Possible return of wflow_open?

[xiangzhu]

Hi John -- I am not sure whether I asked you this before. I apologize if this is a redundant issue.

I wonder if the function wflow_open() could possibly be back to the CRAN version. Ideally, if I type wflow_open('new.Rmd'), it will create a file new.Rmd in analysis folder, with the following header template automatically available:

---
title: xxx
author: xxx
date: xxx
output: workflowr::wflow_html
---

[jdblischak]

@xiangzhu The good news is that I've already started on a re-implementation of wflow_open(). @stephens999 is also interested in this.

Also, based on your previous idea in #100, wflow_open() will try to guess the author name from the Git user.name variable.

I still need to work out some issues with determining the working directory (since in workflowr 1.0+ that can be affected by knit_root_dir in _workflowr.yml). I'll let you know when it's ready for testing.

[jdblischak]

@xiangzhu Could you please test out the minimal reincarnation of wflow_open()? It's on the "dev" branch:

devtools::install_github("jdblischak/workflowr@dev")

I'd specifically like your feedback on:

1. The automatically-populated YAML header

2. Currently there is no magic. Thus if you run wflow_open("new.Rmd") from the root of the project, it creates it in the root of the project. I think this is dangerous, and that a little magic to ensure the file goes to analysis/ is worth it

3. Suggestions for what information to report after running wflow_open()

[xiangzhu]

@jdblischak Thanks for the update!

I just tried this new dev feature, and it seems that's exactly what I want!

Regarding 2, I agree such "magic" is attractive; but I have the habit of setting analysis as the main working directory, and thus 2 is not a big issue for me.

[jdblischak]

I just tried this new dev feature, and it seems that's exactly what I want!

Awesome! Thanks for testing!

Regarding 2, I agree such "magic" is attractive; but I have the habit of setting analysis as the main working directory, and thus 2 is not a big issue for me.

So you manually set the working directory with setwd or the RStudio menu every time you open a workflowr project? Do you ever use wflow_open to open an existing file, or do you only use it to create new files?

[xiangzhu]

So you manually set the working directory with setwd or the RStudio menu every time you open a workflowr project?

Sometimes yes and sometimes no. I guess this has to do with which version of workflowr I am using.

Do you ever use wflow_open to open an existing file, or do you only use it to create new files?

I only use it to create new files; for existing files I am using file.edit().

[jdblischak]

@xiangzhu I made a few more minor updates to wflow_open(). If you have time, please experiment and let me know what you think.

[jdblischak]

@xiangzhu I am finalizing the new implementation of wflow_open() and will be releasing a new version soon. FYI I made some changes to the functionality in 7417fbe. Since you save your R Markdown files in analysis/, I think it should still be fine for your use case.

[xiangzhu]

I look forward to the new release!

Since you save your R Markdown files in analysis/, I think it should still be fine for your use case.

I thought that all Rmd files (whose resulting html files will be shown in the website) should be saved in analysis/; did I misunderstand any part?

[jdblischak]

I thought that all Rmd files (whose resulting html files will be shown in the website) should be saved in analysis/; did I misunderstand any part?

Yes, you are correct that is where they should be saved in order to be included in the website. wflow_open() also allows the creation of an Rmd file in another location if the user sets project = NULL. Probably not used much, but I wanted to allow this possibility.

The main difference you might notice from the previous implementation of wflow_open() is that the filepath must be correct. For example, if you run wflow_open("new.Rmd") from the root of the project, it will throw an error. The correct command would be wflow_open("analysis/new.Rmd"). Since you said that you typically manually switch the working directory to analysis/ anyways, I don't think this will affect you much.

[pcarbo]

I look forward to the new release!

@xiangzhu I believe it is currently implemented in the dev branch if you want to try out the new feature now.

[xiangzhu]

@jdblischak Thanks for the clarification!

@pcarbo thanks for the info! I am not affected by this new feature and I will wait for the formal release.

[jdblischak]

@xiangzhu The new wflow_open() is now available in v1.1.0. You can download it now from the master branch, and it will be available on CRAN in the next few days.

[xiangzhu]

@jdblischak now I understand better one of your replies above

The main difference you might notice from the previous implementation of wflow_open() is that the filepath must be correct. For example, if you run wflow_open("new.Rmd") from the root of the project, it will throw an error. The correct command would be wflow_open("analysis/new.Rmd"). Since you said that you typically manually switch the working directory to analysis/ anyways, I don't think this will affect you much.

> wflow_open(file="grs_compare_logor_chd4_eur.Rmd")
wflow_open:
- New file(s):
  /Users/xiangzhu/GitHub/mvp-cad/analysis/grs_compare_logor_chd4_eur.Rmd
- New working directory: /Users/xiangzhu/GitHub/mvp-cad
> getwd()
[1] "/Users/xiangzhu/GitHub/mvp-cad"

[jdblischak]

@xiangzhu Right, it changed your working directory to the root of the project, which is now the default for new workflowr projects. You can change this in _workflowr.yml if you'd prefer to have the knit directory be analysis/. See the docs for wflow_html.

[xiangzhu]

Thanks! I think I will have to get used to this new default root project.

Here is an example -- it just verifies everything you said before! The error message is very clear to me.

> wflow_open("ashlrt_201peca_31trait.Rmd")
Error: Argument "files" specifies at least one file outside the R Markdown source directory:

/Users/xiangzhu/GitHub/rss-peca/ashlrt_201peca_31trait.Rmd

R Markdown files inside your workflowr project must be in the following directory:

/Users/xiangzhu/GitHub/rss-peca/analysis

Set project=NULL to create an R Markdown file outside of the R Markdown directory of your workflowr project. See
?wflow_open for details.
> wflow_open("analysis/ashlrt_201peca_31trait.Rmd")
wflow_open:
- New file(s):
  /Users/xiangzhu/GitHub/rss-peca/analysis/ashlrt_201peca_31trait.Rmd
- Same working directory: /Users/xiangzhu/GitHub/rss-peca

[pcarbo]

@xiangzhu You do not have to get used to the default root---you can override the default in the _workflowr.yml file.

[jdblischak]

Thanks! I think I will have to get used to this new default root project.

As @pcarbo noted above, you are welcome to either adjust to the new default or continue with the previous setting of executing the code in analysis/. Totally up to you how you'd like to work!

Here is an example -- it just verifies everything you said before! The error message is very clear to me.

I'm glad the error message is informative. Credit to @pcarbo who pays special attention to making sure workflowr error messages are as useful as possible.