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(v2.1.1.9186) replace antibiotics with antimicrobials!

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dr. M.S. (Matthijs) Berends
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
140 changed files with 4870 additions and 4702 deletions
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6
data-raw/_generate_python_wrapper.sh
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@ -115,7 +115,7 @@ example_isolates['date'] = pd.to_datetime(example_isolates['date'])
# microorganisms
microorganisms = pandas2ri.rpy2py(robjects.r('AMR::microorganisms[, !sapply(AMR::microorganisms, is.list)]'))
antibiotics = pandas2ri.rpy2py(robjects.r('AMR::antibiotics[, !sapply(AMR::antibiotics, is.list)]'))
antimicrobials = pandas2ri.rpy2py(robjects.r('AMR::antimicrobials[, !sapply(AMR::antimicrobials, is.list)]'))
clinical_breakpoints = pandas2ri.rpy2py(robjects.r('AMR::clinical_breakpoints[, !sapply(AMR::clinical_breakpoints, is.list)]'))
base.options(warn = 0)
@ -125,7 +125,7 @@ EOL
echo "from .datasets import example_isolates" >> $init_file
echo "from .datasets import microorganisms" >> $init_file
echo "from .datasets import antibiotics" >> $init_file
echo "from .datasets import antimicrobials" >> $init_file
echo "from .datasets import clinical_breakpoints" >> $init_file
@ -239,7 +239,7 @@ for rd_file in "$rd_dir"/*.Rd; do
}
# Skip functions matching the regex pattern
if (func_name_py ~ /^(x |facet|scale|set|get|NA_|microorganisms|antibiotics|clinical_breakpoints|example_isolates)/) {
if (func_name_py ~ /^(x |facet|scale|set|get|NA_|microorganisms|antimicrobials|clinical_breakpoints|example_isolates)/) {
next
}