add tests and docs for python plugin

countess/plugins/python.py

@@ -70,6 +70,7 @@ class PythonPlugin(PandasTransformDictToDictPlugin):
     """ + " ".join(
         AVAILABLE_FUNCTIONS
     )
+    link = "https://countess-project.github.io/CountESS/included-plugins/#python-code"
 
     version = VERSION
 

docs/included-plugins/index.md

@@ -201,6 +201,28 @@ when pivoted with index on Variant, pivot on Replicate and expanding Count becom
 | `2` | `3` | `9` |
 | `3` | `0` | `6` |
 
+### Python Code
+
+This lets you embed simple Python expressions into your data processing.
+
+Add one or more Python expressions to the "Python Code".
+Each row is processed separately, with column values appearing as local variables.
+
+Functions available:
+```
+abs acos acosh all any ascii asin asinh atan atan2 atanh
+bin bool cbrt ceil chr comb compile copysign cos cosh
+degrees dist erf erfc escape exp exp2 expm1
+fabs factorial findall finditer float floor fmod
+format frexp frozenset fsum fullmatch gamma gcd
+hash hex hypot inf int isclose isfinite isinf isinf
+isnan isnan isqrt lcm ldexp len lgamma log log10 log1p log2
+match max mean median min modf nan nextafter ord
+perm pow prod purge radians range remainder round
+search sin sinh sorted split sqrt std str sub subn
+sum sumprod tan tanh template trunc type ulp var zip
+```
+
 ## Bioinformatics
 
 ### FASTQ Load

tests/plugins/test_python.py

@@ -0,0 +1,49 @@
+import pandas as pd
+import numpy as np
+import pytest
+
+from countess.core.logger import ConsoleLogger
+from countess.plugins.python import PythonPlugin
+
+logger = ConsoleLogger()
+
+
+dfi = pd.DataFrame([[1,1,2,7,11],[2,2,3,8,1],[3,3,4,9,3],[4,4,5,10,4],[5,5,6,12,7]], columns=['a','b','c','d','e'])
+
+def test_python_builtins():
+    plugin = PythonPlugin()
+    plugin.set_parameter("code", """
+x = mean(a,b,c,d,e)
+y = std(a,b,c,d,e)
+z = sqrt(pow(a,2) + pow(b,2))
+v = var(a,b,c,d,e)
+    """)
+
+    plugin.prepare(["test"], None)
+    dfo = plugin.process_dataframe(dfi, logger)
+    output = dfo.to_records()
+
+    assert output[0]["x"] == 4.4
+    assert 2.48 < output[1]["y"] < 2.49
+    assert 4.24 < output[2]["z"] < 4.25
+    assert 5.43 < output[3]["v"] < 5.45
+
+
+def test_python_dropna():
+    plugin = PythonPlugin()
+    plugin.set_parameter("code", """
+a = None
+n = None
+if d >= 10: d = None
+    """)
+    plugin.set_parameter("dropna", True)
+
+    plugin.prepare(["test"], None)
+    dfo = plugin.process_dataframe(dfi, logger)
+
+    assert "a" not in dfo.columns
+    assert "n" not in dfo.columns
+    assert "d" in dfo.columns
+
+    assert any(np.isnan(dfo['d']))
+    assert not any(np.isnan(dfo['b']))