diff --git a/dev/assets/warner.js b/dev/assets/warner.js index e818482..5531c88 100644 --- a/dev/assets/warner.js +++ b/dev/assets/warner.js @@ -37,7 +37,7 @@ function maybeAddWarning () { document.body.removeChild(div); }); const href = window.documenterBaseURL + '/../' + window.DOCUMENTER_STABLE; - div.innerHTML = 'This documentation is not for the latest version.
Go to the latest documentation.'; + div.innerHTML = 'This documentation is not for the latest stable release, but for either the development version or an older release.
Click here to go to the documentation for the latest stable release.'; div.appendChild(closer); document.body.appendChild(div); }; diff --git a/dev/customprocessing/index.html b/dev/customprocessing/index.html index 5e51614..49da468 100644 --- a/dev/customprocessing/index.html +++ b/dev/customprocessing/index.html @@ -1,5 +1,5 @@ -5. Custom pre- and post-processing · Literate.jl
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5. Custom pre- and post-processing

Since all packages are different, and may have different demands on how to create a nice example for the documentation it is important that the package maintainer does not feel limited by the by default provided syntax that this package offers. While you can generally come a long way by utilizing line filtering there might be situations where you need to manually hook into the generation and change things. In Literate this is done by letting the user supply custom pre- and post-processing functions that may do transformation of the content.

All of the generators (Literate.markdown, Literate.notebook and Literate.script) accept preprocess and postprocess keyword arguments. The default "transformation" is the identity function. The input to the transformation functions is a String, and the output should be the transformed String.

preprocess is sent the raw input that is read from the source file (modulo the default line ending transformation). postprocess is given different things depending on the output: For markdown and script output postprocess is given the content String just before writing it to the output file, but for notebook output postprocess is given the dictionary representing the notebook, since, in general, this is more useful.

Example: Adding current date

As an example, lets say we want to splice the date of generation into the output. We could of course update our source file before generating the docs, but we could instead use a preprocess function that splices the date into the source for us. Consider the following source file:

# # Example
+5. Custom pre- and post-processing · Literate.jl
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5. Custom pre- and post-processing
Since all packages are different, and may have different demands on how to create a nice example for the documentation it is important that the package maintainer does not feel limited by the by default provided syntax that this package offers. While you can generally come a long way by utilizing line filtering there might be situations where you need to manually hook into the generation and change things. In Literate this is done by letting the user supply custom pre- and post-processing functions that may do transformation of the content.
All of the generators (Literate.markdown, Literate.notebook and Literate.script) accept preprocess and postprocess keyword arguments. The default "transformation" is the identity function. The input to the transformation functions is a String, and the output should be the transformed String.
preprocess is sent the raw input that is read from the source file (modulo the default line ending transformation). postprocess is given different things depending on the output: For markdown and script output postprocess is given the content String just before writing it to the output file, but for notebook output postprocess is given the dictionary representing the notebook, since, in general, this is more useful.
Example: Adding current date
As an example, lets say we want to splice the date of generation into the output. We could of course update our source file before generating the docs, but we could instead use a preprocess function that splices the date into the source for us. Consider the following source file:
# # Example
 # This example was generated DATEOFTODAY
 
 x = 1 // 3
where DATEOFTODAY is a placeholder, to make it easier for our preprocess function to find the location. Now, lets define the preprocess function, for example
function update_date(content)
@@ -26,4 +26,4 @@ include("file2.jl")
Let's say we have saved this fi
     end
     return str
 end

(of course replace included with your respective files)

Finally, you simply pass this function to e.g. Literate.markdown as

Literate.markdown("examples.jl", "path/to/save/markdown";
-                  name = "markdown_file_name", preprocess = replace_includes)

and you will see that in the final output file (here markdown_file_name.md) the include statements are replaced with the actual code to be included!

This approach is used for generating the examples in the documentation of the TimeseriesPrediction.jl package. The example files, included together in the stexamples.jl file, are processed by literate via this make.jl file to generate the markdown and code cells of the documentation.

+ name = "markdown_file_name", preprocess = replace_includes)

and you will see that in the final output file (here markdown_file_name.md) the include statements are replaced with the actual code to be included!

This approach is used for generating the examples in the documentation of the TimeseriesPrediction.jl package. The example files, included together in the stexamples.jl file, are processed by literate via this make.jl file to generate the markdown and code cells of the documentation.

diff --git a/dev/documenter/index.html b/dev/documenter/index.html index b5ec49f..ba47709 100644 --- a/dev/documenter/index.html +++ b/dev/documenter/index.html @@ -1,5 +1,5 @@ -6. Interaction with Documenter.jl · Literate.jl
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6. Interaction with Documenter.jl

Literate can be used for any purpose, it spits out regular markdown files, and notebooks. Typically, though, these files will be used to render documentation for your package. The generators (Literate.markdown, Literate.notebook and Literate.script) supports a keyword argument documenter that lets the generator perform some extra things, keeping in mind that the source code have been written with Documenter.jl in mind. So let's take a look at what will happen if we set documenter = true:

Literate.markdown:

Literate.script:

  • Documenter style @refs and @id will be removed. This means that you can use @ref and @id in the source file without them leaking to the script.
diff --git a/dev/fileformat/index.html b/dev/fileformat/index.html index 78b365d..62d247e 100644 --- a/dev/fileformat/index.html +++ b/dev/fileformat/index.html @@ -1,5 +1,5 @@ -2. File format · Literate.jl
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2. File format

The source file format for Literate is a regular, commented, julia (.jl) scripts. The idea is that the scripts also serve as documentation on their own and it is also simple to include them in the test-suite, with e.g. include, to make sure the examples stay up do date with other changes in your package.

