Feature/coverage

.coveragerc

@@ -0,0 +1,7 @@
+[run]
+branch = True
+[report]
+include = 
+    *.ipynb
+    *.py
+    python/*.py

.travis.yml

@@ -21,7 +21,15 @@ install:
 
   - conda env create -n test-environment python=$TRAVIS_PYTHON_VERSION -f binder/environment.yml
   - source activate test-environment
+  #Packages for testing only -- don't need in user environment.
+  - pip3 install codecov pytest-cov pytest_notebook nbval papermill
+  - ipython kernel install --user --name=galactic-spin 
 
 before_script: cd binder
 script:
-- travis_wait 60 py.test
+- pytest --cov=./ --cov-report=xml --nbval --current-env --cov-config=../.coveragerc
+- papermill --prepare-only -p galaxy NGC5533 07_Bonus_Bulge_Rotation_Curve.ipynb 07_Bonus_Bulge_Rotation_Curve_NGC5533.ipynb
+- papermill --prepare-only -p galaxy NGC7814 07_Bonus_Bulge_Rotation_Curve.ipynb 07_Bonus_Bulge_Rotation_Curve_NGC7814.ipynb
+- pytest --cov=./ --cov-report=xml --nbval-lax 07_Bonus_Bulge_Rotation_Curve_NGC????.ipynb --cov-append --current-env --cov-config=../.coveragerc
+after_script:
+- codecov

binder/01_DM_Rotation_Curve_Intro.ipynb

@@ -375,6 +375,8 @@
     }
    ],
    "source": [
+    "#NBVAL_IGNORE_OUTPUT\n",
+    "#Because the calculation time naturally varies.\n",
     "# Calculation time\n",
     "executionTime3 = (time.time() - startTime)\n",
     "ttt3=executionTime3/60\n",

binder/02_Widget_NGC5533_DMonly.ipynb

@@ -542,6 +542,8 @@
     }
    ],
    "source": [
+    "#NBVAL_IGNORE_OUTPUT\n",
+    "#Because the figure doesn't save to the repository correctly.\n",
     "# Widget\n",
     "VBox([button,out,interactive_plot(f)])"
    ]
@@ -603,7 +605,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.9"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,

binder/03_Measured_Data_Plotting.ipynb

@@ -250,6 +250,8 @@
     }
    ],
    "source": [
+    "#NBVAL_IGNORE_OUTPUT\n",
+    "#Because the timing won't be exactly the same each time.\n",
     "# Time\n",
     "executionTime = (time.time() - startTime)\n",
     "ttt=executionTime/60\n",
@@ -295,7 +297,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.9"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,

binder/04_Plotting_Rotation_Curves.ipynb

@@ -497,6 +497,8 @@
     }
    ],
    "source": [
+    "#NBVAL_IGNORE_OUTPUT\n",
+    "#Because the timing won't be exactly the same each time.\n",
     "# Time\n",
     "executionTime = (time.time() - startTime)\n",
     "ttt = executionTime/60\n",

binder/05_Widget_NGC5533_All_Components.ipynb

@@ -381,6 +381,8 @@
     }
    ],
    "source": [
+    "#NBVAL_IGNORE_OUTPUT\n",
+    "#Because the figure doesn't save to the repository correctly.\n",
     "# Widget\n",
     "VBox([button,out,interactive_plot(f)])"
    ]
@@ -446,7 +448,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.9"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,

