From bad2f70c18cd9f57c0d382914327613bcfc9298f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 29 Jul 2024 08:06:08 +0200 Subject: Move coverage to pkgdown docs The coverage report is neither successful on Travis nor in the github workflow set up with the usethis package. Therefore the code coverage report is generated locally and linked into the pkgdown docs. --- .github/workflows/test-coverage.yaml | 61 -- GNUmakefile | 3 +- NEWS.md | 4 +- README.md | 2 - _pkgdown.yml | 3 + docs/404.html | 112 ++-- docs/articles/index.html | 129 ++-- docs/articles/mkin.html | 136 ++-- docs/authors.html | 124 ++-- docs/index.html | 136 ++-- docs/news/index.html | 117 ++-- docs/reference/BIC.mmkin.html | 8 + docs/reference/FOCUS_2006_A.html | 8 + docs/reference/FOCUS_2006_B.html | 8 + docs/reference/FOCUS_2006_C.html | 8 + docs/reference/FOCUS_2006_D.html | 8 + docs/reference/FOCUS_2006_E.html | 8 + docs/reference/FOCUS_2006_F.html | 8 + docs/reference/NAFTA_SOP_Appendix_B.html | 8 + docs/reference/NAFTA_SOP_Appendix_D.html | 8 + docs/reference/Rplot001.png | Bin 13993 -> 1011 bytes docs/reference/[.mhmkin.html | 8 + docs/reference/aw.mixed.mmkin.html | 8 + docs/reference/aw.mkinfit.html | 8 + docs/reference/aw.mmkin.html | 8 + docs/reference/aw.multistart.html | 8 + docs/reference/backtransform_odeparms.html | 8 + docs/reference/best.default.html | 8 + docs/reference/best.html | 8 + docs/reference/check_failed.html | 100 +++ docs/reference/ds_dfop.html | 8 + docs/reference/ds_dfop_sfo.html | 8 + docs/reference/ds_fomc.html | 8 + docs/reference/ds_hs.html | 8 + docs/reference/ds_sfo.html | 8 + docs/reference/f_time_norm_focus.mkindsg.html | 8 + docs/reference/f_time_norm_focus.numeric.html | 8 + docs/reference/hierarchical_kinetics.html | 125 ++-- docs/reference/html_listing.html | 8 + docs/reference/illparms.mhmkin.html | 8 + docs/reference/illparms.mkinfit.html | 8 + docs/reference/illparms.mmkin.html | 8 + docs/reference/illparms.saem.mmkin.html | 8 + docs/reference/index.html | 725 ++++++++++++---------- docs/reference/intervals.html | 8 + docs/reference/invilr.html | 8 + docs/reference/loftest.mkinfit.html | 8 + docs/reference/lrtest.html | 8 + docs/reference/lrtest.mmkin.html | 8 + docs/reference/max_twa_dfop.html | 8 + docs/reference/max_twa_fomc.html | 8 + docs/reference/max_twa_hs.html | 8 + docs/reference/max_twa_sfo.html | 8 + docs/reference/mhmkin.list.html | 8 + docs/reference/mhmkin.mmkin.html | 8 + docs/reference/mixed.mmkin.html | 8 + docs/reference/mkinpredict.mkinfit.html | 8 + docs/reference/mkinpredict.mkinmod.html | 8 + docs/reference/mkinsub.html | 234 +------ docs/reference/multistart.saem.mmkin.html | 8 + docs/reference/nlme_data.html | 8 + docs/reference/parms.mkinfit.html | 8 + docs/reference/parms.mmkin.html | 8 + docs/reference/parms.multistart.html | 8 + docs/reference/parms.saem.mmkin.html | 8 + docs/reference/parplot.multistart.saem.mmkin.html | 8 + docs/reference/plot_err.html | 8 + docs/reference/plot_res.html | 8 + docs/reference/plot_sep.html | 8 + docs/reference/print.illparms.mhmkin.html | 8 + docs/reference/print.illparms.mkinfit.html | 8 + docs/reference/print.illparms.mmkin.html | 8 + docs/reference/print.illparms.saem.mmkin.html | 8 + docs/reference/print.mhmkin.html | 8 + docs/reference/print.mixed.mmkin.html | 8 + docs/reference/print.mkinds.html | 194 +----- docs/reference/print.mkindsg.html | 8 + docs/reference/print.mkinmod.html | 214 +------ docs/reference/print.mmkin.html | 194 +----- docs/reference/print.multistart.html | 8 + docs/reference/print.nafta.html | 8 + docs/reference/print.nlme.mmkin.html | 8 + docs/reference/print.saem.mmkin.html | 8 + docs/reference/print.status.mhmkin.html | 8 + docs/reference/print.status.mmkin.html | 8 + docs/reference/print.summary.mkinfit.html | 8 + docs/reference/print.summary.mmkin.html | 8 + docs/reference/print.summary.nlme.mmkin.html | 8 + docs/reference/print.summary.saem.mmkin.html | 8 + docs/reference/saem.mmkin.html | 8 + docs/reference/saemix_data.html | 8 + docs/reference/saemix_model.html | 8 + docs/reference/schaefer07_complex_results.html | 8 + docs/reference/set_nd_nq_focus.html | 8 + docs/reference/status.mhmkin.html | 8 + docs/reference/status.mmkin.html | 8 + docs/reference/tex_listing.html | 149 +---- docs/reference/update.nlme.mmkin.html | 8 + docs/reference/which.best.default.html | 8 + docs/reference/which.best.html | 8 + docs/search.json | 2 +- docs/sitemap.xml | 469 ++++---------- 102 files changed, 1671 insertions(+), 2202 deletions(-) delete mode 100644 .github/workflows/test-coverage.yaml create mode 100644 docs/reference/BIC.mmkin.html create mode 100644 docs/reference/FOCUS_2006_A.html create mode 100644 docs/reference/FOCUS_2006_B.html create mode 100644 docs/reference/FOCUS_2006_C.html create mode 100644 docs/reference/FOCUS_2006_D.html create mode 100644 docs/reference/FOCUS_2006_E.html create mode 100644 docs/reference/FOCUS_2006_F.html create mode 100644 docs/reference/NAFTA_SOP_Appendix_B.html create mode 100644 docs/reference/NAFTA_SOP_Appendix_D.html create mode 100644 docs/reference/[.mhmkin.html create mode 100644 docs/reference/aw.mixed.mmkin.html create mode 100644 docs/reference/aw.mkinfit.html create mode 100644 docs/reference/aw.mmkin.html create mode 100644 docs/reference/aw.multistart.html create mode 100644 docs/reference/backtransform_odeparms.html create mode 100644 docs/reference/best.default.html create mode 100644 docs/reference/best.html create mode 100644 docs/reference/check_failed.html create mode 100644 docs/reference/ds_dfop.html create mode 100644 docs/reference/ds_dfop_sfo.html create mode 100644 docs/reference/ds_fomc.html create mode 100644 docs/reference/ds_hs.html create mode 100644 docs/reference/ds_sfo.html create mode 100644 docs/reference/f_time_norm_focus.mkindsg.html create mode 100644 docs/reference/f_time_norm_focus.numeric.html create mode 100644 docs/reference/html_listing.html create mode 100644 docs/reference/illparms.mhmkin.html create mode 100644 docs/reference/illparms.mkinfit.html create mode 100644 docs/reference/illparms.mmkin.html create mode 100644 docs/reference/illparms.saem.mmkin.html create mode 100644 docs/reference/intervals.html create mode 100644 docs/reference/invilr.html create mode 100644 docs/reference/loftest.mkinfit.html create mode 100644 docs/reference/lrtest.html create mode 100644 docs/reference/lrtest.mmkin.html create mode 100644 docs/reference/max_twa_dfop.html create mode 100644 docs/reference/max_twa_fomc.html create mode 100644 docs/reference/max_twa_hs.html create mode 100644 docs/reference/max_twa_sfo.html create mode 100644 docs/reference/mhmkin.list.html create mode 100644 docs/reference/mhmkin.mmkin.html create mode 100644 docs/reference/mixed.mmkin.html create mode 100644 docs/reference/mkinpredict.mkinfit.html create mode 100644 docs/reference/mkinpredict.mkinmod.html create mode 100644 docs/reference/multistart.saem.mmkin.html create mode 100644 docs/reference/nlme_data.html create mode 100644 docs/reference/parms.mkinfit.html create mode 100644 docs/reference/parms.mmkin.html create mode 100644 docs/reference/parms.multistart.html create mode 100644 docs/reference/parms.saem.mmkin.html create mode 100644 docs/reference/parplot.multistart.saem.mmkin.html create mode 100644 docs/reference/plot_err.html create mode 100644 docs/reference/plot_res.html create mode 100644 docs/reference/plot_sep.html create mode 100644 docs/reference/print.illparms.mhmkin.html create mode 100644 docs/reference/print.illparms.mkinfit.html create mode 100644 docs/reference/print.illparms.mmkin.html create mode 100644 docs/reference/print.illparms.saem.mmkin.html create mode 100644 docs/reference/print.mhmkin.html create mode 100644 docs/reference/print.mixed.mmkin.html create mode 100644 docs/reference/print.mkindsg.html create mode 100644 docs/reference/print.multistart.html create mode 100644 docs/reference/print.nafta.html create mode 100644 docs/reference/print.nlme.mmkin.html create mode 100644 docs/reference/print.saem.mmkin.html create mode 100644 docs/reference/print.status.mhmkin.html create mode 100644 docs/reference/print.status.mmkin.html create mode 100644 docs/reference/print.summary.mkinfit.html create mode 100644 docs/reference/print.summary.mmkin.html create mode 100644 docs/reference/print.summary.nlme.mmkin.html create mode 100644 docs/reference/print.summary.saem.mmkin.html create mode 100644 docs/reference/saem.mmkin.html create mode 100644 docs/reference/saemix_data.html create mode 100644 docs/reference/saemix_model.html create mode 100644 docs/reference/schaefer07_complex_results.html create mode 100644 docs/reference/set_nd_nq_focus.html create