fix: bad links and refs

code-workflow-logic/about-python-functions.md

@@ -15,18 +15,6 @@ jupyter:
     name: python3
 ---
 
-:::{toctree}
-:hidden:
-:maxdepth: 2
-
-About Python Functions <self>
-write-python-functions
-python-function-checks
-python-functions-multi-parameters
-python-conditionals
-python-conditionals2
-python-common-exceptions
-:::
 
 
 <!-- #region editable=true slideshow={"slide_type": ""} -->

code-workflow-logic/intro.md

@@ -0,0 +1,36 @@
+---
+jupytext:
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.16.4
+kernelspec:
+  display_name: Python 3 (ipykernel)
+  language: python
+  name: python3
+---
+
+# Optimize your code
+
+
+:::{toctree}
+:caption: functions & checks
+:maxdepth: 2
+
+about-python-functions
+write-python-functions
+python-functions-multi-parameters
+python-function-checks
+python-common-exceptions
+
+:::
+
+:::{toctree}
+:caption: conditionals
+:maxdepth: 2
+
+python-conditionals
+python-conditionals2
+
+:::

index.md

@@ -44,8 +44,8 @@ TODO: let's merge this with the conditional lesson
 :::{card} [✿ Share Code ✿](publish-share-code/intro)
 :class-card: left-aligned
 
-* [Share code on GitHub](share-code)
-* [Get DOI with Zenodo](cite-code)
+* [Share code on GitHub](share-your-code)
+* [Get DOI with Zenodo](cite-your-code)
 
 :::
 ::::
@@ -57,7 +57,6 @@ TODO: let's merge this with the conditional lesson
 These lessons help scientists understand best practices and tools used in the Python ecosystem. We will be adding new lessons over the next year.
 
 :::{toctree}
-:hidden:
 :caption: Clean Code
 :maxdepth: 2
 
@@ -69,7 +68,7 @@ Clean Code <clean-modular-code/intro-clean-code>
 :caption: Optimize Code
 :maxdepth: 2
 
-Optimize Code <code-workflow-logic/about-functions>
+Optimize Code <code-workflow-logic/intro>
 :::
 
 :::{toctree}

publish-share-code/cite-code.md

@@ -13,17 +13,39 @@ kernelspec:
 
 +++ {"editable": true, "slideshow": {"slide_type": ""}}
 
-(cite-code)=
+(cite-your-code)=
 # Cite your code
 
-[Share your code on an online platform like GitHub or GitLab](share-code) using an [open license](open-license) is a great way to share your code. It's also important to consider making your code citable. To understand citations, it's important to understand what a DOI is.
+[Share your code on an online platform like GitHub or GitLab](share-your-code) using an [open license](open-license) is a great way to share your code. It's also important to consider making your code citable. To understand citations, it's important to understand what a DOI is.
 
 ## What is a DOI?
 
 A **DOI**, or **Digital Object Identifier**, is a unique, permanent identifier assigned to digital content such as academic papers, datasets, software, and other research outputs. It acts like a stable web link that always directs users to the reference content, even if the location of the content changes. DOIs are commonly used in academic publishing to ensure that citations remain valid and materials are easily accessible. By using a DOI, creators can make their work more discoverable and citable, enabling others to locate and reference the material reliably now or in future research.
 
