Merge pull request #46 from ericmjl/ghpages

ericmjl · web-flow · commit 7307b4b6c0c1 · 2019-01-20T18:00:19.000-05:00
ran notebooks manually to check that they at least run
diff --git a/.travis.yml b/.travis.yml
@@ -2,7 +2,7 @@
 before_script:
   - "export DISPLAY=:99.0"
   - "sh -e /etc/init.d/xvfb start"
-- sleep 5 # give xvfb some time to start
+  - sleep 5 # give xvfb some time to start
 
 language: python
 matrix:
diff --git a/environment.yml b/environment.yml
@@ -22,5 +22,6 @@ dependencies:
 - xarray
 - pandoc
 - black
+- nbstripout
 - pip:
   - arviz
diff --git a/notebooks/01-Instructor-Probability_a_simulated_introduction.ipynb b/notebooks/01-Instructor-Probability_a_simulated_introduction.ipynb
@@ -808,9 +808,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "bayesian-modelling-tutorial",
    "language": "python",
-   "name": "python3"
+   "name": "bayesian-modelling-tutorial"
   },
   "language_info": {
    "codemirror_mode": {
@@ -822,7 +822,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.6"
+   "version": "3.7.2"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/01-Student-Probability_a_simulated_introduction.ipynb b/notebooks/01-Student-Probability_a_simulated_introduction.ipynb
@@ -811,9 +811,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "bayesian-modelling-tutorial",
    "language": "python",
-   "name": "python3"
+   "name": "bayesian-modelling-tutorial"
   },
   "language_info": {
    "codemirror_mode": {
@@ -825,7 +825,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.6"
+   "version": "3.7.2"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/02-Instructor-Parameter_estimation_hypothesis_testing.ipynb b/notebooks/02-Instructor-Parameter_estimation_hypothesis_testing.ipynb
@@ -480,7 +480,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Assume we have a website and want to redesign the layout (_A_) and test whether the new layout (_B_) results in a higher click through rate. When people come to our website we randomly show them layout _A_ or _B_ and see how many people click through for each. First let's generate the data we need:"
+    "Assume we have a website and want to redesign the layout (*A*) and test whether the new layout (*B*) results in a higher click through rate. When people come to our website we randomly show them layout *A* or *B* and see how many people click through for each. First let's generate the data we need:"
    ]
   },
   {
@@ -605,9 +605,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "bayesian-modelling-tutorial",
    "language": "python",
-   "name": "python3"
+   "name": "bayesian-modelling-tutorial"
   },
   "language_info": {
    "codemirror_mode": {
@@ -619,7 +619,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.7.2"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/02-Student-Parameter_estimation_hypothesis_testing.ipynb b/notebooks/02-Student-Parameter_estimation_hypothesis_testing.ipynb
@@ -595,9 +595,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "bayesian-modelling-tutorial",
    "language": "python",
-   "name": "python3"
+   "name": "bayesian-modelling-tutorial"
   },
   "language_info": {
    "codemirror_mode": {
@@ -609,7 +609,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.7.2"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/03-instructor-two-group-iq.ipynb b/notebooks/03-instructor-two-group-iq.ipynb
@@ -338,7 +338,7 @@
    "source": [
     "fig, [ax1, ax2] = plt.subplots(nrows=1, ncols=2, sharex=True)\n",
     "\n",
-    "x, y = ECDF(samples['drug'])  # Want ECDF of drug-treatment PPC samples\n",
+    "x, y = ECDF(samples['drug'].flatten())  # Want ECDF of drug-treatment PPC samples\n",
     "ax1.plot(x, y, label='ppc')\n",
     "x, y = ECDF(df[drug_filter]['iq'])  # Want ECDF of drug-treatment data\n",
     "ax1.plot(x, y, label='data')\n",
@@ -347,7 +347,7 @@
     "ax1.set_xlabel('IQ')\n",
     "ax1.set_ylabel('Cumulative Fraction')\n",
     "\n",
-    "x, y = ECDF(samples['placebo'])  # Want ECDF of placebo-treatment PPC samples\n",
+    "x, y = ECDF(samples['placebo'].flatten())  # Want ECDF of placebo-treatment PPC samples\n",
     "ax2.plot(x, y, label='ppc')\n",
     "x, y = ECDF(df[placebo_filter]['iq'])  # Want ECDF of placebo-treatment data\n",
