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mirror of https://github.com/msberends/AMR.git synced 2024-12-25 18:06:12 +01:00

(v2.1.1.9102) fix sir

This commit is contained in:
dr. M.S. (Matthijs) Berends 2024-10-18 10:58:57 +02:00
parent 11b1dc2b02
commit da6321c504
6 changed files with 23 additions and 20 deletions

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@ -49,7 +49,6 @@ if command -v Rscript > /dev/null; then
if [ "$(Rscript -e 'cat(all(c('"'pkgload'"', '"'devtools'"', '"'dplyr'"') %in% rownames(installed.packages())))')" = "TRUE" ]; then if [ "$(Rscript -e 'cat(all(c('"'pkgload'"', '"'devtools'"', '"'dplyr'"') %in% rownames(installed.packages())))')" = "TRUE" ]; then
Rscript -e "source('data-raw/_pre_commit_checks.R')" Rscript -e "source('data-raw/_pre_commit_checks.R')"
currentpkg=$(Rscript -e "cat(pkgload::pkg_name())") currentpkg=$(Rscript -e "cat(pkgload::pkg_name())")
bash data-raw/AMRforRGPT.sh
echo "- Adding changed files in ./data-raw and ./man to this commit" echo "- Adding changed files in ./data-raw and ./man to this commit"
git add data-raw/* git add data-raw/*
git add man/* git add man/*
@ -112,4 +111,7 @@ echo ""
# Save the version number for use in the commit-msg hook # Save the version number for use in the commit-msg hook
echo "${currentversion}" > .git/commit_version.tmp echo "${currentversion}" > .git/commit_version.tmp
# Generate GPT knowledge info for our Assistant (https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant)
bash data-raw/_generate_GPT_knowledge_input.sh "${currentversion}"
exit 0 exit 0

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@ -59,9 +59,9 @@ jobs:
bash _generate_python_wrapper.sh bash _generate_python_wrapper.sh
- name: Publish to PyPI - name: Publish to PyPI
# env: env:
# TWINE_USERNAME: "__token__" TWINE_USERNAME: "__token__"
# TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }} TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
run: | run: |
cd data-raw/python_wrapper/AMR cd data-raw/python_wrapper/AMR
python -m twine upload dist/* python -m twine upload dist/*

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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 2.1.1.9100 Version: 2.1.1.9102
Date: 2024-10-17 Date: 2024-10-18
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by

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@ -1,4 +1,4 @@
# AMR 2.1.1.9100 # AMR 2.1.1.9102
*(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).)* *(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).)*

12
R/sir.R
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@ -1739,12 +1739,12 @@ summary.sir <- function(object, ...) {
c.sir <- function(...) { c.sir <- function(...) {
lst <- list(...) lst <- list(...)
guideline <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$guideline %||% NA_character_) guideline <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$guideline %or% NA_character_)
mo <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$mo %||% NA_character_) mo <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$mo %or% NA_character_)
ab <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$ab %||% NA_character_) ab <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$ab %or% NA_character_)
method <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$method %||% NA_character_) method <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$method %or% NA_character_)
ref_tbl <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$ref_tbl %||% NA_character_) ref_tbl <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$ref_tbl %or% NA_character_)
ref_breakpoints <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$ref_breakpoints %||% NA_character_) ref_breakpoints <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$ref_breakpoints %or% NA_character_)
out <- as.sir(unlist(lapply(list(...), as.character))) out <- as.sir(unlist(lapply(list(...), as.character)))

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@ -7,10 +7,11 @@ if [ "$(basename "$PWD")" != "AMR" ]; then
fi fi
# Define the output file, located in ./data-raw # Define the output file, located in ./data-raw
output_file="data-raw/gpt_training_text.txt" version="$1"
output_file="data-raw/gpt_training_text_v${version}.txt"
# Clear the output file if it exists # Clear the output file if it exists
echo "This files contains all context you must know about the AMR package for R."> "$output_file" echo "This files contains all context you must know about the AMR package for R." > "$output_file"
echo -e "\n\n\n\n" >> "$output_file" echo -e "\n\n\n\n" >> "$output_file"
# Function to remove header block (delimited by # ======) # Function to remove header block (delimited by # ======)
@ -20,7 +21,7 @@ remove_header() {
# Process all .R files in the 'R' folder # Process all .R files in the 'R' folder
for file in R/*.R; do for file in R/*.R; do
echo "THE NEXT PART CONTAINS CONTENTS FROM FILE $file" >> "$output_file" echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
echo -e "\n\n" >> "$output_file" echo -e "\n\n" >> "$output_file"
remove_header "$file" >> "$output_file" remove_header "$file" >> "$output_file"
echo -e "\n\n" >> "$output_file" echo -e "\n\n" >> "$output_file"
@ -28,7 +29,7 @@ done
# Process all .Rmd files in the 'vignettes' folder # Process all .Rmd files in the 'vignettes' folder
for file in vignettes/*.Rmd; do for file in vignettes/*.Rmd; do
echo "THE NEXT PART CONTAINS CONTENTS FROM FILE $file" >> "$output_file" echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
echo -e "\n\n" >> "$output_file" echo -e "\n\n" >> "$output_file"
remove_header "$file" >> "$output_file" remove_header "$file" >> "$output_file"
echo -e "\n\n" >> "$output_file" echo -e "\n\n" >> "$output_file"
@ -37,7 +38,7 @@ done
# Process important metadata files (DESCRIPTION, NAMESPACE, index.md) # Process important metadata files (DESCRIPTION, NAMESPACE, index.md)
for file in DESCRIPTION NAMESPACE index.md; do for file in DESCRIPTION NAMESPACE index.md; do
if [[ -f $file ]]; then if [[ -f $file ]]; then
echo "THE NEXT PART CONTAINS CONTENTS FROM FILE $file" >> "$output_file" echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
echo -e "\n\n" >> "$output_file" echo -e "\n\n" >> "$output_file"
cat "$file" >> "$output_file" cat "$file" >> "$output_file"
echo -e "\n\n" >> "$output_file" echo -e "\n\n" >> "$output_file"
@ -46,7 +47,7 @@ done
# Process test files (if available) in the 'tests' folder # Process test files (if available) in the 'tests' folder
for file in tests/*.R; do for file in tests/*.R; do
echo "THE NEXT PART CONTAINS CONTENTS FROM FILE $file" >> "$output_file" echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
echo -e "\n\n" >> "$output_file" echo -e "\n\n" >> "$output_file"
remove_header "$file" >> "$output_file" remove_header "$file" >> "$output_file"
echo -e "\n\n" >> "$output_file" echo -e "\n\n" >> "$output_file"
@ -54,7 +55,7 @@ done
# Process all .Rd files from the 'man' folder # Process all .Rd files from the 'man' folder
for file in man/*.Rd; do for file in man/*.Rd; do
echo "THE NEXT PART CONTAINS CONTENTS FROM FILE $file" >> "$output_file" echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
echo -e "\n\n" >> "$output_file" echo -e "\n\n" >> "$output_file"
remove_header "$file" >> "$output_file" remove_header "$file" >> "$output_file"
echo -e "\n\n" >> "$output_file" echo -e "\n\n" >> "$output_file"