Check the examples in the tests

This ensure they don't fall behind the API changes

.gitignore

@@ -5,3 +5,4 @@ chemfiles.egg-info/
 .tox/
 MANIFEST
 .coverage
+*.pyc

doc/tutorials.rst

@@ -28,28 +28,20 @@ Then we open a Trajectory and read the first frame:
    :language: python
    :lines: 7-8
 
-We can now create a list to store the indices of the atoms with ``x < 5``, and
-get the positions of the atoms in the frame with the :py:func:`Frame.positions`
-function
+Iterating through the atoms in the frame, we store the indices of the atoms with
+``x < 5`` in a list. ``len(frame.atoms)`` gives the number of atoms in the
+frame, which is also the size of the ``frame.positions`` array. This array is a
+numpy array which shape is ``(len(frame), 3)``.
 
 .. literalinclude:: ../examples/indexes.py
    :language: python
-   :lines: 10-11
+   :lines: 10-13
 
-Iterating through the atoms in the frame, we get the ones matching our
-condition. ``len(frame)`` gives the number of atoms in the frame, which is also
-the size of the ``positions`` array. This array is a numpy array which shape is
-``(len(frame), 3)``.
+We can then print our results
 
 .. literalinclude:: ../examples/indexes.py
    :language: python
-   :lines: 13-15
-
-And finally we can print our results
-
-.. literalinclude:: ../examples/indexes.py
-   :language: python
-   :lines: 17-19
+   :lines: 15-17
 
 .. htmlhidden::
     :toggle: Click here to see the whole program
@@ -62,7 +54,7 @@ And finally we can print our results
 For more information about reading frame in a trajectory, see the following
 functions:
 
-- :py:func:`Trajectory.nsteps` gives the number of frame in a Trajectory.
+- :py:attr:`Trajectory.nsteps` is the number of frame in a Trajectory.
 - :py:func:`Trajectory.read_step` to directlty read a given step.
 - :py:func:`Trajectory.set_cell` and :py:func:`Trajectory.set_topology` to
   specify an unit cell or a topology for all frames in a trajectory.
@@ -98,28 +90,28 @@ We can then set the atomic positions:
 
 .. literalinclude:: ../examples/generate.py
    :language: python
-   :lines: 20-23
+   :lines: 20-22
 
 Another possibility is to directly add atoms to the frame. Here we define a
 second molecule representing carbon dioxyde. :py:func:`Frame.add_atom` takes
 two arguments: the atom, and the position of the atom as a 3-element list
 
 .. literalinclude:: ../examples/generate.py
    :language: python
-   :lines: 25-29
+   :lines: 24-28
 
 Finally, we can set the :py:class:`UnitCell` associated with this frame.
 
 .. literalinclude:: ../examples/generate.py
    :language: python
-   :lines: 31
+   :lines: 30
 
 Now that our frame is constructed, it is time to write it to a file. For that,
 we open a trajectory in write (``'w'``) mode, and write to it.
 
 .. literalinclude:: ../examples/generate.py
    :language: python
-   :lines: 33-34
+   :lines: 32-33
 
 .. htmlhidden::
     :toggle: Click here to see the whole program
@@ -176,13 +168,20 @@ frame.
    :language: python
    :lines: 14-15
 
-Finally, we can write the cleaned frame to the output file, and start the next
+We can then write the cleaned frame to the output file, and start the next
 iteration.
 
 .. literalinclude:: ../examples/select.py
    :language: python
    :lines: 16
 
+Finally, we close the input and output files to ensure that all the written data
+is flushed to the disk.
+
+.. literalinclude:: ../examples/select.py
+   :language: python
+   :lines: 18-19
+
 .. htmlhidden::
     :toggle: Click here to see the whole program
     :before-not-html: The whole program look like this:

examples/generate.py

@@ -6,29 +6,28 @@
 from chemfiles import Topology, Frame, Atom, UnitCell, Trajectory
 
 topology = Topology()
-topology.add_atom(Atom("H"))
-topology.add_atom(Atom("O"))
-topology.add_atom(Atom("H"))
+topology.atoms.append(Atom("H"))
+topology.atoms.append(Atom("O"))
+topology.atoms.append(Atom("H"))
 
 topology.add_bond(0, 1)
 topology.add_bond(2, 1)
 
 frame = Frame()
 frame.resize(3)
-frame.set_topology(topology)
+frame.topology = topology
 