     "ax2.plot(x, y, label='data')\n",
@@ -378,7 +378,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "az.plot_posterior(trace=trace, var_names=['diff_means', 'effect_size'])"
+    "az.plot_posterior(trace, var_names=['diff_means', 'effect_size'])"
    ]
   },
   {
@@ -489,7 +489,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "traces = az.traceplot(trace_alt)"
+    "traces = az.plot_trace(trace_alt)"
    ]
   },
   {
@@ -522,9 +522,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "bayesian-modelling-tutorial",
    "language": "python",
-   "name": "python3"
+   "name": "bayesian-modelling-tutorial"
   },
   "language_info": {
    "codemirror_mode": {
@@ -536,7 +536,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.7.2"
   },
   "toc": {
    "base_numbering": 1,
diff --git a/notebooks/03-student-two-group-iq.ipynb b/notebooks/03-student-two-group-iq.ipynb
@@ -522,9 +522,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "bayesian-modelling-tutorial",
    "language": "python",
-   "name": "python3"
+   "name": "bayesian-modelling-tutorial"
   },
   "language_info": {
    "codemirror_mode": {
@@ -536,7 +536,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.7.2"
   },
   "toc": {
    "base_numbering": 1,
diff --git a/notebooks/04-instructor-multi-group-comparsion-sterilization.ipynb b/notebooks/04-instructor-multi-group-comparsion-sterilization.ipynb
@@ -225,7 +225,7 @@
    "outputs": [],
    "source": [
     "# Plot the trace plots.\n",
-    "az.plot_trace(trace)"
+    "traces = az.plot_trace(trace)"
    ]
   },
   {
@@ -242,7 +242,7 @@
    "outputs": [],
    "source": [
     "# Use the `plot_forest` or `plot_posterior` functions.\n",
-    "az.plot_forest(trace, var_names=['perc_reduction'], ylabels=sorted(mapping))"
+    "az.plot_forest(trace, var_names=['perc_reduction'], credible_interval=0.95)"
    ]
   },
   {
@@ -289,7 +289,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.7.2"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/04-student-multi-group-comparsion-sterilization.ipynb b/notebooks/04-student-multi-group-comparsion-sterilization.ipynb
@@ -273,9 +273,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "bayesian-modelling-tutorial",
    "language": "python",
-   "name": "python3"
+   "name": "bayesian-modelling-tutorial"
   },
   "language_info": {
    "codemirror_mode": {
@@ -287,7 +287,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.7.2"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/05-instructor-two-group-comparison-finches.ipynb b/notebooks/05-instructor-two-group-comparison-finches.ipynb
@@ -309,7 +309,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.7.2"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/05-student-two-group-comparison-finches.ipynb b/notebooks/05-student-two-group-comparison-finches.ipynb
@@ -279,9 +279,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "bayesian-modelling-tutorial",
    "language": "python",
-   "name": "python3"
+   "name": "bayesian-modelling-tutorial"
   },
   "language_info": {
    "codemirror_mode": {
@@ -293,7 +293,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.7.2"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/06-instructor-hierarchical-baseball.ipynb b/notebooks/06-instructor-hierarchical-baseball.ipynb
@@ -179,7 +179,7 @@
    "outputs": [],
    "source": [
     "ylabels = ylabels = \"AB: \" + df['AB'].astype(str) + ', H: ' + df['H'].astype('str')\n",
-    "az.plot_forest(baseline_trace, ylabels=ylabels, xlim=[0, 1])"
+    "az.plot_forest(baseline_trace)"
    ]
   },
   {
@@ -290,8 +290,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ylabels = \"AB: \" + df['AB'].astype(str) + ', H: ' + df['H'].astype('str')\n",
-    "az.plot_trace(trace, var_names=['thetas'], ylabels=ylabels, xlim=[0, 1])"
+    "# ylabels = \"AB: \" + df['AB'].astype(str) + ', H: ' + df['H'].astype('str')\n",
+    "traceplots = az.plot_trace(trace, var_names=['thetas']) # old stuff (need to raise issue with arviz) ylabels=ylabels, xlim=[0, 1]"
    ]
   },
   {
@@ -373,13 +373,20 @@
     "\n",
     "The data come from the [Baseball Data Bank](https://github.com/chadwickbureau/baseballdatabank), and are redistributed with this repository for educational purposes."
