This is the current build warnings for the sphinx-tomyst migration tool

▶ make clean && make myst
Removing everything under '_build'...
Running Sphinx v3.1.2
making output directory... done
WARNING: html_static_path entry '_static' does not exist
building [mo]: targets for 0 po files that are out of date
building [myst]: targets for 59 source files that are out of date
updating environment: [new config] 59 added, 0 changed, 0 removed
checking for /Users/matthewmckay/repos-collab/lecture-python-advanced/source/rst/_static/quant-econ.bib in bibtex cache... not found                   
parsing bibtex file /Users/matthewmckay/repos-collab/lecture-python-advanced/source/rst/_static/quant-econ.bib... parsed 218 entries

/Users/matthewmckay/repos-collab/lecture-python-advanced/source/rst/index_time_series_models.rst:16: WARNING: toctree contains reference to nonexisting document 'knowing_forecasts_of_others'
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
CONFIG [definition_list] support for definition list in myst requires:                                                                                 
            myst_deflist_enable = True
        to be specified in the conf.py
writing output... [100%] zreferences                                                                                                                   
/Users/matthewmckay/repos-collab/lecture-python-advanced/source/rst/additive_functionals.rst:1367: WARNING: unknown document: likelihood_ratio_process
/Users/matthewmckay/repos-collab/lecture-python-advanced/source/rst/additive_functionals.rst:1371: WARNING: unknown document: likelihood_ratio_process
WARNING: SKIP amss [transition] objects are not supported by sphinx-tomyst
WARNING: SKIP amss [transition] objects are not supported by sphinx-tomyst
WARNING: SKIP amss2 [transition] objects are not supported by sphinx-tomyst
WARNING: SKIP amss2 [transition] objects are not supported by sphinx-tomyst
WARNING: SKIP amss3 [transition] objects are not supported by sphinx-tomyst
WARNING: SKIP amss3 [transition] objects are not supported by sphinx-tomyst

Hi @mmcky , I find that footnotes and their numbers are in different lines.

e.g., in lecture knowing_forecasts_of_others (left: RST; right: MYST):

There is a reported execution error in opt_tax_recur.md

in this cell

nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
π = np.array([[0, 1, 0,   0,   0,  0],
              [0, 0, 1,   0,   0,  0],
              [0, 0, 0, 0.5, 0.5,  0],
              [0, 0, 0,   0,   0,  1],
              [0, 0, 0,   0,   0,  1],
              [0, 0, 0,   0,   0,  1]])

g = np.array([0.1, 0.1, 0.1, 0.2, 0.1, 0.1])
crra_pref = CRRAutility()

# Solve sequential problem
seq = SequentialLS(crra_pref, π=π, g=g)
sHist_h = np.array([0, 1, 2, 3, 5, 5, 5])
sHist_l = np.array([0, 1, 2, 4, 5, 5, 5])
sim_seq_h = seq.simulate(1, 0, 7, sHist_h)
sim_seq_l = seq.simulate(1, 0, 7, sHist_l)

fig, axes = plt.subplots(3, 2, figsize=(14, 10))
titles = ['Consumption', 'Labor Supply', 'Government Debt',
          'Tax Rate', 'Government Spending', 'Output']

for ax, title, sim_l, sim_h in zip(axes.flatten(),
                                   titles,
                                   sim_seq_l[:6],
                                   sim_seq_h[:6]):
    ax.set(title=title)
    ax.plot(sim_l, '-ok', sim_h, '-or', alpha=0.7)
    ax.grid()

plt.tight_layout()
plt.show()
------------------

results in

ValueError: setting an array element with a sequence. The requested array would exceed the maximum number of dimension of 1.

The latest version of sphinx-exercise supports code through the use of gated directives

https://ebp-sphinx-exercise.readthedocs.io/en/latest/syntax.html#alternative-gated-syntax

so we can now migrate the lecture series to use this package for nice looking exercise and solution admonitions.

The ipywidget objects are again not showing through quantecon-book-theme

• matsuyama
• black_litterman

This is an issue that a code is not compiled.

