From 7eee7302158569800595bf64aa2f0ae99fa12550 Mon Sep 17 00:00:00 2001 From: Markus <66058642+mhovd@users.noreply.github.com> Date: Wed, 17 Sep 2025 12:12:57 +0200 Subject: [PATCH 1/2] pkgdown actions --- .github/workflows/pkgdown.yaml | 11 +-- .gitignore | 1 + DESCRIPTION | 4 +- _pkgdown.yml | 138 +-------------------------------- 4 files changed, 11 insertions(+), 143 deletions(-) diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 6e60a1592..bfc9f4db3 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -4,12 +4,13 @@ on: push: branches: [main, master] pull_request: - branches: [main, master] release: types: [published] workflow_dispatch: -name: pkgdown +name: pkgdown.yaml + +permissions: read-all jobs: pkgdown: @@ -22,7 +23,7 @@ jobs: permissions: contents: write steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 @@ -32,7 +33,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::pkgdown, any::rsconnect, local::. + extra-packages: any::pkgdown, local::. needs: website - name: Build site @@ -41,7 +42,7 @@ jobs: - name: Deploy to GitHub pages 🚀 if: github.event_name != 'pull_request' - uses: JamesIves/github-pages-deploy-action@v4.4.1 + uses: JamesIves/github-pages-deploy-action@v4.5.0 with: clean: false branch: gh-pages diff --git a/.gitignore b/.gitignore index 7e9bd16a6..42495ec78 100644 --- a/.gitignore +++ b/.gitignore @@ -30,3 +30,4 @@ inst/rust/template/* inst/options/PMoptions.json inst/options/PMoptions.json inst/doc +docs diff --git a/DESCRIPTION b/DESCRIPTION index 2728e0771..3fb170a00 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -28,7 +28,7 @@ Authors@R: c( person("Robert", "Leary", email = "", role = "ctb") ) Version: 2.1.1 -URL: https://lapkb.github.io/Pmetrics/ +URL: https://lapkb.github.io/Pmetrics/, https://lapkb.github.io/Pmetrics_rust/ BugReports: https://github.com/LAPKB/Pmetrics/issues Depends: R (>= 4.0.0) @@ -79,7 +79,7 @@ Suggests: reticulate, rmarkdown, testthat -RoxygenNote: 7.3.2 +RoxygenNote: 7.3.3 Encoding: UTF-8 Config/testthat/edition: 3 VignetteBuilder: knitr diff --git a/_pkgdown.yml b/_pkgdown.yml index ffe344eeb..ef5af71a1 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,138 +1,4 @@ -url: https://lapkb.github.io/Pmetrics/ +url: https://lapkb.github.io/Pmetrics_rust/ template: bootstrap: 5 - bootswatch: flatly -navbar: - structure: - left: [intro, reference, articles, tutorials, news] - right: [search, github] - components: - intro: - text: Start Here - href: articles/pmetrics.html - articles: - text: Articles - menu: - - text: Introduction - href: articles/intro.html - - text: Overview - href: articles/overview.html - - text: Workflow - href: articles/workflow.html - - text: Data Objects - href: articles/data.html - - text: Model Objects - href: articles/models.html - - text: Running the fit - href: articles/running.html - - text: Created Objects - href: articles/objects.html - - text: Simulation - href: articles/simulation.html - - text: Plotly plots - href: articles/plotly.html -home: - sidebar: - structure: [links, license, community, citation, authors, dev] - components: - custom: - title: Discussion - text: Discussion board - href: https://github.com/LAPKB/Pmetrics/discussions -reference: -- title: R6 objects - desc: Create Pmetrics R6 objects -- contents: - - starts_with("PM_") - - ab - - additive - - combination - - covariate - - errorPoly - - fixed - - msd - - proportional - - build_model -- title: Make functions - desc: Functions for making Pmetrics objects -- contents: - - PMtree - - starts_with("make") -- title: Optimal sampling - desc: Functions to calculate optimal sample times -- contents: - - Dopt - - MM_opt -- title: Plot - desc: Functions for plotting Pmetrics output -- contents: - - starts_with("plot") - - ab_line - - add_shapes - - add_smooth - - export_plotly - - sub_plot -- title: Summary - desc: Functions for summarizing Pmetrics output -- contents: starts_with("summary") -- title: Print - desc: Functions for printing Pmetrics output -- contents: starts_with("print") -- title: Run - desc: Run functions for modeling or simulating data -- contents: ends_with("run") -- title: Parse/load - desc: Parse functions for loading modeled or simulated data -- contents: - - ends_with("parse") - - PMload -- title: Auxilliary - desc: Auxilliary functions -- contents: - - qgrowth - - zBMI - - ss.PK - - mtsknn.eq - - PMcompare - - PMgetCRCL - - PMstep -- title: Datasets - desc: Pmetrics datasets -- contents: has_keyword("datasets") -- title: Data processing - desc: Data processing and interconversion -- contents: - - NM2PM - - PMwrk2csv - - PMmb2csv - - PMmatrixRelTime - - PMreadMatrix - - PMwriteMatrix -- title: Utility - desc: Utility functions -- contents: - - PMFortranConfig - - PMbuild - - PMcheck - - PMcode - - PMlogin - - PMlogout - - PMpatch - - PMregister - - PMreport - - ERRreport - - PMsave - - PMtest - - PMupdate - - getPMoptions - - setPMoptions - - editPMoptions - - movePMoptions - - update_gfortran -- title: Reference - desc: Reference functions -- contents: - - PMFortranConfig - - PMmanual - - PMnews - - Pmetrics-package + From 621fb816033963f64e5f169f8e82de7223a9b694 Mon Sep 17 00:00:00 2001 From: Markus <66058642+mhovd@users.noreply.github.com> Date: Wed, 17 Sep 2025 12:21:52 +0200 Subject: [PATCH 2/2] Disable tutorials to avoid rsconnect error --- _pkgdown.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/_pkgdown.yml b/_pkgdown.yml index ef5af71a1..453ad57b6 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -2,3 +2,4 @@ url: https://lapkb.github.io/Pmetrics_rust/ template: bootstrap: 5 +tutorials: false \ No newline at end of file