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Hello again. And this video, I want to talk about organizing notebooks as I've promised.

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So we've talked about how do we make charts? That's been a lot of what we've been talking about here.

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But I wanted to talk about how do we actually put together a notebook that's presenting these charts and presenting our conclusions from them.

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So learning outcomes for this video are for you to be able to use markdown document structure to organize a notebook, to use the Jupiter,

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a markdown features to format text in a notebook to create a notebook that clearly tells the story of a data analysis.

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First thing to understand is that a notebook is a document. It is a convenient way to run Python code and to see the results of it.

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But the notebook structure is first and foremost a document. It's meant to be read.

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And there's some structure imposed in the document because it has to read in the same order as the code is going to execute.

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But. We want to be able to actually read it and understand what's going on as we walk through the notebook.

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So we also want to factor particularly complex computations out of the notebook.

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So far, nothing. We've been doing a super complex.

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But if I have a large, complicated data processing operation, training and an extensive set of machine learning models or something,

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I'll put those out of the notebook and other scripts and other modules and leave the notebook for communicating the results of my data analysis.

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So a notebook has two primary types of cells. We have code cells, which you've seen a lot.

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The Python code and its output. And we have marked down cells that contain formatted text.

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Could keep you. I recommend keeping your code cells relatively short.

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One, a few lines. One function definition. If you're defining an entire class and it's taking 100 lines within a code cell.

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That's a good sign you to pull that out into a python module of some kind.

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If helpful, show results after the cell. I do this a lot, particularly in development.

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But if you have too much of it, it can make it hard to read the final notebook because you have all of these outputs.

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And the notebook wins it being a sea of charts and tables.

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And it's difficult to find your way through the notebook and find the pieces that you need to look at.

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So go ahead. Do a lot of them, especially while you're debugging in your prototyping before you submit.

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Maybe go through and clean up, remove things that were just there for you to test how something worked and leave the cells in

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your notebook being the ones that help the reader understand the results of what you're doing.

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Remember, the purpose of the presentation is to show the reader what you learned and how you know it's true.

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Cells that didn't help you do that. Maybe you can consider removing, though, or that don't help you do that.

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At the end of the day, they might have helped you figure out how to do that.

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You can save up a copy of your notebook before doing the cleanup so you don't lose them.

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You can have a supplementary notebook that has maybe Pazz, you went down.

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That didn't work out. Another thing you can consider doing is having an appendix.

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So you've got all of the main content, the notebook. And then down at the end, you have a big heading appendix.

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And there you have extra things. You want to make sure you can still run from top to bottom.

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But there you have some of the other things that maybe dove into more details about the building blocks of some of your computations.

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But it is good to show the results after loading data and after doing a complex manipulation,

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especially one that significantly changes the shape of the data that you're working with.

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And they talk mostly in this video, though, about markdown sales,

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because markdown sells or what you use to build up the structure of your document and make it tell a story,

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not just be a kind of strange way to present Python code.

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So markdown is a text syntax for simple markup. I'm going to provide a link to the markdown documentation in the class notes that go with this video.

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But there's several inline formatting things. If you put two stars around some text, that'll make it bold.

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One star will make it italics. You can indicate a code using the fit, something that's going to show up as the fixed width code layout using back Tex.

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This is one that I see ignored very frequently in and writing up because it's really,

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really useful for function names, variable names, things like that.

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To be able to set apart like this is a special thing. This is a function name also.

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Then you can use tech math syntax by putting it between dollar signs in this markdown notebook.

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Pay attention to the details of what your markdown code or what your text formatted text looks like after you render it in the notebook.

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Make sure it reads well. Make sure it's clear. Ask yourself if I weren't the one who right wrote this.

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What? I like reading this and clean it up and pay attention to those details, to make it look,

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to make it look good and to make it be effective at communicating and so that the reader

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can clearly understand what the different pieces are and what needs to be emphasized,

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etc. Markdown also has a number of block elements.

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The basic one is a paragraph, paragraphs or just text separated by blank lines.

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You can also have bulleted and numbered lists. You can have code blocks for if you need to have a little.

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These aren't super common in a notebook because a lot of your code is in the code cells that you execute.

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But if you need to have a little code that you don't execute for some reason,

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you can put it in the code block and markdown and then you can also block mathematics, a line on its own that begins and ends with two dollar signs.