mode 100644 docs/reference/status.mhmkin.html create mode 100644 docs/reference/status.mmkin.html create mode 100644 docs/reference/update.nlme.mmkin.html create mode 100644 docs/reference/which.best.default.html create mode 100644 docs/reference/which.best.html diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml deleted file mode 100644 index fefc52e2..00000000 --- a/.github/workflows/test-coverage.yaml +++ /dev/null @@ -1,61 +0,0 @@ -# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples -# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help -on: - push: - branches: [main, master] - pull_request: - branches: [main, master] - -name: test-coverage - -permissions: read-all - -jobs: - test-coverage: - runs-on: ubuntu-latest - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - - steps: - - uses: actions/checkout@v4 - - - uses: r-lib/actions/setup-r@v2 - with: - use-public-rspm: true - - - uses: r-lib/actions/setup-r-dependencies@v2 - with: - extra-packages: any::covr, any::xml2 - needs: coverage - - - name: Test coverage - run: | - cov <- covr::package_coverage( - quiet = FALSE, - clean = FALSE, - install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") - ) - covr::to_cobertura(cov) - shell: Rscript {0} - - - uses: codecov/codecov-action@v4 - with: - fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} - file: ./cobertura.xml - plugin: noop - disable_search: true - token: ${{ secrets.CODECOV_TOKEN }} - - - name: Show testthat output - if: always() - run: | - ## -------------------------------------------------------------------- - find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true - shell: bash - - - name: Upload test results - if: failure() - uses: actions/upload-artifact@v4 - with: - name: coverage-test-failures - path: ${{ runner.temp }}/package diff --git a/GNUmakefile b/GNUmakefile index 76163ab6..23f994a1 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -125,8 +125,7 @@ pd_all: roxygen git add -A coverage: - mkdir -p docs/dev/coverage - "$(RBIN)/Rscript" -e "covr::report(file = 'coverage/coverage.html')" + "$(RBIN)/Rscript" -e "covr::report(file = 'docs/coverage/coverage.html')" r-forge: git archive main > $(HOME)/git/mkin/mkin.tar;\ diff --git a/NEWS.md b/NEWS.md index d6139aae..69d6b6f7 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,11 +2,11 @@ - 'R/create_deg_func.R: Make sure that no reversible reactions are specified in the case of two observed variables, as this is not supported -# mkin 1.2.8 +# mkin 1.2.8 (unreleased) - 'R/{mhmkin,status}.R': Deal with 'saem' fits that fail when updating an 'mhmkin' object -# mkin 1.2.7 +# mkin 1.2.7 (unreleased) - 'R/illparms.R': Fix a bug that prevented an ill-defined random effect to be found if there was only one random effect in the model. Also add a test for this. diff --git a/README.md b/README.md index dee59ed9..8d7952ee 100644 --- a/README.md +++ b/README.md @@ -4,10 +4,8 @@ [![](https://www.r-pkg.org/badges/version/mkin)](https://cran.r-project.org/package=mkin) [![mkin status badge](https://jranke.r-universe.dev/badges/mkin)](https://jranke.r-universe.dev/ui/#package:mkin) [![Build Status](https://app.travis-ci.com/jranke/mkin.svg?token=Sq9VuYWyRz2FbBLxu6DK&branch=main)](https://app.travis-ci.com/jranke/mkin) -[![Codecov test coverage](https://codecov.io/gh/jranke/mkin/branch/main/graph/badge.svg)](https://app.codecov.io/gh/jranke/mkin?branch=main) - The [R](https://www.r-project.org) package **mkin** provides calculation routines for the analysis of chemical degradation data, including multicompartment kinetics as needed for modelling the formation and decline of transformation products, or diff --git a/_pkgdown.yml b/_pkgdown.yml index 34220df8..0902ced9 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -67,6 +67,7 @@ reference: - multistart - llhist - parplot + - check_failed - title: Datasets and known results contents: - ds_mixed @@ -178,5 +179,7 @@ navbar: href: articles/twa.html - text: Example evaluation of NAFTA SOP Attachment examples href: articles/web_only/NAFTA_examples.html + - text: Test coverage + href: coverage/coverage.html - text: News href: news/index.html diff --git a/docs/404.html b/docs/404.html index b85f954e..22e29157 100644 --- a/docs/404.html +++ b/docs/404.html @@ -8,87 +8,73 @@ Page not found (404) • mkin - - - - + Skip to contents - -