2.1. Syntax

The basic syntax is simple:

  • lines starting with # are treated as markdown,
  • all other lines are treated as julia code.

Leading whitespace is allowed before #, but it will be removed when generating the output. Since #-lines are treated as markdown we can not use that for regular julia comments, for this you can instead use ##, which will render as # in the output.

Lets look at a simple example:

# # Rational numbers
+2. File format · Literate.jl
Edit on GitHub
2. File format
The source file format for Literate is a regular, commented, julia (.jl) scripts. The idea is that the scripts also serve as documentation on their own and it is also simple to include them in the test-suite, with e.g. include, to make sure the examples stay up do date with other changes in your package.
2.1. Syntax
The basic syntax is simple:
  • lines starting with # are treated as markdown,
  • all other lines are treated as julia code.
Leading whitespace is allowed before #, but it will be removed when generating the output. Since #-lines are treated as markdown we can not use that for regular julia comments, for this you can instead use ##, which will render as # in the output.
Lets look at a simple example:
# # Rational numbers
 #
 # In julia rational numbers can be constructed with the `//` operator.
 # Lets define two rational numbers, `x` and `y`:
@@ -29,4 +29,4 @@ blah blah blah
 #md # Literate.notebook
 #md # Literate.script
 #md # ```
The lines in the example above would be filtered out in the preprocessing step, unless we are generating a markdown file. When generating a markdown file we would simply remove the leading #md from the lines. Beware that the space after the tag is also removed.
The #src token can also be placed at the end of a line. This is to make it possible to have code lines exclusive to the source code, and not just comment lines. For example, if the source file is included in the test suite we might want to add a @test at the end without this showing up in the outputs:
using Test                      #src
-@test result == expected_result #src
2.3. Default replacements
The following convenience "macros"/source placeholders are always expanded:
  • @__NAME__:
    expands to the name keyword argument to Literate.markdown, Literate.notebook and Literate.script (defaults to the filename of the input file).
  • @__REPO_ROOT_URL__:
    Can be used to link to files in the repository. For example @__REPO_ROOT_URL__/src/Literate.jl would link to the source of the Literate module. This variable is automatically determined on Travis CI, GitHub Actions and GitLab CI, but can be configured, see Configuration.
  • @__NBVIEWER_ROOT_URL__:
    Can be used if you want a link that opens the generated notebook in http://nbviewer.jupyter.org/. This variable is automatically determined on Travis CI, GitHub Actions and GitLab CI, but can be configured, see Configuration.
  • @__BINDER_ROOT_URL__:
    Can be used if you want a link that opens the generated notebook in https://mybinder.org/. For example, to add a binder-badge in e.g. the HTML output you can use:
    [![Binder](https://mybinder.org/badge_logo.svg)](@__BINDER_ROOT_URL__/path/to/notebook.inpynb)
    This variable is automatically determined on Travis CI, GitHub Actions and GitLab CI, but can be configured, see Configuration.

+@test result == expected_result #src

2.3. Default replacements

The following convenience "macros"/source placeholders are always expanded:

  • @__NAME__:

    expands to the name keyword argument to Literate.markdown, Literate.notebook and Literate.script (defaults to the filename of the input file).

  • @__REPO_ROOT_URL__:

    Can be used to link to files in the repository. For example @__REPO_ROOT_URL__/src/Literate.jl would link to the source of the Literate module. This variable is automatically determined on Travis CI, GitHub Actions and GitLab CI, but can be configured, see Configuration.

  • @__NBVIEWER_ROOT_URL__:

    Can be used if you want a link that opens the generated notebook in http://nbviewer.jupyter.org/. This variable is automatically determined on Travis CI, GitHub Actions and GitLab CI, but can be configured, see Configuration.

  • @__BINDER_ROOT_URL__:

    Can be used if you want a link that opens the generated notebook in https://mybinder.org/. For example, to add a binder-badge in e.g. the HTML output you can use:

    [![Binder](https://mybinder.org/badge_logo.svg)](@__BINDER_ROOT_URL__/path/to/notebook.inpynb)

    This variable is automatically determined on Travis CI, GitHub Actions and GitLab CI, but can be configured, see Configuration.

diff --git a/dev/generated/example.ipynb b/dev/generated/example.ipynb index c1b34f4..862ecea 100644 --- a/dev/generated/example.ipynb +++ b/dev/generated/example.ipynb @@ -278,87 +278,87 @@ "\n", "\n", "\n", - " \n", + " \n", " \n", " \n", "\n", - "\n", "\n", - " \n", + " \n", " \n", " \n", "\n", - "\n", "\n", - " \n", + " \n", " \n", " \n", "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n" + "\n" ], "image/svg+xml": [ "\n", "\n", "\n", - " \n", + " \n", " \n", " \n", "\n", - "\n", "\n", - " \n", + " \n", " \n", " \n", "\n", - "\n", "\n", - " \n", + " \n", " \n", " \n", "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n" + "\n" ] }, "metadata": {}, diff --git a/dev/generated/example/index.html b/dev/generated/example/index.html index 496a289..3ebea7a 100644 --- a/dev/generated/example/index.html +++ b/dev/generated/example/index.html @@ -1,5 +1,5 @@ -8. Example · Literate.jl
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8. Example

This is an example generated with Literate based on this source file: example.jl. You are seeing the HTML-output which Documenter has generated based on a markdown file generated with Literate. The corresponding notebook can be viewed in nbviewer here: example.ipynb, and opened in binder here: example.ipynb, and the plain script output can be found here: example.jl.

