Updating entire website

[jennysjaarda]

Hello,

First of all thanks very much for your package - it's a great resource! I have a question about updating the entire site when the analysis/_site.yml file is updated, for example. When I use the dry_run feature, the result suggests that all html files would be rebuilt, but when I attempt it, I get an error that says no files were added. Specifically:

> wflow_publish("analysis/_site.yml", republish = TRUE, dry_run = TRUE)

Summary from wflow_publish

**Step 1: Commit analysis files**

Summary from wflow_git_commit

The following would be attempted:

  $ git add analysis/_site.yml
  $ git commit -m "wflow_publish(\"analysis/_site.yml\", republish = TRUE, dry_run = TRUE)"

**Step 2: Build HTML files**

Summary from wflow_build

Settings:
 republish: TRUE clean_fig_files: TRUE

The following would be built externally each in their own fresh R
session:

docs/about.html
docs/cnv.html
docs/create_custom_cluster_files.html
docs/data_processing_in_genomestudio.html
docs/data_sources.html
docs/extract_genetic_data.html
docs/GWAS_method.html
docs/GWAS_results.html
docs/GWAS_test.html
docs/index.html
docs/info.html
docs/license.html
docs/pheno_quality_control.html
docs/plans.html
docs/setup.html

**Step 3: Commit HTML files**

Summary from wflow_git_commit

The following would be attempted:

  $ git add docs/about.html docs/cnv.html docs/create_custom_cluster_files.html docs/data_processing_in_genomestudio.html docs/data_sources.html docs/extract_genetic_data.html docs/GWAS_method.html docs/GWAS_results.html docs/GWAS_test.html docs/index.html docs/info.html docs/license.html docs/pheno_quality_control.html docs/plans.html docs/setup.html docs/figure/about.Rmd docs/figure/cnv.Rmd docs/figure/create_custom_cluster_files.Rmd docs/figure/data_processing_in_genomestudio.Rmd docs/figure/data_sources.Rmd docs/figure/extract_genetic_data.Rmd docs/figure/GWAS_method.Rmd docs/figure/GWAS_results.Rmd docs/figure/GWAS_test.Rmd docs/figure/index.Rmd docs/figure/info.Rmd docs/figure/license.Rmd docs/figure/pheno_quality_control.Rmd docs/figure/plans.Rmd docs/figure/setup.Rmd docs/site_libs docs/.nojekyll
  $ git commit -m "Build site."
>
> wflow_publish("analysis/_site.yml", republish = TRUE)
Error: Commit failed because no files were added. Attempted to commit the
following files: /data/sgg2/jenny/projects/PSYMETAB/analysis/_site.yml

Any untracked files must manually specified even if `all = TRUE`.

Am I missing something obvious? Any thoughts/advice would be appreciated - thanks!

[stephens999]

i'm not sure but it looks like it might be failing at the first step.
can you check that the file /data/sgg2/jenny/projects/PSYMETAB/analysis/_site.yml
actually exists in your repo?

[jennysjaarda]

Hello, thanks for your response. The file does indeed exist: ``` master:PSYMETAB$ cat /data/sgg2/jenny/projects/PSYMETAB/analysis/_site.yml name: PSYMETAB output_dir: ../docs navbar: title: PSYMETAB left: - text: Home href: index.html - text: About href: about.html - text: Setup href: setup.html - text: Project menu: - text: GWAS menu: - text: "GWAS methods" href: GWAS_method.html - text: "GWAS results" href: GWAS_results.html - text: Meetings menu: - text: "Update 25-09-2020" href: Update_meeting_25_09_2020.html right: - icon: fa-github text: Source code href: https://github.com/jennysjaarda/PSYMETAB output: workflowr::wflow_html: toc: yes toc_float: yes theme: readable highlight: textmate ```

[jennysjaarda]

Just an update, the _site.yml file has already been committed and pushed, so perhaps the problem is that the _site.yml file itself had already been ahead of updating the other Rmd files? And so the function doesn't recognize that the website is behind?

[jdblischak]

Just an update, the _site.yml file has already been committed and pushed, so perhaps the problem is that the _site.yml file itself had already been ahead of updating the other Rmd files?

Yes, that's the issue. You are requesting that analysis/_site.yml be added and committed, but when worklowr runs add and commit, the commit is empty and thus Git throws an error. To update the entire website, run

wflow_publish(republish = TRUE)

In general, these are the recommended steps for updating the style of the website:

1. Edit analysis/_site.yml
2. Run wflow_build("analysis/index.Rmd") to preview the changes (you can choose any file that runs quickly)
3. Repeat 1 & 2 until you are happy with the change
4. Commit the changes to analysis/_site.yml and then rebuild all the published Rmd files
   1. In one step:

      wflow_publish("analysis/_site.yml", republish = TRUE)
      

   2. In two steps:

      wflow_git_commit("analysis/_site.yml") # alternatively, use Git in the terminal
      wflow_publish(republish = TRUE)