implement unit tests

tests/data/media_db.tsv

@@ -1,73 +1,4 @@
 medium	description	compound	name
-RICH	LB plus other carbon sources	adn	Adenosine
-RICH	LB plus other carbon sources	ala__L	L-Alanine
-RICH	LB plus other carbon sources	amp	AMP
-RICH	LB plus other carbon sources	arg__L	L-Arginine
-RICH	LB plus other carbon sources	aso3	Arsenite 
-RICH	LB plus other carbon sources	asp__L	L-Aspartate
-RICH	LB plus other carbon sources	ca2	Ca2+
-RICH	LB plus other carbon sources	cbl1	Vitamin B12
-RICH	LB plus other carbon sources	cd2	Cadmium 
-RICH	LB plus other carbon sources	cl	Cl-
-RICH	LB plus other carbon sources	cmp	CMP
-RICH	LB plus other carbon sources	cobalt2	Co2+
-RICH	LB plus other carbon sources	cro4	Chromate 
-RICH	LB plus other carbon sources	cu2	Cu2+
-RICH	LB plus other carbon sources	cys__L	L-Cysteine
-RICH	LB plus other carbon sources	dad_2	Deoxyadenosine 
-RICH	LB plus other carbon sources	dcyt	Deoxycytidine
-RICH	LB plus other carbon sources	fe2	Fe2+
-RICH	LB plus other carbon sources	fe3	Fe3+
-RICH	LB plus other carbon sources	fol	Folate
-RICH	LB plus other carbon sources	glc__D	D-Glucose
-RICH	LB plus other carbon sources	glu__L	L-Glutamate
-RICH	LB plus other carbon sources	gly	Glycine
-RICH	LB plus other carbon sources	gmp	GMP
-RICH	LB plus other carbon sources	gsn	Guanosine
-RICH	LB plus other carbon sources	h2o	H2O
-RICH	LB plus other carbon sources	h2s	Hydrogen sulfide
-RICH	LB plus other carbon sources	h	H+
-RICH	LB plus other carbon sources	hg2	Hg2+ 
-RICH	LB plus other carbon sources	his__L	L-Histidine
-RICH	LB plus other carbon sources	hxan	Hypoxanthine
-RICH	LB plus other carbon sources	ile__L	L-Isoleucine
-RICH	LB plus other carbon sources	ins	Inosine
-RICH	LB plus other carbon sources	k	K+
-RICH	LB plus other carbon sources	leu__L	L-Leucine
-RICH	LB plus other carbon sources	lipoate	Lipoate
-RICH	LB plus other carbon sources	lys__L	L-Lysine
-RICH	LB plus other carbon sources	met__L	L-Methionine
-RICH	LB plus other carbon sources	mg2	Mg
-RICH	LB plus other carbon sources	mn2	Mn2+
-RICH	LB plus other carbon sources	mobd	Molybdate
-RICH	LB plus other carbon sources	na1	Na+
-RICH	LB plus other carbon sources	nac	Isonicotinic acid
-RICH	LB plus other carbon sources	nh4	Ammonium
-RICH	LB plus other carbon sources	ni2	Ni2+
-RICH	LB plus other carbon sources	o2	O2
-RICH	LB plus other carbon sources	phe__L	L-Phenylalanine
-RICH	LB plus other carbon sources	pheme	Protoheme
-RICH	LB plus other carbon sources	pi	Phosphate
-RICH	LB plus other carbon sources	pnto__R	PAN
-RICH	LB plus other carbon sources	pro__L	L-Proline
-RICH	LB plus other carbon sources	pydx	Pyridoxal
-RICH	LB plus other carbon sources	ribflv	Riboflavin
-RICH	LB plus other carbon sources	ser__L	L-Serine
-RICH	LB plus other carbon sources	so4	Sulfate
-RICH	LB plus other carbon sources	thm	Thiamin
-RICH	LB plus other carbon sources	thr__L	L-Threonine
-RICH	LB plus other carbon sources	thymd	Thymidine
-RICH	LB plus other carbon sources	trp__L	L-Tryptophan
-RICH	LB plus other carbon sources	tyr__L	L-Tyrosine
-RICH	LB plus other carbon sources	ump	UMP
-RICH	LB plus other carbon sources	ura	Uracil
-RICH	LB plus other carbon sources	uri	Uridine
-RICH	LB plus other carbon sources	val__L	L-Valine
-RICH	LB plus other carbon sources	zn2	Zn2+
-RICH	LB plus other carbon sources	ac	acetate
-RICH	LB plus other carbon sources	etoh	ethanol
-RICH	LB plus other carbon sources	lac__D	lactate
-RICH	LB plus other carbon sources	pyr	pyruvate
 LB	Lysogeny broth	adn	Adenosine
 LB	Lysogeny broth	ala__L	L-Alanine
 LB	Lysogeny broth	amp	AMP
@@ -133,70 +64,6 @@ LB	Lysogeny broth	ura	Uracil
 LB	Lysogeny broth	uri	Uridine
