Updated tutorial

.github/workflows/main.yml

@@ -27,8 +27,9 @@ jobs:
           - {os: macos-latest,   r: 'release'}
 
           - {os: windows-latest, r: 'release'}
-          # use 4.0 or 4.1 to check with rtools40's older compiler
-          - {os: windows-latest, r: 'oldrel-4'}
+          # switched to oldrel-1 b/c -4 has compatibility issues with bioconductor
+          # used 4.0 or 4.1 to check with rtools40's older compiler
+          - {os: windows-latest, r: 'oldrel-1'}
 
           - {os: ubuntu-latest,  r: 'devel'}
           - {os: ubuntu-latest,  r: 'release'}

.github/workflows/pkgdown.yaml

@@ -33,11 +33,11 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::.
+          extra-packages: any::pkgdown
           needs: website
 
       - name: Build site
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = TRUE)
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀

.gitignore

@@ -3,13 +3,12 @@
 .RData
 docs/
 issues/
-R-deprecated/
-data-raw/
-tests/
-vignettes-manual-export/
-/doc/
-/Meta/
+assets/
 gggenomes.Rcheck
-.vscode
 gggenomes_*.tar.gz
 vignettes/gggenomes_cache
+vignettes/.Rhistory
+vignettes/.RData
+vignettes/bin
+vignettes/data
+.vscode

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: gggenomes
 Title: A Grammar of Graphics for Comparative Genomics
-Version: 1.1.3
+Version: 1.1.3.9000
 Authors@R: c(
   person("Thomas", "Hackl", email = "t.hackl@rug.nl", role = c("aut", "cre")),
   person("Markus J.", "Ankenbrand", email = "iimog@iimog.org", role = c("aut")),

vignettes/_vignettes.qmd

@@ -0,0 +1,25 @@
+
+These are internal notes. `_`-prefixed vignettes are not rendered by pkgdown
+
+# General notes
+
+My goal is to have reproducible vignettes that can be easily run by users. The main issue is that I cannot bundle the raw data files with the package because they are too big for CRAN. Therefore, I have to prerender the figures in the vignette and make the raw data available as assets on the github repo.
+
+- Figures in the vignette are prerendered because we render html with pkgdown from non-bundled sources. 
+- Raw data files cannot be bundled because it would be to slow/big for CRAN. 
+- Raw data are made available as assets on the github repo.
+- The vignette rmd files and figures, however, still need to be under version control, while raw data needs to be .gitignored. That makes it tricky to set up a good directory structure.
+
+```{zsh}
+# to upload the raw data to github as an asset, run the following command in the terminal:
+tar --dereference -czf ../assets/vignettes.tar.gz .
+gh release upload v1.1.3 ../assets/vignettes.tar.gz
+```
+
+# EMALES vignette - demonstrating main functionality of the package
+
+2026-08-28 (for Nature Methods revision):
+- [x] package raw data for bash stuff for easy download with somewhat perm link,
+ maybe github asset?
+- [x] consider packaging binaries for prodigal, minimap2, seqkit, mmseqs2, blastp,
+ gff-clean, gff2cds, cluster-ids, seq-gc. Maybe switch to diamond, which comes in single bin as well. Or maybe just provide a docker image with all of that installed.