From 6efa317a814ee9a1e80c49d59c27db47eff4cd19 Mon Sep 17 00:00:00 2001
From: Matthijs Berends <m.s.berends@umcg.nl>
Date: Mon, 27 Jan 2025 11:51:40 +0100
Subject: [PATCH] (v2.1.1.9128) fix for bug-drug combinations

---
 DESCRIPTION                                   |   2 +-
 NEWS.md                                       |   2 +-
 PythonPackage/AMR/AMR.egg-info/PKG-INFO       |   2 +-
 ...ny.whl => AMR-2.1.1.9128-py3-none-any.whl} | Bin 10179 -> 10176 bytes
 PythonPackage/AMR/dist/amr-2.1.1.9127.tar.gz  | Bin 10020 -> 0 bytes
 PythonPackage/AMR/dist/amr-2.1.1.9128.tar.gz  | Bin 0 -> 10009 bytes
 PythonPackage/AMR/setup.py                    |   2 +-
 R/bug_drug_combinations.R                     |   8 +-
 ....txt => gpt_training_text_v2.1.1.9128.txt} |  85 +++++++++---------
 9 files changed, 50 insertions(+), 51 deletions(-)
 rename PythonPackage/AMR/dist/{AMR-2.1.1.9127-py3-none-any.whl => AMR-2.1.1.9128-py3-none-any.whl} (52%)
 delete mode 100644 PythonPackage/AMR/dist/amr-2.1.1.9127.tar.gz
 create mode 100644 PythonPackage/AMR/dist/amr-2.1.1.9128.tar.gz
 rename data-raw/{gpt_training_text_v2.1.1.9127.txt => gpt_training_text_v2.1.1.9128.txt} (99%)

diff --git a/DESCRIPTION b/DESCRIPTION
index b49b83390..139b89e64 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9127
+Version: 2.1.1.9128
 Date: 2025-01-27
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
diff --git a/NEWS.md b/NEWS.md
index 9f354c607..a9c4aa550 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 2.1.1.9127
+# AMR 2.1.1.9128
 
 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
 
diff --git a/PythonPackage/AMR/AMR.egg-info/PKG-INFO b/PythonPackage/AMR/AMR.egg-info/PKG-INFO
index bbf2afcfc..b80d3fc6e 100644
--- a/PythonPackage/AMR/AMR.egg-info/PKG-INFO
+++ b/PythonPackage/AMR/AMR.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: AMR
-Version: 2.1.1.9127
+Version: 2.1.1.9128
 Summary: A Python wrapper for the AMR R package
 Home-page: https://github.com/msberends/AMR
 Author: Matthijs Berends
diff --git a/PythonPackage/AMR/dist/AMR-2.1.1.9127-py3-none-any.whl b/PythonPackage/AMR/dist/AMR-2.1.1.9128-py3-none-any.whl
similarity index 52%
rename from PythonPackage/AMR/dist/AMR-2.1.1.9127-py3-none-any.whl
rename to PythonPackage/AMR/dist/AMR-2.1.1.9128-py3-none-any.whl
index c15c6ef5b39fd15bc3726ccde728bab96dca3181..2a5f62f2f6ed109af570b38105a2eb6c14cb2009 100644
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literal 0
HcmV?d00001

diff --git a/PythonPackage/AMR/setup.py b/PythonPackage/AMR/setup.py
index 49c451f84..b48a98844 100644
--- a/PythonPackage/AMR/setup.py
+++ b/PythonPackage/AMR/setup.py
@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name='AMR',
-    version='2.1.1.9127',
+    version='2.1.1.9128',
     packages=find_packages(),
     install_requires=[
         'rpy2',
diff --git a/R/bug_drug_combinations.R b/R/bug_drug_combinations.R
index 17e933d7e..dd4ee82c7 100755
--- a/R/bug_drug_combinations.R
+++ b/R/bug_drug_combinations.R
@@ -172,16 +172,16 @@ bug_drug_combinations <- function(x,
     res
   }
   
-  if (include_n_rows == FALSE) {
-    out <- out[, colnames(out)[colnames(out) != "total_rows"], drop = FALSE]
-  }
-  
   if (data_has_groups) {
     out <- apply_group(x, "run_it", groups)
   } else {
     out <- run_it(x)
   }
   
