[med-svn] [python-cobra] 01/03: Imported Upstream version 0.5.8

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository python-cobra.

commit dd7da32c13154ea7d247e84f6993ec11202f6d61
Author: Afif Elghraoui <afif at debian.org>
Date:   Mon Dec 12 22:32:15 2016 -0800

    Imported Upstream version 0.5.8
---
 INSTALL.rst              | 29 +++++++++++++++++++++++++----
 cobra/VERSION            |  2 +-
 cobra/test/__init__.py   | 13 ++++++++++---
 develop-requirements.txt |  1 +
 setup.py                 |  1 +
 5 files changed, 38 insertions(+), 8 deletions(-)

diff --git a/INSTALL.rst b/INSTALL.rst
index 869902f..fb43ae7 100644
--- a/INSTALL.rst
+++ b/INSTALL.rst
@@ -50,7 +50,7 @@ Get the `detailed contribution instructions <CONTRIBUTING.rst>`_ for contributin
 Installation of optional dependencies
 =====================================
 
-Optional Dependencies
+Optional dependencies
 ~~~~~~~~~~~~~~~~~~~~~
 
 On windows, these can downloaded from [this site]
@@ -71,6 +71,15 @@ yum).
 4. `scipy <http://scipy.org>`_ >= 0.11 for ArrayBasedModel and saving to \*.mat files.
 
    -  `Windows scipy installer <http://www.lfd.uci.edu/~gohlke/pythonlibs/#scipy>`_
+5. `pytest <http://docs.pytest.org/en/latest/>`_ and `pytest-benchmark
+   <http://pytest-benchmark.readthedocs.io/en/latest/>`_ are required
+   for testing
+
+You can install all packages directly by
+
+.. code:: shell
+
+    pip install "cobra[all]"
 
 Other solvers
 ~~~~~~~~~~~~~
@@ -103,8 +112,20 @@ using rational operations, giving exact solutions.
 Testing your installation
 =========================
 
-1. Start python
-2. Type the following into the Python shell
+While it is not a hard requirement for using cobrapy, you need pytest and
+pytest-benchmark to run its tests. First do
+
+.. code:: shell
+
+    pip install pytest pytest-benchmark
+
+or to install cobrapy directly with the test dependencies
+
+.. code:: shell
+
+   pip install "cobra[test]"
+
+Then start python and type the following into the Python shell
 
 .. code:: python
 
@@ -112,4 +133,4 @@ Testing your installation
     test_all()
 
 You should see some skipped tests and expected failures, and the
-function should return ``False``.
+function should return ``True``.
diff --git a/cobra/VERSION b/cobra/VERSION
index b49b253..659914a 100644
--- a/cobra/VERSION
+++ b/cobra/VERSION
@@ -1 +1 @@
-0.5.6
+0.5.8
diff --git a/cobra/test/__init__.py b/cobra/test/__init__.py
index e30f8bb..5e6d441 100644
--- a/cobra/test/__init__.py
+++ b/cobra/test/__init__.py
@@ -1,6 +1,10 @@
 from os.path import join, abspath, dirname
 from cobra.io import read_sbml_model
-import pytest
+try:
+    import pytest
+    import pytest_benchmark
+except ImportError:
+    pytest = None
 try:
     from cPickle import load as _load
 except ImportError:
@@ -38,5 +42,8 @@ def create_test_model(model_name="salmonella"):
 def test_all():
     """ alias for running all unit-tests on installed cobra
     """
-    return pytest.main(
-        ['--pyargs', 'cobra', '--benchmark-skip', '-v', '-rs']) == 0
+    if pytest:
+        return pytest.main(
+            ['--pyargs', 'cobra', '--benchmark-skip', '-v', '-rs']) == 0
+    else:
+        raise ImportError('missing package pytest required for testing')
diff --git a/develop-requirements.txt b/develop-requirements.txt
index 2380179..cb2a77b 100644
--- a/develop-requirements.txt
+++ b/develop-requirements.txt
@@ -14,3 +14,4 @@ tabulate
 tox
 pep8
 pytest
+pytest-benchmark
diff --git a/setup.py b/setup.py
index 173c115..3efc7af 100644
--- a/setup.py
+++ b/setup.py
@@ -136,6 +136,7 @@ extras = {
     'matlab': ["pymatbridge"],
     'sbml': ["python-libsbml", "lxml"],
     'array': ["numpy>=1.6", "scipy>=0.11.0"],
+    'test': ["pytest", "pytest-benchmark"],
     'display': ["matplotlib", "palettable", "pandas>=0.17.0", "tabulate"]
 }
 

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