AMR 2.1.1.9126__py3-none-any.whl → 2.1.1.9128__py3-none-any.whl

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Files changed (6) hide show
  1. AMR/datasets.py +6 -0
  2. {AMR-2.1.1.9126.dist-info → AMR-2.1.1.9128.dist-info}/METADATA +42 -43
  3. AMR-2.1.1.9128.dist-info/RECORD +7 -0
  4. AMR-2.1.1.9126.dist-info/RECORD +0 -7
  5. {AMR-2.1.1.9126.dist-info → AMR-2.1.1.9128.dist-info}/WHEEL +0 -0
  6. {AMR-2.1.1.9126.dist-info → AMR-2.1.1.9128.dist-info}/top_level.txt +0 -0
AMR/datasets.py CHANGED
@@ -19,6 +19,9 @@ r_lib_path = os.path.join(venv_path, "R_libs")
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  os.makedirs(r_lib_path, exist_ok=True)
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  # Set the R library path in .libPaths
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  base = importr('base')
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+ # Turn off warnings
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+ base.options(warn = -1)
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+
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  base._libPaths(r_lib_path)
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  r_amr_lib_path = base._libPaths()[0]
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@@ -46,6 +49,9 @@ if r_amr_version != python_amr_version:
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  except Exception as e:
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  print(f"{BLUE}AMR:{RESET} Could not update: {e}{RESET}", flush=True)
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+ # Restore warnings to default
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+ base.options(warn = 0)
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+
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  print(f"{BLUE}AMR:{RESET} Setting up R environment and AMR datasets...", flush=True)
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  # Activate the automatic conversion between R and pandas DataFrames
{AMR-2.1.1.9126.dist-info → AMR-2.1.1.9128.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.2
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  Name: AMR
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- Version: 2.1.1.9126
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+ Version: 2.1.1.9128
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  Summary: A Python wrapper for the AMR R package
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  Home-page: https://github.com/msberends/AMR
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  Author: Matthijs Berends
@@ -98,48 +98,6 @@ print(df)
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  * **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".
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-
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- ## Taxonomic Data Sets Now in Python!
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-
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- 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:
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-
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- ```python
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- AMR.microorganisms
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- ```
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-
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- | mo | fullname | status | kingdom | gbif | gbif_parent | gbif_renamed_to | prevalence |
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- |--------------|------------------------------------|----------|----------|-----------|-------------|-----------------|------------|
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- | B_GRAMN | (unknown Gram-negatives) | unknown | Bacteria | None | None | None | 2.0 |
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- | B_GRAMP | (unknown Gram-positives) | unknown | Bacteria | None | None | None | 2.0 |
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- | B_ANAER-NEG | (unknown anaerobic Gram-negatives) | unknown | Bacteria | None | None | None | 2.0 |
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- | B_ANAER-POS | (unknown anaerobic Gram-positives) | unknown | Bacteria | None | None | None | 2.0 |
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- | B_ANAER | (unknown anaerobic bacteria) | unknown | Bacteria | None | None | None | 2.0 |
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- | ... | ... | ... | ... | ... | ... | ... | ... |
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- | B_ZYMMN_POMC | Zymomonas pomaceae | accepted | Bacteria | 10744418 | 3221412 | None | 2.0 |
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- | B_ZYMPH | Zymophilus | synonym | Bacteria | None | 9475166 | None | 2.0 |
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- | B_ZYMPH_PCVR | Zymophilus paucivorans | synonym | Bacteria | None | None | None | 2.0 |
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- | B_ZYMPH_RFFN | Zymophilus raffinosivorans | synonym | Bacteria | None | None | None | 2.0 |
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- | F_ZYZYG | Zyzygomyces | unknown | Fungi | None | 7581 | None | 2.0 |
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-
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- ```python
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- AMR.antibiotics
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- ```
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-
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- | ab | cid | name | group | oral_ddd | oral_units | iv_ddd | iv_units |
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- |-----|-------------|----------------------|----------------------------|----------|------------|--------|----------|
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- | AMA | 4649.0 | 4-aminosalicylic acid| Antimycobacterials | 12.00 | g | NaN | None |
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- | ACM | 6450012.0 | Acetylmidecamycin | Macrolides/lincosamides | NaN | None | NaN | None |
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- | ASP | 49787020.0 | Acetylspiramycin | Macrolides/lincosamides | NaN | None | NaN | None |
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- | ALS | 8954.0 | Aldesulfone sodium | Other antibacterials | 0.33 | g | NaN | None |
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- | AMK | 37768.0 | Amikacin | Aminoglycosides | NaN | None | 1.0 | g |
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- | ... | ... | ... | ... | ... | ... | ... | ... |
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- | VIR | 11979535.0 | Virginiamycine | Other antibacterials | NaN | None | NaN | None |
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- | VOR | 71616.0 | Voriconazole | Antifungals/antimycotics | 0.40 | g | 0.4 | g |
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- | XBR | 72144.0 | Xibornol | Other antibacterials | NaN | None | NaN | None |
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- | ZID | 77846445.0 | Zidebactam | Other antibacterials | NaN | None | NaN | None |
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- | ZFD | NaN | Zoliflodacin | None | NaN | None | NaN | None |
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-
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-
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  ## Calculating AMR
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  ```python
@@ -190,6 +148,47 @@ print(result2b)
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  In this example, we generate an antibiogram by selecting various antibiotics.
