AMR 2.1.1.9103__py3-none-any.whl → 2.1.1.9106__py3-none-any.whl

AMR/datasets.py

@@ -4,31 +4,48 @@ RESET = '\033[0m'
 
 print(f"{BLUE}AMR:{RESET} Setting up R environment and AMR datasets...", flush=True)
 
+
+import os
 from rpy2 import robjects
 from rpy2.robjects import pandas2ri
 from rpy2.robjects.packages import importr, isinstalled
 import pandas as pd
-# import importlib.metadata as metadata
+import importlib.metadata as metadata
+
+# Get the path to the virtual environment
+venv_path = os.getenv('VIRTUAL_ENV')  # Path to the active virtual environment
+if not venv_path:
+    raise EnvironmentError("No virtual environment detected. Please activate your Python virtual environment.")
 
-# Check if AMR package is installed in R
+# Define R library path within the venv
+r_lib_path = os.path.join(venv_path, "R_libs")
+# Ensure the R library path exists
+os.makedirs(r_lib_path, exist_ok=True)
+# Set the R library path in .libPaths
+base = importr('base')
+base._libPaths(r_lib_path)
+
+# Check if the AMR package is installed in R
 if not isinstalled('AMR'):
     utils = importr('utils')
-    utils.install_packages('AMR', repos='https://msberends.r-universe.dev')
+    utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True)
 
 # Python package version of AMR
-python_amr_version = metadata.version('AMR')
+try:
+    python_amr_version = metadata.version('AMR')
+except metadata.PackageNotFoundError:
+    python_amr_version = None
+
 # R package version of AMR
-# r_amr_version = robjects.r('packageVersion("AMR")')[0]
+r_amr_version = robjects.r(f'as.character(packageVersion("AMR", lib.loc = "{r_lib_path}"))')[0]
 
 # Compare R and Python package versions
-# if r_amr_version != python_amr_version:
-#     print(f"{BLUE}AMR:{RESET} Version mismatch detected. Updating AMR R package version to {python_amr_version}...", flush=True)
-#     try:
-#         # Re-install the specific version of AMR in R
-#         utils = importr('utils')
-#         utils.install_packages('AMR', repos='https://msberends.r-universe.dev')
-#     except Exception as e:
-#         print(f"{BLUE}AMR:{RESET} Could not update: {e}{RESET}", flush=True)
+if python_amr_version and r_amr_version != python_amr_version:
+    try:
+        utils = importr('utils')
+        utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True)
+    except Exception as e:
+        print(f"{BLUE}AMR:{RESET} Could not update: {e}{RESET}", flush=True)
 
 # Activate the automatic conversion between R and pandas DataFrames
 pandas2ri.activate()

{AMR-2.1.1.9103.dist-info → AMR-2.1.1.9106.dist-info}/METADATA

@@ -1,13 +1,12 @@
 Metadata-Version: 2.1
 Name: AMR
-Version: 2.1.1.9103
+Version: 2.1.1.9106
 Summary: A Python wrapper for the AMR R package
 Home-page: https://github.com/msberends/AMR
 Author: Dr. Matthijs Berends
 Author-email: m.s.berends@umcg.nl
 License: GPL 2
 Project-URL: Bug Tracker, https://github.com/msberends/AMR/issues
-Platform: UNKNOWN
 Classifier: Programming Language :: Python :: 3
 Classifier: Operating System :: OS Independent
 Requires-Python: >=3.6
@@ -187,5 +186,3 @@ With the `AMR` Python package, Python users can now effortlessly call R function
 By just running `import AMR`, users can seamlessly integrate the robust features of the R `AMR` package into Python workflows.
 
 Whether you're cleaning data or analysing resistance patterns, the `AMR` Python package makes it easy to work with AMR data in Python.
-
-

AMR-2.1.1.9106.dist-info/RECORD

@@ -0,0 +1,7 @@
+AMR/__init__.py,sha256=Jzrh0SVD8tXP1_sJAnElOPAJcvMgtleTzdSnY3RI3HY,7315
+AMR/datasets.py,sha256=mmbhbTk9MF3F4d50CzIiK01disCRcFOpjdAUo8UHNZg,2502
+AMR/functions.py,sha256=XDN7fo0N3gGnZHYL0pdkG_9jwlsrvj0fo5IqLS7gWBM,43615
+AMR-2.1.1.9106.dist-info/METADATA,sha256=zBIitXz4LjqqV9IozMG0ktLuegaqqglS6YS-XlugWa4,9394
+AMR-2.1.1.9106.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+AMR-2.1.1.9106.dist-info/top_level.txt,sha256=7K6Mq_X_OHdXOzQM5y06VUadXjYkze6yzufL1d7_6xc,4
+AMR-2.1.1.9106.dist-info/RECORD,,

{AMR-2.1.1.9103.dist-info → AMR-2.1.1.9106.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.44.0)
+Generator: setuptools (75.6.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

AMR-2.1.1.9103.dist-info/RECORD

@@ -1,7 +0,0 @@
-AMR/__init__.py,sha256=Jzrh0SVD8tXP1_sJAnElOPAJcvMgtleTzdSnY3RI3HY,7315
-AMR/datasets.py,sha256=rZyCubWpEMEHoY0Wmh7HHHo4Exsys8Cq8JobVl5YgHg,2022
-AMR/functions.py,sha256=XDN7fo0N3gGnZHYL0pdkG_9jwlsrvj0fo5IqLS7gWBM,43615
-AMR-2.1.1.9103.dist-info/METADATA,sha256=6NamjGS5HgvSg_1uDTSXndnwi7H9Vh7qb1XH4FMnWWw,9414
-AMR-2.1.1.9103.dist-info/WHEEL,sha256=eOLhNAGa2EW3wWl_TU484h7q1UNgy0JXjjoqKoxAAQc,92
-AMR-2.1.1.9103.dist-info/top_level.txt,sha256=7K6Mq_X_OHdXOzQM5y06VUadXjYkze6yzufL1d7_6xc,4
-AMR-2.1.1.9103.dist-info/RECORD,,