Solve warnings when building html

Author: enekomartinmartinez

build_rst.py

@@ -8,10 +8,11 @@
 
 notebooks = glob.glob('source/analyses/*/*.ipynb')
 notebooks += glob.glob('source/data/*/*.ipynb')
-
 # Remove 'workbook' files
 notebooks = [Path(nbf) for nbf in notebooks if '_Workbook' not in nbf]
-errors = []
+figures = glob.glob('source/analyses/*/*.png')
+figures += glob.glob('source/data/*/*.png')
+figures = [Path(file) for file in figures]
 
 for infile in notebooks:
     # convert notebook in its local directory
@@ -42,3 +43,8 @@
             shutil.rmtree(destdir)
         # !mv $movedir $dest
         shutil.move(str(movedir), str(dest))
+
+for infile in figures:
+    # Copy extra figures
+    dest = _docs / Path(*infile.parts[1:])
+    shutil.copy(infile, dest)

docs/analyses/data_handling/index_data_handling.rst

@@ -7,4 +7,5 @@ Data Handling
    :glob:
 
    pandas
-   Writing_to_Database
+   Writing_to_Database
+   exogenous_timeseries

docs/analyses/design_policy/index_desing_policy.rst

@@ -0,0 +1,9 @@
+Desing Policy
+=============
+
+
+.. toctree::
+   :maxdepth: 2
+   :glob:
+
+   *

docs/analyses/fitting/index_fitting.rst

@@ -9,4 +9,5 @@ Model Fitting
    Fitting_with_Optimization
    Step_at_a_time_optimization
    Massively_Parallel_Fitting
-   MCMC_for_fitting_models
+   MCMC_for_fitting_models
+   *

docs/analyses/getting_started/index_getting_started.rst

@@ -11,4 +11,5 @@ Getting Started
    Python
    Notebook
    Git_and_Github
-   Hello_World_Teacup
+   Hello_World_Teacup
+   PySD_Challenge_1

docs/analyses/model_comparison/index_model_comparison.rst

@@ -0,0 +1,9 @@
+Model Comparison
+================
+
+
+.. toctree::
+   :maxdepth: 2
+   :glob:
+
+   *

docs/analyses/sensitivity/index_sensitivity.rst

@@ -0,0 +1,9 @@
+Sensitivity
+===========
+
+
+.. toctree::
+   :maxdepth: 2
+   :glob:
+
+   *

docs/analyses/testing/index_testing.rst

@@ -0,0 +1,9 @@
+Testing
+=======
+
+
+.. toctree::
+   :maxdepth: 2
+   :glob:
+
+   *

docs/analyses/visualization/index_visualization.rst

@@ -5,7 +5,10 @@ Visualization
 .. toctree::
    :maxdepth: 2
    :glob:
-   
+
    matplotlib
    other_visualization_libraries
-   phase_portraits
+   phase_portraits
+   marginal_density_plot
+   marginal_density_plot_interactive
+   *

docs/analyses/wrapper_EMAWorkbench/index_wrapper_EMAWorkbench.rst

@@ -0,0 +1,9 @@
+Wrapper EMAWorkbench
+====================
+
+
+.. toctree::
+   :maxdepth: 2
+   :glob:
+
+   *

docs/data/index_data.rst

@@ -16,3 +16,4 @@ The notebooks listed here show how each set was collected or generated.
    Ebola/*
    Emails/*
    MA_Towns/*
+   SD_Fever/*

docs/index.rst

@@ -41,12 +41,18 @@ Contents
 
    analyses/getting_started/index_getting_started
    analyses/data_handling/index_data_handling
+   analyses/design_policy/index_desing_policy.rst
    analyses/visualization/index_visualization
    analyses/fitting/index_fitting
    analyses/geo/index_geo
+   analyses/model_comparison/index_model_comparison.rst
+   analyses/sensitivity/index_sensitivity.rst
    analyses/surrogating_functions/index_surrogate
+   analyses/testing/index_testing.rst
    analyses/realtime/index_realtime
    analyses/workflow/index_workflow
+   analyses/wrapper_EMAWorkbench/index_wrapper_EMAWorkbench.rst
+
    data/index_data
    future
    endnotes

source/analyses/data_handling/exogenous_timeseries.ipynb

@@ -58,7 +58,7 @@
     "\n",
     "Pandas gives us a comprehensive set of tools for loading data from [a variety of sources](http://pandas.pydata.org/pandas-docs/version/0.18.1/io.html), including CSV, Excel, SQL, JSON, and Stata, amongst others. In this demonstration, we'll read a comma separated value file of global emissions data from the year 1751 until 2011.\n",
     "\n",
-    "The `.read_csv` [method]() gives us options for how we want to format the data as we read it in. In reading in our data file, we want to skip the second row (indexed as `1`!) and use the column `Time` as the index of our resulting `DataFrame`."
+    "The `.read_csv` [method](https://pandas.pydata.org/docs/reference/api/pandas.read_csv.html) gives us options for how we want to format the data as we read it in. In reading in our data file, we want to skip the second row (indexed as `1`!) and use the column `Time` as the index of our resulting `DataFrame`."
    ]
   },
   {
@@ -2798,7 +2798,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.12"
+   "version": "3.8.10"
   },
   "vscode": {
    "interpreter": {

source/analyses/data_handling/pandas.ipynb

@@ -1,11 +1,16 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# PySD EMAWorkbench Connector Demo"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 9,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -34,9 +39,7 @@
   {
    "cell_type": "code",
    "execution_count": 5,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "model = ema.connectors.PySDConnector(mdl_file='../../models/Climate/Atmospheric_Bathtub.mdl',\n",
@@ -51,9 +54,7 @@
   {
    "cell_type": "code",
    "execution_count": 14,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -83,23 +84,23 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.12"
+   "pygments_lexer": "ipython3",
+   "version": "3.7.12"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 0
+ "nbformat_minor": 1
 }

source/analyses/design_policy/PySD_EMA_Connector_Demo.ipynb

@@ -39,7 +39,7 @@
    "source": [
     "The model that we'll try to fit is simple 'Susceptible-Infectious' model. This model assumes that everyone is either susceptible, or infectious. It assumes that there is no recovery, or death; and doesn't account for changes in behavior due to the presence of the disease. But it is super simple, and so we'll accept those limitations for now, until we've seen it's fit to the data.\n",
     "\n",
-    "<img src=\"../../models/Epidemic/SI Model.png\" alt=\"Stock and Flow diagram of Susceptible-Infectious model\" style=\"width: 600px;\"/>"
+    "<img src=\"../../models/Epidemic/SI_Model.png\" alt=\"Stock and Flow diagram of Susceptible-Infectious model\" style=\"width: 600px;\"/>"
    ]
   },
   {
@@ -55,7 +55,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "model = pysd.read_vensim('../../models/Epidemic/SI Model.mdl')"
+    "model = pysd.read_vensim('../../models/Epidemic/SI_Model.mdl')"
    ]
   },
   {

source/analyses/fitting/Fitting_with_Optimization.ipynb

@@ -41,7 +41,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "model = pysd.read_vensim('../../models/SI Model/SI Model.mdl')"
+    "model = pysd.read_vensim('../../models/SI_Model/SI_Model.mdl')"
    ]
   },
   {
@@ -232,7 +232,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3.8.10 64-bit",
    "language": "python",
    "name": "python3"
   },
@@ -246,7 +246,12 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.12"
+   "version": "3.8.10"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "916dbcbb3f70747c44a77c7bcd40155683ae19c65e1c03b4aa3499c5328201f1"
+   }
   }
  },
  "nbformat": 4,