(v2.1.1.9186) replace antibiotics with antimicrobials!

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

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: AMR
-Version: 2.1.1.9183
+Version: 2.1.1.9186
 Summary: A Python wrapper for the AMR R package
 Home-page: https://github.com/msberends/AMR
 Author: Matthijs Berends
@@ -175,7 +175,7 @@ In this example, we generate an antibiogram by selecting various antibiotics.
 
 ## Taxonomic Data Sets Now in Python!
 
-As a Python user, you might like that the most important data sets of the `AMR` R package, `microorganisms`, `antibiotics`, `clinical_breakpoints`, and `example_isolates`, are now available as regular Python data frames:
+As a Python user, you might like that the most important data sets of the `AMR` R package, `microorganisms`, `antimicrobials`, `clinical_breakpoints`, and `example_isolates`, are now available as regular Python data frames:
 
 ```python
 AMR.microorganisms
@@ -196,7 +196,7 @@ AMR.microorganisms
 | F_ZYZYG      | Zyzygomyces                        | unknown  | Fungi    | None      | 7581        | None            | 2.0        |
 
 ```python
-AMR.antibiotics
+AMR.antimicrobials
 ```
 
 | ab  | cid         | name                 | group                      | oral_ddd | oral_units | iv_ddd | iv_units |

PythonPackage/AMR/AMR/__init__.py

@@ -1,6 +1,6 @@
 from .datasets import example_isolates
 from .datasets import microorganisms
-from .datasets import antibiotics
+from .datasets import antimicrobials
 from .datasets import clinical_breakpoints
 from .functions import ab_class
 from .functions import ab_selector
@@ -138,7 +138,6 @@ from .functions import semi_join_microorganisms
 from .functions import anti_join_microorganisms
 from .functions import key_antimicrobials
 from .functions import all_antimicrobials
-from .functions import antimicrobials_equal
 from .functions import kurtosis
 from .functions import like
 from .functions import mdro

PythonPackage/AMR/AMR/datasets.py

@@ -71,7 +71,7 @@ example_isolates['date'] = pd.to_datetime(example_isolates['date'])
 
 # microorganisms
 microorganisms = pandas2ri.rpy2py(robjects.r('AMR::microorganisms[, !sapply(AMR::microorganisms, is.list)]'))
-antibiotics = pandas2ri.rpy2py(robjects.r('AMR::antibiotics[, !sapply(AMR::antibiotics, is.list)]'))
+antimicrobials = pandas2ri.rpy2py(robjects.r('AMR::antimicrobials[, !sapply(AMR::antimicrobials, is.list)]'))
 clinical_breakpoints = pandas2ri.rpy2py(robjects.r('AMR::clinical_breakpoints[, !sapply(AMR::clinical_breakpoints, is.list)]'))
 
 base.options(warn = 0)

PythonPackage/AMR/AMR/functions.py

@@ -444,9 +444,6 @@ def key_antimicrobials(x = None, *args, **kwargs):
 def all_antimicrobials(x = None, *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.all_antimicrobials(x = None, *args, **kwargs))
-def antimicrobials_equal(y, *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.antimicrobials_equal(y, *args, **kwargs))
 def kurtosis(x, *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.kurtosis(x, *args, **kwargs))

PythonPackage/AMR/README.md

@@ -147,7 +147,7 @@ In this example, we generate an antibiogram by selecting various antibiotics.
 
 ## Taxonomic Data Sets Now in Python!
 
-As a Python user, you might like that the most important data sets of the `AMR` R package, `microorganisms`, `antibiotics`, `clinical_breakpoints`, and `example_isolates`, are now available as regular Python data frames:
+As a Python user, you might like that the most important data sets of the `AMR` R package, `microorganisms`, `antimicrobials`, `clinical_breakpoints`, and `example_isolates`, are now available as regular Python data frames:
 
 ```python
 AMR.microorganisms
@@ -168,7 +168,7 @@ AMR.microorganisms
 | F_ZYZYG      | Zyzygomyces                        | unknown  | Fungi    | None      | 7581        | None            | 2.0        |
 
 ```python
-AMR.antibiotics
+AMR.antimicrobials
 ```
 
 | ab  | cid         | name                 | group                      | oral_ddd | oral_units | iv_ddd | iv_units |

PythonPackage/AMR/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name='AMR',
-    version='2.1.1.9183',
+    version='2.1.1.9186',
     packages=find_packages(),
     install_requires=[
         'rpy2',