Merge branch 'main' into ci-warnings-action

Author: mmcky

.github/workflows/cache.yml

@@ -17,7 +17,7 @@ jobs:
           auto-update-conda: true
           auto-activate-base: true
           miniconda-version: 'latest'
-          python-version: "3.12"
+          python-version: "3.13"
           environment-file: environment.yml
           activate-environment: quantecon
       - name: Install JAX, Numpyro, PyTorch

.github/workflows/ci.yml

@@ -18,7 +18,7 @@ jobs:
           auto-update-conda: true
           auto-activate-base: true
           miniconda-version: 'latest'
-          python-version: "3.12"
+          python-version: "3.13"
           environment-file: environment.yml
           activate-environment: quantecon
       - name: Install JAX, Numpyro, PyTorch
@@ -56,7 +56,7 @@ jobs:
         uses: actions/upload-artifact@v4
         if: failure()
         with:
-          name: execution-reports
+          name: execution-reports-notebooks
           path: _build/jupyter/reports
       - name: Build PDF from LaTeX
         shell: bash -l {0}

.github/workflows/linkcheck.yml

@@ -2,7 +2,7 @@ name: Link Checker (lychee)
 on:
   schedule:
     # UTC 23:00 is early morning in Australia (9am)
-    - cron:  '0 23 * * *'
+    - cron:  '0 23 * * 1'
   workflow_dispatch:
 jobs:
   link-checking:
@@ -21,7 +21,7 @@ jobs:
         uses: lycheeverse/lychee-action@v2
         with:
           fail: false
-          args: --accept 403,503 *.html
+          args: --accept 200,403,503 *.html
       - name: Create Issue From File
         if: steps.lychee.outputs.exit_code != 0
         uses: peter-evans/create-issue-from-file@v5

.github/workflows/publish.yml

@@ -16,7 +16,7 @@ jobs:
           auto-update-conda: true
           auto-activate-base: true
           miniconda-version: 'latest'
-          python-version: "3.12"
+          python-version: "3.13"
           environment-file: environment.yml
           activate-environment: quantecon
       - name: Install JAX, Numpyro, PyTorch

environment.yml

@@ -2,17 +2,18 @@ name: quantecon
 channels:
   - default
 dependencies:
-  - python=3.12
-  - anaconda=2024.10
+  - python=3.13
+  - anaconda=2025.06
   - pip
   - pip:
-    - jupyter-book==1.0.3
-    - quantecon-book-theme==0.7.6
-    - sphinx-tojupyter==0.3.0
+    - jupyter-book==1.0.4post1
+    - quantecon-book-theme==0.9.0
+    - sphinx-tojupyter==0.3.1
     - sphinxext-rediraffe==0.2.7
-    - sphinx-reredirects==0.1.4
     - sphinx-exercise==1.0.1
-    - sphinx-proof==0.2.0
-    - ghp-import==1.1.0
-    - sphinxcontrib-youtube==1.3.0 #Version 1.3.0 is required as quantecon-book-theme is only compatible with sphinx<=5
+    - sphinx-proof==0.2.1
+    - sphinxcontrib-youtube==1.4.1
     - sphinx-togglebutton==0.3.2
+    - sphinx-reredirects==0.1.4
+
+

lectures/_config.yml

@@ -37,6 +37,7 @@ sphinx:
     # false-positive links
     linkcheck_ignore: ['https://online.stat.psu.edu/stat415/book/export/html/834']
     bibtex_reference_style: author_year
+    suppress_warnings: ["mystnb.unknown_mime_type"]
     nb_mime_priority_overrides: [
        # HTML
        ['html', 'application/vnd.jupyter.widget-view+json', 10],
@@ -97,6 +98,9 @@ sphinx:
       advanced:
         - "https://python-advanced.quantecon.org"
         - null
+      jax:
+        - "https://jax.quantecon.org/"
+        - null
     mathjax3_config:
       tex:
         macros:

lectures/_static/quant-econ.bib

@@ -2,6 +2,46 @@
 QuantEcon Bibliography File used in conjuction with sphinxcontrib-bibtex package
 Note: Extended Information (like abstracts, doi, url's etc.) can be found in quant-econ-extendedinfo.bib file in _static/
 ###
+
+@article{blume2018case,
+  title={A case for incomplete markets},
+  author={Blume, Lawrence E and Cogley, Timothy and Easley, David A and Sargent, Thomas J and Tsyrennikov, Viktor},
+  journal={Journal of Economic Theory},
+  volume={178},
+  pages={191--221},
+  year={2018},
+  publisher={Elsevier}
+}
+
+@article{shannon1948mathematical,
+  title={A mathematical theory of communication},
+  author={Shannon, Claude E},
+  journal={The Bell system technical journal},
+  volume={27},
+  number={3},
+  pages={379--423},
+  year={1948},
+  publisher={Nokia Bell Labs}
+}
+
+@article{kullback1951information,
+  title={On Information and Sufficiency},
+  author={Kullback, Solomon and Leibler, Richard A},
+  journal={The Annals of Mathematical Statistics},
+  volume={22},
+  number={1},
+  pages={79--86},
+  year={1951},
+  publisher={JSTOR}
+}
+
+@book{kullback1997information,
+  title={Information theory and statistics},
+  author={Kullback, Solomon},
+  year={1997},
+  publisher={Courier Corporation}
+}
+
 @book{friedman1953essays,
   title={Essays in positive economics},
   author={Friedman, Milton},

lectures/_toc.yml

@@ -33,7 +33,10 @@ parts:
 - caption: Statistics and Information 
   numbered: true
   chapters:
+  - file: divergence_measures
   - file: likelihood_ratio_process
+  - file: likelihood_ratio_process_2
+  - file: likelihood_var
   - file: imp_sample
   - file: wald_friedman
   - file: wald_friedman_2

lectures/aiyagari.md

@@ -57,7 +57,6 @@ Let's start with some imports:
 
 ```{code-cell} ipython3
 import matplotlib.pyplot as plt
-plt.rcParams["figure.figsize"] = (11, 5)  #set default figure size
 import numpy as np
 from quantecon.markov import DiscreteDP
 from numba import jit

lectures/back_prop.md

@@ -16,25 +16,17 @@ kernelspec:
 ```{include} _admonition/gpu.md
 ```
 
-```{code-cell} ipython3
-:tags: [skip-execution]
-
-!pip install --upgrade jax
-```
-
-```{code-cell} ipython3
-import jax
-## to check that gpu is activated in environment
-print(f"JAX backend: {jax.devices()[0].platform}")
-```
-
 In addition to what's included in base Anaconda, we need to install the following packages
 
 ```{code-cell} ipython3
 :tags: [hide-output]
 
-!pip install kaleido
-!conda install -y -c plotly plotly plotly-orca retrying
+!pip install -U kaleido plotly
+!conda install -y -c plotly plotly-orca
+
+# kaleido needs chrome to build images
+import kaleido
+kaleido.get_chrome_sync()
 ```
 
 ```{note}
@@ -44,6 +36,19 @@ the Python packages. However this lecture will still execute as Google Colab
 has `plotly` installed.
 ```
 
+We also need to install JAX to run this lecture
+
+```{code-cell} ipython3
+:tags: [skip-execution]
+
+!pip install --upgrade jax
+```
+
+```{code-cell} ipython3
+import jax
+print(f"JAX backend: {jax.devices()[0].platform}") # to check that gpu is activated in environment
+```
+
 ## Overview
 
 Substantial parts of **machine learning** and **artificial intelligence** are about