more

.devel/sphinx/genieclust_inequality.rst

@@ -1,5 +1,5 @@
 genieclust.inequality
-===================
+=====================
 
 .. automodule:: genieclust.inequality
     :members:

.devel/sphinx/weave/Makefile

@@ -1,28 +1,29 @@
 # Copyright (c) 2013-2023, Marek Gagolewski <https://www.gagolewski.com>
 
 FILES_RMD = \
+	basics.Rmd              \
+	sklearn_toy_example.Rmd \
 	r.Rmd
 
 
 FILES_RSTW = \
-	sklearn_toy_example.rstw \
-	basics.rstw              \
 	benchmarks_ar.rstw       \
 	benchmarks_details.rstw  \
 	benchmarks_approx.rstw   \
 	noise.rstw               \
-	sparse.rstw              \
-	string.rstw              \
 	timings.rstw
 
+#	string.rstw              \
+#	sparse.rstw              \
+
 
 RMD_MD_OUTPUTS=$(patsubst %.Rmd,%.md,$(FILES_RMD))
 #RMD_RST_OUTPUTS=$(patsubst %.Rmd,%.rst,$(FILES_RMD))
 
 RSTW_RST_OUTPUTS=$(patsubst %.rstw,%.rst,$(FILES_RSTW))
 
 %.md: %.Rmd
-	Rscript -e 'knitr::knit("$<", "$@")'
+	./Rmd2md.sh "$<"
 
 #%.rst: %.md
 #	pandoc -f markdown+grid_tables --wrap=none "$<" -o "$@"

.devel/sphinx/weave/Rmd2md-patch.R

@@ -0,0 +1,11 @@
+# Copyright (C) 2020-2023, Marek Gagolewski <https://www.gagolewski.com>
+
+# I only want ```{r...``` and ```{python...``` to be recognised as
+# chunks to-be processed by knitr so that they can be placed within
+# MyST's nested admonitions
+
+all_patterns_new <- knitr:::all_patterns
+all_patterns_new$md$chunk.begin <- "^[\t >]*```\\s*\\{((r|python)( *[ ,].*)?)\\}\\s*$"
+all_patterns_new$md$chunk.end <- "^[\t >]*```\\s*$"
+unlockBinding("all_patterns", getNamespace("knitr"))
+assign("all_patterns", all_patterns_new, getNamespace("knitr"))

.devel/sphinx/weave/Rmd2md.sh

@@ -0,0 +1,95 @@
+#!/bin/bash
+
+# Copyright (C) 2020-2023, Marek Gagolewski <https://www.gagolewski.com>
+
+set -e
+
+if [ ! -f "${1}" ]; then
+    echo "The input file does not exist or was not provided."
+    exit 1
+fi
+
+basename="${1/%.Rmd/}"
+tmpdir="${1/%.Rmd/}"
+knitrfile="tmp-md-${1}"
+outfile="${1/%.Rmd/.md}"
+
+echo "Rmd2md ${1} → ${outfile}..."
+
+rm -f "${knitrfile}"
+rm -f "${outfile}"
+
+#mkdir -p "cache"
+
+touch "${knitrfile}"
+
+echo "\`\`\`{r __rinit__,echo=FALSE,warning=FALSE,message=FALSE,results='hide'}" >> "${knitrfile}"
+cat options.R >> "${knitrfile}"
+echo "\`\`\`" >> "${knitrfile}"
+echo "" >> "${knitrfile}"
+
+echo "\`\`\`{python __pyinit__,echo=FALSE,warning=FALSE,message=FALSE,results='hide'}" >> "${knitrfile}"
+cat options.py >> "${knitrfile}"
+echo "\`\`\`" >> "${knitrfile}"
+echo "" >> "${knitrfile}"
+
+cat "${1}" >> "${knitrfile}"
+
+# remove HTML comments <!-- ... -->  (in a brute force way; beware)
+perl -0pi -e 's/(?s)<!--.*?-->\n?//g' "${knitrfile}"
+
+Rscript -e "\
+    library('knitr');                              \
+    source('Rmd2md-patch.R');               \
+    opts_knit\$set(
+        progress=FALSE,                    \
+        verbose=TRUE,                      \
+        unnamed.chunk.label='${basename}'  \
+    );  \
+    opts_chunk\$set(                               \
+        cache.path='${tmpdir}-cache/',     \
+        fig.path='${tmpdir}-figures/'      \
+    );                                             \
+    knit('${knitrfile}', '${outfile}')
+"
+
+rm -f "${knitrfile}"
+
+
+if [ -d "${tmpdir}-figures" ]
+then
+    for f in ${tmpdir}-figures/*.pdf
+    do
+        if [ "$f" -nt "${f/.pdf/.png}" ]
+        then
+            echo "Converting ${f} to png...."
+            convert -density 96 "$f" "${f/.pdf/.png}"
+        fi
+    done
+fi
+
+# move #> comments inside code blocks outside
+Rscript -e "\
+    source('extract-code-comments.R'); \
+    extract_code_comments('${outfile}')
+"
+
+# convert paths: sphinx/chapter/ → ./
+sed -ri -e's/sphinx\/chapter\///g' "${outfile}"
+
+# {chapref}`ref` → {numref}`Chapter %s <ref>`
+sed -ri -e's/\{numref\}`chap:([^`]+)`/{numref}`Chapter %s <chap:\1>`/g' "${outfile}"
+
+# {help}`topic` → {command}`help`{code}`("topic")`
+sed -ri -e's/\{help\}`([^`]+)`/{command}`help`{code}`("\1")`/g' "${outfile}"
+
+# horizontal lines are bigskips
+sed -i -e 's/^\-\-\-$/```{raw} latex\n\\bigskip\n```\n\n```{raw} html\n<div style="margin-top: 1em"><\/div>\n```\n/g' "${outfile}"
+
+# merge input and output chunks:
+sed -rz --in-place 's/(\s)```\n\n+```\n/\1/g' "${outfile}"
+# merge output and input chunks:
+sed -rz --in-place 's/(\s)```\n\n+```r\n/\1/g' "${outfile}"
+sed -rz --in-place 's/(\s)```\n\n+```python\n/\1/g' "${outfile}"
+
+echo "Rmd2md ${1} → ${outfile} DONE."