Skip to content

tjmahr/notestar

Folders and files

NameName
Last commit message
Last commit date

Latest commit

Β 

History

52 Commits
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 
Β 

Repository files navigation

notestar πŸ““β­

R-CMD-check

notestar is a notebook system built on the targets package: notes with targets.

Installation

You can install notestar from GitHub with:

# install.packages("devtools")
devtools::install_github("tjmahr/notestar")

A demo notebook

Here is an example project/notebook showing how notestar combines various .Rmd files into a single HTML file: https://github.com/tjmahr/notestar-demo.

Big picture idea of how notestar works

First, we follow a targets-based workflow. We develop datasets and models and so on, writing functions in R/functions.R and describing a build pipeline in _targets.R. Some familiarity with the big ideas of the targets packages is required.

We then work with our data-analysis products in RMarkdown .Rmd files in a notebook directory. We read in these targets using targets::tar_read(), and we might develop several entries notebook as we tackle different parts of our analysis problem.

In the _targets.R file, there are special notebook-related targets. When we run targets::tar_make(), notestar does the following:

  • For each .Rmd file, it knits (knitr::knit()) the corresponding .md output file: computing running the code, printing the results, saving and inserting figures.

  • These .md files are collated and assembled into a single-page bookdown document. It looks kind of a data-analysis blog (a page with a sequence of entries in reverse-chronological order).

Importantly, notestar only does these jobs when needed. For example, a notebook entry’s .md file will only be created if it is outdated. That is,

  • if the .md has not been created yet.
  • if the .Rmd source file has changed at all.
  • if a dependency loaded via targets (i.e., data <- targets::tar_read(data)) in the .Rmd source file has changed.
  • if any other dependencies for the .md file have changed. (For example, there is an R script that run before knitting each entry that sets knitr options. If that changes, then the notebook entry is outdated.)

notestar’s role in all of this is to link the data analysis targets to the .Rmd files and then orchestrate the assembly of a notebook from these entries.

Packages that help make this happen

Let’s highlight some packages that are indispensable for this scheme to work.

  • targets (backend)
  • knitr (running R code in .Rmd files to .md files)
  • bookdown (assembling .md files into a .md file)
  • rmarkdown / pandoc (for converting markdown into other formats)
  • cleanrmd (theme/template for final html document)
  • usethis (functions for setting up R-based data analysis projects)

Most important functions for users

Below I show a worked example and describe things in great detail. But before that I want to note that as a user, I only really use 3–4 functions from this package.

  • use_notestar() to set up a notestar project
  • (optional) use_notestar_makefile() to set up a Makefile that runs targets::tar_make(). I then use the RStudio’s Build commands to build projects.
  • (optional) use_notestar_references() to set up a .bib and .csl file for the notebook.
  • notebook_create_page() to create a new notebook entry
  • notebook_browse() to open the final notebook file in a browser.

A worked example

notestar works best inside of a data analysis project and specifically, as a part of an RStudio project. That is, we have some directory for our project. Everything we do or create will live in that directory, and that directory is the default working directory for all of our R code.

For demonstration, let’s create a new directory inside of a temporary directory and make that the home base for our project.

project_dir <- file.path(tempdir(), pattern = "my-project")
dir.create(project_dir)
setwd(project_dir)

Nothing here!

fs::dir_tree(all = TRUE)
#> .

Initial file skeleton

use_notestar() will populate the project directory with the basic skeleton for the project. We set the theme to "water-dark" so that the screenshots below stick out better from the white background on GitHub.

library(notestar)
use_notestar(cleanrmd_theme = "water-dark")

fs::dir_tree(all = TRUE)
#> .
#> β”œβ”€β”€ .here
#> β”œβ”€β”€ config.yml
#> β”œβ”€β”€ notebook
#> β”‚   β”œβ”€β”€ 0000-00-00-references.Rmd
#> β”‚   β”œβ”€β”€ book
#> β”‚   β”‚   └── assets
#> β”‚   β”œβ”€β”€ index.Rmd
#> β”‚   └── knitr-helpers.R
#> β”œβ”€β”€ R
#> β”‚   └── functions.R
#> └── _targets.R

The file config.yml is a config-package configuration file. These configuration options were set when we called use_notestar(), so these are all the default configuration options (except for cleanrmd_theme). Each of these is described by a comment field.