It is recommended to have the source file available when reading this, to better understand how the syntax in the source file corresponds to the output you are seeing.

Basic syntax

The basic syntax for Literate is simple, lines starting with # is interpreted as markdown, and all the other lines are interpreted as code. Here is some code:

x = 1//3
+8. Example · Literate.jl
Edit on GitHub
8. Example
 
This is an example generated with Literate based on this source file: example.jl. You are seeing the HTML-output which Documenter has generated based on a markdown file generated with Literate. The corresponding notebook can be viewed in nbviewer here: example.ipynb, and opened in binder here: example.ipynb, and the plain script output can be found here: example.jl.
It is recommended to have the source file available when reading this, to better understand how the syntax in the source file corresponds to the output you are seeing.
Basic syntax
The basic syntax for Literate is simple, lines starting with # is interpreted as markdown, and all the other lines are interpreted as code. Here is some code:
x = 1//3
 y = 2//5
2//5
In markdown sections we can use markdown syntax. For example, we can write text in italic font, text in bold font and use links.
It is possible to filter out lines depending on the output using the #md, #nb, #jl and #src tags (see Filtering lines):
  • This line starts with #md and is thus only visible in the markdown output.
The source file is parsed in chunks of markdown and code. Starting a line with #- manually inserts a chunk break. For example, if we want to display the output of the following operations we may insert #- in between. These two code blocks will now end up in different @example-blocks in the markdown output, and two different notebook cells in the notebook output.
x + y
11//15
x * y
2//15
Output capturing
Code chunks are by default placed in Documenter @example blocks in the generated markdown. This means that the output will be captured in a block when Documenter is building the docs. In notebooks the output is captured in output cells, if the execute keyword argument is set to true. Output to stdout/stderr is also captured.
Note
Note that Documenter currently only displays output to stdout/stderr if there is no other result to show. Since the vector [1, 2, 3, 4] is returned from foo, the printing of "This string is printed to stdout." is hidden.
function foo()
     println("This string is printed to stdout.")
     return [1, 2, 3, 4]
@@ -16,87 +16,87 @@ y2 = cos.(x)
 plot(x, [y1, y2])

 
 
-  
+  
     
   
 
-
 
-  
+  
     
   
 
-
 
-  
+  
     
   
 
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
 
Custom processing
It is possible to give Literate custom pre- and post-processing functions. For example, here we insert a placeholder value y = 321 in the source, and use a preprocessing function that replaces it with y = 321 in the rendered output.
x = 123
123
In this case the preprocessing function is defined by
function pre(s::String)
     s = replace(s, "x = 123" => "y = 321")
     return s
-end
pre (generic function with 1 method)
Documenter.jl interaction
In the source file it is possible to use Documenter.jl style references, such as @ref and @id. These will be filtered out in the notebook output. For example, here is a link, but it is only visible as a link if you are reading the markdown output. We can also use equations:
\[\int_\Omega \nabla v \cdot \nabla u\ \mathrm{d}\Omega = \int_\Omega v f\ \mathrm{d}\Omega\]
using Documenters math syntax. Documenters syntax is automatically changed to \begin{equation} ... \end{equation} in the notebook output to display correctly.
This page was generated using Literate.jl.

+end
pre (generic function with 1 method)

Documenter.jl interaction

In the source file it is possible to use Documenter.jl style references, such as @ref and @id. These will be filtered out in the notebook output. For example, here is a link, but it is only visible as a link if you are reading the markdown output. We can also use equations:

\[\int_\Omega \nabla v \cdot \nabla u\ \mathrm{d}\Omega = \int_\Omega v f\ \mathrm{d}\Omega\]

using Documenters math syntax. Documenters syntax is automatically changed to \begin{equation} ... \end{equation} in the notebook output to display correctly.

This page was generated using Literate.jl.

diff --git a/dev/generated/name/index.html b/dev/generated/name/index.html index a6c5814..5b6c91e 100644 --- a/dev/generated/name/index.html +++ b/dev/generated/name/index.html @@ -1,2 +1,2 @@ -Rational numbers · Literate.jl
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Rational numbers

In julia rational numbers can be constructed with the // operator. Lets define two rational numbers, x and y:

x = 1//3
1//3
y = 2//5
2//5

When adding x and y together we obtain a new rational number:

z = x + y
11//15
+Rational numbers · Literate.jl
Edit on GitHub

Rational numbers

In julia rational numbers can be constructed with the // operator. Lets define two rational numbers, x and y:

x = 1//3
1//3
y = 2//5
2//5

When adding x and y together we obtain a new rational number:

z = x + y
11//15
diff --git a/dev/index.html b/dev/index.html index 368322e..610365f 100644 --- a/dev/index.html +++ b/dev/index.html @@ -1,2 +1,2 @@ -1. Introduction · Literate.jl
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1. Introduction

Welcome to the documentation for Literate – a simplistic package for Literate Programming.

