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mirror of https://github.com/msberends/AMR.git synced 2024-12-25 18:46:11 +01:00

(v2.1.1.9107) new pkg knowledge for AMR

This commit is contained in:
dr. M.S. (Matthijs) Berends 2024-11-21 12:02:58 +01:00
parent 31a0da0d3a
commit 0fda130a0b
10 changed files with 20380 additions and 138101 deletions

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@ -1,5 +1,5 @@
Package: AMR
Version: 2.1.1.9106
Version: 2.1.1.9107
Date: 2024-11-21
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

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@ -1,4 +1,4 @@
# AMR 2.1.1.9106
# AMR 2.1.1.9107
*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*

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@ -6,13 +6,17 @@ if [ "$(basename "$PWD")" != "AMR" ]; then
exit 1
fi
rm -rf data-raw/gpt_training_text_v*
# Define the output file, located in ./data-raw
version="$1"
output_file="data-raw/gpt_training_text_v${version}.txt"
# Clear the output file if it exists
echo "This files contains all context you must know about the AMR package for R." > "$output_file"
echo -e "\n\n\n\n" >> "$output_file"
echo "First and foremost, you are trained on version ${version}. Remember this whenever someone asks which AMR package version youre at." >> "$output_file"
echo "--------------------------------" >> "$output_file"
echo "" >> "$output_file"
# Function to remove header block (delimited by # ======)
remove_header() {
@ -20,43 +24,51 @@ remove_header() {
}
# Process all .R files in the 'R' folder
for file in R/*.R; do
echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
echo -e "\n\n" >> "$output_file"
# for file in R/*.R; do
# echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE '$file':" >> "$output_file"
# echo -e "\n" >> "$output_file"
# remove_header "$file" >> "$output_file"
# echo -e "\n\n" >> "$output_file"
# done
# Process important metadata files (DESCRIPTION, NAMESPACE, index.md)
for file in NAMESPACE index.md; do
if [[ -f $file ]]; then
echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE '$file':" >> "$output_file"
echo -e "\n" >> "$output_file"
cat "$file" >> "$output_file"
echo -e "\n\n" >> "$output_file"
fi
done
# Process all .Rd files from the 'man' folder
for file in man/*.Rd; do
echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE '$file':" >> "$output_file"
echo -e "\n" >> "$output_file"
remove_header "$file" >> "$output_file"
echo -e "\n\n" >> "$output_file"
done
# Process all .Rmd files in the 'vignettes' folder
for file in vignettes/*.Rmd; do
echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
echo -e "\n\n" >> "$output_file"
echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE '$file':" >> "$output_file"
echo -e "\n" >> "$output_file"
remove_header "$file" >> "$output_file"
echo -e "\n\n" >> "$output_file"
done
# Process important metadata files (DESCRIPTION, NAMESPACE, index.md)
for file in DESCRIPTION NAMESPACE index.md; do
if [[ -f $file ]]; then
echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
echo -e "\n\n" >> "$output_file"
cat "$file" >> "$output_file"
echo -e "\n\n" >> "$output_file"
fi
# Process all .Rmd files in the 'vignettes' folder
echo "THE PART HEREAFTER CONTAINS THE README OF OUR PYTHON PACKAGE" >> "$output_file"
echo -e "\n" >> "$output_file"
for file in PythonPackage/AMR/README.md; do
remove_header "$file" >> "$output_file"
echo -e "\n\n" >> "$output_file"
done
# Process test files (if available) in the 'tests' folder
for file in tests/*.R; do
echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
echo -e "\n\n" >> "$output_file"
remove_header "$file" >> "$output_file"
echo -e "\n\n" >> "$output_file"
done
# Process all .Rd files from the 'man' folder
for file in man/*.Rd; do
echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
echo -e "\n\n" >> "$output_file"
remove_header "$file" >> "$output_file"
echo -e "\n\n" >> "$output_file"
done
# for file in tests/*.R; do
# echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE '$file':" >> "$output_file"
# echo -e "\n" >> "$output_file"
# remove_header "$file" >> "$output_file"
# echo -e "\n\n" >> "$output_file"
# done

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@ -46,9 +46,6 @@ BLUE = '\033[94m'
GREEN = '\033[32m'
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
@ -58,8 +55,6 @@ import importlib.metadata as metadata
# 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")
@ -86,11 +81,14 @@ r_amr_version = robjects.r(f'as.character(packageVersion("AMR", lib.loc = "{r_li
# Compare R and Python package versions
if python_amr_version and r_amr_version != python_amr_version:
try:
print(f"{BLUE}AMR:{RESET} Updating package version{RESET}", flush=True)
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)
print(f"{BLUE}AMR:{RESET} Setting up R environment and AMR datasets...", flush=True)
# Activate the automatic conversion between R and pandas DataFrames
pandas2ri.activate()

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