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And you can actually span multiple lines so long as there aren't any blanks that's going to be treated as a piece of block mathematics.

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It's not in line in a sentence, but it becomes its own block and the rendered self.

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Headings are an important one to pay attention to. So Mark Down headings are lines that start with one, two,

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three up to six hash marks and then a space in the heading text having one heading to hitting three.

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Something that's important to know is the hashes do not mean big and bold.

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That's what they look like. But that's not what they mean. What they mean is heading.

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And so you need to have an outline structure to your notebook using the headings.

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And you need to nest them properly, so within each one, you have your H 2s.

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And then you have your H threes. You don't go straight from H one to H for you.

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You have H three in the middle. Start the notebook with an H one that has the notebook title and that that will become in a lot of rendering context.

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That becomes the title at the top of your notebook. And then all your other headings are two or lower.

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Also you might if you have an appendix, you might have Appendix B, another H1, but also the section headers should be short, not sentences.

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If you're writing an entire sentence in your section header. You're you're putting too much there.

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The section header should be a short title and then the section content comes after it.

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Now, one of the few reasons why it's important to use the section headers heading levels properly.

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One is just visually, it helps break up your notebook so we can easily see which component we're at.

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Second, there are extensions that will do things like no your headings or give you a Browsr Bowl table of contents.

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You can use to navigate the notebook by heading what? I'm rendering notebooks as a part of the course website.

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You'll see this over in the right hand side. You can jump directly to notebook headings.

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That only works because I'm consistently using the heading levels to build the structure and outline based structure of my notebook.

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Another a third reason is for accessibility. If someone's reading your notebook with an assistive technology such as a screen reader,

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the section headings are very important to help them navigate to the parts. The notebook that are both relevant to them at a given time.

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So on the section headers, one additional little rule is if your section editor has to wrap onto a second line, really rethink.

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It's almost certainly too long particularly.

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Don't put an entire question in the section. Maybe. Usually.

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Occasionally it's OK to put a whole question, but maybe put a brief like three to five word summary of the questions topic and

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then write this question itself as the first paragraph of the of the section.

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But pay attention to these different formatting features.

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You can build a well-structured notebook that communicates clearly and draws the reader's emphasis to the places where it needs to go.

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Writing the text itself. Use the document to tell a story. What's the goal of what you're doing?

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Either the whole notebook or of individual pieces of analysis. What's the data that we're doing?

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What do we know about it going in at the up at the top, either at the very top of your notebook or where you're loading the data?

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It's useful to write some, especially at the notebooks and we report you submit to somebody.

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It's useful to write there. What do you know? Where did you get the data? How was it collected?

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Not a full data sheet, but at least some summary information to help the reader understand what it is that we're going to be going and looking at.

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Why are we doing each piece of the analysis? What's the purpose here?

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How does it fit into our broader picture, into our broader goals? What approach are we using?

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We don't want to just repeat the code writing a a numbered list here.

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The steps and those steps are just a literal translation of the code doesn't help understanding.

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It creates an opportunity for a code and documentation to become mismatched.

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But explain if there's anything tricky in the code.

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Explain why that does the job. Explain the conceptual idea behind why you're approaching things the way you are.

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If you're doing a data clean up, explain why that what that cleanup's doing and why that's the right cleanup for your data.

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And then what do we learn from it? So oftentimes what I do with us, with an individual piece of it, like a chart.

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All right. What question the charge is supposed to be answering.

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Or at least the purpose of the chart that we have the code to generate the chart itself.

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And then we have a tech cell that has observations about what we learn from the chart.

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So what are we doing? How are we going to do it if that's not immediately clear code results?

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And then what do we observe from these results?

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So the over then the high level document structure that I recommend is to start start with the title and intros.

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You've got your title. You're heading one. Then what's the notebook for?

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Why does this notebook exist? Are there to include links?

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There's hyperlinks and taxes and markdown as well. Read the markdown documentation to see how to use that.

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But where does this go? Are there things we need to know?

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Background about where why this documents being created?

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Where did the data come from? If we have defined research questions, what are those research questions?

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You can write those right in the intro, the notebook. Then I have a set up.

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I almost always have a setup section that comes next. That has input. I import my python libraries.

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I've maybe defined some help or functions that I'm going to be using throughout the

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notebook helper function specific to one section I might define in that section.

