search

lcolladotor / biocthis

Automate package and project setup for Bioconductor packages
https://lcolladotor.github.io/biocthis/
50 stars 17 forks source link

Recognise both master and main branches #24

Closed bschilder closed 2 years ago

bschilder commented 3 years ago

Context

thanks so much for this really helpful package!

I'm trying to use it to get GitHub Actions to work for my Bioc package orthogene using the following:

biocthis::use_bioc_github_action()

GitHub now defaults to calling the 'master' branch the 'main' branch. I manually added the following OR statements (||) throughout, but It would be great to have the function generate this automatically. You can see my edited yaml here.

Example:

...
...
...
- name: Test coverage
        if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main') && env.run_covr == 'true' && runner.os == 'Linux'
        run: |
          covr::codecov()
        shell: Rscript {0}
...
...
...

R session information

```R ─ Session info ────────────────────────────────────────────────────────────────── setting value version R version 4.1.0 (2021-05-18) os macOS Big Sur 11.4 system x86_64, darwin17.0 ui RStudio language (EN) collate en_GB.UTF-8 ctype en_GB.UTF-8 tz America/New_York date 2021-10-24 ─ Packages ────────────────────────────────────────────────────────────────────── package * version date lib source abind 1.4-5 2016-07-21 [1] CRAN (R 4.1.0) askpass 1.1 2019-01-13 [1] CRAN (R 4.1.0) assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0) babelgene 21.4 2021-04-26 [1] CRAN (R 4.1.0) backports 1.2.1 2020-12-09 [1] CRAN (R 4.1.0) badger 0.1.0 2021-04-21 [1] CRAN (R 4.1.0) BiocManager 1.30.16 2021-06-15 [1] CRAN (R 4.1.0) BiocStyle * 2.21.4 2021-10-12 [1] Bioconductor biocthis * 1.3.8 2021-08-10 [1] Bioconductor bitops 1.0-7 2021-04-24 [1] CRAN (R 4.1.0) bookdown 0.24 2021-09-02 [1] CRAN (R 4.1.0) broom 0.7.9 2021-07-27 [1] CRAN (R 4.1.0) bslib 0.3.1 2021-10-06 [1] CRAN (R 4.1.0) cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.0) callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.0) car 3.0-11 2021-06-27 [1] CRAN (R 4.1.0) carData 3.0-4 2020-05-22 [1] CRAN (R 4.1.0) cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.1.0) cli 3.0.1 2021-07-17 [1] CRAN (R 4.1.0) colorspace 2.0-2 2021-06-24 [1] CRAN (R 4.1.0) crayon 1.4.1 2021-02-08 [1] CRAN (R 4.1.0) credentials 1.3.1 2021-07-25 [1] CRAN (R 4.1.0) curl 4.3.2 2021-06-23 [1] CRAN (R 4.1.0) data.table 1.14.2 2021-09-27 [1] CRAN (R 4.1.0) DBI 1.1.1 2021-01-15 [1] CRAN (R 4.1.0) desc 1.4.0 2021-09-28 [1] CRAN (R 4.1.0) devtools 2.4.2 2021-06-07 [1] CRAN (R 4.1.0) digest 0.6.28 2021-09-23 [1] CRAN (R 4.1.0) dlstats 0.1.4 2021-04-23 [1] CRAN (R 4.1.0) downlit 0.2.1 2020-11-04 [1] CRAN (R 4.1.0) dplyr 1.0.7 2021-06-18 [1] CRAN (R 4.1.0) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0) evaluate 0.14 2019-05-28 [1] CRAN (R 4.1.0) fansi 0.5.0 2021-05-25 [1] CRAN (R 4.1.0) farver 2.1.0 2021-02-28 [1] CRAN (R 4.1.0) fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.0) forcats 0.5.1 2021-01-27 [1] CRAN (R 4.1.0) foreign 0.8-81 2020-12-22 [1] CRAN (R 4.1.0) fs 1.5.0 2020-07-31 [1] CRAN (R 4.1.0) generics 0.1.0 2020-10-31 [1] CRAN (R 4.1.0) GenomeInfoDbData 1.2.7 2021-10-20 [1] Bioconductor gert 1.4.1 2021-09-16 [1] CRAN (R 4.1.0) ggplot2 3.3.5 2021-06-25 [1] CRAN (R 4.1.0) ggpubr 0.4.0 2020-06-27 [1] CRAN (R 4.1.0) ggsignif 0.6.3 2021-09-09 [1] CRAN (R 4.1.0) gh 1.3.0 2021-04-30 [1] CRAN (R 4.1.0) gitcreds 0.1.1 2020-12-04 [1] CRAN (R 4.1.0) glue 1.4.2 2020-08-27 [1] CRAN (R 4.1.0) gprofiler2 0.2.1 2021-08-23 [1] CRAN (R 4.1.0) grr 0.9.5 2016-08-26 [1] CRAN (R 4.1.0) gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0) haven 2.4.3 2021-08-04 [1] CRAN (R 4.1.0) hms 1.1.1 2021-09-26 [1] CRAN (R 4.1.0) homologene 1.4.68.19.3.27 2019-03-28 [1] CRAN (R 4.1.0) htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.1.0) htmlwidgets 1.5.4 2021-09-08 [1] CRAN (R 4.1.0) httr 1.4.2 2020-07-20 [1] CRAN (R 4.1.0) jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.1.0) jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.1.0) knitr 1.36 2021-09-29 [1] CRAN (R 4.1.0) labeling 0.4.2 2020-10-20 [1] CRAN (R 4.1.0) lattice 0.20-45 2021-09-22 [1] CRAN (R 4.1.0) lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.1.0) lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.0) magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.1.0) Matrix 1.3-4 2021-06-01 [1] CRAN (R 4.1.0) Matrix.utils 0.9.8 2020-02-26 [1] CRAN (R 4.1.0) memoise 2.0.0 2021-01-26 [1] CRAN (R 4.1.0) munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0) openssl 1.4.5 2021-09-02 [1] CRAN (R 4.1.0) openxlsx 4.2.4 2021-06-16 [1] CRAN (R 4.1.0) orthogene * 0.99.8 2021-10-21 [1] Bioconductor patchwork 1.1.1 2020-12-17 [1] CRAN (R 4.1.0) pillar 1.6.4 2021-10-18 [1] CRAN (R 4.1.0) pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.1.0) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0) pkgdown 1.6.1 2020-09-12 [1] CRAN (R 4.1.0) pkgload 1.2.3 2021-10-13 [1] CRAN (R 4.1.0) plotly 4.10.0 2021-10-09 [1] CRAN (R 4.1.0) prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0) processx 3.5.2 2021-04-30 [1] CRAN (R 4.1.0) ps 1.6.0 2021-02-28 [1] CRAN (R 4.1.0) purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.0) R.cache 0.15.0 2021-04-30 [1] CRAN (R 4.1.0) R.methodsS3 1.8.1 2020-08-26 [1] CRAN (R 4.1.0) R.oo 1.24.0 2020-08-26 [1] CRAN (R 4.1.0) R.utils 2.11.0 2021-09-26 [1] CRAN (R 4.1.0) R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.0) ragg 1.1.3 2021-06-09 [1] CRAN (R 4.1.0) RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.1.0) Rcpp 1.0.7 2021-07-07 [1] CRAN (R 4.1.0) RCurl 1.98-1.5 2021-09-17 [1] CRAN (R 4.1.0) readxl 1.3.1 2019-03-13 [1] CRAN (R 4.1.0) rematch2 2.1.2 2020-05-01 [1] CRAN (R 4.1.0) remotes 2.4.1 2021-09-29 [1] CRAN (R 4.1.0) rio 0.5.27 2021-06-21 [1] CRAN (R 4.1.0) rlang 0.4.12 2021-10-18 [1] CRAN (R 4.1.0) rmarkdown 2.11 2021-09-14 [1] CRAN (R 4.1.0) rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.1.0) rstatix 0.7.0 2021-02-13 [1] CRAN (R 4.1.0) rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.0) rvcheck 0.2.1 2021-10-22 [1] CRAN (R 4.1.0) sass 0.4.0 2021-05-12 [1] CRAN (R 4.1.0) scales 1.1.1 2020-05-11 [1] CRAN (R 4.1.0) sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.1.0) stringi 1.7.5 2021-10-04 [1] CRAN (R 4.1.0) stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0) styler 1.6.2 2021-09-23 [1] CRAN (R 4.1.0) sys 3.4 2020-07-23 [1] CRAN (R 4.1.0) systemfonts 1.0.3 2021-10-13 [1] CRAN (R 4.1.0) testthat 3.1.0 2021-10-04 [1] CRAN (R 4.1.0) textshaping 0.3.6 2021-10-13 [1] CRAN (R 4.1.0) tibble 3.1.5 2021-09-30 [1] CRAN (R 4.1.0) tidyr 1.1.4 2021-09-27 [1] CRAN (R 4.1.0) tidyselect 1.1.1 2021-04-30 [1] CRAN (R 4.1.0) usethis 2.1.0 2021-10-16 [1] CRAN (R 4.1.0) utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.0) vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.0) viridisLite 0.4.0 2021-04-13 [1] CRAN (R 4.1.0) whisker 0.4 2019-08-28 [1] CRAN (R 4.1.0) withr 2.4.2 2021-04-18 [1] CRAN (R 4.1.0) xfun 0.27 2021-10-18 [1] CRAN (R 4.1.0) xml2 1.3.2 2020-04-23 [1] CRAN (R 4.1.0) yaml 2.2.1 2020-02-01 [1] CRAN (R 4.1.0) yulab.utils 0.0.4 2021-10-09 [1] CRAN (R 4.1.0) zip 2.2.0 2021-05-31 [1] CRAN (R 4.1.0) [1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library ```
lcolladotor commented 2 years ago

Hi,

I'm not in favor of doing this. Currently, you can use the pkgdown_covr_branch argument https://github.com/lcolladotor/biocthis/blob/master/R/use_bioc_github_action.R#L103 to specify which branch you want the GHA workflow to apply to. That information is then used by pkgdown_covr_branch in the template file at https://github.com/lcolladotor/biocthis/blob/master/inst/templates/check-bioc.yml.

Best, Leo

bschilder commented 2 years ago

Ok, good to know, thank you!