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(v2.1.1.9133) (v2.1.1.9132) unit test, final fixes

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dr. M.S. (Matthijs) Berends
2025-01-27 22:06:32 +01:00
parent f03933940c
commit 9520977a10
14 changed files with 25 additions and 21 deletions
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4
data-raw/_generate_python_wrapper.sh
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@ -62,6 +62,8 @@ os.makedirs(r_lib_path, exist_ok=True)
base = importr('base')
utils = importr('utils')
base.options(warn = -1)
# Override R library paths globally for the session
robjects.r(f'.Library <- "{r_lib_path}"') # Replace default library
robjects.r(f'.Library.site <- "{r_lib_path}"') # Replace site-specific library
@ -117,6 +119,8 @@ microorganisms = pandas2ri.rpy2py(robjects.r('AMR::microorganisms[, !sapply(AMR:
antibiotics = pandas2ri.rpy2py(robjects.r('AMR::antibiotics[, !sapply(AMR::antibiotics, is.list)]'))
clinical_breakpoints = pandas2ri.rpy2py(robjects.r('AMR::clinical_breakpoints[, !sapply(AMR::clinical_breakpoints, is.list)]'))
base.options(warn = 0)
print(f"AMR: Done.", flush=True)
EOL