ENH: Fix for bringing code in from a file (#16)

* use ifp as a test case'

* update lecture files to new syntax for executable code from file

* install myst_nb from the branch

* remove debug cell at the top of lecture

* install mysb_nb from branch for testing

* add mathjax cdn address

* update sources lecture-python (9ae923d) using tomyst (b06cacb)

* fix for newline bug in wald_friedman

* update config for latest sphinxcontrib-bibtex (#84)

* update environment for testing from branch mystnb:code-from-file

* upload build folder as an artifact

* fix path

* update timeout for exection to 10min

* migrate from :file: to :load: (myst-nb)

* remove install of myst_nb from branch and include latest jupyter-book master install

Author: mmcky

.github/workflows/ci.yml

@@ -32,6 +32,11 @@ jobs:
         shell: bash -l {0}
         run: |
           jb build lectures --path-output ./
+      - name: Save Build as Artifact
+        uses: actions/upload-artifact@v1
+        with:
+          name: _build
+          path: _build
       - name: Preview Deploy to Netlify
         uses: nwtgck/[email protected]
         with:

.gitignore

@@ -1 +1,2 @@
-lectures/_build
+_build/
+lectures/_build/

lectures/_config.yml

@@ -5,7 +5,10 @@ description: This website presents a set of lectures on quantitative economic mo
 
 execute:
   execute_notebooks: "cache"
-  timeout: 60
+  timeout: 600
+
+bibtex_bibfiles:
+   - _static/quant-econ.bib
 
 bibtex_bibfiles:
    - _static/quant-econ.bib
@@ -50,6 +53,7 @@ sphinx:
       og_logo_url: https://assets.quantecon.org/img/qe-og-logo.png
       description: This website presents a set of lectures on quantitative economic modeling, designed and written by Thomas J. Sargent and John Stachurski.
       keywords: Python, QuantEcon, Quantitative Economics, Economics, Sloan, Alfred P. Sloan Foundation, Tom J. Sargent, John Stachurski
+    mathjax_path: https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
     rediraffe_redirects:
       index_toc.md: intro.md
     tojupyter_static_file_path: ["source/_static", "_static"]

lectures/cake_eating_numerical.md

@@ -72,7 +72,8 @@ where $u$ is the CRRA utility function.
 The analytical solutions for the value function and optimal policy were found
 to be as follows.
 
-```{literalinclude} _static/lecture_specific/cake_eating_numerical/analytical.py
+```{code-cell} python3
+:load: _static/lecture_specific/cake_eating_numerical/analytical.py
 ```
 
 Our first aim is to obtain these analytical solutions numerically.

lectures/coleman_policy_iter.md

@@ -267,7 +267,8 @@ As in our {doc}`previous study <optgrowth_fast>`, we continue to assume that
 
 This will allow us to compare our results to the analytical solutions
 
-```{literalinclude} _static/lecture_specific/optgrowth/cd_analytical.py
+```{code-cell} python3
+:load: _static/lecture_specific/optgrowth/cd_analytical.py
 ```
 
 As discussed above, our plan is to solve the model using time iteration, which
@@ -278,7 +279,8 @@ For this we need access to the functions $u'$ and $f, f'$.
 These are available in a class called `OptimalGrowthModel` that we
 constructed in an {doc}`earlier lecture <optgrowth_fast>`.
 
-```{literalinclude} _static/lecture_specific/optgrowth_fast/ogm.py
+```{code-cell} python3
+:load: _static/lecture_specific/optgrowth_fast/ogm.py
 ```
 
 Now we implement a method called `euler_diff`, which returns
@@ -374,7 +376,8 @@ Here is a function called `solve_model_time_iter` that takes an instance of
 `OptimalGrowthModel` and returns an approximation to the optimal policy,
 using time iteration.
 
-```{literalinclude} _static/lecture_specific/coleman_policy_iter/solve_time_iter.py
+```{code-cell} python3
+:load: _static/lecture_specific/coleman_policy_iter/solve_time_iter.py
 ```
 
 Let's call it:
@@ -439,7 +442,8 @@ Compute and plot the optimal policy.
 
 We use the class `OptimalGrowthModel_CRRA` from our {doc}`VFI lecture <optgrowth_fast>`.
 
