Remove the conda r-dependency example

As discussed in the PR this does not need to be
explicitly shown. Instead I have added this more expliiclty to the
documentation.

Author: Vito Zanotelli

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():

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.
+  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`.

utils/quarto/test/.gitignore

@@ -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",