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(v2.1.1.9129) unit test fix

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dr. M.S. (Matthijs) Berends
2025-01-27 16:17:03 +01:00
parent 6efa317a81
commit 1149360b27
66 changed files with 94 additions and 80 deletions
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36
data-raw/_generate_python_wrapper.sh
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@ -42,10 +42,6 @@ description_file="../DESCRIPTION"
# Write header to the datasets Python file, including the convert_to_python function
cat <<EOL > "$datasets_file"
BLUE = '\033[94m'
GREEN = '\033[32m'
RESET = '\033[0m'
import os
import sys
from rpy2 import robjects
@ -61,18 +57,22 @@ venv_path = sys.prefix
r_lib_path = os.path.join(venv_path, "R_libs")
# Ensure the R library path exists
os.makedirs(r_lib_path, exist_ok=True)
# Set the R library path in .libPaths
base = importr('base')
# Turn off warnings
base.options(warn = -1)
base._libPaths(r_lib_path)
# Import base and utils
base = importr('base')
utils = importr('utils')
# 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
base._libPaths(r_lib_path) # Override .libPaths() as well
# Get the effective library path
r_amr_lib_path = base._libPaths()[0]
# Check if the AMR package is installed in R
if not isinstalled('AMR', lib_loc = r_amr_lib_path):
utils = importr('utils')
print(f"{BLUE}AMR:{RESET} Installing AMR package to {BLUE}{r_amr_lib_path}/{RESET}...", flush=True)
if not isinstalled('AMR', lib_loc=r_amr_lib_path):
print(f"AMR: Installing latest AMR R package to {r_amr_lib_path}...", flush=True)
utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True)
# Python package version of AMR
@ -87,16 +87,12 @@ r_amr_version = robjects.r(f'as.character(packageVersion("AMR", lib.loc = "{r_li
# Compare R and Python package versions
if r_amr_version != python_amr_version:
try:
print(f"{BLUE}AMR:{RESET} Updating AMR package in {BLUE}{r_amr_lib_path}/{RESET}...", flush=True)
utils = importr('utils')
print(f"AMR: Updating AMR package in {r_amr_lib_path}...", flush=True)
utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True)
except Exception as e:
print(f"{BLUE}AMR:{RESET} Could not update: {e}{RESET}", flush=True)
print(f"AMR: Could not update: {e}", flush=True)
# Restore warnings to default
base.options(warn = 0)
print(f"{BLUE}AMR:{RESET} Setting up R environment and AMR datasets...", flush=True)
print(f"AMR: Setting up R environment and AMR datasets...", flush=True)
# Activate the automatic conversion between R and pandas DataFrames
pandas2ri.activate()
@ -121,7 +117,7 @@ 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)]'))
print(f"{BLUE}AMR:{RESET} {GREEN}Done.{RESET}", flush=True)
print(f"AMR: Done.", flush=True)
EOL
echo "from .datasets import example_isolates" >> $init_file