Conjugate step notebook update

.pre-commit-config.yaml

@@ -3,11 +3,11 @@ ci:
 
 repos:
 - repo: https://github.com/psf/black
-  rev: 24.4.2
+  rev: 24.10.0
   hooks:
     - id: black-jupyter
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.8.5
+  rev: 1.9.1
   hooks:
     - id: nbqa-isort
       additional_dependencies: [isort==5.6.4]
@@ -35,7 +35,7 @@ repos:
             |examples/samplers/MLDA_variance_reduction_linear_regression\.ipynb$
 
 - repo: https://github.com/FlamingTempura/bibtex-tidy
-  rev: v1.11.0
+  rev: v1.14.0
   hooks:
     - id: bibtex-tidy
       files: examples/references.bib
@@ -99,7 +99,7 @@ repos:
       language: pygrep
       types_or: [markdown, rst, jupyter]
 - repo: https://github.com/mwouts/jupytext
-  rev: v1.16.3
+  rev: v1.16.5
   hooks:
   - id: jupytext
     files: ^examples/.+\.ipynb$

CONTRIBUTING.md

@@ -1,34 +1,44 @@
 # Guidelines for Contributing
 As part of the PyMC3 library documentation, the guidelines to contribute to
-pymc-examples are based on [PyMC3 contributing guidelines](https://github.com/pymc-devs/pymc3/blob/master/CONTRIBUTING.md). Please refer there
-for a detailed description of the Fork-PR contributing workflow, see "Steps" section,
-and note that you'll need to update the repository URLs and branch names.
+pymc-examples are based on 
+[PyMC3 contributing guidelines](https://github.com/pymc-devs/pymc3/blob/master/CONTRIBUTING.md). 
+Please refer there for a detailed description of the Fork-PR contributing workflow, 
+see "Steps" section,and note that you'll need to update the repository URLs and 
+branch names.
 
-This document therefore covers only some specific guidelines specific to this repository, mainly,
-an adapted version of the "Pull Request Checklist" and some extra guidelines for
-efficient collaboration with Jupyter notebooks.
+This document therefore covers only some specific guidelines specific to this 
+repository, mainly, an adapted version of the "Pull Request Checklist" and some
+extra guidelines for efficient collaboration with Jupyter notebooks.
 
 ## Before submitting a pull request
-The notebooks in pymc-examples are in the process of being updated and reexecuted.
-The main progress tracker is [this GitHub project](https://github.com/pymc-devs/pymc-examples/projects/1).
+The notebooks in `pymc-examples` are in the process of being updated and reexecuted.
+The main progress tracker is 
+[this GitHub project](https://github.com/pymc-devs/pymc-examples/projects/1).
 
 ### About the notebook tracker project
-This project serves as both tracker and organizer of the work needed on each of the example notebooks in this repo.
-Each notebook will have its own issue where we can point out things to fix and discuss them.
-These issue tickets are placed on one of the columns in this project based on the state of the notebook:
-
-* **To Do:** notebooks in this column are potentially outdated, run on v3, don't follow the style guide,
-  don't use best practices when using PyMC...
-* **Best practices (v3):** notebooks in this column use ArviZ and PyMC v3 best practices.
-* **v4 (auto)**: Notebooks in this column have been updated and reexecuted with PyMC v4,
-  but following v3 style and patterns, and are not taking advantage of the new features
-  introduced in v4.
-* **Book style**: Notebooks in this column have had their content, style and formatting updated
-  to take advantage of all the pymc-examples website features, but still need work
-  on the code side (either because they still use v3 or because they use v4 but don't
-  take advantage of its new features). There is a [webinar](https://pymc-data-umbrella.xyz/en/latest/webinars/contributing_to_documentation/index.html)
-  about the pymc examples repo and contributing to it, part of the PyMC Data Umbrella series.
-* **Done:** notebooks in this column use ArviZ and have been updated and executed with pymc3 v4.
+This project serves as both tracker and organizer of the work needed on each of 
+the example notebooks in this repo.
+Each notebook will have its own issue where we can point out things to fix and 
+discuss them.
+These issue tickets are placed on one of the columns in this project based on 
+the state of the notebook:
+
+* **To Do:** notebooks in this column are potentially outdated, run on v3, don't
+  follow the style guide, don't use best practices when using PyMC...
+* **Best practices (v3):** notebooks in this column use ArviZ and PyMC v3 best 
+  practices.
+* **v4 (auto)**: Notebooks in this column have been updated and reexecuted with 
+  PyMC v4, but following v3 style and patterns, and are not taking advantage of
+  the new features introduced in v4.
+* **Book style**: Notebooks in this column have had their content, style and
+  formatting updated to take advantage of all the pymc-examples website features,
+  but still need work on the code side (either because they still use v3 or 
+  because they use v4 but don't take advantage of its new features). There is a 
+  [webinar](https://pymc-data-umbrella.xyz/en/latest/webinars/contributing_to_documentation/index.html)
+  about the pymc examples repo and contributing to it, part of the PyMC Data 
+  Umbrella series.
+* **Done:** notebooks in this column use ArviZ and have been updated and 
+  executed with PyMC v4.
 