Here is an example:
Left:RST Right:MyST```

This occurs in:
16
32
33
35
39
40
41
42
43

cc: @mmcky

Consider quantecon lecture on Houthaker's paper
Uploading Houthaker_REStud_Pareto_55.pdf…

Hi @mmcky , I find that inserted figures are not centered.

e.g., (left: RST; right: MYST):

See QuantEcon/lecture-python.myst#165

Hi @mmcky I inspect that the latex code \color{blue} in the following lecture is not working:

• hs_recursive_models

e.g., (left: RST; right: MYST):

This issue occurs in this section.

The equation(31.4) is not compiled properly like below:

I could not figure it out why this occurs from the code in MyST below.

```{math}
:label: eq_55

x_t = \sum^{t-1}_{j=0} L^{-1}_{t,t-j}\, \varepsilon_{t-j}\

cc: @mmcky

This is an issue that some hyperlinks which refer to other lectures have different names from that current website shows in MyST.

For example, Left:RST Right:MyST

This issue occurs when RST codes up the hyperlink as follows:
:doc:`file_name`

Then MyST convert this as follows:
{doc}`file_name <file_name>`

For example, in the above screenshot case,
RST : :doc:`smoothing_tax`

MyST: {doc}`smoothing_tax <smoothing_tax>`

I wonder whether there is any solution for this or the individual links should be manually changed via PR.

So far, this issue occurs in
6
7
31
34
35

cc: @mmcky

This is an issue that \argmin and \col does not work properly in MyST.

These screenshots show the examples. (in this lecture)
Left: RST Right: MyST

I checked all lectures to see whether any other cases needs to be fixed. But no other cases except \argmin& \col cause the issue. (I searched and checked the possible cases from \RR to \argmin in this list.)

cc: @mmcky

Hi @mmcky , I find when there are some italic parts in titles, they don't look very consistent with our new bold style titles.

e.g., in lecture (left: RST; right: MYST):

In the case that equation in lecture is so long, equation reference in MyST does not show well like below. Equation reference covers equation.

Here is MyST.

comparing to RST

This happens in this lecture

cc: @mmcky

The fonts and text are misaligned between the Figure {number} and the actual title given to figure directive

I suggest unifying jitclass names in the advanced lectures with CamelCase.

E.g.,

• https://python-advanced.quantecon.org/arellano

Hi @jstac and @mmcky , I find that there are some error messages in lecture chang_ramsey(MYST-version's code cells are not compiled, but we can see those error messages in RST-version). Also in chang_credible.

Do you think it would be a good idea to get rid of these errors? If so then I would try my best to figure out the issue and create a PR for this.

e.g., (left: RST; right: MYST):

@Smit-create can you take a look at the additive_functionals lecture

AttributeError: module 'quantecon' has no attribute 'lss'

Must be due to a change in quantecon package?

coming from this block

------------------
ϕ_1, ϕ_2, ϕ_3, ϕ_4 = 0.5, -0.2, 0, 0.5
σ = 0.01
ν = 0.01   # Growth rate

# A matrix should be n x n
A = np.array([[ϕ_1, ϕ_2, ϕ_3, ϕ_4],
              [  1,   0,   0,   0],
              [  0,   1,   0,   0],
              [  0,   0,   1,   0]])

# B matrix should be n x k
B = np.array([[σ, 0, 0, 0]]).T

D = np.array([1, 0, 0, 0]) @ A
F = np.array([1, 0, 0, 0]) @ B

amf = AMF_LSS_VAR(A, B, D, F, ν=ν)

T = 150
x, y = amf.lss.simulate(T)

fig, ax = plt.subplots(2, 1, figsize=(10, 9))

ax[0].plot(np.arange(T), y[amf.nx, :], color='k')
ax[0].set_title('Path of $y_t$')
ax[1].plot(np.arange(T), y[0, :], color='g')
ax[1].axhline(0, color='k', linestyle='-.')
ax[1].set_title('Associated path of $x_t$')
plt.show()
------------------

@HumphreyYang there are some execution errors with the new software stack

https://github.com/QuantEcon/lecture-python-advanced.myst/actions/runs/6477683196/job/17588255103