What?

Literate is a package that generates markdown pages (for e.g. Documenter.jl), and Jupyter notebooks, from the same source file. There is also an option to "clean" the source from all metadata, and produce a pure Julia script.

The main design goal is simplicity. It should be simple to use, and the syntax should be simple. In short, all you have to do is to write a commented julia script!

The public interface consists of three functions, all of which take the same script file as input, but generate different output:

  • Literate.markdown generates a markdown file. Code snippets can be executed and the results included in the output.
  • Literate.notebook generates a notebook. Code snippets can be executed and the results included in the output.
  • Literate.script generates a plain script file scrubbed from all metadata and special syntax.

Why?

Examples are (probably) the best way to showcase your awesome package, and examples are often the best way for a new user to learn how to use it. It is therefore important that the documentation of your package contains examples for users to read and study. However, people are different, and we all prefer different ways of trying out a new package. Some people want to RTFM, others want to explore the package interactively in, for example, a notebook, and some people want to study the source code. The aim of Literate is to make it easy to give the user all of these options, while still keeping maintenance to a minimum.

It is quite common that packages have "example notebooks" to showcase the package. Notebooks are great for showcasing a package, but they are not so great with version control, like git. The reason being that a notebook is a very "rich" format since it contains output and other metadata. Changes to the notebook thus result in large diffs, which makes it harder to review the actual changes.

It is also common that packages include examples in the documentation, for example by using Documenter.jl @example-blocks. This is also great, but it is not quite as interactive as a notebook, for the users who prefer that.

Literate tries to solve the problems above by creating the output as a part of the doc build. Literate generates the output based on a single source file which makes it easier to maintain, test, and keep the manual and your example notebooks in sync.

+1. Introduction · Literate.jl
Edit on GitHub

1. Introduction

Welcome to the documentation for Literate – a simplistic package for Literate Programming.

What?

Literate is a package that generates markdown pages (for e.g. Documenter.jl), and Jupyter notebooks, from the same source file. There is also an option to "clean" the source from all metadata, and produce a pure Julia script.

The main design goal is simplicity. It should be simple to use, and the syntax should be simple. In short, all you have to do is to write a commented julia script!

The public interface consists of three functions, all of which take the same script file as input, but generate different output:

  • Literate.markdown generates a markdown file. Code snippets can be executed and the results included in the output.
  • Literate.notebook generates a notebook. Code snippets can be executed and the results included in the output.
  • Literate.script generates a plain script file scrubbed from all metadata and special syntax.

Why?

Examples are (probably) the best way to showcase your awesome package, and examples are often the best way for a new user to learn how to use it. It is therefore important that the documentation of your package contains examples for users to read and study. However, people are different, and we all prefer different ways of trying out a new package. Some people want to RTFM, others want to explore the package interactively in, for example, a notebook, and some people want to study the source code. The aim of Literate is to make it easy to give the user all of these options, while still keeping maintenance to a minimum.

It is quite common that packages have "example notebooks" to showcase the package. Notebooks are great for showcasing a package, but they are not so great with version control, like git. The reason being that a notebook is a very "rich" format since it contains output and other metadata. Changes to the notebook thus result in large diffs, which makes it harder to review the actual changes.

It is also common that packages include examples in the documentation, for example by using Documenter.jl @example-blocks. This is also great, but it is not quite as interactive as a notebook, for the users who prefer that.

Literate tries to solve the problems above by creating the output as a part of the doc build. Literate generates the output based on a single source file which makes it easier to maintain, test, and keep the manual and your example notebooks in sync.

diff --git a/dev/outputformats/index.html b/dev/outputformats/index.html index 93bb3b2..18a0a27 100644 --- a/dev/outputformats/index.html +++ b/dev/outputformats/index.html @@ -1,5 +1,5 @@ -4. Output formats · Literate.jl
Edit on GitHub

4. Output formats

When the source is parsed, and has been processed it is time to render the output. We will consider the following source snippet:

# # Rational numbers
+4. Output formats · Literate.jl
Edit on GitHub
4. Output formats
When the source is parsed, and has been processed it is time to render the output. We will consider the following source snippet:
# # Rational numbers
 #
 # In julia rational numbers can be constructed with the `//` operator.
 # Lets define two rational numbers, `x` and `y`:
@@ -42,7 +42,7 @@ x = 1//3
 ````
 ````
 1//3
-````
In this example the output is just plain text. However, if the resulting value of the code block can be displayed as an image (image/png or image/jpeg), HTML (text/html) or markdown (text/markdown) Literate will include the richest representation of the output.
Note
Since Documenter executes and captures results of @example block it is not necessary to use execute=true for markdown output that is meant to be used as input to Documenter.
See the section about Configuration for more information about how to configure the behavior and resulting output of Literate.markdown.
Literate.markdown — Function
Literate.markdown(inputfile, outputdir=pwd(); config::AbstractDict=Dict(), kwargs...)
Generate a markdown file from inputfile and write the result to the directory outputdir.
See the manual section on Configuration for documentation of possible configuration with config and other keyword arguments.
source
Markdown flavors
Literate can output markdown in different flavors. The flavor is specified using the flavor keyword argument. The following flavors are currently supported:
  • flavor = Literate.DocumenterFlavor(): this is the default flavor and the output is meant to be used as input to Documenter.jl.
  • flavor = Literate.CommonMarkFlavor(): this outputs markdown that has the flavor of the CommonMark specification.
  • flavor = Literate.FranklinFlavor(): this outputs markdown meant to be used as input to Franklin.jl.
4.2. Notebook output
Notebook output is generated by Literate.notebook. The (default) notebook output of the source snippet can be seen here: notebook.ipynb.
We note that lines starting with # are placed in markdown cells, and the code lines have been placed in code cells. By default the notebook is also executed and output cells populated. The current working directory is set to the specified output directory the notebook is executed.
See the section about Configuration for how to configure the behavior and resulting output of Literate.notebook.
Literate.notebook — Function
Literate.notebook(inputfile, outputdir=pwd(); config::AbstractDict=Dict(), kwargs...)
Generate a notebook from inputfile and write the result to outputdir.
See the manual section on Configuration for documentation of possible configuration with config and other keyword arguments.
source
Notebook metadata
Jupyter notebook cells (both code cells and markdown cells) can contain metadata. This is enabled in Literate by the %% token, similar to Jupytext. The format is as follows
%% optional ignored text [type] {optional metadata JSON}
Cell metadata can, for example, be used for nbgrader and the reveal.js notebook extension RISE.
The following would create a 3 slide deck with RISE:
#nb # %% A slide [markdown] {"slideshow": {"slide_type": "slide"}}
+````
In this example the output is just plain text. However, if the resulting value of the code block can be displayed as an image (image/png or image/jpeg), HTML (text/html) or markdown (text/markdown) Literate will include the richest representation of the output.
Note
Since Documenter executes and captures results of @example block it is not necessary to use execute=true for markdown output that is meant to be used as input to Documenter.
See the section about Configuration for more information about how to configure the behavior and resulting output of Literate.markdown.
Literate.markdown — Function
Literate.markdown(inputfile, outputdir=pwd(); config::AbstractDict=Dict(), kwargs...)
Generate a markdown file from inputfile and write the result to the directory outputdir.
See the manual section on Configuration for documentation of possible configuration with config and other keyword arguments.
source
Markdown flavors
Literate can output markdown in different flavors. The flavor is specified using the flavor keyword argument. The following flavors are currently supported:
  • flavor = Literate.DocumenterFlavor(): this is the default flavor and the output is meant to be used as input to Documenter.jl.
  • flavor = Literate.CommonMarkFlavor(): this outputs markdown that has the flavor of the CommonMark specification.
  • flavor = Literate.FranklinFlavor(): this outputs markdown meant to be used as input to Franklin.jl.
4.2. Notebook output
Notebook output is generated by Literate.notebook. The (default) notebook output of the source snippet can be seen here: notebook.ipynb.
We note that lines starting with # are placed in markdown cells, and the code lines have been placed in code cells. By default the notebook is also executed and output cells populated. The current working directory is set to the specified output directory the notebook is executed.
See the section about Configuration for how to configure the behavior and resulting output of Literate.notebook.
Literate.notebook — Function
Literate.notebook(inputfile, outputdir=pwd(); config::AbstractDict=Dict(), kwargs...)
Generate a notebook from inputfile and write the result to outputdir.
See the manual section on Configuration for documentation of possible configuration with config and other keyword arguments.
source
Notebook metadata
Jupyter notebook cells (both code cells and markdown cells) can contain metadata. This is enabled in Literate by the %% token, similar to Jupytext. The format is as follows
%% optional ignored text [type] {optional metadata JSON}
Cell metadata can, for example, be used for nbgrader and the reveal.js notebook extension RISE.
The following would create a 3 slide deck with RISE:
#nb # %% A slide [markdown] {"slideshow": {"slide_type": "slide"}}
 # # Some title
 #
 # We're using `#nb` so the metadata is only included in notebook output
@@ -56,4 +56,4 @@ y = 2//5
 