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "bayesian-modelling-tutorial",
    "language": "python",
-   "name": "python3"
+   "name": "bayesian-modelling-tutorial"
   },
   "language_info": {
    "codemirror_mode": {
@@ -391,7 +398,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.7.2"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/06-student-hierarchical-baseball.ipynb b/notebooks/06-student-hierarchical-baseball.ipynb
@@ -379,9 +379,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "bayesian-modelling-tutorial",
    "language": "python",
-   "name": "python3"
+   "name": "bayesian-modelling-tutorial"
   },
   "language_info": {
    "codemirror_mode": {
@@ -393,7 +393,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.7.2"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/07-instructor-hierarchical-finches.ipynb b/notebooks/07-instructor-hierarchical-finches.ipynb
@@ -240,9 +240,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "bayesian-modelling-tutorial",
    "language": "python",
-   "name": "python3"
+   "name": "bayesian-modelling-tutorial"
   },
   "language_info": {
    "codemirror_mode": {
@@ -254,7 +254,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.7.2"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/07-student-hierarchical-finches.ipynb b/notebooks/07-student-hierarchical-finches.ipynb
@@ -211,9 +211,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "bayesian-modelling-tutorial",
    "language": "python",
-   "name": "python3"
+   "name": "bayesian-modelling-tutorial"
   },
   "language_info": {
    "codemirror_mode": {
@@ -225,7 +225,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.7.2"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/08-bayesian-curve-regression.ipynb b/notebooks/08-bayesian-curve-regression.ipynb
diff --git a/notebooks/bonus-exploration-finches.ipynb b/notebooks/bonus-exploration-finches.ipynb
diff --git a/notebooks/data.py b/notebooks/data.py

-Original file line number
+Diff line change
 - xarray
 - pandoc
 - black
 +- nbstripout
 - pip:
   - arviz
Original file line number	Diff line number	Diff line change
`@@ -225,7 +225,7 @@`
`225`	`225`	`"outputs": [],`
`226`	`226`	`"source": [`
`227`	`227`	`"# Plot the trace plots.\n",`
`228`		`- "az.plot_trace(trace)"`
	`228`	`+ "traces = az.plot_trace(trace)"`
`229`	`229`	`]`
`230`	`230`	`},`
`231`	`231`	`{`
`@@ -242,7 +242,7 @@`
`242`	`242`	`"outputs": [],`
`243`	`243`	`"source": [`
`244`	`244`	"# Use the `plot_forest` or `plot_posterior` functions.\n",
`245`		`- "az.plot_forest(trace, var_names=['perc_reduction'], ylabels=sorted(mapping))"`
	`245`	`+ "az.plot_forest(trace, var_names=['perc_reduction'], credible_interval=0.95)"`
`246`	`246`	`]`
`247`	`247`	`},`
`248`	`248`	`{`
`@@ -289,7 +289,7 @@`
`289`	`289`	`"name": "python",`
`290`	`290`	`"nbconvert_exporter": "python",`
`291`	`291`	`"pygments_lexer": "ipython3",`
`292`		`- "version": "3.6.8"`
	`292`	`+ "version": "3.7.2"`
`293`	`293`	`}`
`294`	`294`	`},`
`295`	`295`	`"nbformat": 4,`