/home/runner/work/lecture-python-advanced.myst/lecture-python-advanced.myst/lectures/five_preferences.md: WARNING: Executing notebook failed: CellExecutionError [mystnb.exec]

Would you have time to take a look?

This work should be done here and tagged manual-change

QuantEcon/lecture-python-advanced#138

Implement the model in Overborrowing and Systemic Externalities in the Business Cycle

On http://www.javierbianchi.com/research.html there is Matlab code.

Can anyone reproduce Fig 1 of the paper in Python or Julia? I've had a go but couldn't get the same output. If you run main.m in the Matlab zip file you'll see that the code seems to roughly reproduce Fig 1.

It would be enough just to replicate the decentralized equilibrium, which is up to line 162 in main.m

CC @Smit-create @chien-y @Flintro @natashawatkins @cc7768 @shlff --- in case anyone feels like a small coding challenge :-)

The AMSS lectures are not currently executing through github actions

Hi @jstac and @mmcky , I find that there are several UserWarning, ComplexWarning and RuntimeWarning in the following lectures (updating):

• arma
• estspec
• opt_tax_recur
• amss

Do you think we should get rid of these warnings? If so, then I would create a PR to solve them.

e.g., (left: RST; right: MYST):

Some codes make too big figure outputs.

Unlike lecture-python-programming.myst, I think we cannot use the solution to use plt.rcParams["figure.figsize"] = (11, 5) #set default figure size.

This is because each code sets up own figure size in code, for example, byfig, (ax1, ax2, ax3, ax4) = plt.subplots(1, 4, figsize=(16, 4)).

Here is the example screenshot.

Here is lectures that contain oversized figure outputs (to-be-updated):
11
12
16
22
28
38

Possibly in:
4
6
7
13
26
27
34
37

cc: @mmcky

Hi @mmcky and @jstac , I find that we have a very good feature to collapse/fold a long-line code cell in our RST-version lectures.

Do you think it is a good idea to translate this feature to the new MYST lectures as well?

e.g., in lecture amss (left: RST; right: MYST):

Hi @mmcky and @jstac , I find that there are some outputs of code cells that occupy too many lines and spaces in the following lectures:

• amss

Do you think it would be a good idea to find an elegant way to compress the output? I came up with three ideas that we can either

• fold the output like what we did for long code cells in the RST-version lectures or like what we did for outputs of !pip install --upgrade in every lecture or
• we can put those outputs just in one output cell or
• we modify the code a bit to just print some of the results.

e.g., this output list is very long and I just show the very first part (left: RST; right: MYST):

Hi @mmcky , \argmin is not compiled in the following lectures (updating):

• 1_orth_proj

\col is not compiled in the following lectures (updating):

• 1_orth_proj

E.g., please find the issue of \argmin from the screenshots (left: RST, right: MYST):

E.g., please find the issue of \argmin from the screenshots (left: RST, right: MYST):

Hi @jstac and @mmcky , I find there are some equations uncentered, which might be easier to read if we centralise them in lectures (updating):

• BCG_incomplete_mkts

Do you think it would be better to make these equations centred in these cases? If so, then I would create a PR for this.

e.g., (left: RST; right: MYST):

Hi @mmcky and @jstac , I find there are some links to external websites written explicitly.

Do you think it would be better to write the link implicitly, like this reference? If so then I would create a PR to improve it.

e.g., in lecture orth_proj (left: RST; right: MYST):

and this

There are two lectures that contain ipywidgets that need to be updated to show the figure some how

• matsuyama
• black_litterman