-positions = frame.positions()
-positions[0, :] = np.array([1.0, 0.0, 0.0])
-positions[1, :] = np.array([0.0, 0.0, 0.0])
-positions[2, :] = np.array([0.0, 1.0, 0.0])
+frame.positions[0, :] = np.array([1.0, 0.0, 0.0])
+frame.positions[1, :] = np.array([0.0, 0.0, 0.0])
+frame.positions[2, :] = np.array([0.0, 1.0, 0.0])
 
 frame.add_atom(Atom("O"), [5.0, 0.0, 0.0])
 frame.add_atom(Atom("C"), [6.0, 0.0, 0.0])
 frame.add_atom(Atom("O"), [7.0, 0.0, 0.0])
 frame.add_bond(3, 4)
 frame.add_bond(4, 5)
 
-frame.set_cell(UnitCell(10, 10, 10))
+frame.cell = UnitCell(10, 10, 10)
 
-trajectory = Trajectory("water-co2.pdb", 'w')
-trajectory.write(frame)
+with Trajectory("water-co2.pdb", 'w') as trajectory:
+    trajectory.write(frame)

examples/indexes.py

@@ -4,14 +4,12 @@
 #!/usr/bin/env python
 from chemfiles import Trajectory
 
-trajectory = Trajectory("filename.xyz")
-frame = trajectory.read()
+with Trajectory("filename.xyz") as trajectory:
+    frame = trajectory.read()
 
 less_than_five = []
-positions = frame.positions()
-
-for i in range(len(frame)):
-    if positions[i, 0] < 5:
+for i in range(len(frame.atoms)):
+    if frame.positions[i, 0] < 5:
         less_than_five.append(i)
 
 print("Atoms with x < 5: ")

examples/select.py

@@ -14,3 +14,6 @@
     for i in reversed(sorted(to_remove)):
         frame.remove(i)
     output.write(frame)
+
+trajectory.close()
+output.close()

tests/examples.py

@@ -0,0 +1,57 @@
+# -*- coding=utf-8 -*-
+from __future__ import absolute_import, print_function, unicode_literals
+import unittest
+import tempfile
+import shutil
+import os
+
+from chemfiles import Trajectory, Frame, Atom
+
+ROOT = os.path.dirname(__file__)
+
+
+class TestExamples(unittest.TestCase):
+    @classmethod
+    def setUpClass(cls):
+        cls._cwd = os.getcwd()
+        cls._tmpdir = tempfile.mkdtemp()
+        os.chdir(cls._tmpdir)
+
+    @classmethod
+    def tearDownClass(cls):
+        os.chdir(cls._cwd)
+        shutil.rmtree(cls._tmpdir)
+
+    def test_generate(self):
+        path = os.path.join(ROOT, "..", "examples", "generate.py")
+        exec(open(path).read(), globals())
+
+    def test_indexes(self):
+        # Create an input file
+        frame = Frame()
+        for i in range(120):
+            frame.add_atom(Atom('X'), [i % 10, i + 1 % 10, i + 2 % 10])
+
+        with Trajectory("filename.xyz", "w") as file:
+            file.write(frame)
+
+        path = os.path.join(ROOT, "..", "examples", "indexes.py")
+        # disable output
+        exec(open(path).read(), globals(), {'print': lambda _: None})
+
+    def test_select(self):
+        # Create an input file
+        frame = Frame()
+        NAMES = ["N", "Zn", "C", "O"]
+        for i in range(120):
+            frame.add_atom(Atom(NAMES[i % 4]), [i % 10, i + 1 % 10, i + 2 % 10])
+
+        with Trajectory("input.arc", "w")as file:
+            file.write(frame)
+
+        path = os.path.join(ROOT, "..", "examples", "select.py")
+        exec(open(path).read(), globals())
+
+
+if __name__ == "__main__":
+    unittest.main()