 Therefore, all notebooks will be progressively updated along this path:
 
@@ -38,8 +48,8 @@ To Do --> Best Practices (v3) --<                          >--> Done
                                  \ -->   v4 (auto)     -- /
 ```
 
-See https://github.com/pymc-devs/pymc-examples/wiki/Notebook-updates-overview for a more detailed
-description of what each of the statuses mean.
+See https://github.com/pymc-devs/pymc-examples/wiki/Notebook-updates-overview 
+for a more detailed description of what each of the statuses mean.
 
 Each pull request should update a single notebook 1-2 positions to the right.
 Before starting a work on a pull request look at the tracker issue of the
@@ -73,21 +83,24 @@ but not being receiving such ping does not mean you won't get unassigned.
 If you know you won't be able to work during two weeks but plan to
 continue your work afterwards, let us know by commenting when you'll be able
 to retake the work.
-Alternatively, you can also contact your reviewers on [Discourse](https://discourse.pymc.io/)
-
-As for review timeline, while you may get some reviews in a few hours or even some minutes
-if we happen to be working on related things, _you should not expect that to be the norm_.
-You should expect to receive review(s) for your PRs in 1-2 days. If two and a half days
-after submitting you still have not received any comment, let us know (i.e. tag whoever
-opened the issue you are addressing in a new PR comment. If at any point we were
-overwhelmed by PRs and delay this timeline, we will comment on your PR with an estimate
-of when you can expect a proper review.
+Alternatively, you can also contact your reviewers on 
+[Discourse](https://discourse.pymc.io/)
+
+As for review timeline, while you may get some reviews in a few hours or even 
+some minutes if we happen to be working on related things, 
+_you should not expect that to be the norm_.
+You should expect to receive review(s) for your PRs in 1 - 2 days. If 2 1/2 days
+after submitting you still have not received any comment, let us know 
+(i.e. tag whoever opened the issue you are addressing in a new PR comment). 
+If at any point we were overwhelmed by PRs and delay this timeline, we will 
+comment on your PR with an estimate of when you can expect a proper review.
 
 ### In the event of a conflict
 In the event of two or more people working on the same issue,
 the general precedence will go to the person who first commented in the issue.
 If no comments it will go to the first person to submit a PR for review.
-Each situation will differ though, and the core contributors will make the best judgement call if needed.
+Each situation will differ though, and the core contributors will make the best
+judgement call if needed.
 
 ### If the issue ticket has someone assigned to it
 If the issue is assigned then precedence goes to the assignee.
@@ -96,33 +109,49 @@ the ticket is open for all again and will be unassigned.
 
 ## Pull request checklist
 
-We recommended that your contribution complies with the following guidelines before you submit a pull request:
+We recommended that your contribution complies with the following guidelines 
+before you submit a pull request:
 
-*  Use the pull request title to describe the issue and mention the issue number in the pull request description. This will make sure a link back to the original issue is created. For example, use `Use ArviZ in sampler stats notebook` as a title and link to [#46](https://github.com/pymc-devs/pymc-examples/issues/46) in the description.
-   * Please do not submit PRs that are not addressing an issue already present in the issue tracker.
-   * If you want to add a new notebook and no issue related to it is present yet, open one so we can
-     discuss the best way to add the content to the repo. We have an issue template for that.
+* Use the pull request title to describe the issue and mention the issue number
