(v2.1.1.9125) replace 'antibiotic selectors' with 'antimicrobial selectors'

PythonPackage/AMR/AMR.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: AMR
-Version: 2.1.1.9123
+Version: 2.1.1.9125
 Summary: A Python wrapper for the AMR R package
 Home-page: https://github.com/msberends/AMR
 Author: Matthijs Berends

PythonPackage/AMR/AMR/__init__.py

@@ -2,6 +2,8 @@ from .datasets import example_isolates
 from .datasets import microorganisms
 from .datasets import antibiotics
 from .datasets import clinical_breakpoints
+from .functions import ab_class
+from .functions import ab_selector
 from .functions import ab_from_text
 from .functions import ab_name
 from .functions import ab_cid
@@ -24,8 +26,8 @@ from .functions import clear_custom_microorganisms
 from .functions import age
 from .functions import age_groups
 from .functions import antibiogram
-from .functions import ab_class
-from .functions import ab_selector
+from .functions import amr_class
+from .functions import amr_selector
 from .functions import aminoglycosides
 from .functions import aminopenicillins
 from .functions import antifungals

PythonPackage/AMR/AMR/functions.py

@@ -36,6 +36,12 @@ def convert_to_python(r_output):
     
     # Fall-back
     return r_output
+def ab_class(*args, **kwargs):
+    """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+    return convert_to_python(amr_r.ab_class(*args, **kwargs))
+def ab_selector(*args, **kwargs):
+    """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+    return convert_to_python(amr_r.ab_selector(*args, **kwargs))
 def ab_from_text(*args, **kwargs):
     """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
     return convert_to_python(amr_r.ab_from_text(*args, **kwargs))
@@ -102,15 +108,15 @@ def age_groups(x, *args, **kwargs):
 def antibiogram(*args, **kwargs):
     """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
     return convert_to_python(amr_r.antibiogram(*args, **kwargs))
-def ab_class(ab_class, *args, **kwargs):
+def amr_class(*args, **kwargs):
     """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
-    return convert_to_python(amr_r.ab_class(ab_class, *args, **kwargs))
-def ab_selector(filter, *args, **kwargs):
+    return convert_to_python(amr_r.amr_class(*args, **kwargs))
+def amr_selector(*args, **kwargs):
     """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
-    return convert_to_python(amr_r.ab_selector(filter, *args, **kwargs))
-def aminoglycosides(only_sir_columns = False, *args, **kwargs):
+    return convert_to_python(amr_r.amr_selector(*args, **kwargs))
+def aminoglycosides(*args, **kwargs):
     """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
-    return convert_to_python(amr_r.aminoglycosides(only_sir_columns = False, *args, **kwargs))
+    return convert_to_python(amr_r.aminoglycosides(*args, **kwargs))
 def aminopenicillins(only_sir_columns = False, *args, **kwargs):
     """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
     return convert_to_python(amr_r.aminopenicillins(only_sir_columns = False, *args, **kwargs))
@@ -120,15 +126,15 @@ def antifungals(only_sir_columns = False, *args, **kwargs):
 def antimycobacterials(only_sir_columns = False, *args, **kwargs):
     """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
     return convert_to_python(amr_r.antimycobacterials(only_sir_columns = False, *args, **kwargs))
-def betalactams(only_sir_columns = False, *args, **kwargs):
+def betalactams(*args, **kwargs):
     """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
-    return convert_to_python(amr_r.betalactams(only_sir_columns = False, *args, **kwargs))
+    return convert_to_python(amr_r.betalactams(*args, **kwargs))
 def betalactams_with_inhibitor(only_sir_columns = False, *args, **kwargs):
     """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
     return convert_to_python(amr_r.betalactams_with_inhibitor(only_sir_columns = False, *args, **kwargs))
-def carbapenems(only_sir_columns = False, *args, **kwargs):
+def carbapenems(*args, **kwargs):
     """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
-    return convert_to_python(amr_r.carbapenems(only_sir_columns = False, *args, **kwargs))
+    return convert_to_python(amr_r.carbapenems(*args, **kwargs))
 def cephalosporins(only_sir_columns = False, *args, **kwargs):
     """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
     return convert_to_python(amr_r.cephalosporins(only_sir_columns = False, *args, **kwargs))
@@ -153,9 +159,9 @@ def fluoroquinolones(only_sir_columns = False, *args, **kwargs):
 def glycopeptides(only_sir_columns = False, *args, **kwargs):
     """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
     return convert_to_python(amr_r.glycopeptides(only_sir_columns = False, *args, **kwargs))
-def lincosamides(only_sir_columns = False, *args, **kwargs):
+def lincosamides(*args, **kwargs):
     """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
-    return convert_to_python(amr_r.lincosamides(only_sir_columns = False, *args, **kwargs))
+    return convert_to_python(amr_r.lincosamides(*args, **kwargs))
 def lipoglycopeptides(only_sir_columns = False, *args, **kwargs):
     """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
     return convert_to_python(amr_r.lipoglycopeptides(only_sir_columns = False, *args, **kwargs))
@@ -174,9 +180,9 @@ def penicillins(only_sir_columns = False, *args, **kwargs):
 def phenicols(only_sir_columns = False, *args, **kwargs):
     """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
     return convert_to_python(amr_r.phenicols(only_sir_columns = False, *args, **kwargs))
-def polymyxins(only_sir_columns = False, *args, **kwargs):
+def polymyxins(*args, **kwargs):
     """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
-    return convert_to_python(amr_r.polymyxins(only_sir_columns = False, *args, **kwargs))
+    return convert_to_python(amr_r.polymyxins(*args, **kwargs))
 def quinolones(only_sir_columns = False, *args, **kwargs):
     """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
     return convert_to_python(amr_r.quinolones(only_sir_columns = False, *args, **kwargs))

PythonPackage/AMR/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name='AMR',
-    version='2.1.1.9123',
+    version='2.1.1.9125',
     packages=find_packages(),
     install_requires=[
         'rpy2',