497 automate website

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Comparison is base (7fc5faa) 72.32% compared to head (d0fd5ff) 72.40%. Report is 1 commits behind head on develop.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop #500 +/- ## =========================================== + Coverage 72.32% 72.40% +0.07% =========================================== Files 63 63 Lines 4286 4298 +12 =========================================== + Hits 3100 3112 +12 Misses 1186 1186 ```

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[pchelle]

Is there actually a difference between this action and pages build and deployment with artifacts-next action ? If not, we can drop this PR

[Yuri05]

@pchelle The action code is almost identical between devel and release and between repositories (more or less only installed prerequisites differ). I have moved the code to a reusable OSP-global workflow - s. the PR https://github.com/Open-Systems-Pharmacology/Workflows/pull/18 Once this PR is merged, the dev-website yaml can be reduced to this:

name: Update dev website
on:
  push: 
    branches:
      - develop    

# The action needs permissions to update the branch
permissions:
  contents: write

jobs:
  update_dev_website:
    uses: Open-Systems-Pharmacology/Workflows/.github/workflows/CreateGitHubPagesForR.yml@main
    with:
      pkgdown_mode: 'devel'
      extra_r_packages: 'github::Open-Systems-Pharmacology/OSPSuite.RUtils'

Similar for the release yaml.

[Yuri05]

@pchelle I tested the reusable workflow for the dev site here - works pretty nice. However the website creation produced some warnings which might lead to the wrong display of some images (s. below). You can check the created website here: https://htmlpreview.github.io/?https://github.com/Yuri05/TLF-Library/blob/gh-pages/docs/dev/index.html

Warning messages:
1: Missing images in 'vignettes/atom-plots.Rmd': 'atom-plots_files/figure-html/initializePlot%20minimal%20example-1.png', 'atom-plots_files/figure-html/initializePlot%20with%20plot%20configuration-1.png', 'atom-plots_files/figure-html/initializePlot%20with%20smart%20plot%20configuration%20on%20metaData-1.png', 'atom-plots_files/figure-html/initializePlot%20with%20smart%20plot%20configuration%20on%20data-1.png', 'atom-plots_files/figure-html/initializePlot%20with%20smart%20plot%20configuration%20overwritten-1.png', 'atom-plots_files/figure-html/addScatter%20data-1.png', 'atom-plots_files/figure-html/addScatter%20with%20smart%20plot%20configuration%20overwritten-1.png', 'atom-plots_files/figure-html/addScatter%20xy-1.png', 'atom-plots_files/figure-html/addScatter%20xy%20with%20plot%20configuration%20overwritten-1.png', 'atom-plots_files/figure-html/addScatter%20xy%20with%20optional%20properties-1.png', 'atom-plots_files/figure-html/addScatter%20with%20plotObject-1.png', 'atom-plots_files/figure-html/addScatter%20with%20plotObject-2.png', 'atom-plots_files/figure-html/addLine%20xy-1.png', 'atom-plots_files/figure-html/addLine%20xy%20with%20optional%20properties-1.png', 'atom-plots_files/figure-html/addRibbon%20data-1.png', 'atom-plots_files/figure-html/addRibbon%20xy-1.png', 'atom-plots_files/figure-html/addRibbon%20optional%20inputs-1.png', 'atom-plots_files/figure-html/addErrorbar%20xy-1.png', 'atom-plots_files/figure-html/addErrorbar%20optional%20inputs-1.png', 'atom-plots_files/figure-html/addErrorbar%20and%20Scatter-1.png', 'atom-plots_files/figure-html/addErrorbar%20and%20Scatter-2.png'
ℹ pkgdown can only use images in 'man/figures' and 'vignettes' 
2: Missing images in 'vignettes/box-whisker-vignette.Rmd': 'box-whisker-vignette_files/figure-html/minimal%20example-1.png', 'box-whisker-vignette_files/figure-html/boxplot-country%20x-1.png'
ℹ pkgdown can only use images in 'man/figures' and 'vignettes' 
3: Missing images in 'vignettes/plot-configuration.Rmd': 'plot-configuration_files/figure-html/show-smart-scatter%201-1.png', 'plot-configuration_files/figure-html/show-smart-scatter%202-1.png'
ℹ pkgdown can only use images in 'man/figures' and 'vignettes' 
4: Missing images in 'vignettes/plot-time-profile.Rmd': 'plot-time-profile_files/figure-html/examples%20single%20simulation-1.png', 'plot-time-profile_files/figure-html/examples%20single%20simulation-2.png', 'plot-time-profile_files/figure-html/examples%20single%20simulation%20with%20confidence%20interval-1.png', 'plot-time-profile_files/figure-html/examples%20single%20simulation%20with%20confidence%20interval-2.png', 'plot-time-profile_files/figure-html/examples%20multiple%20simulations%20no%20caption-1.png', 'plot-time-profile_files/figure-html/examples%20multiple%20simulations-1.png', 'plot-time-profile_files/figure-html/examples%20multiple%20simulations%20with%20confidence%20interval-1.png', 'plot-time-profile_files/figure-html/examples%20single%20observation-1.png', 'plot-time-profile_files/figure-html/examples%20single%20observation-2.png', 'plot-time-profile_files/figure-html/examples%20single%20observation%20with%20confidence%20interval%20as%20error-1.png', 'plot-time-profile_files/figure-html/examples%20single%20observation%20with%20confidence%20interval%20as%20ymin-ymax-1.png', 'plot-time-profile_files/figure-html/examples%20multiple%20observations%20no%20caption-1.png', 'plot-time-profile_files/figure-html/examples%20multiple%20observations%20with%20confidence%20interval-1.png', 'plot-time-profile_files/figure-html/examples%20mdv-1.png', 'plot-time-profile_files/figure-html/combine%20simulated%20and%20observed-1.png', 'plot-time-profile_files/figure-html/combine%20simulated%20and%20observed-2.png', 'plot-time-profile_files/figure-html/combine%20simulated%20and%20observed%20with%20ci-1.png', 'plot-time-profile_files/figure-html/combine%20simulated%20and%20observed%20with%20ci-2.png', 'plot-time-profile_files/figure-html/combine%20multiple%20simulated%20and%20observed-1.png', 'plot-time-profile_files/figure-html/update%20legend%20properties-1.png', 'plot-time-profile_files/figure-html/combine%20simulated%20and%20observed%20sharing%20legend-1.png', 'plot-time-profile_files/figure-html/combine%20multiple%20simulated%20and%20observed%20with%20ci-1.png', 'plot-time-profile_files/figure-html/time%20profile%20plot%20using%20plot%20configuration-1.png'
ℹ pkgdown can only use images in 'man/figures' and 'vignettes' 

[pchelle]

pkgdown can only use images

I double checked the figures were correctly added. From what I read of pkgdown, this is likely a false warning: https://github.com/r-lib/pkgdown/issues/2194