+  in the pull request description. This will make sure a link back to the original
+  issue is created. For example, use `Use ArviZ in sampler stats notebook` as a
+  title and link to [#46](https://github.com/pymc-devs/pymc-examples/issues/46)
+  in the description.
+  * Please do not submit PRs that are not addressing an issue already present
+    in the issue tracker.
+  * If you want to add a new notebook and no issue related to it is present yet,
+    open one so we can discuss the best way to add the content to the repo. 
+    We have an issue template for that.
 
-*  Prefix the title of incomplete contributions with `[WIP]` (to indicate a work in progress). WIPs may be useful to (1) indicate you are working on something to avoid duplicated work, (2) request broad review of functionality or API, or (3) seek collaborators.
+* Prefix the title of incomplete contributions with `[WIP]` (to indicate a work
+  in progress). WIPs may be useful to (1) indicate you are working on something 
+  to avoid duplicated work, (2) request broad review of functionality or API, 
+  or (3) seek collaborators.
 
-* Make sure to run the whole notebook sequentially on a fresh kernel. You can do that with the
-  "Restart & Run All" option before saving.
+* Make sure to run the whole notebook sequentially on a fresh kernel. You can do
+  that with the "Restart & Run All" option before saving.
 
-* No `pre-commit` errors: see the [Jupyter Notebook style](https://github.com/pymc-devs/pymc3/wiki/PyMC3-Jupyter-Notebook-Style-Guide) (and [Python code style](https://github.com/pymc-devs/pymc3/wiki/PyMC3-Python-Code-Style)) page from our Wiki on how to install and run it.
+* No `pre-commit` errors: see the 
+  [Jupyter Notebook style](https://github.com/pymc-devs/pymc3/wiki/PyMC3-Jupyter-Notebook-Style-Guide)
+  (and [Python code style](https://github.com/pymc-devs/pymc3/wiki/PyMC3-Python-Code-Style)) 
+  page from our Wiki on how to install and run it.
 
-* Indicate how are you aiming to update the notebook (i.e. what is the target end column in the tracker). The pull request template has a template for this.
+* Indicate how are you aiming to update the notebook (i.e. what is the target
+  end column in the tracker). The pull request template has a template for this.
 
 ## Contributor guide
-In order to work and run the example notebooks you need to install the packages in
-`requirements-write.txt`. To see how the notebook looks rendered, you can follow
-the instructions in the following paragraph or open a PR to see the preview in
-readthedocs.
-
-The markdown cells in the notebook can use MyST, a superset of CommonMark markdown. See
-https://myst-parser.readthedocs.io/en/latest/ and https://myst-nb.readthedocs.io/en/latest/
-for documentation on their features and syntax.
-
-To generate the draft standalone notebook gallery, you need to have installed all the packages in
-`requirements-docs.txt` and to run `sphinx-build examples/ _build -b html` from the repository
-home directory. After building, you can see the preview of the docs
-by opening `_build/index.html` file with your browser.
+In order to work and run the example notebooks you need to install the packages
+in `requirements-write.txt`. To see how the notebook looks rendered, you can 
+follow the instructions in the following paragraph or open a PR to see the 
+preview in **readthedocs**.
+
+The markdown cells in the notebook can use MyST, a superset of CommonMark markdown.
+See https://myst-parser.readthedocs.io/en/latest/ and 
+https://myst-nb.readthedocs.io/en/latest/ for documentation on their features 
+and syntax.
+
+To generate the draft standalone notebook gallery, you need to have installed
+all the packages in `requirements-docs.txt` and to run 
+`sphinx-build examples/ _build -b html` from the repository home directory. 
+After building, you can see the preview of the docs by opening `_build/index.html` 
+file with your browser.