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commit dd7da32c13154ea7d247e84f6993ec11202f6d61 Author: Afif Elghraoui <[email protected]> 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"] } -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-cobra.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