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But then and then I LOEs load the data. Sometimes I load the data as a part of the setup.

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So it's OK. Important modules and then load my data. Sometimes if specially if I have more to say about the data, it's its own section.

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But then as I load each table, I just show the first few rows of it often so that I can see, OK, I've loaded this data and then it's right there.

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We can see as we're going through the rest of the notebook. What is the data just loaded look like?

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Then we perform our analysis and this might be two sections. It might be five, six, seven, eight sections.

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And then finally at the end, we can summarize and conclude this is going to be really I don't always do this in

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my research notebook because often that's the material that goes in the paper.

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But this is going to be something particularly in our assignment, and we're submitting notebooks.

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Put that at the end of the notebook. What do we learn from this?

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Sometimes they going to have specific directions for things.

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I want you to reflect on there when like an assignment one, I've broken down the different requirements.

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Those become good candidates for your age to your level. Two headings for each of those.

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So we've got, I think six require six different requirements. An assignment one.

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H2, heading a primary section of your document for each of those is a good starting point for your layout.

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In addition to you're probably gonna have another one up at the top for the setup and maybe another for the data load.

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But think about this. This the flow, your document be able to communicate.

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What are we doing? What are the prerequisites in terms of and data?

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How are we actually doing it? And then at the end, what do we learn?

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So you're going to write a lot of cells and produce a lot of outputs in your notebook while you're debugging,

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before you submit to before you share in other contexts. Spend some time cleaning up your notebook,

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remove dead ends and extraneous outputs that you included for debugging, but don't fit in the flow of the story.

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Consider putting them in a supplementary notebook. If you want to keep them around and then make sure you can rerun your notebook from top to bottom.

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So when the Jupiter interface is the kernel, when you click that and choose, restart and rerun all.

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And it will restart the python kernel that's actually running your code so all your variables disappear.

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Your data is no longer loaded. And then it starts running the notebook from top to bottom.

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You want that to succeed so that someone else working with the notebook can actually rerun and reproduce your results.

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If that doesn't succeed, then that means either you deleted something that's that's important or you're the order of

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your source in the notebook does not match the order in which it actually has to be executed.

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But make sure it succeeds and also read back to the notebook to make sure that the charts all still look right.

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The data is the conclusions are all still correct, etc. before you submit the final notebook.

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So when you're writing an up of two, you also need to know your audience and your purpose.

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For example, the notebooks I'm writing for you for teaching purposes here.

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They the things I write in them differ from what I'm going to write in a research notebook that I share with my collaborators,

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or I use my own purposes because my purpose partially in their notebooks, is to explain how they're working.

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So I'm going to say more in these notebooks about how exactly the what exactly the code is

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doing is that you can learn how the code works that I would expect in a research notebook.

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But also, you're your own internal your own personal use sharing with your adviser or your supervisor,

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sharing with the public, either the professional public working on your topic or the general public.

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These are all different audiences and they're going to need different levels of explanation and different things highlighted in your notebook.

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Also, not all audiences are well served for notebooks.

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Notebooks are fantastic for internal reports, collaboration, et cetera, sharing the results of a data analysis with colleagues or with yourself.

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But for final publication, you're often going to need a separate final report.

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I don't know that it's possible to write a research paper and Jupiter notebooks. Somebody might have tried, but.

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But I'll still have the notebook where I explain the analysis. I often make that notebook available.

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So for a lot of my a lot of my published research papers, you can download a zip file or a get repository that contains the notebooks and you

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can rerun the experiment and rerun my analysis with the notebooks in the notebook.

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Then also I write the files out to disk. And we're not going to see this quite yet.

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We're going to see it later when we start talking about workflow. Because right now I'm just having to submit notebooks.

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But the note, the figures as they show up in the notebook aren't very high resolution.

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So we're gonna want to render a higher resolution version of them to a PMG file or a PDA file or a

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postscript file that we can then include in our document and word or law tech or whatever we're writing.

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So to wrap up, your notebook is first and foremost a document that contains code to generate the results that you're trying to discuss.

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Take advantage of the document structure and use it as a store to tell the story of your analysis.

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The conclusion you come to in why we should believe them. Pay attention to the examples I'm giving you in class.

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I'm also going to be trying to give you some examples of research oriented notebooks that you can look at to see examples of good notebook practice.

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