+  if (include_n_rows == FALSE) {
+    out <- out[, colnames(out)[colnames(out) != "total_rows"], drop = FALSE]
+  }
+  
   out <- out %pm>% pm_arrange(mo, ab)
   out <- as_original_data_class(out, class(x.bak)) # will remove tibble groups
   rownames(out) <- NULL
diff --git a/data-raw/gpt_training_text_v2.1.1.9127.txt b/data-raw/gpt_training_text_v2.1.1.9128.txt
similarity index 99%
rename from data-raw/gpt_training_text_v2.1.1.9127.txt
rename to data-raw/gpt_training_text_v2.1.1.9128.txt
index e030aade0..ad94c68c8 100644
--- a/data-raw/gpt_training_text_v2.1.1.9127.txt
+++ b/data-raw/gpt_training_text_v2.1.1.9128.txt
@@ -1,5 +1,5 @@
 This files contains all context you must know about the AMR package for R.
-First and foremost, you are trained on version 2.1.1.9127. Remember this whenever someone asks which AMR package version you’re at.
+First and foremost, you are trained on version 2.1.1.9128. Remember this whenever someone asks which AMR package version you’re at.
 --------------------------------
 
 THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'NAMESPACE':
@@ -10044,48 +10044,6 @@ print(df)
 
 * **ab_name**: Similarly, this function standardises antimicrobial names. The different representations of ciprofloxacin (e.g., "Cipro", "CIP", "J01MA02", and "Ciproxin") are all converted to the standard name, "Ciprofloxacin".
 