 y = 2//5
 
-z = x + y
We note that lines starting with # are removed and only the code lines have been kept.
See the section about Configuration for how to configure the behavior and resulting output of Literate.script.
Literate.script — Function
Literate.script(inputfile, outputdir=pwd(); config::AbstractDict=Dict(), kwargs...)
Generate a plain script file from inputfile and write the result to outputdir.
See the manual section on Configuration for documentation of possible configuration with config and other keyword arguments.
source
4.4. Configuration
The behavior of Literate.markdown, Literate.notebook and Literate.script can be configured by keyword arguments. There are two ways to do this; pass config::Dict as a keyword argument, or pass individual keyword arguments.
Configuration precedence
Individual keyword arguments take precedence over the config dictionary, so for e.g. Literate.markdown(...; config = Dict("name" => "hello"), name = "world") the resulting configuration for name will be "world". Both individual keyword arguments and the config dictionary take precedence over the default.
Available configurations with description and default values are given in the reference for Literate.DEFAULT_CONFIGURATION just below.
Literate.DEFAULT_CONFIGURATION — Constant
DEFAULT_CONFIGURATION
Default configuration for Literate.markdown, Literate.notebook and Literate.script which is used for everything not specified by the user. Configuration can be passed as individual keyword arguments or as a dictionary passed with the config keyword argument. See the manual section about Configuration for more information.
Available options:
  • name (default: filename(inputfile)): Name of the output file (excluding the file extension).
  • preprocess (default: identity): Custom preprocessing function mapping a String to a String. See Custom pre- and post-processing.
  • postprocess (default: identity): Custom preprocessing function mapping a String to a String. See Custom pre- and post-processing.
  • credit (default: true): Boolean for controlling the addition of This file was generated with Literate.jl ... to the bottom of the page. If you find Literate.jl useful then feel free to keep this.
  • keep_comments (default: false): When true, keeps markdown lines as comments in the output script. Only applicable for Literate.script.
  • execute (default: true for notebook, false for markdown): Whether to execute and capture the output. Only applicable for Literate.notebook and Literate.markdown.
  • codefence (default: "````@example $(name)" => "````" for DocumenterFlavor() and "````julia" => "````" otherwise): Pair containing opening and closing code fence for wrapping code blocks.
  • flavor (default: Literate.DocumenterFlavor()) Output flavor for markdown, see Markdown flavors. Only applicable for Literate.markdown.
  • devurl (default: "dev"): URL for "in-development" docs, see Documenter docs. Unused if repo_root_url/ nbviewer_root_url/binder_root_url are set.
  • repo_root_url: URL to the root of the repository. Determined automatically on Travis CI, GitHub Actions and GitLab CI. Used for @__REPO_ROOT_URL__.
  • nbviewer_root_url: URL to the root of the repository as seen on nbviewer. Determined automatically on Travis CI, GitHub Actions and GitLab CI. Used for @__NBVIEWER_ROOT_URL__.
  • binder_root_url: URL to the root of the repository as seen on mybinder. Determined automatically on Travis CI, GitHub Actions and GitLab CI. Used for @__BINDER_ROOT_URL__.
  • repo_root_path: Filepath to the root of the repository. Determined automatically on Travis CI, GitHub Actions and GitLab CI. Used for computing Documenters EditURL.
  • image_formats: A vector of (mime, ext) tuples, with the default Tuple{MIME, String}[(MIME type image/svg+xml, ".svg"), (MIME type image/png, ".png"), (MIME type image/jpeg, ".jpeg")]. Results which are showable with a MIME type are saved with the first match, with the corresponding extension.
source

+z = x + y

We note that lines starting with # are removed and only the code lines have been kept.

See the section about Configuration for how to configure the behavior and resulting output of Literate.script.

Literate.script — Function
Literate.script(inputfile, outputdir=pwd(); config::AbstractDict=Dict(), kwargs...)

Generate a plain script file from inputfile and write the result to outputdir.

See the manual section on Configuration for documentation of possible configuration with config and other keyword arguments.

source

4.4. Configuration

The behavior of Literate.markdown, Literate.notebook and Literate.script can be configured by keyword arguments. There are two ways to do this; pass config::Dict as a keyword argument, or pass individual keyword arguments.

Configuration precedence

Individual keyword arguments take precedence over the config dictionary, so for e.g. Literate.markdown(...; config = Dict("name" => "hello"), name = "world") the resulting configuration for name will be "world". Both individual keyword arguments and the config dictionary take precedence over the default.

Available configurations with description and default values are given in the reference for Literate.DEFAULT_CONFIGURATION just below.

Literate.DEFAULT_CONFIGURATION — Constant
DEFAULT_CONFIGURATION

Default configuration for Literate.markdown, Literate.notebook and Literate.script which is used for everything not specified by the user. Configuration can be passed as individual keyword arguments or as a dictionary passed with the config keyword argument. See the manual section about Configuration for more information.

Available options:

  • name (default: filename(inputfile)): Name of the output file (excluding the file extension).
  • preprocess (default: identity): Custom preprocessing function mapping a String to a String. See Custom pre- and post-processing.
  • postprocess (default: identity): Custom preprocessing function mapping a String to a String. See Custom pre- and post-processing.
  • credit (default: true): Boolean for controlling the addition of This file was generated with Literate.jl ... to the bottom of the page. If you find Literate.jl useful then feel free to keep this.
  • keep_comments (default: false): When true, keeps markdown lines as comments in the output script. Only applicable for Literate.script.
  • execute (default: true for notebook, false for markdown): Whether to execute and capture the output. Only applicable for Literate.notebook and Literate.markdown.
  • codefence (default: "````@example $(name)" => "````" for DocumenterFlavor() and "````julia" => "````" otherwise): Pair containing opening and closing code fence for wrapping code blocks.
  • flavor (default: Literate.DocumenterFlavor()) Output flavor for markdown, see Markdown flavors. Only applicable for Literate.markdown.
  • devurl (default: "dev"): URL for "in-development" docs, see Documenter docs. Unused if repo_root_url/ nbviewer_root_url/binder_root_url are set.
  • repo_root_url: URL to the root of the repository. Determined automatically on Travis CI, GitHub Actions and GitLab CI. Used for @__REPO_ROOT_URL__.
  • nbviewer_root_url: URL to the root of the repository as seen on nbviewer. Determined automatically on Travis CI, GitHub Actions and GitLab CI. Used for @__NBVIEWER_ROOT_URL__.
  • binder_root_url: URL to the root of the repository as seen on mybinder. Determined automatically on Travis CI, GitHub Actions and GitLab CI. Used for @__BINDER_ROOT_URL__.
  • repo_root_path: Filepath to the root of the repository. Determined automatically on Travis CI, GitHub Actions and GitLab CI. Used for computing Documenters EditURL.
  • image_formats: A vector of (mime, ext) tuples, with the default Tuple{MIME, String}[(MIME type image/svg+xml, ".svg"), (MIME type image/png, ".png"), (MIME type image/jpeg, ".jpeg")]. Results which are showable with a MIME type are saved with the first match, with the corresponding extension.
source
diff --git a/dev/pipeline/index.html b/dev/pipeline/index.html index 6ff8566..38b80d1 100644 --- a/dev/pipeline/index.html +++ b/dev/pipeline/index.html @@ -1,5 +1,5 @@ -3. Processing pipeline · Literate.jl
Edit on GitHub

