Merge pull request #35 from takluyver/travis-nbval

Run notebook tests on Travis

Author: fangohr

.travis.yml

@@ -8,6 +8,7 @@ sudo: false
 before_install:
   # We do this conditionally because it saves us some downloading if the
   # version is the same.
+  - deactivate  # Deactivate virtualenv
   - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
       wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
     else
@@ -19,7 +20,7 @@ before_install:
 install:
   - conda create -q -y -n fidimag-test python=$TRAVIS_PYTHON_VERSION cython matplotlib pytest scipy pytest-cov
   - source activate fidimag-test
-  - pip install pyvtk six
+  - pip install pyvtk six nbval
   # Download and compile FFTW & Sundials locally
   - bash bin/install.sh
 
@@ -36,6 +37,7 @@ before_script:
 # command to run tests
 script:
   - make test-without-run-oommf
+  - make test-ipynb
 
 
 notifications:

Makefile

@@ -44,7 +44,7 @@ test-quick:
 
 
 test-ipynb: create-dirs
-	cd doc/ipynb && py.test . -v --ipynb --sanitize-with sanitize_file --junitxml=$(PROJECT_DIR)/test-reports/junit/test-ipynb-pytest.xml
+	cd doc/ipynb && py.test . -v --nbval --sanitize-with sanitize_file --junitxml=$(PROJECT_DIR)/test-reports/junit/test-ipynb-pytest.xml
 
 test-oommf:
 	py.test -v -m "oommf"

doc/ipynb/1d_domain_wall.ipynb

@@ -105,6 +105,7 @@
     }
    ],
    "source": [
+    "# PYTEST_VALIDATE_IGNORE_OUTPUT\n",
     "Ms = 8.6e5  # magnetisation saturation (A/m)\n",
     "A = 1.3e-11  # exchange energy constant (J/m)\n",
     "K1 = 1.86e5  # anisotropy energy constant (J/m**3)\n",

doc/ipynb/current-driven-domain-wall.ipynb

@@ -320,7 +320,7 @@
     "x = np.arange(len(m0_z))\n",
     "index_max = np.argmax(np.abs(m0_z))\n",
     "\n",
-    "print 'Maximum |m_z| at x =', x[index_max]"
+    "print('Maximum |m_z| at x = %s' % x[index_max])"
    ]
   },
   {
@@ -952,6 +952,7 @@
     }
    ],
    "source": [
+    "# PYTEST_VALIDATE_IGNORE_OUTPUT\n",
     "excite_system(mesh, 1.5e-9, 151);"
    ]
   },

doc/ipynb/isolated_skyrmion.ipynb

@@ -1257,6 +1257,7 @@
     }
    ],
    "source": [
+    "# PYTEST_VALIDATE_IGNORE_OUTPUT\n",
     "# Relax the system to its equilibrium.\n",
     "sim.relax(dt=1e-13, stopping_dmdt=0.01, max_steps=5000, save_m_steps=None, save_vtk_steps=None)"
    ]

doc/ipynb/spin-polarised-current-driven-skyrmion.ipynb

@@ -105,6 +105,7 @@
     }
    ],
    "source": [
+    "# PYTEST_VALIDATE_IGNORE_OUTPUT\n",
     "Ms = 1e6  # magnetisation saturation (A/m)\n",
     "A = 13e-11  # exchange stiffness (J/m)\n",
     "D = 5e-2  # DMI constant (J/m**2)\n",
@@ -289,6 +290,7 @@
     }
    ],
    "source": [
+    "# PYTEST_VALIDATE_IGNORE_OUTPUT\n",
     "sim2  = Sim(mesh, driver='llg_stt')  # create simulation object\n",
     "\n",
     "# Set parameters.\n",

doc/ipynb/standard_problem_4.ipynb

@@ -154,7 +154,7 @@
     "sim.add(UniformExchange(A=A))\n",
     "sim.add(Demag())\n",
     "\n",
-    "H0 = [Ms/sqrt(3) for _ in xrange(3)]\n",
+    "H0 = [Ms/sqrt(3) for _ in range(3)]\n",
     "Ht = lambda t: 1 - t / 0.5e-9 if t < 0.5e-9 else 0\n",
     "sim.add(TimeZeeman(H0, Ht))  # saturating field which is reduced over 0.5 nanoseconds"
    ]
@@ -909,7 +909,7 @@
     }
    ],
    "source": [
-    "%%time\n",
+    "# PYTEST_VALIDATE_IGNORE_OUTPUT\n",
     "sim.set_m((1.0, 0.25, 0.1))\n",
     "sim.set_tols(rtol=1e-10, atol=1e-10)\n",
     "sim.relax(dt=1e-13, stopping_dmdt=0.01, max_steps=5000, save_m_steps=None, save_vtk_steps=None);\n",
@@ -998,7 +998,7 @@
     }
    ],
    "source": [
-    "%%time\n",
+    "# PYTEST_VALIDATE_IGNORE_OUTPUT\n",
     "mu0 = 4 * np.pi * 1e-7  # magnetic constant (H/m)\n",
     "mT = 1e-3 / mu0  # millitesla\n",
     "\n",
@@ -1050,6 +1050,7 @@
     }
    ],
    "source": [
+    "# PYTEST_VALIDATE_IGNORE_OUTPUT\n",
     "import matplotlib.pyplot as plt\n",
     "%matplotlib inline\n",
     "from fidimag.common.fileio import DataReader\n",

doc/ipynb/tutorial-basics.ipynb

@@ -1330,6 +1330,7 @@
     }
    ],
    "source": [
+    "# PYTEST_VALIDATE_IGNORE_OUTPUT\n",
     "sim.relax(dt=1e-11, stopping_dmdt=0.01, max_steps=1000, save_m_steps=10, save_vtk_steps=100)"
    ]
   },
@@ -1456,7 +1457,8 @@
     }
    ],
    "source": [
-    "ls"
+    "# PYTEST_VALIDATE_IGNORE_OUTPUT\n",
+    "%ls"
    ]
   },
   {