replace nose with pytest in docs and comments. (mdtraj#1404)

replace nose with pytest in docs and comments.

[ci skip]

Author: marscher

.github/CONTRIBUTING.rst

@@ -18,8 +18,8 @@ Tests
 -----
 
 Writing unit tests in a dynamic language like Python is very important.
-Writing tests is annoying, but it pays off big time. `Nose
-<https://nose.readthedocs.org/en/latest/>`_ makes writing tests pretty
+Writing tests is annoying, but it pays off big time. `PyTest
+<https://pytest.readthedocs.org/en/latest/>`_ makes writing tests pretty
 easy, and MDTraj has some testing infrastructure to make it easier. We will
 probably refuse your pull-request if it doesn't include tests.
 
@@ -50,7 +50,7 @@ for ``XTCTrajectoryFormat.read()`` is below. Note that the signature comes
 before the 1 line summary. ::
 
     """read(n_frames=None, stride=1, atom_indices=None)
-    
+
     Read data from an XTC file
 
     Parameters
@@ -76,5 +76,5 @@ before the 1 line summary. ::
     box : np.ndarray, shape=(n_frames, 3, 3), dtype=np.float32
         The box vectors in each frame.
     """
- 
+
 .. vim: tw=75

docs/installation.rst

@@ -30,14 +30,14 @@ Testing Your Installation
 -------------------------
 
 Running the tests is a great way to verify that everything is working. The test
-suite uses `nose <https://nose.readthedocs.org/en/latest/>`_, which you can pick
+suite uses `pytest <https://pytest.readthedocs.org/en/latest/>`_, which you can pick
 up via ``pip`` if you don't already have it. ::
 
-  pip install nose
+  pip install pytest
 
 Then, to run the tests, execute the command ::
 
-  nosetests mdtraj -v
+  pytest mdtraj -v
 
 Compiling From Source
 ---------------------

docs/requirements.txt

@@ -7,6 +7,6 @@ runipy
 openmm
 pytables
 scikit-learn
-nose
+pytest
 pandas
 numpydoc

tests/test_gro.py

@@ -32,7 +32,7 @@
 
 def teardown_module(module):
     """remove the temporary file created by tests in this file
-    this gets automatically called by nose"""
+    this gets automatically called by pytest"""
     os.unlink(temp)
 
 

tests/test_hdf5.py

@@ -39,7 +39,7 @@
 fd, temp = tempfile.mkstemp(suffix='.h5')
 def teardown_module(module):
     """remove the temporary file created by tests in this file
-    this gets automatically called by nose"""
+    this gets automatically called by pytest"""
     os.close(fd)
     os.unlink(temp)
 
@@ -252,13 +252,13 @@ def test_do_overwrite():
     with HDF5TrajectoryFile(temp, 'w', force_overwrite=True) as f:
         f.write(np.random.randn(10,5,3))
 
-        
+
 def test_vsite_elements(get_fn):
     #  Test case for issue #265
     pdb_filename = get_fn('GG-tip4pew.pdb')
     trj = md.load(pdb_filename)
     trj.save_hdf5(temp)
-    
+
     trj2 = md.load(temp, top=pdb_filename)
 
 def test_dont_overwrite():

tests/test_io.py

@@ -36,7 +36,7 @@
 
 def teardown_module(module):
     """remove the temporary file created by tests in this file
-    this gets automatically called by nose"""
+    this gets automatically called by pytest"""
     os.unlink(temp)
 
 

tests/test_lammpstrj.py

@@ -33,7 +33,7 @@
 fd, temp = tempfile.mkstemp(suffix='.lammpstrj')
 def teardown_module(module):
     """Remove the temporary file created by tests in this file
-    this gets automatically called by nose. """
+    this gets automatically called by pytest. """
     os.close(fd)
     os.unlink(temp)
 

tests/test_lh5.py

@@ -40,7 +40,7 @@
 
 def teardown_module(module):
     """remove the temporary file created by tests in this file
-    this gets automatically called by nose"""
+    this gets automatically called by pytest"""
     os.close(fd)
     os.unlink(temp)
 

tests/test_mdcrd.py

@@ -32,7 +32,7 @@
 
 def teardown_module(module):
     """remove the temporary file created by tests in this file
-    this gets automatically called by nose"""
+    this gets automatically called by pytest"""
     os.close(fd)
     os.unlink(temp)
 

tests/test_netcdf.py

@@ -42,7 +42,7 @@
 
 def teardown_module(module):
     """remove the temporary file created by tests in this file
-    this gets automatically called by nose"""
+    this gets automatically called by pytest"""
     os.close(fd)
     os.close(fd2)
     os.unlink(temp)