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Merge pull request #16 from choldgraf/advanced_section
adding advanced section
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‎_data/navigation.yml‎

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url: guide/05_publish
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- title: Frequently Asked Questions
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url: guide/06_faq
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- title: Advanced topics and information
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url: guide/07_advanced

‎_guide/01_overview.md‎

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@@ -23,57 +23,8 @@ The build process in general goes something like this:
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* Tell GitHub you want to build a website from your fork of the repository.
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* That's it!
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See the rest of this guide for more detailed instructions on this process.
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For a more complete description of the relevant files for this repository,
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see the [Advanced topics section](../07_advanced).
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## Relevant files
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First off, a short description of this repository. The following list contains some
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of the more important files/folders worth knowing about.
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### Website materials
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* `_posts` contains a collection of posts that are displayed chronologically
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with Jekyll's `posts` page.
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* `<XXX>.md` all files in the site's room ending in `.md` will be built into HTML
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and available as pages on the final website.
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### Course materials
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* `notebooks/` contains all course content in Jupyter notebook form
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* `data/` contains the CSV data files used in the course textbook
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* `images/` contains images referenced in the course
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* `SUMMARY.md` contains a markdown list of chapters / paths to your textbook files. For
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example, here is a sample from the Data 8 textbook:
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```
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* [1. Data Science](notebooks/01/what-is-data-science.md)
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* [1.1 Introduction](notebooks/01/1/intro.ipynb)
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* [1.1.1 Computational Tools](notebooks/01/1/1/computational-tools.md)
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* [1.2 Why Data Science?](notebooks/01/2/why-data-science.md)
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* [2. Causality and Experiments](notebooks/02/causality-and-experiments.ipynb)
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* [2.1 John Snow and the Broad Street Pump](notebooks/02/1/observation-and-visualization-john-snow-and-the-broad-street-pump.md)
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* [2.2 Snow’s “Grand Experiment”](notebooks/02/2/snow-s-grand-experiment.ipynb)
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```
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### Auto-generated folders and files
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* `images/chapters` contains images *generated* during the notebook conversion
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* `_chapters/` contain notebooks automatically converted to markdown in the build process
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* `_site/` contains the HTML for the built site. It is created by Jekyll, and should only exist if you build the site locally
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* `_data/textbook.yml` contains information generated in the textbook build process.
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### Repository configuration and build files
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* `_config.yml` contains all site configuration.
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* `_data/navigation.yml` contains site navigation as well as auto-generated sidebar yaml
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* `assets/css` contains CSS for the textbook and website
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* `environment.yml` contains the environment needed to build the textbook
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* `_includes/textbook.html` contains Javascript and HTML needed to set up the textbook
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### Helper scripts
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* `scripts/` contains scripts to generate the textbook from the Jupyter notebooks
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* `scripts/generate_textbook.py` will generate the markdown and sidebar for your textbook. After you make any changes
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in `notebook/`, you should run this script via `make textbook` so your site stays up-to-date.
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* `scripts/clean.py` is used to clean out any auto-generated files
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* `scripts/execute_all_notebooks.py` will use nbconvert to execute all notebooks in `notebooks/` in-place.
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* `scripts/generate_summary_from_folders.py` is a helper script to automatically gneerate a `SUMMARY.md` file from
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the files/folders in `notebooks/`.
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See the rest of this guide in the links to the left for detailed
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instructions on this process. The next section covers [Setting up your environment](../02_setup).

‎_guide/07_advanced.md‎

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---
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title: Advanced topics
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---
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This page contains more advanced and complete information about the
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`textbooks-with-jupyter` repository. See the sections below.
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## Relevant files
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There are a few moving parts associated with `textbooks-with-jupyter`, and this
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section tries to cover most of the relevant pieces. The following list contains some
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of the more important files/folders worth knowing about.
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### Website materials
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* `_posts` contains a collection of posts that are displayed chronologically
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with Jekyll's `posts` page.
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* `<XXX>.md` all files in the site's room ending in `.md` will be built into HTML
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and available as pages on the final website.
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### Course materials
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* `notebooks/` contains all course content in Jupyter notebook form
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* `data/` contains the CSV data files used in the course textbook
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* `images/` contains images referenced in the course
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* `SUMMARY.md` contains a markdown list of chapters / paths to your textbook files. For
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example, here is a sample from the Data 8 textbook:
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```
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* [1. Data Science](notebooks/01/what-is-data-science.md)
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* [1.1 Introduction](notebooks/01/1/intro.ipynb)
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* [1.1.1 Computational Tools](notebooks/01/1/1/computational-tools.md)
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* [1.2 Why Data Science?](notebooks/01/2/why-data-science.md)
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* [2. Causality and Experiments](notebooks/02/causality-and-experiments.ipynb)
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* [2.1 John Snow and the Broad Street Pump](notebooks/02/1/observation-and-visualization-john-snow-and-the-broad-street-pump.md)
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* [2.2 Snow’s “Grand Experiment”](notebooks/02/2/snow-s-grand-experiment.ipynb)
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```
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### Auto-generated folders and files
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* `images/chapters` contains images *generated* during the notebook conversion
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* `_chapters/` contain notebooks automatically converted to markdown in the build process
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* `_site/` contains the HTML for the built site. It is created by Jekyll, and should only exist if you build the site locally
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* `_data/textbook.yml` contains information generated in the textbook build process.
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### Repository configuration and build files
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* `_config.yml` contains all site configuration.
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* `_data/navigation.yml` contains site navigation as well as auto-generated sidebar yaml
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* `assets/css` contains CSS for the textbook and website
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* `environment.yml` contains the environment needed to build the textbook
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* `_includes/textbook.html` contains Javascript and HTML needed to set up the textbook
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### Helper scripts
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* `scripts/` contains scripts to generate the textbook from the Jupyter notebooks
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* `scripts/generate_textbook.py` will generate the markdown and sidebar for your textbook. After you make any changes
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in `notebook/`, you should run this script via `make textbook` so your site stays up-to-date.
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* `scripts/clean.py` is used to clean out any auto-generated files
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* `scripts/execute_all_notebooks.py` will use nbconvert to execute all notebooks in `notebooks/` in-place.
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* `scripts/generate_summary_from_folders.py` is a helper script to automatically gneerate a `SUMMARY.md` file from
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the files/folders in `notebooks/`.

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