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(v2.1.1.9098) update Py vigettes

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dr. M.S. (Matthijs) Berends
2024-10-17 11:52:01 +02:00
parent 40edc16fdf
commit a9e753b1dc
5 changed files with 64 additions and 51 deletions
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25
data-raw/_generate_python_wrapper.sh
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@ -50,14 +50,31 @@ from rpy2 import robjects
from rpy2.robjects import pandas2ri
from rpy2.robjects.packages import importr, isinstalled
import pandas as pd
# import importlib.metadata as metadata
# Check if the R package is installed
# Check if AMR package is installed in R
if not isinstalled('AMR'):
utils = importr('utils')
utils.install_packages('AMR')
utils.install_packages('AMR', repos='https://msberends.r-universe.dev')
# Python package version of AMR
python_amr_version = metadata.version('AMR')
# R package version of AMR
# r_amr_version = robjects.r('packageVersion("AMR")')[0]
# Compare R and Python package versions
# if r_amr_version != python_amr_version:
# print(f"{BLUE}AMR:{RESET} Version mismatch detected. Updating AMR R package version to {python_amr_version}...", flush=True)
# try:
# # Re-install the specific version of AMR in R
# utils = importr('utils')
# utils.install_packages('AMR', repos='https://msberends.r-universe.dev')
# except Exception as e:
# print(f"{BLUE}AMR:{RESET} Could not update: {e}{RESET}", flush=True)
# Activate the automatic conversion between R and pandas DataFrames
pandas2ri.activate()
# example_isolates
example_isolates = pandas2ri.rpy2py(robjects.r('''
df <- AMR::example_isolates
@ -68,6 +85,7 @@ df[] <- lapply(df, function(x) {
x
}
})
df <- df[, !sapply(df, is.list)]
df
'''))
example_isolates['date'] = pd.to_datetime(example_isolates['date'])
@ -75,7 +93,7 @@ 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)]'))
clinical_breakpoints = pandas2ri.rpy2py(robjects.r('AMR::clinical_breakpoints'))
clinical_breakpoints = pandas2ri.rpy2py(robjects.r('AMR::clinical_breakpoints[, !sapply(AMR::clinical_breakpoints, is.list)]'))
print(f"{BLUE}AMR:{RESET} {GREEN}Done.{RESET}", flush=True)
EOL
@ -220,6 +238,7 @@ echo "Python wrapper functions generated in $functions_file."
echo "Python wrapper functions listed in $init_file."
cp ../vignettes/AMR_for_Python.Rmd python_wrapper/AMR/README.md
sed -i '1,/^# Introduction$/d' python_wrapper/AMR/README.md
echo "README copied"