-```{literalinclude} _static/lecture_specific/optgrowth_fast/ogm_crra.py
+```{code-cell} python3
+:load: _static/lecture_specific/optgrowth_fast/ogm_crra.py
 ```
 
 Let's create an instance:

lectures/egm_policy_iter.md

@@ -160,12 +160,14 @@ where
 
 This will allow us to make comparisons with the analytical solutions
 
-```{literalinclude} _static/lecture_specific/optgrowth/cd_analytical.py
+```{code-cell} python3
+:load: _static/lecture_specific/optgrowth/cd_analytical.py
 ```
 
 We reuse the `OptimalGrowthModel` class
 
-```{literalinclude} _static/lecture_specific/optgrowth_fast/ogm.py
+```{code-cell} python3
+:load: _static/lecture_specific/optgrowth_fast/ogm.py
 ```
 
 ### The Operator
@@ -216,7 +218,8 @@ grid = og.grid
 
 Here's our solver routine:
 
-```{literalinclude} _static/lecture_specific/coleman_policy_iter/solve_time_iter.py
+```{code-cell} python3
+:load: _static/lecture_specific/coleman_policy_iter/solve_time_iter.py
 ```
 
 Let's call it:

lectures/ifp.md

@@ -475,7 +475,8 @@ start to iterate.
 The following function iterates to convergence and returns the approximate
 optimal policy.
 
-```{literalinclude} _static/lecture_specific/coleman_policy_iter/solve_time_iter.py
+```{code-cell} python3
+:load: _static/lecture_specific/coleman_policy_iter/solve_time_iter.py
 ```
 
 Let's carry this out using the default parameters of the `IFP` class:
@@ -518,7 +519,8 @@ In this case, our income fluctuation problem is just a cake eating problem.
 We know that, in this case, the value function and optimal consumption policy
 are given by
 
-```{literalinclude} _static/lecture_specific/cake_eating_numerical/analytical.py
+```{code-cell} python3
+:load: _static/lecture_specific/cake_eating_numerical/analytical.py
 ```
 
 Let's see if we match up:

lectures/markov_perf.md

@@ -431,7 +431,8 @@ Consider the previously presented duopoly model with parameter values of:
 
 From these, we compute the infinite horizon MPE using the preceding code
 
-```{literalinclude} _static/lecture_specific/markov_perf/duopoly_mpe.py
+```{code-cell} python3
+:load: _static/lecture_specific/markov_perf/duopoly_mpe.py
 ```
 
 Running the code produces the following output.

lectures/optgrowth.md

@@ -624,7 +624,8 @@ whether our code works for this particular case.
 
 In Python, the functions above can be expressed as:
 
-```{literalinclude} _static/lecture_specific/optgrowth/cd_analytical.py
+```{code-cell} python3
+:load: _static/lecture_specific/optgrowth/cd_analytical.py
 ```
 
 Next let's create an instance of the model with the above primitives and assign it to the variable `og`.
@@ -700,7 +701,8 @@ We are clearly getting closer.
 We can write a function that iterates until the difference is below a particular
 tolerance level.
 
-```{literalinclude} _static/lecture_specific/optgrowth/solve_model.py
+```{code-cell} python3
+:load: _static/lecture_specific/optgrowth/solve_model.py
 ```
 
 Let's use this function to compute an approximate solution at the defaults.

lectures/optgrowth_fast.md

@@ -103,7 +103,8 @@ In particular, the algorithm is unchanged, and the only difference is in the imp
 
 As before, we will be able to compare with the true solutions
 
-```{literalinclude} _static/lecture_specific/optgrowth/cd_analytical.py
+```{code-cell} python3
+:load: _static/lecture_specific/optgrowth/cd_analytical.py
 ```
 
 ## Computation
@@ -125,7 +126,8 @@ class.
 
 This is where we sacrifice flexibility in order to gain more speed.
 
-```{literalinclude} _static/lecture_specific/optgrowth_fast/ogm.py
+```{code-cell} python3
+:load: _static/lecture_specific/optgrowth_fast/ogm.py
 ```
 
 The class includes some methods such as `u_prime` that we do not need now
@@ -186,7 +188,8 @@ def T(v, og):
 
 We use the `solve_model` function to perform iteration until convergence.
 
-```{literalinclude} _static/lecture_specific/optgrowth/solve_model.py
+```{code-cell} python3
+:load: _static/lecture_specific/optgrowth/solve_model.py
 ```
 
 Let's compute the approximate solution at the default parameters.
@@ -317,7 +320,8 @@ value function iteration, the JIT-compiled code is usually an order of magnitude
 
 Here's our CRRA version of `OptimalGrowthModel`:
 
-```{literalinclude} _static/lecture_specific/optgrowth_fast/ogm_crra.py
+```{code-cell} python3
+:load: _static/lecture_specific/optgrowth_fast/ogm_crra.py
 ```
 
 Let's create an instance: