Merge branch 'main' into adding_fornax

Author: bsipocz

.github/dependabot.yml

@@ -9,3 +9,9 @@ updates:
     directory: "/"
     schedule:
       interval: "monthly"
+    groups:
+      actions:
+        patterns:
+          - "*"
+    labels:
+      - "dependencies"

.github/workflows/create-meeting-issue.yml

@@ -10,7 +10,7 @@ jobs:
   create-team-issue:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v5
       - uses: JasonEtco/create-an-issue@v2
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/linkcheck.yml

@@ -1,16 +1,20 @@
 name: Build documentation
 
 on:
+  schedule:
+  # Once a month is enough
+    - cron: '0 1 15 * *'
   pull_request:
+  workflow_dispatch:
 
 jobs:
   check-links:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v5
+      - uses: actions/setup-python@v6
         with:
-          python-version: '3.9'
+          python-version: '3.13'
           cache: 'pip'
 
       - name: Build the documentation
@@ -21,7 +25,7 @@ jobs:
       # ref: https://github.com/lycheeverse/lychee-action
       # ref: https://github.com/lycheeverse/lychee#commandline-parameters
       - name: Link Checker
-        uses: lycheeverse/lychee-action@v1.5.4
+        uses: lycheeverse/lychee-action@v2.6.1
         env:
           GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
         with:

.readthedocs.yml

@@ -12,3 +12,4 @@ python:
 sphinx:
   builder: dirhtml
   fail_on_warning: true
+  configuration: docs/conf.py

docs/blog/2020-08-07-announce-book.md

@@ -125,10 +125,10 @@ Jupyter Book and its related projects will continue to be developed as a part of
 
 If you'd like to learn more about Jupyter Book or get started building your own books, then check out [the new Jupyter Book documentation](https://jupyterbook.org). Jupyter Book is still in beta and is constantly being improved, so your [feedback and contributions are always welcome](https://github.com/executablebooks/jupyter-book/issues/new/choose).
 
-If there are particular features you'd like to see, open an issue or give a 👍 to a pre-existing issue, and [it will be bumped up on the feature request leaderboard](https://executablebooks.org/en/latest/feature-vote.html).
+If there are particular features you'd like to see, open an issue or give a 👍 to a pre-existing issue, and [it will be bumped up on the feature request leaderboard](https://executablebooks.org/en/latest/feature-vote).
 
 ## Get involved
 
-If you'd like to contribute to any of the projects listed in this post, you are highly encouraged to do so! The Executable Book Project (and thus Jupyter Book) is run as an open project that [welcomes contributions from others](https://executablebooks.org/en/latest/contributing.html).
+If you'd like to contribute to any of the projects listed in this post, you are highly encouraged to do so! The Executable Book Project (and thus Jupyter Book) is run as an open project that [welcomes contributions from others](https://executablebooks.org/en/latest/contributing).
 
 We are excited about all the new features and improvements in the new Jupyter Book, and look forward to seeing the new books that the community creates with this stack!

