setup.py, doc (install) and .travis.yml updated

.travis.yml

@@ -15,7 +15,8 @@ before_install:
 # scipy requirements
 - sudo apt-get install gcc gfortran python-dev libblas-dev liblapack-dev cython
 # matplotlib additional requirements
-- sudo apt-get install libpng-dev libfreetype6-dev
+- sudo apt-get install pkg-config libfreetype6 libfreetype6-dev libpng-dev
+- pip install --upgrade pip
 - pip install 'setuptools >=14.0'
 
 install: pip install .

doc/source/install.rst

@@ -8,16 +8,27 @@ micca requires `Python <https://www.python.org/>`_ >=2.7, `NumPy
 <http://scipy.org/>`_ (>= 1.8.0) and the software required in order to
 install `SciPy <http://scipy.org/>`_ (>= 0.13.0) through pip.
 
-On Ubuntu Linux >=12.04
-^^^^^^^^^^^^^^^^^^^^^^^
+On Ubuntu Linux >= 12.04
+^^^^^^^^^^^^^^^^^^^^^^^^
 
-In Linux, we suggest install NumPy and requirements for SciPy through
-the package manager. In Ubuntu Linux you can use `apt-get install`:
+In Ubuntu Linux >= 12.04, we suggest install NumPy and the requirements for
+SciPy and matplotlib through the package manager:
 
 .. code-block:: sh
 
+   sudo apt-get -qq update
+   sudo apt-get install build-essential
    sudo apt-get install python-numpy
-   sudo apt-get install gcc gfortran python-dev libblas-dev liblapack-dev cython 
+   sudo apt-get install gcc gfortran python-dev libblas-dev liblapack-dev cython
+   sudo apt-get install pkg-config libfreetype6 libfreetype6-dev libpng-dev
+
+Then, upgrade pip and install setuptools:
+
+.. code-block:: sh
+
+   pip install --upgrade pip
+   pip install 'setuptools >=14.0'
+
 
 On OS X
 ^^^^^^^
@@ -26,18 +37,24 @@ In OS X, we recommend to install Python from `Homebrew <http://brew.sh/>`_:
 
    #. Install `Xcode <https://developer.apple.com/xcode/>`_;
    #. Install `Homebrew <http://brew.sh/>`_;
+   #. Make sure the environment variable ``PATH`` is properly setted in your
+      ``~/.bash_profile`` or ``~/.bashrc``::
+
+      .. code-block:: sh
+         export PATH=/usr/local/bin:$PATH
+
    #. Install Python and gfortran:
-      
+
       .. code-block:: sh
-      
+
          brew update
          brew install python
          brew install gfortran
 
 Install NumPy:
-   
+
       .. code-block:: sh
-         
+
 	 pip install numpy
 
 
@@ -49,7 +66,7 @@ The easiest way to install micca is to using pip, from PYPI:
 .. code-block:: sh
 
    sudo pip install micca
-   
+
 or from the tarball (https://github.com/compmetagen/micca/releases):
 
 .. code-block:: sh
@@ -65,7 +82,7 @@ In order to install micca from sources (with the standard procedure
 (>= 1.8.0) and SciPy (>= 0.13.0), the following Python packages must be
 installed:
 
-   * Pandas >=0.17.0, <0.18.0
+   * Pandas >=0.17.0
    * matplotlib >=1.3.0
    * Biopython >=1.50
    * cutadapt >=1.9
@@ -74,17 +91,16 @@ installed:
 The easiest way to install these packages is to  is using pip:
 
 .. code-block:: sh
- 
-   sudo pip install 'pandas >=0.17.0, <0.18.0' 'matplotlib >=1.3.0' 'biopython >= 1.50' 'cutadapt >=1.9' 'biom-format >=1.3.1'
+
+   sudo pip install 'pandas >=0.17.0' 'matplotlib >=1.3.0' 'biopython >= 1.50' 'cutadapt >=1.9' 'biom-format >=1.3.1'
 
 Download the latest version from
 https://github.com/compmetagen/micca/releases and complete the
 installation:
 
 .. code-block:: sh
-    
+
    tar -zxvf micca-X.Y.Z.tar.gz
-   python setup.py build
    sudo python setup.py install
 
 If you don’t have root access, install micca in a local directory by
@@ -96,10 +112,10 @@ specifying the ``--prefix`` argument. Then you need to set
    python setup.py install --prefix=/path/to/modules
    export PYTHONPATH=$PYTHONPATH:/path/to/modules/lib/python{version}/site-packages
 
-.. note:: 
+.. note::
 
    In order to export the variable permanently add the command
-   at the bottom of your ``.bashrc`` file.
+   at the bottom of your ``~/.bash_profile`` or ``~/.bashrc`` file.
 
 
 Testing the installation
@@ -108,7 +124,7 @@ Testing the installation
 .. code-block:: sh
 
    micca -h
-   
+
 
 Install RDP classifier (optional)
 ---------------------------------
@@ -126,19 +142,19 @@ can be used in the :doc:`/commands/classify` command (option
 Download and unzip the file (RDP cladssifier v2.11 2015-09-14):
 
 .. code-block:: sh
-   
+
    wget https://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_2.11.zip
    unzip rdp_classifier_2.11.zip
 
 Now you must set the environment variable ``RDPPATH`` by typing:
 
 .. code-block:: sh
-    
+
    $ export RDPPATH=/path-to-rdp-classifier/rdp_classifier_2.11/
 
-e.g. ``export RDPPATH=/Users/David/rdp_classifier_2.11``. 
+e.g. ``export RDPPATH=/Users/David/rdp_classifier_2.11``.
 
 .. note::
-   
+
    In order to export the variable permanently add the latest command
    at the bottom of your ``.bashrc`` file.

setup.py

@@ -122,8 +122,6 @@ def run(self):
     author_email='[email protected]',
     maintainer='Davide Albanese',
     maintainer_email='[email protected]',
-    # setup_requires must be repeated in install_requires
-    setup_requires=['numpy >= 1.8.0'],
     install_requires=[
         'numpy >= 1.8.0',
         'scipy >=0.14.0',