writeLines(readLines("config.yml"))
---
default:
  notestar:
    dir_notebook:
      comment: >
        directory location for user-edited notebook entries (as
        RMarkdown files)
      value: "notebook"
    dir_md:
      comment: >
        directory location for knitted/rendered notebook entries
        (as markdown files)
      value: "notebook/book"
    notebook_helper:
      comment: >
        path to an R script that is run before knitting each notebook
        entry
      value: "notebook/knitr-helpers.R"
    cleanrmd_theme:
      comment: >
        CSS theme to use for the notebook. Anything printed by
        cleanrmd::cleanrmd_themes() should work.
      value: "water-dark"
    notebook_filename:
      comment: >
        Name to use for the final html file. Defaults to "notebook"
        which produces "notebook.html"
      value: "notebook"
---

Two .Rmd files are automatically included: index.Rmd and 0000-00-00.Rmd. These are the first and last entries (top and bottom parts) of the notebook. index.Rmd houses metadata for the notebook:

writeLines(readLines("notebook/index.Rmd"))
---
title: "Notebook title"
author: "Author Name"
date: > 
  `r knitr::inline_expr('format(Sys.time(), "Updated on %A, %B %d, %Y %I:%M %p")')`
site: bookdown::bookdown_site
link-citations: true
---

The yaml metadata in index.Rmd is created automatically inside the _targets.R file. More on that later.

0000-00-00.Rmd is not meant to be edited. As it tells us, it provides a β€œReferences” heading. When the bibliography is appended to the end of the notebook, it will be printed under this heading.

writeLines(readLines("notebook/0000-00-00-references.Rmd"))
<!-- Chapters/posts are collated in reverse chronological order so  -->
<!-- this last one is a dummy entry to tell bookdown where to drop  -->
<!-- the references. -->

## References

The file _targets.R orchestrates the compilation of the notebook using the targets package. targets::tar_make() compiles the notebook by:

  • knitting each .Rmd file in notebook if necessary to produce a corresponding .md file notebook/book/.
  • collating the .md files in notebook/book/ into a single-document bookdown book with bookdown/RMarkdown/pandoc (if necessary).

I say β€œif necessary” because targets only builds the targets in workflow if the target has not been built yet or if the target is out of date. Thus, notestar doesn’t waste time regenerating earlier entries if they or their dependencies have not changed.

Finally, .here is a sentinel file for the here package. It indicates where the project root is located. R/functions.R is an (as-yet empty) R script that is source()-ed at the start of _targets.R.

Building, rebuilding

Here we build the notebook and see targets build each target.

targets::tar_make()
#> β€’ start target notebook_output_yaml
#> β€’ built target notebook_output_yaml
#> β€’ start target notebook_deps_in_index_yml
#> β€’ built target notebook_deps_in_index_yml
#> β€’ start target entry_0000_00_00_references_rmd
#> β€’ built target entry_0000_00_00_references_rmd
#> β€’ start target notebook_index_yml
#> β€’ built target notebook_index_yml
#> β€’ start target notebook_helper_user
#> β€’ built target notebook_helper_user
#> β€’ start target spellcheck_exceptions
#> β€’ built target spellcheck_exceptions
#> β€’ start target notebook_index_rmd
#> β€’ built target notebook_index_rmd
#> β€’ start target notebook_helper
#> β€’ built target notebook_helper
#> β€’ start target notebook_rmds
#> β€’ built target notebook_rmds
#> β€’ start target entry_index_md
#> β€’ built target entry_index_md
#> β€’ start target entry_0000_00_00_references_md
#> β€’ built target entry_0000_00_00_references_md
#> β€’ start target spellcheck_notebook
#> β€’ built target spellcheck_notebook
#> β€’ start target notebook_mds
#> β€’ built target notebook_mds
#> β€’ start target spellcheck_report_results_change
#> β€’ built target spellcheck_report_results_change
#> β€’ start target notebook_bookdown_yaml
#> β€’ built target notebook_bookdown_yaml
#> β€’ start target spellcheck_report_results
#> No spelling errors found.
#> β€’ built target spellcheck_report_results
#> β€’ start target notebook
#> 
#> 
#> processing file: index.Rmd
#>   |                                                                              |                                                                      |   0%  |                                                                              |......................................................................| 100%
#>    inline R code fragments
#> 
#> 
#> output file: index.knit.md
#> 
#> "C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS notebook.md --to html5 --from markdown+autolink_bare_uris+tex_math_single_backslash --output notebook.html --lua-filter "C:\Users\trist\AppData\Local\R\win-library\4.2\bookdown\rmarkdown\lua\custom-environment.lua" --lua-filter "C:\Users\trist\AppData\Local\R\win-library\4.2\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\trist\AppData\Local\R\win-library\4.2\rmarkdown\rmarkdown\lua\latex-div.lua" --metadata-file "C:\Users\trist\AppData\Local\Temp\RtmpOE7W2v\file58d87b347c18" --self-contained --variable disable-fontawesome --variable title-in-header --highlight-style pygments --table-of-contents --toc-depth 3 --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --template "C:/Users/trist/AppData/Local/R/win-library/4.2/cleanrmd/template/cleanrmd.html" --include-in-header "C:\Users\trist\AppData\Local\Temp\RtmpOE7W2v\rmarkdown-str58d82cc775d5.html" 
#> 
#> Output created: docs/notebook.html
#> β€’ built target notebook
#> β€’ end pipeline