docs/blog/2021-12-18-agu-2021.md

@@ -4,7 +4,7 @@
 :author: Chris Holdgraf
 ```
 
-The [AGU 2021 conference](https://www.agu.org/Fall-Meeting) just wrapped up, and Jupyter Book made a few appearances at the conference this year.
+The AGU 2021 conference just wrapped up, and Jupyter Book made a few appearances at the conference this year.
 Below are a few links to videos and Google Slides for each session.
 
 ## Jupyter Book 101: A tutorial introduction to Jupyter Book

docs/feature-vote.md

@@ -3,8 +3,7 @@
 
 You can help us to prioritise development of new features by leaving a [👍 reaction](https://github.blog/2016-03-10-add-reactions-to-pull-requests-issues-and-comments/) on the first comment of any `enhancement` issue.
 
-Below is a list of all current enhancement issues from our core repositories,[^a] ordered by 👍
-Click the `+` to see more details.
+Below is a list of all current enhancement issues from our core repositories,[^a] ordered by 👍.
 
 [^a]: The data in this table is updated every day.
 

docs/gallery.yml

@@ -1,3 +1,26 @@
+- name: The image analysis field guide
+  website: https://imaging.epfl.ch/field-guide/
+  repository: https://github.com/EPFL-Center-for-Imaging/image-analysis-field-guide
+  image: https://imaging.epfl.ch/field-guide/_images/epfl.jpeg
+- name: Understanding Quantitative Finance
+  website: https://quantgirluk.github.io/Understanding-Quantitative-Finance/intro.html
+  repository: https://github.com/quantgirluk/Understanding-Quantitative-Finance
+  image: https://quantgirluk.github.io/Understanding-Quantitative-Finance/_static/puzzle.jpeg
+- name: "Taming LLMs: A Practical Guide to LLM Pitfalls with Open Source Software"
+  website: https://www.souzatharsis.com/tamingLLMs/
+  repository: https://github.com/souzatharsis/tamingLLMs
+  image: https://raw.githubusercontent.com/souzatharsis/tamingLLMs/master/tamingllms/_static/cover_curve.png
+- name: Real-Time Digital Signal Processing
+  website: https://realtimedsp.net/lab/
+  repository: https://github.com/Real-Time-DSP/lab
+  image: https://realtimedsp.net/lab/_static/logo.png
+- name: "Discrete-Event Simulation in Python"
+  website: https://health-data-science-or.github.io/simpy-streamlit-tutorial
+  repository: https://github.com/health-data-science-OR/simpy-streamlit-tutorial
+- name: Show the Physics
+  website: https://interactivetextbooks.tudelft.nl/showthephysics/
+  repository: https://github.com/TeachBooks/Showing-Physics
+  image: https://interactivetextbooks.tudelft.nl/showthephysics/_images/coverbook.jpg
 - name: Developing with QIIME 2
   website: https://develop.qiime2.org
   repository: https://github.com/caporaso-lab/developing-with-qiime2
@@ -14,10 +37,6 @@
   website: https://numpy.org/numpy-tutorials/
   repository: https://github.com/numpy/numpy-tutorials
   image: https://raw.githubusercontent.com/numpy/numpy-tutorials/main/site/_static/numpylogo.svg
-- name: CVE.icu
-  website: https://cve.icu
-  repository: https://github.com/jgamblin/cve.icu
-  image: https://raw.githubusercontent.com/jgamblin/cve.icu/main/ambulance.png
 - name: Open Source in Environmental Sustainability
   website: https://report.opensustain.tech/
   repository: https://github.com/protontypes/open-source-in-environmental-sustainability
@@ -101,6 +120,10 @@
 - name: NASA VirtualObservatory Notebooks
   website: https://nasa-navo.github.io/navo-workshop/
   repository: https://github.com/NASA-NAVO/navo-workshop
+- name: NASA/IPAC Infrared Science Archive Python Notebook Tutorials
+  website: https://caltech-ipac.github.io/irsa-tutorials/
+  repository: https://github.com/Caltech-IPAC/irsa-tutorials
+  image: https://raw.githubusercontent.com/Caltech-IPAC/irsa-tutorials/main/_static/irsa_logo.png
 - name: Solving Partial Differential Equations
   image: https://aquaulb.github.io/book_solving_pde_mooc/_static/logo.png
   website: https://aquaulb.github.io/book_solving_pde_mooc/solving_pde_mooc/notebooks/01_Introduction/01_00_Preface.html
@@ -158,11 +181,11 @@
   repository: https://github.com/YannDubs/Neural-Process-Family
   image: https://yanndubs.github.io/Neural-Process-Family/_static/logo.gif
 - name: "The Turing Way: A guide to reproducible, ethical, inclusive and collaborative data science"
-  website: https://the-turing-way.netlify.app
-  repository: https://github.com/alan-turing-institute/the-turing-way
-  image: https://raw.githubusercontent.com/alan-turing-institute/the-turing-way/master/book/website/figures/logo/logo.png
+  website: https://book.the-turing-way.org
+  repository: https://github.com/the-turing-way/the-turing-way
+  image: https://raw.githubusercontent.com/the-turing-way/the-turing-way/main/book/figures/logo/logo.png
 - name: Deep Learning for Molecules and Materials
-  website: https://whitead.github.io/dmol-book/
+  website: https://dmol.pub
   repository: https://github.com/whitead/dmol-book
   image: https://raw.githubusercontent.com/whitead/dmol-book/master/_static/images/logo.png
 - name: genome-sampler Software Documentation
@@ -246,10 +269,6 @@
   repository: https://github.com/euroargodev/argoonlineschool
   image: https://euroargodev.github.io/argoonlineschool/_static/logoAoS.png
   website: https://euroargodev.github.io/argoonlineschool
-- name: "PVSC pvlib python Tutorial"
-  repository: https://github.com/PVSC-Python-Tutorials/PVSC48-Python-Tutorial
-  image: https://raw.githubusercontent.com/pvlib/pvlib-python/master/docs/sphinx/source/_images/pvlib_logo_vert.png
-  website: https://pvsc-python-tutorials.github.io/PVSC48-Python-Tutorial/index.html
 # Temporarily down
 # - name: An Introduction to Applied Bioinformatics
 #   website: http://readIAB.org
@@ -355,7 +374,7 @@
   website: https://climateestimate.net
   repository: https://github.com/atrisovic/weather-panel.github.io/
   image: https://climateestimate.net/_static/climate_estimate_logo.png
-- name: "Apuntes del Curso Introducción a Big Data"
+- name: "Introducción a Big Data. Apuntes de análisis de datos y ML"
   website: https://fortinux.github.io/bigdata-book/intro.html
   repository: https://github.com/fortinux/bigdata-book/
   image: https://fortinux.com/wp-content/uploads/2022/04/Big-data-stack.png
@@ -410,7 +429,7 @@
 - name: "Environmental Data Science Book"
   website: https://the-environmental-ds-book.netlify.app/
   repository: https://github.com/alan-turing-institute/environmental-ds-book
-  image: https://raw.githubusercontent.com/alan-turing-institute/environmental-ds-book/master/book/figures/logo/logo.png
+  image: https://raw.githubusercontent.com/eds-book/eds-book/main/book/_static/edsbook_logo-black.png
 - name: Python Coding for Public Policy
   website: https://python-public-policy.afeld.me/
   repository: https://github.com/afeld/python-public-policy
@@ -451,7 +470,47 @@
   repository: https://github.com/FireDynamics/LectureFireSimulation
   website: https://firedynamics.github.io/LectureFireSimulation
   image: https://firedynamics.github.io/LectureFireSimulation/_static/cce_logo.png
+- name: "Topics in Mathematical Biology"
+  repository: https://github.com/abestshef/mas377
+  website: https://abestshef.github.io/mas377
+  image: https://abestshef.github.io/mas377/_static/logo.png
+- name: "Quantum Metrology with Photoelectrons Vol. 3: Analysis methodologies"
+  repository: https://github.com/phockett/Quantum-Metrology-with-Photoelectrons-Vol3
+  website: https://phockett.github.io/Quantum-Metrology-with-Photoelectrons-Vol3
+  image: https://raw.githubusercontent.com/phockett/Quantum-Metrology-with-Photoelectrons-Vol3/main/notes/cover_art/quantum_met_cover_mock_vol3_070823.png
 - name: "NeuroML"
   repository: https://github.com/NeuroML/Documentation/
   website: https://docs.neuroml.org
   image: https://docs.neuroml.org/_static/logo.png
+- name: "Molecular Simulations"
+  repository: https://github.com/BarakHirshberg/MolecularSimulations
+  website: https://barakhirshberg.github.io/MolecularSimulations
+  image: https://barakhirshberg.github.io/MolecularSimulations/_static/tau_logo.jpg
+- name: "Python Data Science 数据科学"
+  repository: https://github.com/RobinChen121/book-Python-Data-Science-cn
+  website: https://robinchen121.github.io/book-Python-Data-Science-cn
+  image: https://github.com/RobinChen121/book-Python-Data-Science-cn/blob/main/data-science/logo2.png
+- name: "Computational Astrophysics"
+  repository: https://github.com/zingale/computational_astrophysics
+  website: https://zingale.github.io/computational_astrophysics/
+  image: https://github.com/zingale/computational_astrophysics/blob/a756151090ca1da94d0cd6a3e92a8a47cb940630/content/rt_small.png?raw=true
+- name: Computational Problem Solving in the Chemical Sciences
+  repository: https://github.com/rwexler/comp-prob-solv
+  website: https://wexlergroup.github.io/comp-prob-solv/
+  image: https://github.com/wexlergroup/comp-prob-solv/blob/main/logo.png
+- name: Aprendendo Físico-Química com auxílio de Phython
+  repository: https://github.com/leobap01/ebook-fisico-quimica
+  website: https://leobap01.github.io/ebook-fisico-quimica/
+  image: https://leobap01.github.io/ebook-fisico-quimica/_static/logo.png
+- name: Learn Probability
+  repository: https://github.com/snowch/learn_probability
+  website: https://snowch.github.io/learn_probability
+  image: https://snowch.github.io/learn_probability/_static/logo.png
+- name: Fuzzing with Fandango
+  repository: https://github.com/fandango-fuzzer/fandango
+  website: https://fandango-fuzzer.github.io/
+  image: https://fandango-fuzzer.github.io/_static/fandango.png
+- name: Modelling, Uncertainty and Data for Engineers
+  repository: https://github.com/TUDelft-MUDE/book
+  website: https://mude.citg.tudelft.nl/book/2024
+  image: https://files.mude.citg.tudelft.nl/MUDE_Logo-small.png