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https://github.com/msberends/AMR.git
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3 Commits
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7f4ea96c09 | |||
38bb36ca19 | |||
0fda130a0b |
4
.github/prehooks/commit-msg
vendored
4
.github/prehooks/commit-msg
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@ -59,4 +59,8 @@ else
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echo "No version number to prepend to commit message."
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fi
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git add data-raw/*
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git add PythonPackage/*
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git add -u
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exit 0
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5
.github/prehooks/pre-commit
vendored
5
.github/prehooks/pre-commit
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@ -113,6 +113,11 @@ echo "${currentversion}" > .git/commit_version.tmp
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# Generate GPT knowledge info for our Assistant (https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant)
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bash data-raw/_generate_GPT_knowledge_input.sh "${currentversion}"
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cd data-raw
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bash _generate_python_wrapper.sh
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cd ..
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git add data-raw/*
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git add PythonPackage/*
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git add -u
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exit 0
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 2.1.1.9106
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Version: 2.1.1.9109
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Date: 2024-11-21
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
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# AMR 2.1.1.9106
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# AMR 2.1.1.9109
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*(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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@ -1,6 +1,6 @@
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Metadata-Version: 2.1
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Name: AMR
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Version: 2.1.1.9103
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Version: 2.1.1.9109
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Summary: A Python wrapper for the AMR R package
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Home-page: https://github.com/msberends/AMR
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Author: Dr. Matthijs Berends
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@ -2,9 +2,6 @@ BLUE = '\033[94m'
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GREEN = '\033[32m'
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RESET = '\033[0m'
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print(f"{BLUE}AMR:{RESET} Setting up R environment and AMR datasets...", flush=True)
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import os
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from rpy2 import robjects
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from rpy2.robjects import pandas2ri
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@ -14,8 +11,6 @@ import importlib.metadata as metadata
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# Get the path to the virtual environment
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venv_path = os.getenv('VIRTUAL_ENV') # Path to the active virtual environment
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if not venv_path:
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raise EnvironmentError("No virtual environment detected. Please activate your Python virtual environment.")
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# Define R library path within the venv
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r_lib_path = os.path.join(venv_path, "R_libs")
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@ -42,11 +37,14 @@ r_amr_version = robjects.r(f'as.character(packageVersion("AMR", lib.loc = "{r_li
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# Compare R and Python package versions
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if python_amr_version and r_amr_version != python_amr_version:
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try:
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print(f"{BLUE}AMR:{RESET} Updating package version{RESET}", flush=True)
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utils = importr('utils')
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utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True)
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except Exception as e:
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print(f"{BLUE}AMR:{RESET} Could not update: {e}{RESET}", flush=True)
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print(f"{BLUE}AMR:{RESET} Setting up R environment and AMR datasets...", flush=True)
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# Activate the automatic conversion between R and pandas DataFrames
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pandas2ri.activate()
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Binary file not shown.
BIN
PythonPackage/AMR/dist/amr-2.1.1.9103.tar.gz
vendored
BIN
PythonPackage/AMR/dist/amr-2.1.1.9103.tar.gz
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BIN
PythonPackage/AMR/dist/amr-2.1.1.9109.tar.gz
vendored
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BIN
PythonPackage/AMR/dist/amr-2.1.1.9109.tar.gz
vendored
Normal file
Binary file not shown.
@ -2,7 +2,7 @@ from setuptools import setup, find_packages
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setup(
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name='AMR',
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version='2.1.1.9103',
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version='2.1.1.9109',
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packages=find_packages(),
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install_requires=[
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'rpy2',
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@ -6,13 +6,17 @@ if [ "$(basename "$PWD")" != "AMR" ]; then
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exit 1
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fi
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rm -rf data-raw/gpt_training_text_v*
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# Define the output file, located in ./data-raw
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version="$1"
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output_file="data-raw/gpt_training_text_v${version}.txt"
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# Clear the output file if it exists
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echo "This files contains all context you must know about the AMR package for R." > "$output_file"
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echo -e "\n\n\n\n" >> "$output_file"
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echo "First and foremost, you are trained on version ${version}. Remember this whenever someone asks which AMR package version you’re at." >> "$output_file"
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echo "--------------------------------" >> "$output_file"
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echo "" >> "$output_file"
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# Function to remove header block (delimited by # ======)
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remove_header() {
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@ -20,43 +24,51 @@ remove_header() {
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}
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# Process all .R files in the 'R' folder
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for file in R/*.R; do
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echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
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echo -e "\n\n" >> "$output_file"
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# for file in R/*.R; do
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# echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE '$file':" >> "$output_file"
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# echo -e "\n" >> "$output_file"
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# remove_header "$file" >> "$output_file"
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# echo -e "\n\n" >> "$output_file"
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# done
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# Process important metadata files (DESCRIPTION, NAMESPACE, index.md)
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for file in NAMESPACE index.md; do
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if [[ -f $file ]]; then