 ## TODO Add a section on citation.cff files
 
+## Ways to make your code citable
+
+Add overview on using a platform like Zenodo - what is zenodo --  or publishing 
+
+
+(zenodo)=
+## What is Zenodo?
+TODO: Add more here
+
+### How does Zenodo work?
+
+Creating a DOI for your GitHub repository using Zenodo is a straightforward way to ensure your code is citable and easily discoverable. Zenodo integrates seamlessly with GitHub, allowing you to generate a persistent DOI for any release of your project. To start, link your GitHub account to Zenodo by authorizing access through the Zenodo website. Once connected, navigate to the Zenodo settings and enable the repository you want to archive. After pushing a new release on GitHub, Zenodo will automatically archive it and generate a unique DOI. This DOI can be included in your publications or shared with others, ensuring proper credit for your work. Zenodo also supports versioning, so each release will have its own DOI while maintaining a link to the overall repository.
+
+The video below will walk you through how to set this all up. 
+
+:::{important} 21 October 2024
+This video is a DRAFT and will be updated over the next two months. A more polished version of it will be available soon. 
+:::
+
+
+<div style="padding:75% 0 0 0;position:relative;"><iframe src="https://player.vimeo.com/video/1021839955?badge=0&amp;autopause=0&amp;player_id=0&amp;app_id=58479" frameborder="0" allow="autoplay; fullscreen; picture-in-picture; clipboard-write" style="position:absolute;top:0;left:0;width:100%;height:100%;" title="zenodo-rough-cut"></iframe></div><script src="https://player.vimeo.com/api/player.js"></script>
+
 
 ## CrossRef vs. Zenodo DOIs - What's the difference?
 
@@ -39,15 +61,4 @@ Both types of DOIs ensure your work is easily found and cited. CrossRef is more
 
 By using the right DOI for your work, you help others find and cite it easily, no matter where or how it’s shared!
 
-## How does Zenodo work?
-
-Creating a DOI for your GitHub repository using Zenodo is a straightforward way to ensure your code is citable and easily discoverable. Zenodo integrates seamlessly with GitHub, allowing you to generate a persistent DOI for any release of your project. To start, link your GitHub account to Zenodo by authorizing access through the Zenodo website. Once connected, navigate to the Zenodo settings and enable the repository you want to archive. After pushing a new release on GitHub, Zenodo will automatically archive it and generate a unique DOI. This DOI can be included in your publications or shared with others, ensuring proper credit for your work. Zenodo also supports versioning, so each release will have its own DOI while maintaining a link to the overall repository.
-
-The video below will walk you through how to set this all up. 
 
-:::{important} 21 October 2024
-This video is a DRAFT and will be updated over the next two months. A more polished version of it will be available soon. 
-:::
-
-
-<div style="padding:75% 0 0 0;position:relative;"><iframe src="https://player.vimeo.com/video/1021839955?badge=0&amp;autopause=0&amp;player_id=0&amp;app_id=58479" frameborder="0" allow="autoplay; fullscreen; picture-in-picture; clipboard-write" style="position:absolute;top:0;left:0;width:100%;height:100%;" title="zenodo-rough-cut"></iframe></div><script src="https://player.vimeo.com/api/player.js"></script>

publish-share-code/intro.md

@@ -23,6 +23,7 @@ kernelspec:
 Intro <self>
 Share your Code <share-code>
 Cite your Code <cite-code>
+Publish your Code <publish-code>
 :::
 
 :::{toctree}

publish-share-code/share-code.md

@@ -13,12 +13,12 @@ kernelspec:
 
 +++ {"editable": true, "slideshow": {"slide_type": ""}}
 
-(share-code)=
+(share-your-code)=
 # Share Your Code
 
 Sharing your code online using [open licenses](https://www.pyopensci.org/python-package-guide/documentation/repository-files/license-files.html) is a powerful way to make your work more open and collaborative, supporting the principles of open science. By openly sharing your code, you can set clear guidelines on how others can use, modify, and distribute it through licensing, ensuring that your contributions are respected.
 
-When your code is hosted on a shared platform, others can easily download, install, and use it, making it more accessible and useful to the broader community. Additionally, you can set up proper citations for your code, giving contributors and yourself credit for the work and promoting transparency. [Learn more about setting up citation in our lesson on citing code.](cite-code)
+When your code is hosted on a shared platform, others can easily download, install, and use it, making it more accessible and useful to the broader community. Additionally, you can set up proper citations for your code, giving contributors and yourself credit for the work and promoting transparency. [Learn more about setting up citation in our lesson on citing code.](cite-your-code)
 
 There are several ways to share code. 
 1. You can post your code to an online repository like GitHub or GitLab.