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+ ## Taxonomic Data Sets Now in Python!
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+
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+ 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:
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+
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+ ```python
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+ AMR.microorganisms
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+ ```
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+
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+ | mo | fullname | status | kingdom | gbif | gbif_parent | gbif_renamed_to | prevalence |
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+ |--------------|------------------------------------|----------|----------|-----------|-------------|-----------------|------------|
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+ | B_GRAMN | (unknown Gram-negatives) | unknown | Bacteria | None | None | None | 2.0 |
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+ | B_GRAMP | (unknown Gram-positives) | unknown | Bacteria | None | None | None | 2.0 |
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+ | B_ANAER-NEG | (unknown anaerobic Gram-negatives) | unknown | Bacteria | None | None | None | 2.0 |
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+ | B_ANAER-POS | (unknown anaerobic Gram-positives) | unknown | Bacteria | None | None | None | 2.0 |
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+ | B_ANAER | (unknown anaerobic bacteria) | unknown | Bacteria | None | None | None | 2.0 |
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+ | ... | ... | ... | ... | ... | ... | ... | ... |
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+ | B_ZYMMN_POMC | Zymomonas pomaceae | accepted | Bacteria | 10744418 | 3221412 | None | 2.0 |
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+ | B_ZYMPH | Zymophilus | synonym | Bacteria | None | 9475166 | None | 2.0 |
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+ | B_ZYMPH_PCVR | Zymophilus paucivorans | synonym | Bacteria | None | None | None | 2.0 |
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+ | B_ZYMPH_RFFN | Zymophilus raffinosivorans | synonym | Bacteria | None | None | None | 2.0 |
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+ | F_ZYZYG | Zyzygomyces | unknown | Fungi | None | 7581 | None | 2.0 |
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+
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+ ```python
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+ AMR.antibiotics
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+ ```
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+
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+ | ab | cid | name | group | oral_ddd | oral_units | iv_ddd | iv_units |
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+ |-----|-------------|----------------------|----------------------------|----------|------------|--------|----------|
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+ | AMA | 4649.0 | 4-aminosalicylic acid| Antimycobacterials | 12.00 | g | NaN | None |
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+ | ACM | 6450012.0 | Acetylmidecamycin | Macrolides/lincosamides | NaN | None | NaN | None |
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+ | ASP | 49787020.0 | Acetylspiramycin | Macrolides/lincosamides | NaN | None | NaN | None |
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+ | ALS | 8954.0 | Aldesulfone sodium | Other antibacterials | 0.33 | g | NaN | None |
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+ | AMK | 37768.0 | Amikacin | Aminoglycosides | NaN | None | 1.0 | g |
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+ | ... | ... | ... | ... | ... | ... | ... | ... |
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+ | VIR | 11979535.0 | Virginiamycine | Other antibacterials | NaN | None | NaN | None |
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+ | VOR | 71616.0 | Voriconazole | Antifungals/antimycotics | 0.40 | g | 0.4 | g |
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+ | XBR | 72144.0 | Xibornol | Other antibacterials | NaN | None | NaN | None |
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+ | ZID | 77846445.0 | Zidebactam | Other antibacterials | NaN | None | NaN | None |
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+ | ZFD | NaN | Zoliflodacin | None | NaN | None | NaN | None |
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+
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+
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  # Conclusion
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  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.
AMR-2.1.1.9128.dist-info/RECORD ADDED
@@ -0,0 +1,7 @@
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+ AMR/__init__.py,sha256=-3zoWVuhybnYkXePzljDrtcxxaAQscPpCPP75EiqLfQ,7540
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+ AMR/datasets.py,sha256=tNLt7ERRxR-HYWD_gY6NwkMjdTIkg0bqtdi98U7sCyQ,2673
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+ AMR/functions.py,sha256=JSh-0_mfrAj7ajpazlv2KFyEtRAglj7oQV9Iiaux7eo,45557
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+ AMR-2.1.1.9128.dist-info/METADATA,sha256=QnZSp517HzD7Z-fb-IBsRM2Yl0rrcib0ikS4di8j2gE,9624
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+ AMR-2.1.1.9128.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
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+ AMR-2.1.1.9128.dist-info/top_level.txt,sha256=7K6Mq_X_OHdXOzQM5y06VUadXjYkze6yzufL1d7_6xc,4
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+ AMR-2.1.1.9128.dist-info/RECORD,,
AMR-2.1.1.9126.dist-info/RECORD DELETED
@@ -1,7 +0,0 @@
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- AMR/__init__.py,sha256=-3zoWVuhybnYkXePzljDrtcxxaAQscPpCPP75EiqLfQ,7540
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- AMR/datasets.py,sha256=DtzZAmuaFK3H4LZIycEfCDS7BIY5iyNxDzfTj2bGsdU,2574
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- AMR/functions.py,sha256=JSh-0_mfrAj7ajpazlv2KFyEtRAglj7oQV9Iiaux7eo,45557
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- AMR-2.1.1.9126.dist-info/METADATA,sha256=3PIASuWvjNhLvT6r17T7tuTO_10GnMzk_EDNTgIUxUk,9625
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- AMR-2.1.1.9126.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
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- AMR-2.1.1.9126.dist-info/top_level.txt,sha256=7K6Mq_X_OHdXOzQM5y06VUadXjYkze6yzufL1d7_6xc,4
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- AMR-2.1.1.9126.dist-info/RECORD,,