In this case,
 be sure to compile with *PyROOT* support. Additionally, for Python to see the *PyROOT* bindings,
-the following environment variables have to be set correctly (:
+the following environment variables have to be set correctly:
 
     .. code:: bash
 
@@ -121,7 +128,6 @@ the following environment variables have to be set correctly (:
 
 For more info, refer to `<http://root.cern.ch/drupal/content/pyroot>`_.
 
-
 -----------------
 Install `iminuit`
 -----------------
@@ -210,11 +216,7 @@ Installation notes (Windows)
 The recommended Python distribution for working with *kafe* under Windows is
 `WinPython <https://winpython.github.io/>`_, which has the advantage that it is
 portable and comes with a number of useful pre-installed packages. Particularly,
-*NumPy*, *SciPy* and *matplotlib* are all pre-installed in *WinPython*, as are
-all *Qt*-related dependencies.
-
-Be sure to install *WinPython* version **2.7**, since *kafe* does not currently
-run under Python 3.
+*NumPy*, *SciPy* and *matplotlib* are all pre-installed in *WinPython*.
 
 -----------------
 Install `iminuit`