3. Processing pipeline

The generation of output follows the same pipeline for all output formats:

  1. Pre-processing
  2. Parsing
  3. Document generation
  4. Post-processing
  5. Writing to file

3.1. Pre-processing

The first step is pre-processing of the input file. The file is read to a String. The first processing step is to apply the user specified pre-processing function, see Custom pre- and post-processing.

The next step is to perform all of the built-in default replacements. CRLF style line endings ("\r\n") are replaced with LF line endings ("\n") to simplify internal processing. Next, line filtering is performed, see Filtering lines, meaning that lines starting with #md, #nb or #jl are handled (either just the token itself is removed, or the full line, depending on the output target). The last pre-processing step is to expand the convenience "macros" described in Default replacements is expanded.

3.2. Parsing

After the preprocessing the file is parsed. The first step is to categorize each line and mark them as either markdown or code according to the rules described in the Syntax section. Lets consider the example from the previous section with each line categorized:

# # Rational numbers                                                     <- markdown
+3. Processing pipeline · Literate.jl
Edit on GitHub
3. Processing pipeline
The generation of output follows the same pipeline for all output formats:
  1. Pre-processing
  2. Parsing
  3. Document generation
  4. Post-processing
  5. Writing to file
3.1. Pre-processing
The first step is pre-processing of the input file. The file is read to a String. The first processing step is to apply the user specified pre-processing function, see Custom pre- and post-processing.
The next step is to perform all of the built-in default replacements. CRLF style line endings ("\r\n") are replaced with LF line endings ("\n") to simplify internal processing. Next, line filtering is performed, see Filtering lines, meaning that lines starting with #md, #nb or #jl are handled (either just the token itself is removed, or the full line, depending on the output target). The last pre-processing step is to expand the convenience "macros" described in Default replacements is expanded.
3.2. Parsing
After the preprocessing the file is parsed. The first step is to categorize each line and mark them as either markdown or code according to the rules described in the Syntax section. Lets consider the example from the previous section with each line categorized:
# # Rational numbers                                                     <- markdown
 #                                                                        <- markdown
 # In julia rational numbers can be constructed with the `//` operator.   <- markdown
 # Lets define two rational numbers, `x` and `y`:                         <- markdown
@@ -29,4 +29,4 @@ x = 1 // 3
 y = 2 // 5
Chunk #3:
When adding `x` and `y` together we obtain a new rational number:
Chunk #4:
z = x + y
It is then up to the Document generation step to decide how these chunks should be treated.
Custom control over chunk splits
Sometimes it is convenient to be able to manually control how the chunks are split. For example, if you want to split a block of code into two, such that they end up in two different @example blocks or notebook cells. The #- token can be used for this purpose. All lines starting with #- are used as "chunk-splitters":
x = 1 // 3
 y = 2 // 5
 #-
-z = x + y
The example above would result in two consecutive code-chunks.
Tip
The rest of the line, after #-, is discarded, so it is possible to use e.g. #------------- as a chunk splitter, which may make the source code more readable.
It is also possible to use #+ as a chunk splitter. The difference between #+ and #- is that #+ enables Documenter's "continued"-blocks, see the Documenter manual.
3.3. Document generation
After the parsing it is time to generate the output. What is done in this step is very different depending on the output target, and it is described in more detail in the Output format sections: Markdown output, Notebook output and Script output. Using the default settings, the following is happening:
  • Markdown output: markdown chunks are printed as-is, code chunks are put inside a code fence (defaults to @example-blocks),
  • Notebook output: markdown chunks are printed in markdown cells, code chunks are put in code cells,
  • Script output: markdown chunks are discarded, code chunks are printed as-is.
3.4. Post-processing
When the document is generated the user, again, has the option to hook-into the generation with a custom post-processing function. The reason is that one might want to change things that are only visible in the rendered document. See Custom pre- and post-processing.
3.5. Writing to file
The last step of the generation is writing to file. The result is written to $(outputdir)/$(name)(.md|.ipynb|.jl) where outputdir is the output directory supplied by the user (for example docs/generated), and name is a user supplied filename. It is recommended to add the output directory to .gitignore since the idea is that the generated documents will be generated as part of the build process rather than beeing files in the repo.

+z = x + y

The example above would result in two consecutive code-chunks.

Tip

The rest of the line, after #-, is discarded, so it is possible to use e.g. #------------- as a chunk splitter, which may make the source code more readable.

It is also possible to use #+ as a chunk splitter. The difference between #+ and #- is that #+ enables Documenter's "continued"-blocks, see the Documenter manual.

