AMR 2.1.1.9099__tar.gz → 2.1.1.9106__tar.gz

{AMR-2.1.1.9099 → amr-2.1.1.9106}/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-2.1.1.9099 → amr-2.1.1.9106}/AMR.egg-info/PKG-INFO

@@ -1,17 +1,19 @@
 Metadata-Version: 2.1
 Name: AMR
-Version: 2.1.1.9099
+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
 Description-Content-Type: text/markdown
+Requires-Dist: rpy2
+Requires-Dist: numpy
+Requires-Dist: pandas
 
 
 The `AMR` package for R is a powerful tool for antimicrobial resistance (AMR) analysis. It provides extensive features for handling microbial and antimicrobial data. However, for those who work primarily in Python, we now have a more intuitive option available: the [`AMR` Python Package Index](https://pypi.org/project/AMR/).
@@ -20,7 +22,13 @@ This Python package is a wrapper round the `AMR` R package. It uses the `rpy2` p
 
 # Install
 
-1. First make sure you have R installed. There is **no need to install the `AMR` R package**, as it will be installed automatically.
+1. Since the Python package is available on the official [Python Package Index](https://pypi.org/project/AMR/), you can just run:
+
+    ```bash
+    pip install AMR
+    ```
+
+2. Make sure you have R installed. There is **no need to install the `AMR` R package**, as it will be installed automatically.
 
     For Linux:
 
@@ -41,12 +49,6 @@ This Python package is a wrapper round the `AMR` R package. It uses the `rpy2` p
     
     For Windows, visit the [CRAN download page](https://cran.r-project.org) to download and install R.
 
-2. Since the Python package is available on the official [Python Package Index](https://pypi.org/project/AMR/), you can just run:
-
-    ```bash
-    pip install AMR
-    ```
-
 # Examples of Usage
 
 ## Cleaning Taxonomy
@@ -184,5 +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-2.1.1.9099 → amr-2.1.1.9106}/PKG-INFO

@@ -1,17 +1,19 @@
 Metadata-Version: 2.1
 Name: AMR
-Version: 2.1.1.9099
+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
 Description-Content-Type: text/markdown
+Requires-Dist: rpy2
+Requires-Dist: numpy
+Requires-Dist: pandas
 
 
 The `AMR` package for R is a powerful tool for antimicrobial resistance (AMR) analysis. It provides extensive features for handling microbial and antimicrobial data. However, for those who work primarily in Python, we now have a more intuitive option available: the [`AMR` Python Package Index](https://pypi.org/project/AMR/).
@@ -20,7 +22,13 @@ This Python package is a wrapper round the `AMR` R package. It uses the `rpy2` p
 
 # Install
 
-1. First make sure you have R installed. There is **no need to install the `AMR` R package**, as it will be installed automatically.
+1. Since the Python package is available on the official [Python Package Index](https://pypi.org/project/AMR/), you can just run:
+
+    ```bash
+    pip install AMR
+    ```
+
+2. Make sure you have R installed. There is **no need to install the `AMR` R package**, as it will be installed automatically.
 
     For Linux:
 
@@ -41,12 +49,6 @@ This Python package is a wrapper round the `AMR` R package. It uses the `rpy2` p
     
     For Windows, visit the [CRAN download page](https://cran.r-project.org) to download and install R.
 
-2. Since the Python package is available on the official [Python Package Index](https://pypi.org/project/AMR/), you can just run:
-
-    ```bash
-    pip install AMR
-    ```
-
 # Examples of Usage
 
 ## Cleaning Taxonomy
@@ -184,5 +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-2.1.1.9099 → amr-2.1.1.9106}/README.md

@@ -5,7 +5,13 @@ This Python package is a wrapper round the `AMR` R package. It uses the `rpy2` p
 
 # Install
 
-1. First make sure you have R installed. There is **no need to install the `AMR` R package**, as it will be installed automatically.
+1. Since the Python package is available on the official [Python Package Index](https://pypi.org/project/AMR/), you can just run:
+
+    ```bash
+    pip install AMR
+    ```
+
+2. Make sure you have R installed. There is **no need to install the `AMR` R package**, as it will be installed automatically.
 
     For Linux:
 
@@ -26,12 +32,6 @@ This Python package is a wrapper round the `AMR` R package. It uses the `rpy2` p
     
     For Windows, visit the [CRAN download page](https://cran.r-project.org) to download and install R.
 
-2. Since the Python package is available on the official [Python Package Index](https://pypi.org/project/AMR/), you can just run:
-
-    ```bash
-    pip install AMR
-    ```
-
 # Examples of Usage
 
 ## Cleaning Taxonomy

{AMR-2.1.1.9099 → amr-2.1.1.9106}/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name='AMR',
-    version='2.1.1.9099',
+    version='2.1.1.9106',
     packages=find_packages(),
     install_requires=[
         'rpy2',