-
-## 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:
-
-```python
-AMR.microorganisms
-```
-
-| mo           | fullname                           | status   | kingdom  | gbif      | gbif_parent | gbif_renamed_to | prevalence |
-|--------------|------------------------------------|----------|----------|-----------|-------------|-----------------|------------|
-| B_GRAMN      | (unknown Gram-negatives)           | unknown  | Bacteria | None      | None        | None            | 2.0        |
-| B_GRAMP      | (unknown Gram-positives)           | unknown  | Bacteria | None      | None        | None            | 2.0        |
-| B_ANAER-NEG  | (unknown anaerobic Gram-negatives) | unknown  | Bacteria | None      | None        | None            | 2.0        |
-| B_ANAER-POS  | (unknown anaerobic Gram-positives) | unknown  | Bacteria | None      | None        | None            | 2.0        |
-| B_ANAER      | (unknown anaerobic bacteria)       | unknown  | Bacteria | None      | None        | None            | 2.0        |
-| ...          | ...                                | ...      | ...      | ...       | ...         | ...             | ...        |
-| B_ZYMMN_POMC | Zymomonas pomaceae                 | accepted | Bacteria | 10744418  | 3221412     | None            | 2.0        |
-| B_ZYMPH      | Zymophilus                         | synonym  | Bacteria | None      | 9475166     | None            | 2.0        |
-| B_ZYMPH_PCVR | Zymophilus paucivorans             | synonym  | Bacteria | None      | None        | None            | 2.0        |
-| B_ZYMPH_RFFN | Zymophilus raffinosivorans         | synonym  | Bacteria | None      | None        | None            | 2.0        |
-| F_ZYZYG      | Zyzygomyces                        | unknown  | Fungi    | None      | 7581        | None            | 2.0        |
-
-```python
-AMR.antibiotics
-```
-
-| ab  | cid         | name                 | group                      | oral_ddd | oral_units | iv_ddd | iv_units |
-|-----|-------------|----------------------|----------------------------|----------|------------|--------|----------|
-| AMA | 4649.0      | 4-aminosalicylic acid| Antimycobacterials         | 12.00    | g          | NaN    | None     |
-| ACM | 6450012.0   | Acetylmidecamycin    | Macrolides/lincosamides    | NaN      | None       | NaN    | None     |
-| ASP | 49787020.0  | Acetylspiramycin     | Macrolides/lincosamides    | NaN      | None       | NaN    | None     |
-| ALS | 8954.0      | Aldesulfone sodium   | Other antibacterials       | 0.33     | g          | NaN    | None     |
-| AMK | 37768.0     | Amikacin             | Aminoglycosides            | NaN      | None       | 1.0    | g        |
-| ... | ...         | ...                  | ...                        | ...      | ...        | ...    | ...      |
-| VIR | 11979535.0  | Virginiamycine       | Other antibacterials       | NaN      | None       | NaN    | None     |
-| VOR | 71616.0     | Voriconazole         | Antifungals/antimycotics   | 0.40     | g          | 0.4    | g        |
-| XBR | 72144.0     | Xibornol             | Other antibacterials       | NaN      | None       | NaN    | None     |
-| ZID | 77846445.0  | Zidebactam           | Other antibacterials       | NaN      | None       | NaN    | None     |
-| ZFD | NaN         | Zoliflodacin         | None                       | NaN      | None       | NaN    | None     |
-
-
 ## Calculating AMR
 
 ```python
@@ -10136,6 +10094,47 @@ print(result2b)
 
 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:
+
+```python
+AMR.microorganisms
+```
+
+| mo           | fullname                           | status   | kingdom  | gbif      | gbif_parent | gbif_renamed_to | prevalence |
+|--------------|------------------------------------|----------|----------|-----------|-------------|-----------------|------------|
+| B_GRAMN      | (unknown Gram-negatives)           | unknown  | Bacteria | None      | None        | None            | 2.0        |
+| B_GRAMP      | (unknown Gram-positives)           | unknown  | Bacteria | None      | None        | None            | 2.0        |
+| B_ANAER-NEG  | (unknown anaerobic Gram-negatives) | unknown  | Bacteria | None      | None        | None            | 2.0        |
+| B_ANAER-POS  | (unknown anaerobic Gram-positives) | unknown  | Bacteria | None      | None        | None            | 2.0        |
+| B_ANAER      | (unknown anaerobic bacteria)       | unknown  | Bacteria | None      | None        | None            | 2.0        |
+| ...          | ...                                | ...      | ...      | ...       | ...         | ...             | ...        |
+| B_ZYMMN_POMC | Zymomonas pomaceae                 | accepted | Bacteria | 10744418  | 3221412     | None            | 2.0        |
+| B_ZYMPH      | Zymophilus                         | synonym  | Bacteria | None      | 9475166     | None            | 2.0        |
+| B_ZYMPH_PCVR | Zymophilus paucivorans             | synonym  | Bacteria | None      | None        | None            | 2.0        |
+| B_ZYMPH_RFFN | Zymophilus raffinosivorans         | synonym  | Bacteria | None      | None        | None            | 2.0        |
+| F_ZYZYG      | Zyzygomyces                        | unknown  | Fungi    | None      | 7581        | None            | 2.0        |
+
+```python
+AMR.antibiotics
+```
+
+| ab  | cid         | name                 | group                      | oral_ddd | oral_units | iv_ddd | iv_units |
+|-----|-------------|----------------------|----------------------------|----------|------------|--------|----------|
+| AMA | 4649.0      | 4-aminosalicylic acid| Antimycobacterials         | 12.00    | g          | NaN    | None     |
+| ACM | 6450012.0   | Acetylmidecamycin    | Macrolides/lincosamides    | NaN      | None       | NaN    | None     |
+| ASP | 49787020.0  | Acetylspiramycin     | Macrolides/lincosamides    | NaN      | None       | NaN    | None     |
+| ALS | 8954.0      | Aldesulfone sodium   | Other antibacterials       | 0.33     | g          | NaN    | None     |
+| AMK | 37768.0     | Amikacin             | Aminoglycosides            | NaN      | None       | 1.0    | g        |
+| ... | ...         | ...                  | ...                        | ...      | ...        | ...    | ...      |
+| VIR | 11979535.0  | Virginiamycine       | Other antibacterials       | NaN      | None       | NaN    | None     |
+| VOR | 71616.0     | Voriconazole         | Antifungals/antimycotics   | 0.40     | g          | 0.4    | g        |
+| XBR | 72144.0     | Xibornol             | Other antibacterials       | NaN      | None       | NaN    | None     |
+| ZID | 77846445.0  | Zidebactam           | Other antibacterials       | NaN      | None       | NaN    | None     |
+| ZFD | NaN         | Zoliflodacin         | None                       | NaN      | None       | NaN    | None     |
+
+
 # Conclusion
 
 With the `AMR` Python package, Python users can now effortlessly call R functions from the `AMR` R package. This eliminates the need for complex `rpy2` configurations and provides a clean, easy-to-use interface for antimicrobial resistance analysis. The examples provided above demonstrate how this can be applied to typical workflows, such as standardising microorganism and antimicrobial names or calculating resistance.