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echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE '$file':" >> "$output_file"
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echo -e "\n" >> "$output_file"
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cat "$file" >> "$output_file"
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echo -e "\n\n" >> "$output_file"
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fi
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done
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# Process all .Rd files from the 'man' folder
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for file in man/*.Rd; do
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echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE '$file':" >> "$output_file"
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echo -e "\n" >> "$output_file"
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remove_header "$file" >> "$output_file"
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echo -e "\n\n" >> "$output_file"
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done
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# Process all .Rmd files in the 'vignettes' folder
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for file in vignettes/*.Rmd; do
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echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
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echo -e "\n\n" >> "$output_file"
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echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE '$file':" >> "$output_file"
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echo -e "\n" >> "$output_file"
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remove_header "$file" >> "$output_file"
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echo -e "\n\n" >> "$output_file"
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done
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# Process important metadata files (DESCRIPTION, NAMESPACE, index.md)
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for file in DESCRIPTION NAMESPACE index.md; do
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if [[ -f $file ]]; then
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echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
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echo -e "\n\n" >> "$output_file"
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cat "$file" >> "$output_file"
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echo -e "\n\n" >> "$output_file"
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fi
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# Process all .Rmd files in the 'vignettes' folder
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echo "THE PART HEREAFTER CONTAINS THE README OF OUR PYTHON PACKAGE" >> "$output_file"
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echo -e "\n" >> "$output_file"
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for file in PythonPackage/AMR/README.md; do
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remove_header "$file" >> "$output_file"
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echo -e "\n\n" >> "$output_file"
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done
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# Process test files (if available) in the 'tests' folder
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for file in tests/*.R; do
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echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
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echo -e "\n\n" >> "$output_file"
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remove_header "$file" >> "$output_file"
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echo -e "\n\n" >> "$output_file"
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done
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# Process all .Rd files from the 'man' folder
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for file in man/*.Rd; do
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echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
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echo -e "\n\n" >> "$output_file"
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remove_header "$file" >> "$output_file"
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echo -e "\n\n" >> "$output_file"
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done
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# for file in tests/*.R; do
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# echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE '$file':" >> "$output_file"
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# echo -e "\n" >> "$output_file"
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# remove_header "$file" >> "$output_file"
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# echo -e "\n\n" >> "$output_file"
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# done
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@ -38,7 +38,7 @@ setup_file="../PythonPackage/AMR/setup.py"
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functions_file="../PythonPackage/AMR/AMR/functions.py"
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datasets_file="../PythonPackage/AMR/AMR/datasets.py"
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init_file="../PythonPackage/AMR/AMR/__init__.py"
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description_file="../DESCRIPTION"
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# Write header to the datasets Python file, including the convert_to_python function
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cat <<EOL > "$datasets_file"
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@ -46,9 +46,6 @@ BLUE = '\033[94m'
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GREEN = '\033[32m'
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RESET = '\033[0m'
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print(f"{BLUE}AMR:{RESET} Setting up R environment and AMR datasets...", flush=True)
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import os
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from rpy2 import robjects
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from rpy2.robjects import pandas2ri
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@ -58,8 +55,6 @@ import importlib.metadata as metadata
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# Get the path to the virtual environment
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venv_path = os.getenv('VIRTUAL_ENV') # Path to the active virtual environment
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if not venv_path:
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raise EnvironmentError("No virtual environment detected. Please activate your Python virtual environment.")
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# Define R library path within the venv
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r_lib_path = os.path.join(venv_path, "R_libs")
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@ -86,11 +81,14 @@ r_amr_version = robjects.r(f'as.character(packageVersion("AMR", lib.loc = "{r_li
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# Compare R and Python package versions
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if python_amr_version and r_amr_version != python_amr_version:
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try:
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print(f"{BLUE}AMR:{RESET} Updating package version{RESET}", flush=True)
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utils = importr('utils')
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utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True)
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except Exception as e:
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print(f"{BLUE}AMR:{RESET} Could not update: {e}{RESET}", flush=True)
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print(f"{BLUE}AMR:{RESET} Setting up R environment and AMR datasets...", flush=True)
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# Activate the automatic conversion between R and pandas DataFrames
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pandas2ri.activate()
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@ -260,11 +258,6 @@ cp ../vignettes/AMR_for_Python.Rmd ../PythonPackage/AMR/README.md
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sed -i '1,/^# Introduction$/d' ../PythonPackage/AMR/README.md
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echo "README copied"
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# Path to your DESCRIPTION file
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description_file="../DESCRIPTION"
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# Extract the relevant fields from DESCRIPTION
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version=$(grep "^Version:" "$description_file" | awk '{print $2}')
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10132
data-raw/gpt_training_text_v2.1.1.9109.txt
Normal file
10132
data-raw/gpt_training_text_v2.1.1.9109.txt
Normal file
File diff suppressed because one or more lines are too long
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