If we ask it to build the book again, it skips everythingβ€”none of the dependencies have changedβ€”but a special spell-checking target set to always run.

targets::tar_make()
#> βœ“ skip target notebook_output_yaml
#> βœ“ skip target notebook_deps_in_index_yml
#> βœ“ skip target entry_0000_00_00_references_rmd
#> βœ“ skip target notebook_index_yml
#> βœ“ skip target notebook_helper_user
#> βœ“ skip target spellcheck_exceptions
#> βœ“ skip target notebook_index_rmd
#> βœ“ skip target notebook_helper
#> βœ“ skip target notebook_rmds
#> βœ“ skip target entry_index_md
#> βœ“ skip target entry_0000_00_00_references_md
#> βœ“ skip target spellcheck_notebook
#> βœ“ skip target notebook_mds
#> β€’ start target spellcheck_report_results_change
#> β€’ built target spellcheck_report_results_change
#> βœ“ skip target notebook_bookdown_yaml
#> βœ“ skip target spellcheck_report_results
#> βœ“ skip target notebook
#> β€’ end pipeline

Right now, our compiled notebook ("notebook/book/docs/notebook.html") is just the title page:

If we look at the project tree, we see some additions.

fs::dir_tree(all = TRUE)
#> .
#> β”œβ”€β”€ .here
#> β”œβ”€β”€ config.yml
#> β”œβ”€β”€ notebook
#> β”‚   β”œβ”€β”€ 0000-00-00-references.Rmd
#> β”‚   β”œβ”€β”€ book
#> β”‚   β”‚   β”œβ”€β”€ 0000-00-00-references.md
#> β”‚   β”‚   β”œβ”€β”€ assets
#> β”‚   β”‚   β”œβ”€β”€ docs
#> β”‚   β”‚   β”‚   β”œβ”€β”€ 0000-00-00-references.md
#> β”‚   β”‚   β”‚   β”œβ”€β”€ index.md
#> β”‚   β”‚   β”‚   β”œβ”€β”€ notebook.html
#> β”‚   β”‚   β”‚   └── reference-keys.txt
#> β”‚   β”‚   β”œβ”€β”€ index.Rmd
#> β”‚   β”‚   β”œβ”€β”€ knitr-helpers.R
#> β”‚   β”‚   β”œβ”€β”€ notebook.rds
#> β”‚   β”‚   β”œβ”€β”€ _bookdown.yml
#> β”‚   β”‚   └── _output.yml
#> β”‚   β”œβ”€β”€ index.Rmd
#> β”‚   └── knitr-helpers.R
#> β”œβ”€β”€ R
#> β”‚   └── functions.R
#> β”œβ”€β”€ shot1.png
#> β”œβ”€β”€ _targets
#> β”‚   β”œβ”€β”€ .gitignore
#> β”‚   β”œβ”€β”€ meta
#> β”‚   β”‚   β”œβ”€β”€ meta
#> β”‚   β”‚   β”œβ”€β”€ process
#> β”‚   β”‚   └── progress
#> β”‚   β”œβ”€β”€ objects
#> β”‚   β”‚   β”œβ”€β”€ notebook_deps_in_index_yml
#> β”‚   β”‚   β”œβ”€β”€ notebook_index_yml
#> β”‚   β”‚   β”œβ”€β”€ notebook_rmds
#> β”‚   β”‚   β”œβ”€β”€ spellcheck_exceptions
#> β”‚   β”‚   β”œβ”€β”€ spellcheck_notebook
#> β”‚   β”‚   β”œβ”€β”€ spellcheck_report_results
#> β”‚   β”‚   └── spellcheck_report_results_change
#> β”‚   └── user
#> └── _targets.R