binder/07_Bonus_Bulge_Rotation_Curve.ipynb

@@ -60,7 +60,11 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "parameters"
+    ]
+   },
    "outputs": [],
    "source": [
     "galaxy = \"NGC891\"         # Change this value to select a galaxy out of the 3 choices: NGC5533, NGC891, NGC7814"
@@ -105,6 +109,8 @@
     }
    ],
    "source": [
+    "#NBVAL_IGNORE_OUTPUT\n",
+    "#Because the filepath won't be the same across devices\n",
     "import importlib\n",
     "importlib.reload(b)             # Reload library so the changes take effect"
    ]
@@ -635,6 +641,8 @@
     }
    ],
    "source": [
+    "#NBVAL_IGNORE_OUTPUT\n",
+    "#Because the timing won't be exactly the same each time.\n",
     "executionTime = (time.time() - startTime)\n",
     "print(f'Execution time: {executionTime:.2f} seconds')"
    ]
@@ -682,9 +690,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "galactic-spin",
    "language": "python",
-   "name": "python3"
+   "name": "galactic-spin"
   },
   "language_info": {
    "codemirror_mode": {
@@ -696,7 +704,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.9"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,

binder/08_Interactive_Fitting.ipynb

@@ -269,6 +269,8 @@
     }
    ],
    "source": [
+    "#NBVAL_IGNORE_OUTPUT\n",
+    "#Because there is some randomness to the fit itself\n",
     "f_fit = f_mod.fit(m_velocities, f_params, r = m_radii, weights = weighdata)\n",
     "\n",
     "# Show fit statistics\n",
@@ -454,6 +456,8 @@
     }
    ],
    "source": [
+    "#NBVAL_IGNORE_OUTPUT\n",
+    "#Because the timing won't be exactly the same each time.\n",
     "# Time\n",
     "executionTime = (time.time() - startTime)\n",
     "ttt=executionTime/60\n",

binder/09_Widget_SPARC_Galaxies.ipynb

@@ -135,6 +135,8 @@
     }
    ],
    "source": [
+    "#NBVAL_IGNORE_OUTPUT\n",
+    "#Because the button doesn't save to the repository correctly.\n",
     "print(\"Would you like to download and unzip SPARC data files to your computer?\")\n",
     "dsd.displaybuttons"
    ]
@@ -198,6 +200,8 @@
     }
    ],
    "source": [
+    "#NBVAL_IGNORE_OUTPUT\n",
+    "#Because the dropdown doesn't save to the repository correctly.\n",
     "galaxylist = ['NGC5005']                 # default list of galaxies  \n",
     "def on_change(change):                   # add selected galaxynames to the list\n",
     "    if change['type'] == 'change' and change['name'] == 'value':\n",
@@ -285,6 +289,8 @@
     }
    ],
    "source": [
+    "#NBVAL_IGNORE_OUTPUT\n",
+    "#Because the figure doesn't save to the repository correctly.\n",
     "# Widget Output\n",
     "widget.VBox([widget.button,widget.out,widget.interactive_plot(widget.widgetfunction)])"
    ]
@@ -323,6 +329,8 @@
     }
    ],
    "source": [
+    "#NBVAL_IGNORE_OUTPUT\n",
+    "#Because there is some randomness in the fit itself\n",
     "# Show fit statistics\n",
     "widget.fit"
    ]

binder/10_Bonus_Black_Holes_as_DM.ipynb

@@ -78,6 +78,8 @@
     }
    ],
    "source": [
+    "#NBVAL_IGNORE_OUTPUT\n",
+    "#Because the figure doesn't save to the repository correctly.\n",
     "# Widget Output\n",
     "widget.VBox([widget.button_5533,widget.out_5533,widget.interactive_plot_5533(widget.f5533)])"
    ]
@@ -135,6 +137,8 @@
     }
    ],
    "source": [
+    "#NBVAL_IGNORE_OUTPUT\n",
+    "#Because the figure doesn't save to the repository correctly.\n",
     "%matplotlib inline\n",
     "widget.VBox([widget.button_7814,widget.out_7814,widget.interactive_plot_7814(widget.f7814)])"
    ]
@@ -209,7 +213,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.9"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,

binder/environment.yml

@@ -14,6 +14,7 @@ dependencies:
   - ipywidgets==7.6.5
   - ffmpeg
   - pip
+  - ipykernel
   - pip:
     - lmfit
     - astroquery