3.3. Document generation

After the parsing it is time to generate the output. What is done in this step is very different depending on the output target, and it is described in more detail in the Output format sections: Markdown output, Notebook output and Script output. Using the default settings, the following is happening:

  • Markdown output: markdown chunks are printed as-is, code chunks are put inside a code fence (defaults to @example-blocks),
  • Notebook output: markdown chunks are printed in markdown cells, code chunks are put in code cells,
  • Script output: markdown chunks are discarded, code chunks are printed as-is.

3.4. Post-processing

When the document is generated the user, again, has the option to hook-into the generation with a custom post-processing function. The reason is that one might want to change things that are only visible in the rendered document. See Custom pre- and post-processing.

3.5. Writing to file

The last step of the generation is writing to file. The result is written to $(outputdir)/$(name)(.md|.ipynb|.jl) where outputdir is the output directory supplied by the user (for example docs/generated), and name is a user supplied filename. It is recommended to add the output directory to .gitignore since the idea is that the generated documents will be generated as part of the build process rather than beeing files in the repo.

diff --git a/dev/search/index.html b/dev/search/index.html index be5ce82..843892c 100644 --- a/dev/search/index.html +++ b/dev/search/index.html @@ -1,2 +1,2 @@ -Search · Literate.jl

Loading search...

    +Search · Literate.jl

    Loading search...

      diff --git a/dev/tips/index.html b/dev/tips/index.html index 6a48558..48b60a7 100644 --- a/dev/tips/index.html +++ b/dev/tips/index.html @@ -1,5 +1,5 @@ -7. Tips and tricks · Literate.jl
      Edit on GitHub

      7. Tips and tricks

      This section lists some tips and tricks that might be useful for using Literate.

      Filesize of generated notebooks

      When Literate executes a notebook the return value, i.e. the result of the last Julia expression in each cell is captured. By default Literate generates multiple renderings of the result in different output formats or MIMEs, just like IJulia.jl does. All of these renderings are embedded in the notebook and it is up to the notebook frontend viewer to select the most appropriate format to show to the user.

      A common example is images, which can often be displayed in multiple formats, e.g. PNG (image/png), SVG (image/svg+xml) and HTML (text/html). As a result, the filesize of the generated notebook can become large.

      In order to remedy this you can use the clever Julia package DisplayAs to limit the output capabilities of an object. For example, to "force" an image to be captures as image/png only, you can use

      import DisplayAs
+7. Tips and tricks · Literate.jl
      Edit on GitHub
      7. Tips and tricks
      This section lists some tips and tricks that might be useful for using Literate.
      Filesize of generated notebooks
      When Literate executes a notebook the return value, i.e. the result of the last Julia expression in each cell is captured. By default Literate generates multiple renderings of the result in different output formats or MIMEs, just like IJulia.jl does. All of these renderings are embedded in the notebook and it is up to the notebook frontend viewer to select the most appropriate format to show to the user.
      A common example is images, which can often be displayed in multiple formats, e.g. PNG (image/png), SVG (image/svg+xml) and HTML (text/html). As a result, the filesize of the generated notebook can become large.
      In order to remedy this you can use the clever Julia package DisplayAs to limit the output capabilities of an object. For example, to "force" an image to be captures as image/png only, you can use
      import DisplayAs
 img = plot(...)
 img = DisplayAs.PNG(img)
      This can save some memory, since the image is never captured in e.g. SVG or HTML formats.
      Note
      It is best to always let the object be showable as text/plain. This can be achieved by nested calls to DisplayAs output types. For example, to limit an image img to be showable as just image/png and text/plain you can use
      img = plot(...)
 img = DisplayAs.Text(DisplayAs.PNG(img))
      Adding admonitions using compound line filtering
      Admonitions are a useful feature for drawing attention to particular elements of  documentation. They are documented in Documenter.jl and an example of their use can be seen above in the blue 'note' box. Admonitions is a specific Julia markdown feature, and they are not recognized by either common mark or Jupyter notebooks. The md line filter can be used to make sure admonitions only show up in markdown output, for example:
      #md # !!! note "Be aware!"
@@ -25,4 +25,4 @@ Literate.notebook("example.jl", "tmp/"; preprocess = nb_note
     This is a useful note.
      and a quotation style formatting in the generated notebook cell:
      > *Note*
 > This is a useful note.
      which, in an actual notebook cell, will look similar to:
      Note
      This is a useful note.
      Debugging code execution
      When Literate is executing code (i.e. when execute = true is set), it does so quietly. All the output gets captured and nothing gets printed into the terminal. This can make it tricky to know where things go wrong, e.g. when the execution stalls due to an infinite loop.
      To help debug this, Literate has an @debug statement that prints out each code block that is being executed. In general, to enable the printing of Literate's @debug statements, you can set the JULIA_DEBUG environment variable to "Literate".
      The easiest way to do that is to set the variable in the Julia session before running Literate by doing
      ENV["JULIA_DEBUG"]="Literate"
      Alternatively, you can also set the environment variable before starting the Julia session, e.g.
      $ JULIA_DEBUG=Literate julia
      or by wrapping the Literate calls in an withenv block
      withenv("JULIA_DEBUG" => "Literate") do
     Literate.notebook("myscript.jl"; execute=true)
-end
      
+end