From b1399259e7858f8052474aaf2ac801c81e7d568d Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Thu, 17 Oct 2024 15:22:19 +0200 Subject: [PATCH] (v2.1.1.9100) PyPI update --- .github/workflows/publish-to-pypi.yml | 4 +- DESCRIPTION | 2 +- NEWS.md | 2 +- data-raw/gpt_training_text.txt | 70 +++++++++++++++++++++------ vignettes/AMR_for_Python.Rmd | 14 +++--- 5 files changed, 67 insertions(+), 25 deletions(-) diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml index 5469850e..117889a7 100644 --- a/.github/workflows/publish-to-pypi.yml +++ b/.github/workflows/publish-to-pypi.yml @@ -60,8 +60,8 @@ jobs: - name: Publish to PyPI env: - TWINE_USERNAME: "__token__" - TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }} + # TWINE_USERNAME: "__token__" + # TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }} run: | cd data-raw/python_wrapper/AMR python -m twine upload dist/* diff --git a/DESCRIPTION b/DESCRIPTION index 57bc83c9..340c916b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 2.1.1.9099 +Version: 2.1.1.9100 Date: 2024-10-17 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 5d7b052e..874633bd 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9099 +# AMR 2.1.1.9100 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)* diff --git a/data-raw/gpt_training_text.txt b/data-raw/gpt_training_text.txt index 928967b1..90ebf722 100644 --- a/data-raw/gpt_training_text.txt +++ b/data-raw/gpt_training_text.txt @@ -21728,11 +21728,23 @@ as.sir <- function(x, ...) { UseMethod("as.sir") } -as_sir_structure <- function(x) { - structure(factor(as.character(unlist(unname(x))), - levels = c("S", "SDD", "I", "R", "NI"), - ordered = TRUE), - class = c("sir", "ordered", "factor")) +as_sir_structure <- function(x, + guideline = NULL, + mo = NULL, + ab = NULL, + method = NULL, + ref_tbl = NULL, + ref_breakpoints = NULL) { + out <- structure(factor(as.character(unlist(unname(x))), + levels = c("S", "SDD", "I", "R", "NI"), + ordered = TRUE), + guideline = guideline, + mo = mo, + ab = ab, + method = method, + ref_tbl = ref_tbl, + ref_breakpoints = ref_breakpoints, + class = c("sir", "ordered", "factor")) } #' @rdname as.sir @@ -23043,7 +23055,17 @@ get_skimmers.sir <- function(column) { #' @export #' @noRd print.sir <- function(x, ...) { + x_name <- deparse(substitute(x)) cat("Class 'sir'\n") + if (!is.null(attributes(x)$guideline) && !all(is.na(attributes(x)$guideline))) { + cat(font_blue(word_wrap("These values were interpreted using ", + font_bold(vector_and(attributes(x)$guideline, quotes = FALSE)), + " based on ", + vector_and(attributes(x)$method, quotes = FALSE), + " values. ", + "Use `sir_interpretation_history(", x_name, ")` to return a full logbook."))) + cat("\n") + } print(as.character(x), quote = FALSE) } @@ -23124,7 +23146,27 @@ summary.sir <- function(object, ...) { #' @export #' @noRd c.sir <- function(...) { - as.sir(unlist(lapply(list(...), as.character))) + lst <- list(...) + + guideline <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$guideline %||% NA_character_) + mo <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$mo %||% NA_character_) + ab <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$ab %||% NA_character_) + method <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$method %||% NA_character_) + ref_tbl <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$ref_tbl %||% NA_character_) + ref_breakpoints <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$ref_breakpoints %||% NA_character_) + + out <- as.sir(unlist(lapply(list(...), as.character))) + + if (!all(is.na(guideline))) { + attributes(out)$guideline <- guideline + attributes(out)$mo <- mo + attributes(out)$ab <- ab + attributes(out)$method <- method + attributes(out)$ref_tbl <- ref_tbl + attributes(out)$ref_breakpoints <- ref_breakpoints + } + + out } #' @method unique sir @@ -24740,7 +24782,13 @@ This Python package is a wrapper round the `AMR` R package. It uses the `rpy2` p # Install -1. First make sure you have R installed. There is **no need to install the `AMR` R package**, as it will be installed automatically. +1. Since the Python package is available on the official [Python Package Index](https://pypi.org/project/AMR/), you can just run: + + ```bash + pip install AMR + ``` + +2. Make sure you have R installed. There is **no need to install the `AMR` R package**, as it will be installed automatically. For Linux: @@ -24761,12 +24809,6 @@ This Python package is a wrapper round the `AMR` R package. It uses the `rpy2` p For Windows, visit the [CRAN download page](https://cran.r-project.org) to download and install R. -2. Since the Python package is available on the official [Python Package Index](https://pypi.org/project/AMR/), you can just run: - - ```bash - pip install AMR - ``` - # Examples of Usage ## Cleaning Taxonomy @@ -25982,7 +26024,7 @@ THE NEXT PART CONTAINS CONTENTS FROM FILE DESCRIPTION Package: AMR -Version: 2.1.1.9098 +Version: 2.1.1.9099 Date: 2024-10-17 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/vignettes/AMR_for_Python.Rmd b/vignettes/AMR_for_Python.Rmd index 0b4ec78e..c28f0999 100755 --- a/vignettes/AMR_for_Python.Rmd +++ b/vignettes/AMR_for_Python.Rmd @@ -30,7 +30,13 @@ This Python package is a wrapper round the `AMR` R package. It uses the `rpy2` p # Install -1. First make sure you have R installed. There is **no need to install the `AMR` R package**, as it will be installed automatically. +1. Since the Python package is available on the official [Python Package Index](https://pypi.org/project/AMR/), you can just run: + + ```bash + pip install AMR + ``` + +2. Make sure you have R installed. There is **no need to install the `AMR` R package**, as it will be installed automatically. For Linux: @@ -51,12 +57,6 @@ This Python package is a wrapper round the `AMR` R package. It uses the `rpy2` p For Windows, visit the [CRAN download page](https://cran.r-project.org) to download and install R. -2. Since the Python package is available on the official [Python Package Index](https://pypi.org/project/AMR/), you can just run: - - ```bash - pip install AMR - ``` - # Examples of Usage ## Cleaning Taxonomy