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add Python package to repo

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dr. M.S. (Matthijs) Berends
2024-11-21 10:06:26 +01:00
parent f424c39474
commit 87271d261a
16 changed files with 1417 additions and 34 deletions
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data-raw/_generate_python_wrapper.sh
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@ -30,13 +30,15 @@
# ==================================================================== #
# Clean up
rm -rf python_wrapper/AMR/*
mkdir -p python_wrapper/AMR/AMR
rm -rf ../PythonPackage/AMR/*
mkdir -p ../PythonPackage/AMR/AMR
# Output Python file
functions_file="python_wrapper/AMR/AMR/functions.py"
datasets_file="python_wrapper/AMR/AMR/datasets.py"
init_file="python_wrapper/AMR/AMR/__init__.py"
setup_file="../PythonPackage/AMR/setup.py"
functions_file="../PythonPackage/AMR/AMR/functions.py"
datasets_file="../PythonPackage/AMR/AMR/datasets.py"
init_file="../PythonPackage/AMR/AMR/__init__.py"
# Write header to the datasets Python file, including the convert_to_python function
cat <<EOL > "$datasets_file"
@ -46,31 +48,48 @@ RESET = '\033[0m'
print(f"{BLUE}AMR:{RESET} Setting up R environment and AMR datasets...", flush=True)
import os
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
import importlib.metadata as metadata
# Check if AMR package is installed in R
# Get the path to the virtual environment
venv_path = os.getenv('VIRTUAL_ENV') # Path to the active virtual environment
if not venv_path:
raise EnvironmentError("No virtual environment detected. Please activate your Python virtual environment.")
# Define R library path within the venv
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')
base._libPaths(r_lib_path)
# Check if the AMR package is installed in R
if not isinstalled('AMR'):
utils = importr('utils')
utils.install_packages('AMR', repos='https://msberends.r-universe.dev')
utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True)
# Python package version of AMR
python_amr_version = metadata.version('AMR')
try:
python_amr_version = metadata.version('AMR')
except metadata.PackageNotFoundError:
python_amr_version = None
# R package version of AMR
# r_amr_version = robjects.r('packageVersion("AMR")')[0]
r_amr_version = robjects.r(f'as.character(packageVersion("AMR", lib.loc = "{r_lib_path}"))')[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)
if python_amr_version and r_amr_version != python_amr_version:
try:
utils = importr('utils')
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)
# Activate the automatic conversion between R and pandas DataFrames
pandas2ri.activate()
@ -237,22 +256,20 @@ done
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
cp ../vignettes/AMR_for_Python.Rmd ../PythonPackage/AMR/README.md
sed -i '1,/^# Introduction$/d' ../PythonPackage/AMR/README.md
echo "README copied"
# Path to your DESCRIPTION file
description_file="../DESCRIPTION"
# Output setup.py file
functions_file="python_wrapper/AMR/setup.py"
# Extract the relevant fields from DESCRIPTION
version=$(grep "^Version:" "$description_file" | awk '{print $2}')
# Write the setup.py file
cat <<EOL > "$functions_file"
cat <<EOL > "$setup_file"
from setuptools import setup, find_packages
setup(
@ -283,8 +300,10 @@ setup(
EOL
# Output completion message
echo "setup.py has been generated in $functions_file."
echo "setup.py has been generated in $setup_file."
cd python_wrapper/AMR
python3 setup.py sdist bdist_wheel
cd ../PythonPackage/AMR
pip3 install build
python3 -m build
# python3 setup.py sdist bdist_wheel