_targets/ is a new directory. It is the object and metadata storage for targets. We don’t worry about it.

There are some md files in notebook/book/ as well as some bookdown-related files (_bookdown.yml, _output.yml and notebook.rds file). There is also the output of bookdown in notebook/book/docs. (notebook/book/docs/notebook.html is the file we screenshotted earlier.)

knitr-helpers.R was also copied to the notebook/book/ directory. This copying reflects design decision by the package. Namely, the contents of the notebook/book directory should not be edited by hand. Its contents should be reproducible whether by regenerating files (like the .md files) or by copying files (like knitr-helpers.R. The user should only have to worry about editing files in the notebook/ directory or in _targets.R (or perhaps config.yml).

We can create a new entry from a template using notebook_create_page() and regenerate the notebook. (A slug is some words we include in the filename to help remember what the entry is about.)

notebook_create_page(date = "2022-02-22", slug = "hello-world")
#> βœ“ Setting active project to 'C:/Users/trist/AppData/Local/Temp/Rtmp0CF7CR/my-project'
#> βœ“ Writing 'notebook/2022-02-22-hello-world.Rmd'
#> β€’ Edit 'notebook/2022-02-22-hello-world.Rmd'
#> βœ“ 'notebook/2022-02-22-hello-world.Rmd' created

Now targets has to rebuild the notebook because there is a new entry that needs to be folded in. The network diagram shows that entry_2022_02_hello_world_rmd is outdated (blue) so everything downstream from it is also outdated.

targets::tar_visnetwork(targets_only = TRUE)

When we rebuild the notebook, that entry now appears in the HTML file.

targets::tar_make()
#> [output omitted]

Next steps

From here, we go with the flow. We use targets as we normally would, modifying R/functions.R and targets.R to set up our data-processing pipeline. We can now use our notebook to do reporting and exploration as part of our data-processing pipeline. Things we make with targets can be tar_read() into our notebook entries and tracked as dependencies.

Behind-the-scenes details

In this section, we will describe some behind-the-scenes details about notestar using the worked example.

1. .Rmd/.md files have hidden timestamps

Here is what a minimal Rmd file entry looks like:

writeLines(readLines("notebook/2022-02-22-hello-world.Rmd"))
<!--- Timestamp to trigger book rebuilds: `r Sys.time()` --->

```{r setup, include = FALSE}
# library(tidyverse)
# fit <- targets::tar_read(fit)
# fit
```

## Feb. 22, 2022 (Demo entry)

<small>Source: <code>`r knitr::current_input()`</code></small>

```{r content}

```

That first <!--- comment ---> line on top is an HTML comment. It will not be displayed when we view the final html file, but when the .Rmd file is knitted to produce the corresponding .md, the timestamp will be updated. Here is the first line of that .md file:

writeLines(readLines("notebook/book/2022-02-22-hello-world.md")[1])
<!--- Timestamp to trigger book rebuilds: 2022-03-01 13:35:54 --->

This timestamp allows us to mark a notebook entry as outdated even if none of the text in the .md file has changed. Here is a motivating example. Let’s append a code chunk to the bottom of the notebook entry. It will plot a histogram.

entry_v0 <- readLines("notebook/2022-02-22-hello-world.Rmd")[1:13]
writeLines(
  c(
    entry_v0,
    "Would you look at all these 4's?",
    "```{r old-faithful, fig.width = 4, fig.height = 4}",
    "hist(faithful$eruptions)",
    "```"
  ),
  "notebook/2022-02-22-hello-world.Rmd"
)

And then we regenerate the notebook.

targets::tar_make()
#> [output omitted]

