From 4f9db23684e84f3e1d1d295aea40ae4ab939123f Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Sun, 23 Jun 2024 16:18:42 +0200 Subject: [PATCH] check for windows unit test (no-check) --- .github/prehooks/commit-msg | 57 ------------------- .../{pre-commit => prepare-commit-msg} | 23 +++++--- inst/tinytest/test-sir.R | 1 + 3 files changed, 15 insertions(+), 66 deletions(-) delete mode 100755 .github/prehooks/commit-msg rename .github/prehooks/{pre-commit => prepare-commit-msg} (91%) diff --git a/.github/prehooks/commit-msg b/.github/prehooks/commit-msg deleted file mode 100755 index c3a4a69b..00000000 --- a/.github/prehooks/commit-msg +++ /dev/null @@ -1,57 +0,0 @@ -#!/bin/bash - -# ==================================================================== # -# TITLE: # -# AMR: An R Package for Working with Antimicrobial Resistance Data # -# # -# SOURCE CODE: # -# https://github.com/msberends/AMR # -# # -# PLEASE CITE THIS SOFTWARE AS: # -# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # -# (2022). AMR: An R Package for Working with Antimicrobial Resistance # -# Data. Journal of Statistical Software, 104(3), 1-31. # -# https://doi.org/10.18637/jss.v104.i03 # -# # -# Developed at the University of Groningen and the University Medical # -# Center Groningen in The Netherlands, in collaboration with many # -# colleagues from around the world, see our website. # -# # -# This R package is free software; you can freely use and distribute # -# it for both personal and commercial purposes under the terms of the # -# GNU General Public License version 2.0 (GNU GPL-2), as published by # -# the Free Software Foundation. # -# We created this package for both routine data analysis and academic # -# research and it was publicly released in the hope that it will be # -# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # -# # -# Visit our website for the full manual and a complete tutorial about # -# how to conduct AMR data analysis: https://msberends.github.io/AMR/ # -# ==================================================================== # - -####################################### -# This script runs on commit-msg hook # -####################################### - -# Path to the commit message file -COMMIT_MSG_FILE=$1 - -# Read the current commit message -COMMIT_MSG=$(cat "$COMMIT_MSG_FILE") -# check the commit message, cancel commit if needed -if [[ "$COMMIT_MSG" =~ \(no-check\)|\(no-checks\)|\(no-verify\) ]]; then - exit 0 -fi - -# Path to the DESCRIPTION file -DESCRIPTION_FILE="DESCRIPTION" -# Read the version number from the DESCRIPTION file -if [ -f "$DESCRIPTION_FILE" ]; then - currentversion=$(grep "^Version:" "$DESCRIPTION_FILE" | awk '{print $2}') -else - echo "Error: DESCRIPTION file not found. Unable to prepend version number." - exit 1 -fi - -# Prepend the version number to the commit message -echo "(v${currentversion}) ${COMMIT_MSG}" > "$COMMIT_MSG_FILE" diff --git a/.github/prehooks/pre-commit b/.github/prehooks/prepare-commit-msg similarity index 91% rename from .github/prehooks/pre-commit rename to .github/prehooks/prepare-commit-msg index 36dfc7ed..d4392ad6 100755 --- a/.github/prehooks/pre-commit +++ b/.github/prehooks/prepare-commit-msg @@ -33,23 +33,25 @@ # This script runs before every commit # ######################################## -# try to fetch the commit message from the standard location -COMMIT_MSG_PATH=".git/COMMIT_EDITMSG" -if [ -f "$COMMIT_MSG_PATH" ]; then - COMMIT_MSG=$(cat "$COMMIT_MSG_PATH") +COMMIT_MSG_FILE=".git/COMMIT_EDITMSG" + +# Read the commit message +if [ -f "$COMMIT_MSG_FILE" ]; then + COMMIT_MSG=$(cat "$COMMIT_MSG_FILE") else echo "Commit message file not found." exit 1 fi -# check the commit message, cancel commit if needed -if [[ "$COMMIT_MSG" =~ \(no-check\)|\(no-checks\)|\(no-verify\) ]]; then - echo "Not running pre-commit checks:" - echo "Commit message contains '(no-check)', '(no-checks)', or '(no-verify)." + +# Check the commit message and skip checks if needed +if [[ "$COMMIT_MSG" =~ no-?checks?|no-?verify ]]; then + echo "Not running prehook:" + echo "Commit message contains 'no-check' or 'no-verify'." echo "" exit 0 fi -echo "Running pre-commit checks..." +echo "Running prehook..." # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ if command -v Rscript > /dev/null; then @@ -119,3 +121,6 @@ else echo "- no NEWS.md found!" fi echo "" + +# Prepend the version number to the commit message +echo "(v${currentversion}) ${COMMIT_MSG}" > "$COMMIT_MSG_FILE" diff --git a/inst/tinytest/test-sir.R b/inst/tinytest/test-sir.R index 6c410f79..78c03873 100644 --- a/inst/tinytest/test-sir.R +++ b/inst/tinytest/test-sir.R @@ -326,6 +326,7 @@ expect_identical(out_vet$PRA, rep(NA_sir_, 11)) expect_identical(out_vet$FLR, as.sir(c("S", "S", NA, "S", "S", NA, "I", "R", NA, "R", "R"))) sir_history <- sir_interpretation_history() +print(sir_history$host) expect_identical(sir_history$host, c("poultry", "cattle", "poultry", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "dogs", "horse", "dogs", "horse", "horse", "horse", "cattle", "horse", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "cattle", "dogs", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cats", "cats",