Hi @mmcky , I find that there are some equation numbers are not internal reference so not updated in the following lectures:

• amss2

Do you think it would be a good idea to make them internal referenced? If so then I would creat a PR for it.

e.g., (left: RST; right: MYST):

@Smit-create can you please review the robustness lecture

AttributeError: module 'quantecon' has no attribute 'lqcontrol'

due to this code block

------------------
# Model parameters

a_0 = 100
a_1 = 0.5
ρ = 0.9
σ_d = 0.05
β = 0.95
c = 2
γ = 50.0

θ = 0.002
ac = (a_0 - c) / 2.0

# Define LQ matrices

R = np.array([[0.,   ac,   0.],
            [ac, -a_1,  0.5],
            [0.,  0.5,  0.]])

R = -R  # For minimization
Q = γ / 2

A = np.array([[1., 0., 0.],
            [0., 1., 0.],
            [0., 0., ρ]])
B = np.array([[0.],
            [1.],
            [0.]])
C = np.array([[0.],
            [0.],
            [σ_d]])

# ----------------------------------------------------------------------- #
#                                 Functions
# ----------------------------------------------------------------------- #


def evaluate_policy(θ, F):

    """
    Given θ (scalar, dtype=float) and policy F (array_like), returns the
    value associated with that policy under the worst case path for {w_t},
    as well as the entropy level.
    """

    rlq = qe.robustlq.RBLQ(Q, R, A, B, C, β, θ)
    K_F, P_F, d_F, O_F, o_F = rlq.evaluate_F(F)
    x0 = np.array([[1.], [0.], [0.]])
    value = - x0.T @ P_F @ x0 - d_F
    entropy = x0.T @ O_F @ x0 + o_F
    return list(map(float, (value, entropy)))


def value_and_entropy(emax, F, bw, grid_size=1000):

    """
    Compute the value function and entropy levels for a θ path
    increasing until it reaches the specified target entropy value.

    Parameters
    ==========
    emax: scalar
        The target entropy value

    F: array_like
        The policy function to be evaluated

    bw: str
        A string specifying whether the implied shock path follows best
        or worst assumptions. The only acceptable values are 'best' and
        'worst'.

    Returns
    =======
    df: pd.DataFrame
        A pandas DataFrame containing the value function and entropy
        values up to the emax parameter. The columns are 'value' and
        'entropy'.
    """

    if bw == 'worst':
        θs = 1 / np.linspace(1e-8, 1000, grid_size)
    else:
        θs = -1 / np.linspace(1e-8, 1000, grid_size)

    df = pd.DataFrame(index=θs, columns=('value', 'entropy'))

    for θ in θs:
        df.loc[θ] = evaluate_policy(θ, F)
        if df.loc[θ, 'entropy'] >= emax:
            break

    df = df.dropna(how='any')
    return df


# ------------------------------------------------------------------------ #
#                                    Main
# ------------------------------------------------------------------------ #


# Compute the optimal rule
optimal_lq = qe.lqcontrol.LQ(Q, R, A, B, C, beta=β)
Po, Fo, do = optimal_lq.stationary_values()

# Compute a robust rule given θ
baseline_robust = qe.robustlq.RBLQ(Q, R, A, B, C, β, θ)
Fb, Kb, Pb = baseline_robust.robust_rule()

# Check the positive definiteness of worst-case covariance matrix to
# ensure that θ exceeds the breakdown point
test_matrix = np.identity(Pb.shape[0]) - (C.T @ Pb @ C) / θ
eigenvals, eigenvecs = eig(test_matrix)
assert (eigenvals >= 0).all(), 'θ below breakdown point.'


emax = 1.6e6

optimal_best_case = value_and_entropy(emax, Fo, 'best')
robust_best_case = value_and_entropy(emax, Fb, 'best')
optimal_worst_case = value_and_entropy(emax, Fo, 'worst')
robust_worst_case = value_and_entropy(emax, Fb, 'worst')

fig, ax = plt.subplots()

ax.set_xlim(0, emax)
ax.set_ylabel("Value")
ax.set_xlabel("Entropy")
ax.grid()

for axis in 'x', 'y':
    plt.ticklabel_format(style='sci', axis=axis, scilimits=(0, 0))

