diff --git a/test.py b/test.py index ebe22f23c95..e2a9ccada4c 100644 --- a/test.py +++ b/test.py @@ -6745,19 +6745,6 @@ def test_quarto_simple_noreport(): ) -@skip_if_not_modified -def test_quarto_simple_extra_conda_deps(): - run( - "utils/quarto", - [ - "snakemake", - "--cores", - "1", - "output/extra_datatable_conda.html", - "--use-conda", - ], - ) - @skip_if_not_modified def test_quarto_simple_extra_renv_deps(): diff --git a/utils/quarto/meta.yaml b/utils/quarto/meta.yaml index a9eb3a358cd..909980f9677 100644 --- a/utils/quarto/meta.yaml +++ b/utils/quarto/meta.yaml @@ -46,6 +46,12 @@ params: ``` will be passed to quarto render as `-P project=project -P threads=threads -P mem=mem` notes: | - This wrapper runs quarto to render markdown .qmd notebooks. It supports r-package management via conda and renv, as illustrated - in the examples. - PDF rendering is currently not working. \ No newline at end of file + This wrapper runs quarto to render markdown .qmd notebooks. + It supports r-package management via `conda` and `renv`: + - For `conda` overwrite the conda environment from the `conda:` directive of the rule with an environement with + the r dependencies as well as `r-quarto` installed. + - For `renv` restore an environment before and point the `input.renv` + to the environment folder or a file within (eg `.Rprofile`). The r-version needs used to build the `renv` needs to match + the one of the wrapper or the environment of the wrapper needs to be overwritten with via `conda:` with a matching `r-base` + installation. + PDF rendering is currently not working as tinytex is not properly supported in `conda`. \ No newline at end of file diff --git a/utils/quarto/test/.gitignore b/utils/quarto/test/.gitignore deleted file mode 100644 index 03c0d3a687b..00000000000 --- a/utils/quarto/test/.gitignore +++ /dev/null @@ -1,9 +0,0 @@ -example_proj* -logs/ -env/renv_test -*_files/ -*_input.txt -*_output.txt -*.docx -*.html -output/ \ No newline at end of file diff --git a/utils/quarto/test/Snakefile b/utils/quarto/test/Snakefile index 431acc37700..7ff0e0e701d 100644 --- a/utils/quarto/test/Snakefile +++ b/utils/quarto/test/Snakefile @@ -7,7 +7,6 @@ rule all: # [hide] "output/simple.docx", # [hide] "output/example_proj_full.html", # [hide] "output/example_proj_noreport.txt", # [hide] - "output/extra_datatable_conda.html", # [hide] "output/extra_datatable_renv.html", # [hide] @@ -65,17 +64,21 @@ rule render_quarto_noreport: "master/utils/quarto" -rule render_quarto_extra_conda: - conda: - "env/extra.yaml" - input: - script="extra_datatable.qmd", - output: - report="output/extra_datatable_conda.html", - log: - "logs/conda.log", - wrapper: - "master/utils/quarto" +# To add additional r-dependencies used to render +# the report also the conda: directive can be +# overwritten. The only required dependency +# is r-quarto +# rule render_quarto_extra_conda: +# conda: +# "env/extra.yaml" +# input: +# script="extra_datatable.qmd", +# output: +# report="output/extra_datatable_conda.html", +# log: +# "logs/conda.log", +# wrapper: +# "master/utils/quarto" # Rules for a example using renv @@ -130,6 +133,10 @@ rule restore_renv: rule render_quarto_renv: + # If the renv is build using a different r version + # than the wrapper, the "conda:" directive may can be overwritten + # using an environment with the correct "r-base" & "r-conda" + # installed input: script="extra_datatable.qmd", renv="env/renv_test/restored.Rprofile", diff --git a/utils/quarto/test/env/extra.linux-64.pin.txt b/utils/quarto/test/env/extra.linux-64.pin.txt deleted file mode 100644 index 2f0a7ae48a0..00000000000 --- a/utils/quarto/test/env/extra.linux-64.pin.txt +++ /dev/null @@ -1,139 +0,0 @@ -# This file may be used to create an environment using: -# $ conda create --name --file -# platform: 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/dev/null @@ -1,6 +0,0 @@ -channels: - - conda-forge -dependencies: - - r-quarto=1.4 - - r-data.table=1.15.4 -