Let’s store the current .md file lines so we can compare it to a later version.

entry_v1 <- readLines("notebook/book/2022-02-22-hello-world.md")

Now, suppose we wanted to change size or resolution of the plot. In this case, we will change the fig.width and fig.height values to 6 here and regenerate the notebook

writeLines(
  c(
    entry_v0,
    "Would you look at all these 4's?",
    "```{r old-faithful, fig.width = 6, fig.height = 6}",
    "hist(faithful$eruptions)",
    "```"
  ),
  "notebook/2022-02-22-hello-world.Rmd"
)

targets::tar_make()
#> [output omitted]

The figures image files have definitely changed: they are different sizes! The text in the plots in the two screenshots are different sizes. But the text of the .md files is the sameβ€”except for the timestamp.

entry_v2 <- readLines("notebook/book/2022-02-22-hello-world.md")
entry_v1 == entry_v2
#>  [1] FALSE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#> [13]  TRUE  TRUE
entry_v1[1] 
#> [1] "<!--- Timestamp to trigger book rebuilds: 2022-03-01 13:36:00 --->"
entry_v2[1]
#> [1] "<!--- Timestamp to trigger book rebuilds: 2022-03-01 13:36:07 --->"

This phenomenon, where a change to an .Rmd file would not cause a change in the text of a .md file, is the reason for the timestamp at the top of the .Rmd file.

2. Despite the timestamp, image dependencies are tracked

Our targets graph has a node called entry_2022_02_22_hello_world_md.

targets::tar_visnetwork(
  targets_only = TRUE, 
  names = "entry_2022_02_22_hello_world_md"
)

That node does not represent just the file notebook/book/2022-02-22-hello-world.md. Its plot is also tracked as byproduct of the entry:

targets::tar_read("entry_2022_02_22_hello_world_md")
#> [1] "notebook/book/2022-02-22-hello-world.md"                              
#> [2] "notebook/book/assets/figure/2022-02-22-hello-world/old-faithful-1.png"

Thus, if I removed the image, that notebook entry becomes outdated and needs to be reprocessed.

file.remove(targets::tar_read("entry_2022_02_22_hello_world_md")[2])
#> [1] TRUE

targets::tar_visnetwork(
  targets_only = TRUE, 
  names = "entry_2022_02_22_hello_world_md"
)

(I forget the problem that motivated me to add this layer of tracking on top of the timestamping, but it’s there.)

# undo the deletion before moving on
targets::tar_make()
#> [output omitted]

3. Unused figures are automatically deleted

Think about any other time you’ve used knitr or RMarkdown. When you remove the code to produce a figure in an .Rmd file, what happens to the plot’s image file? Normally, it sticks around, and you eventually find yourself with all kinds of old, no-longer used figures. When knitting a .Rmd file, notestar removes all existing figures associated with an entry beforehand. As a result, only figures that were created during the most recent knitting are retained. This move is what allows image dependencies (see last point) to be inferred: If an image file is created as a result of knitting an .Rmd file, we can associate it with .md file.

Let’s demonstrate this feature. Here are the current notebook assets:

fs::dir_tree("./notebook/book/assets")
#> ./notebook/book/assets
#> └── figure
#>     └── 2022-02-22-hello-world
#>         └── old-faithful-1.png

We will restore the original version of the entry so that the plot is no longer created.

writeLines(entry_v0, "notebook/2022-02-22-hello-world.Rmd")

targets::tar_make()
#> [output omitted]

What we have now is an empty directory.

fs::dir_tree("./notebook/book/assets")
#> ./notebook/book/assets
#> └── figure
#>     └── 2022-02-22-hello-world

This behavior is controlled in the knitr-helpers.R file, specifically the last line:

writeLines(readLines("notebook/knitr-helpers.R"))
# This script is run before knitting each chapter. It sets the knitting root
# directory so that it can see the `_targets` folder, and it sets the chunk
# default settings.
notestar::notebook_set_opts_knit()

notestar::notebook_set_opts_chunk()

notestar::notebook_set_markdown_hooks()

knitr::opts_knit$set(notestar_purge_figures = TRUE)

About

notestar is a notebook system built on the targets package: notes with targets.

Topics

Resources

License

Stars

Watchers

Forks

Languages