Added jupyter{book} for IOOS website

[lohithmunakala]

This PR is in response to the issue https://github.com/ioos/notebooks_demos/issues/386 which was to create a jupyterbook style website for all the notebooks present on IOOS Data Demo Center.

I have created a base jupyter{book} which consist of all the files required to run a jupyterbook on Github pages. As of now, I have only added 2 notebooks and would like to know how we can classify the notebooks into different chapters and subchapters.

@ocefpaf and @MathewBiddle could you please help me out with the addition of the rest of the notebooks to their respective chapters/folders ?

All the files have been added to the folder "jupyterbook".

Here are a few screenshots of the jupyter{book} website and the design.

1. Homepage

2. Other Resources Installation Page

3. A preview of a Notebook

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[lohithmunakala]

After the initial making of the book, I have added all the other notebooks to the jupyter{book} expect for the R Notebooks.

I have divided the classes into 3 types:

• Data Collection
• Data Analysis
• Data PreProcessing

The Data Preprocessing subheading/chapter names have a bit of an issue which can be solved at a later stage.

1. The updated website looks like this now:

2. Notebooks in the Data Collection Chapter

3. Notebooks in the Data Analysis Chapter

4. Notebooks in the Data Preprocessing Chapter

5. A View of the Plot Generated by one of the Notebooks

[ocefpaf]

@MathewBiddle I don't recall the sections we decided in our last meeting (I believe that Tiffany had a really nice idea), did you take notes? I guess they were along the lines of:

• Data Access
• Data Analysis and Visualization
• Standards and Metadata (Data Publication?)

[MathewBiddle]

@ocefpaf, yes those were the sections we discussed. Something like find data, use data, and manage data.

[lohithmunakala]

@ocefpaf, yes those were the sections we discussed. Something like find data, use data, and manage data.

So @ocefpaf @MathewBiddle should I rename the chapters to the following?

• Data Access
• Data Analysis and Visualization
• Data Publication

Also, can you help me with regards to which folder the notebooks should be placed in? I have placed them based on how I have understood the notebooks.

Thanks!

[ocefpaf]

So @ocefpaf @MathewBiddle should I rename the chapters to the following?

Sure. But let's convert this PR to a draft for now as this would probably be part of your GSoC application, correct?

[lohithmunakala]

So @ocefpaf @MathewBiddle should I rename the chapters to the following?

Sure. But let's convert this PR to a draft for now as this would probably be part of your GSoC application, correct?

Yes, it would be a part of my GSoC application although I don't mind merging the PR if it is fine enough. I have some changes to make and the issue with the R notebooks not having the kernel isn't sorted out yet.

[lohithmunakala]

@ocefpaf @MathewBiddle, there is an issue that has come up with regards to the libraries that are being used in the notebooks. The two libraries causing issues are:

1. compliance_checker
2. cf-untis 

Both of the libraries give the error #include "udunits2.h" no such file or directory. I guess compliance_checker is using cf-units hence the same error.

I have googled about these and they seem to be have been made by the IOOS folks themselves. How can I get through this?

[lohithmunakala]

@ocefpaf, yes those were the sections we discussed. Something like find data, use data, and manage data.

So @ocefpaf @MathewBiddle should I rename the chapters to the following?

* Data Access

* Data Analysis and Visualization

* Data Publication

Also, can you help me with regards to which folder the notebooks should be placed in? I have placed them based on how I have understood the notebooks.

Thanks!

@ocefpaf @MathewBiddle I have renamed the folders to the above-mentioned chapters.

Can you help me out with the R Kernel Issue? It doesn't let jupyter build the book. And there are around 5 notebooks which are in R and Matlab.

I have also edited the PR to a draft one for now.

[ocefpaf]

@ocefpaf @MathewBiddle, there is an issue that has come up with regards to the libraries that are being used in the notebooks. The two libraries causing issues are:

1. compliance_checker
2. cf-untis 

Both of the libraries give the error #include "udunits2.h" no such file or directory. I guess compliance_checker is using cf-units hence the same error.

I have googled about these and they seem to be have been made by the IOOS folks themselves. How can I get through this?

How are you installing them? With conda you should not worry about that. There is a section in our page on how to use conda here: https://ioos.github.io/notebooks_demos/other_resources/

Let me know if that helps.

[lohithmunakala]

@ocefpaf @MathewBiddle, there is an issue that has come up with regards to the libraries that are being used in the notebooks. The two libraries causing issues are:

1. compliance_checker
2. cf-untis 

Both of the libraries give the error #include "udunits2.h" no such file or directory. I guess compliance_checker is using cf-units hence the same error. I have googled about these and they seem to be have been made by the IOOS folks themselves. How can I get through this?

How are you installing them? With conda you should not worry about that. There is a section in our page on how to use conda here: https://ioos.github.io/notebooks_demos/other_resources/

Let me know if that helps.

I was trying to install them using pip. Will use conda to get the installation done. Thanks for the help!

[ocefpaf]

I was trying to install them using pip. Will use conda to get the installation done. Thanks for the help!

A lot of packages in the scientific world are not pip installable. We require a full-fledged package managers instead.

[lohithmunakala]

• Adding the R, Matlab notebooks to the jupyter{book}. Solved the issue where the kernel was not being detected.

  Here are some samples

  Basic Home Screen / Landing Page for R and Matlab Notebooks

  

  A Matlab Notebook Primer (Matlab Demo)

  

  Calling R from Python Notebook (R Demo)

  

Any more suggestions would be helpful @ocefpaf @MathewBiddle.

Thanks a ton!

[ocefpaf]

Hi @lohithmunakala are you available for a call to touch base on these details?

[lohithmunakala]

Hi @lohithmunakala are you available for a call to touch base on these details?

Hey @ocefpaf ! When can we have the call?

[ocefpaf]

@lohithmunakala conflicts with notebooks are quite hard to solve correctly. Do you mind re-issuing your PR? It would also be nice so we can take an iterative approach. Sent a PR with as little change as possible to get the basic JB working and we will go from there.

[lohithmunakala]

Sure. I'll reissue a PR. Probably will make the issues go away,