plot_args = {'lw': 2, 'alpha': 0.7}

colors = 'r', 'b'

df_pairs = ((optimal_best_case, optimal_worst_case),
            (robust_best_case, robust_worst_case))


class Curve:

    def __init__(self, x, y):
        self.x, self.y = x, y

    def __call__(self, z):
        return np.interp(z, self.x, self.y)


for c, df_pair in zip(colors, df_pairs):
    curves = []
    for df in df_pair:
        # Plot curves
        x, y = df['entropy'], df['value']
        x, y = (np.asarray(a, dtype='float') for a in (x, y))
        egrid = np.linspace(0, emax, 100)
        curve = Curve(x, y)
        print(ax.plot(egrid, curve(egrid), color=c, **plot_args))
        curves.append(curve)
    # Color fill between curves
    ax.fill_between(egrid,
                    curves[0](egrid),
                    curves[1](egrid),
                    color=c, alpha=0.1)

plt.show()
------------------

Hi @mmcky , I find that there are some lower-resolution plots compiled by code cells compared to our previous plots in RST website in lectures:

• calvo

e.g., (left: RST; right: MYST):

Hi @mmcky , I find that there are some code cells compiled but the plots generated unshown in the following lectures (updating):

• lu_tricks

e.g., (left: RST; right: MYST):

Hi @mmcky , I find that there are some oversized inserted figures.

Do you think it would be a good idea to adjust their size manually like what we did before? If so, then I would investigate all possibly-oversized inserted figures and create a PR to adjust their sizes.

e.g., (left: RST; right: MYST):

NumbaDeprecationWarning occurs in this lecture.

This issue will be fixed by this PR in lecture-python-advanced repo.

To close this issue, it needs to be checked the updated MyST after merging the PR.

cc: @mmcky

This issue is set up to maintain the consistency of style across the lecture series.

Hi @jstac and @mmcky , I also find that the in-text citation styles of footnotes in MYST lectures look different from those in RST lectures before.

e.g., please see knowing_forecasts_of_others's footnote 1 (left: RST; right: MYST):

As discussed with @AakashGfude , we think it would be better to follow the styles in RST lectures--to put the in-text footnote citations in the superscript (as what we did in the picture on the left-hand side above).

Do you think it is a good idea? Looking forward to your comments.

We will need to add input-scroll support for myst-parser as a code-cell tag

Hi @mmcky,

I found the link in the intro page is not working for this series. I will remove that line as we have done in other series.

The following math:

$$
\begin{aligned}
 [\Pi &+ \beta^{1/2} L^{-1} \Lambda (I - \beta^{1/2} L^{-1}
\Delta_h)^{-1} \Theta_h]^\prime [\Pi + \beta^{1/2} L
\Lambda (I - \beta^{1/2} L \Delta_h)^{-1} \Theta_h]\\
&= [\hat\Pi + \beta^{1/2} L^{-1} \hat\Lambda
(I - \beta^{1/2} L^{-1} \Delta_h)^{-1} \Theta_h]^\prime
[\hat\Pi + \beta^{1/2} L \hat\Lambda
(I - \beta^{1/2} L \Delta_h)^{-1} \Theta_h]\end{aligned}
$$

Is breaking pdf build with jupyterbook-latex with the following error:

! Argument of \\aligned@a has an extra }.

in https://github.com/QuantEcon/lecture-python-advanced.myst/blob/main/lectures/hs_recursive_models.md

Hi @mmcky , I find there are some uncompiled code cells in lectures (updating):

• black_litterman
• chang_ramsey
• matsuyama

e.g., (left: RST; right: MYST):

In this lecture, the math equation in the quotes shows redundant > at the beginning and the ending of the equation like below.
Left: RST Right: MyST

This is the same issue #48 in lecture-python.myst

This also occurs in these lectures:
33
43

cc: @mmcky

Thanks to @QBatista for pointing out the timing issue, as per arellano_timing.pdf

This needs to be fixed.

Thanks also for providing JAX code, which uses the correct timing.