(v3.0.1.9071) fix python wrapper

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)

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.
 

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