From ede1cdfd9940cbc65116a737806d3888acbf03d7 Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Sat, 15 Mar 2025 16:14:29 +0100 Subject: [PATCH] (v2.1.1.9205) Fix python wrapper --- .github/workflows/publish-to-pypi.yml | 42 +++++++++---------- DESCRIPTION | 2 +- NEWS.md | 2 +- data-raw/_pre_commit_checks.R | 8 +++- ....txt => gpt_training_text_v2.1.1.9205.txt} | 2 +- 5 files changed, 31 insertions(+), 25 deletions(-) rename data-raw/{gpt_training_text_v2.1.1.9204.txt => gpt_training_text_v2.1.1.9205.txt} (99%) diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml index 43ef09553..b90577ad4 100644 --- a/.github/workflows/publish-to-pypi.yml +++ b/.github/workflows/publish-to-pypi.yml @@ -75,24 +75,24 @@ jobs: python -m twine upload --repository-url https://test.pypi.org/legacy/ dist/* - name: Git push to python-wrapper branch - run: | - git config user.name "GitHub Actions" - git config user.email "<>" - - # Create and switch to python-wrapper branch (orphan if it doesn't exist) - git fetch origin python-wrapper || true - git checkout python-wrapper || git checkout --orphan python-wrapper - - # Delete all existing files from the working tree (safely) - git rm -rf . || true - rm -rf * || true - - # Copy over only PythonPackage/AMR contents from main - git checkout main -- PythonPackage/AMR - mv PythonPackage/AMR/* . - rm -rf PythonPackage - - # Commit and push if changes exist - git add . - git commit -m "Python wrapper update" || echo "No changes to commit" - git push origin python-wrapper --force + run: | + git config user.name "GitHub Actions" + git config user.email "<>" + + # Create and switch to python-wrapper branch (orphan if it doesn't exist) + git fetch origin python-wrapper || true + git checkout python-wrapper || git checkout --orphan python-wrapper + + # Delete all existing files from the working tree (safely) + git rm -rf . || true + rm -rf * || true + + # Copy over only PythonPackage/AMR contents from main + git checkout main -- PythonPackage/AMR + mv PythonPackage/AMR/* . + rm -rf PythonPackage + + # Commit and push if changes exist + git add . + git commit -m "Python wrapper update" || echo "No changes to commit" + git push origin python-wrapper --force diff --git a/DESCRIPTION b/DESCRIPTION index 4e5882a93..59ca6a083 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 2.1.1.9204 +Version: 2.1.1.9205 Date: 2025-03-15 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 0bd207a7f..c8fe47baf 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9204 +# AMR 2.1.1.9205 *(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/_pre_commit_checks.R b/data-raw/_pre_commit_checks.R index 30f40f560..b456ef6c2 100644 --- a/data-raw/_pre_commit_checks.R +++ b/data-raw/_pre_commit_checks.R @@ -636,9 +636,15 @@ styler::style_pkg(include_roxygen_examples = FALSE, exclude_dirs = list.dirs(full.names = FALSE, recursive = FALSE)[!list.dirs(full.names = FALSE, recursive = FALSE) %in% c("R", "tests")]) # Document pkg ------------------------------------------------------------ +files_changed <- function(paths = c("R/", "data/")) { + tryCatch({ + changed_files <- system("git diff --name-only", intern = TRUE) + any(changed_files %like% "^(R|data)/") + }, error = function(e) TRUE) +} if (interactive()) { message("Skipping document in interactive mode") -} else { +} else if (files_changed()) { usethis::ui_info("Documenting package") suppressMessages(devtools::document(quiet = TRUE)) } diff --git a/data-raw/gpt_training_text_v2.1.1.9204.txt b/data-raw/gpt_training_text_v2.1.1.9205.txt similarity index 99% rename from data-raw/gpt_training_text_v2.1.1.9204.txt rename to data-raw/gpt_training_text_v2.1.1.9205.txt index 42fb10780..870a22d94 100644 --- a/data-raw/gpt_training_text_v2.1.1.9204.txt +++ b/data-raw/gpt_training_text_v2.1.1.9205.txt @@ -1,6 +1,6 @@ This knowledge base contains all context you must know about the AMR package for R. You are a GPT trained to be an assistant for the AMR package in R. You are an incredible R specialist, especially trained in this package and in the tidyverse. -First and foremost, you are trained on version 2.1.1.9204. Remember this whenever someone asks which AMR package version you’re at. +First and foremost, you are trained on version 2.1.1.9205. Remember this whenever someone asks which AMR package version you’re at. Below are the contents of the file, the file, and all the files (documentation) in the package. Every file content is split using 100 hypens. ----------------------------------------------------------------------------------------------------