switch from recommonmark to myst_parser

Author: dmey

docs/conf.py

@@ -52,9 +52,9 @@ def copy_overview(f_read: Path, f_write: Path, rebuild=False) -> None:
     "IPython.sphinxext.ipython_directive",
     "IPython.sphinxext.ipython_console_highlighting",
     "nbsphinx",
-	"recommonmark",
     'sphinxcontrib.bibtex',
-    'sphinx_copybutton'
+    'sphinx_copybutton',
+    "myst_parser"
 ]
 
 # Autodoc settings
@@ -71,12 +71,6 @@ def copy_overview(f_read: Path, f_write: Path, rebuild=False) -> None:
 
 copybutton_prompt_text = ">>> "
 
-# For recommonmark
-source_suffix = {
-    '.rst': 'restructuredtext',
-    '.txt': 'restructuredtext',
-    '.md': 'markdown',
-}
 
 nbsphinx_execute = 'always'
 # Some notebooks take longer than the default 30 s limit.

docs/copula.md

@@ -0,0 +1,3 @@
+# Copula
+
+TODO: background information about copulas. For general/maths syntax see [`review.md`](review.md).

docs/copula.rst

@@ -0,0 +1,3 @@
+# Functional Principal Component Analysis (fPCA)
+
+TODO: background information about fPCA. For general/maths syntax see [`review.md`](review.md).

docs/fpca.md

@@ -0,0 +1,8 @@
+@book{ deisenroth_faisal_ong_2020,
+    place={Cambridge},
+    title={Mathematics for Machine Learning},
+    DOI={10.1017/9781108679930},
+    publisher={Cambridge University Press},
+    author={Deisenroth, Marc Peter and Faisal, A. Aldo and Ong, Cheng Soon},
+    year={2020}
+}

docs/fpca.rst

@@ -0,0 +1,65 @@
+# Review
+
+TODO: some background statistical information/review of PDF/CDF and other terms used in `copula.md` and `fpca.md`?
+
+Note: I render files with the [MyST parser](https://myst-parser.readthedocs.io/en/latest/examples/wealth_dynamics_md.html) as it makes it easier to use standard LaTeX syntax. E.g. (from [their example](https://myst-parser.readthedocs.io/en/latest/examples/wealth_dynamics_md.html) -- note that [labels are not aligned correctly in the readthedocs theme](https://github.com/readthedocs/sphinx_rtd_theme/pull/383) but we can fix this later/use another theme in the case all eqs needs to be labelled):
+
+
+## Example: Citations/Reference
+
+I use [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/en/latest/quickstart.html) to render references. This can be used to cite with something like:
+
+For a review, see, for example,
+    {cite}`deisenroth_faisal_ong_2020`.
+
+References are in [`references.bib`](references.bib)
+
+## Example syntax in Markdown with MyST: A Model of Wealth Dynamics
+
+Having discussed inequality measures, let us now turn to wealth
+dynamics.
+
+The model we will study is
+
+$$
+w_{t+1} = (1 + r_{t+1}) s(w_t) + y_{t+1}
+$$
+
+where
+
+- $w_t$ is wealth at time $t$ for a given household,
+- $r_t$ is the rate of return of financial assets,
+- $y_t$ is current non-financial (e.g., labor) income and
+- $s(w_t)$ is current wealth net of consumption
+
+Letting $\{z_t\}$ be a correlated state process of the form
+
+$$z_{t+1} = a z_t + b + \sigma_z \epsilon_{t+1}$$
+
+we'll assume that
+
+$$R_t := 1 + r_t = c_r \exp(z_t) + \exp(\mu_r + \sigma_r \xi_t)$$
+
+and
+
+$$y_t = c_y \exp(z_t) + \exp(\mu_y + \sigma_y \zeta_t)$$
+
+Here $\{ (\epsilon_t, \xi_t, \zeta_t) \}$ is IID and standard normal in
+$\mathbb R^3$.
+
+(md:sav_ah)=
+
+```{math}
+---
+label: md:sav_ah
+---
+s(w) = s_0 w \cdot \mathbb 1\{w \geq \hat w\}
+```
+
+
+where $s_0$ is a positive constant.
+
+
+```{bibliography} references.bib
+:style: alpha
+```

docs/references.bib

@@ -25,9 +25,9 @@ dependencies:
   - sphinx
   - sphinx-autobuild
   - sphinx_rtd_theme
+  - myst-parser
   - m2r
   - nbsphinx
-  - recommonmark
   - gdown
   - sphinxcontrib-bibtex
   - sphinx-copybutton