diff --git a/DESCRIPTION b/DESCRIPTION index b3de6761f..c3946b921 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 3.0.1.9070 +Version: 3.0.1.9071 Date: 2026-06-26 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 44bc617af..0907a1ed3 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 3.0.1.9070 +# AMR 3.0.1.9071 Planned as v3.1.0, end of June 2026. diff --git a/data-raw/_generate_python_wrapper.sh b/data-raw/_generate_python_wrapper.sh index f56b139fd..fc49aa603 100644 --- a/data-raw/_generate_python_wrapper.sh +++ b/data-raw/_generate_python_wrapper.sh @@ -72,7 +72,9 @@ base._libPaths(r_lib_path) # Check if the AMR package is installed in R if not isinstalled('AMR', lib_loc=r_lib_path): print(f"AMR: Installing latest AMR R package to {r_lib_path}...", flush=True) - utils.install_packages('AMR', repos='beta.amr-for-r.org', quiet=True) + utils.install_packages('remotes', quiet=True) + remotes = importr('remotes') + remotes.install_github('msberends/AMR', quiet=True) # Retrieve Python AMR version try: @@ -88,10 +90,15 @@ r_amr_version = str(r_amr_version[0]) if r_amr_version != python_amr_version: try: print(f"AMR: Updating AMR package in {r_lib_path}...", flush=True) - utils.install_packages('AMR', repos='beta.amr-for-r.org', quiet=True) + utils.install_packages('remotes', quiet=True) + remotes = importr('remotes') + remotes.install_github('msberends/AMR', quiet=True) + r_amr_version = robjects.r(f'as.character(packageVersion("AMR", lib.loc = "{r_lib_path}"))') + r_amr_version = str(r_amr_version[0]) except Exception as e: print(f"AMR: Could not update: {e}", flush=True) +print(f"AMR: R package version {r_amr_version} loaded.", flush=True) print(f"AMR: Setting up R environment and AMR datasets...", flush=True) # Activate the automatic conversion between R and pandas DataFrames @@ -204,7 +211,7 @@ def r_to_python(r_func): return wrapper EOL -# Directory where the .Rd files are stored (update path as needed) +# Directory where the .Rd files are stored rd_dir="../man" # Iterate through each .Rd file in the man directory