 LB	Lysogeny broth	val__L	L-Valine
 LB	Lysogeny broth	zn2	Zn2+
-LB[-O2]	Lysogeny broth (anaerobic)	adn	Adenosine
-LB[-O2]	Lysogeny broth (anaerobic)	ala__L	L-Alanine
-LB[-O2]	Lysogeny broth (anaerobic)	amp	AMP
-LB[-O2]	Lysogeny broth (anaerobic)	arg__L	L-Arginine
-LB[-O2]	Lysogeny broth (anaerobic)	aso3	Arsenite 
-LB[-O2]	Lysogeny broth (anaerobic)	asp__L	L-Aspartate
-LB[-O2]	Lysogeny broth (anaerobic)	ca2	Ca2+
-LB[-O2]	Lysogeny broth (anaerobic)	cbl1	Vitamin B12
-LB[-O2]	Lysogeny broth (anaerobic)	cd2	Cadmium 
-LB[-O2]	Lysogeny broth (anaerobic)	cl	Cl-
-LB[-O2]	Lysogeny broth (anaerobic)	cmp	CMP
-LB[-O2]	Lysogeny broth (anaerobic)	cobalt2	Co2+
-LB[-O2]	Lysogeny broth (anaerobic)	cro4	Chromate 
-LB[-O2]	Lysogeny broth (anaerobic)	cu2	Cu2+
-LB[-O2]	Lysogeny broth (anaerobic)	cys__L	L-Cysteine
-LB[-O2]	Lysogeny broth (anaerobic)	dad_2	Deoxyadenosine 
-LB[-O2]	Lysogeny broth (anaerobic)	dcyt	Deoxycytidine
-LB[-O2]	Lysogeny broth (anaerobic)	fe2	Fe2+
-LB[-O2]	Lysogeny broth (anaerobic)	fe3	Fe3+
-LB[-O2]	Lysogeny broth (anaerobic)	fol	Folate
-LB[-O2]	Lysogeny broth (anaerobic)	glc__D	D-Glucose
-LB[-O2]	Lysogeny broth (anaerobic)	glu__L	L-Glutamate
-LB[-O2]	Lysogeny broth (anaerobic)	gly	Glycine
-LB[-O2]	Lysogeny broth (anaerobic)	gmp	GMP
-LB[-O2]	Lysogeny broth (anaerobic)	gsn	Guanosine
-LB[-O2]	Lysogeny broth (anaerobic)	h2o	H2O
-LB[-O2]	Lysogeny broth (anaerobic)	h2s	Hydrogen sulfide
-LB[-O2]	Lysogeny broth (anaerobic)	h	H+
-LB[-O2]	Lysogeny broth (anaerobic)	hg2	Hg2+ 
-LB[-O2]	Lysogeny broth (anaerobic)	his__L	L-Histidine
-LB[-O2]	Lysogeny broth (anaerobic)	hxan	Hypoxanthine
-LB[-O2]	Lysogeny broth (anaerobic)	ile__L	L-Isoleucine
-LB[-O2]	Lysogeny broth (anaerobic)	ins	Inosine
-LB[-O2]	Lysogeny broth (anaerobic)	k	K+
-LB[-O2]	Lysogeny broth (anaerobic)	leu__L	L-Leucine
-LB[-O2]	Lysogeny broth (anaerobic)	lipoate	Lipoate
-LB[-O2]	Lysogeny broth (anaerobic)	lys__L	L-Lysine
-LB[-O2]	Lysogeny broth (anaerobic)	met__L	L-Methionine
-LB[-O2]	Lysogeny broth (anaerobic)	mg2	Mg
-LB[-O2]	Lysogeny broth (anaerobic)	mn2	Mn2+
-LB[-O2]	Lysogeny broth (anaerobic)	mobd	Molybdate
-LB[-O2]	Lysogeny broth (anaerobic)	na1	Na+
-LB[-O2]	Lysogeny broth (anaerobic)	nac	Isonicotinic acid
-LB[-O2]	Lysogeny broth (anaerobic)	nh4	Ammonium
-LB[-O2]	Lysogeny broth (anaerobic)	ni2	Ni2+
-LB[-O2]	Lysogeny broth (anaerobic)	phe__L	L-Phenylalanine
-LB[-O2]	Lysogeny broth (anaerobic)	pheme	Protoheme
-LB[-O2]	Lysogeny broth (anaerobic)	pi	Phosphate
-LB[-O2]	Lysogeny broth (anaerobic)	pnto__R	PAN
-LB[-O2]	Lysogeny broth (anaerobic)	pro__L	L-Proline
-LB[-O2]	Lysogeny broth (anaerobic)	pydx	Pyridoxal
-LB[-O2]	Lysogeny broth (anaerobic)	ribflv	Riboflavin
-LB[-O2]	Lysogeny broth (anaerobic)	ser__L	L-Serine
-LB[-O2]	Lysogeny broth (anaerobic)	so4	Sulfate
-LB[-O2]	Lysogeny broth (anaerobic)	thm	Thiamin
-LB[-O2]	Lysogeny broth (anaerobic)	thr__L	L-Threonine
-LB[-O2]	Lysogeny broth (anaerobic)	thymd	Thymidine
-LB[-O2]	Lysogeny broth (anaerobic)	trp__L	L-Tryptophan
-LB[-O2]	Lysogeny broth (anaerobic)	tyr__L	L-Tyrosine
-LB[-O2]	Lysogeny broth (anaerobic)	ump	UMP
-LB[-O2]	Lysogeny broth (anaerobic)	ura	Uracil
-LB[-O2]	Lysogeny broth (anaerobic)	uri	Uridine
-LB[-O2]	Lysogeny broth (anaerobic)	val__L	L-Valine
-LB[-O2]	Lysogeny broth (anaerobic)	zn2	Zn2+
 M9	M9 minimal medium	ca2	Ca2+
 M9	M9 minimal medium	cl	Cl-
 M9	M9 minimal medium	cobalt2	Co2+
@@ -217,42 +84,3 @@ M9	M9 minimal medium	o2	O2
 M9	M9 minimal medium	pi	Phosphate
 M9	M9 minimal medium	so4	Sulfate
 M9	M9 minimal medium	zn2	Zn2+
-M9[-O2]	M9 minimal medium (anaerobic)	ca2	Ca2+
-M9[-O2]	M9 minimal medium (anaerobic)	cl	Cl-
-M9[-O2]	M9 minimal medium (anaerobic)	cobalt2	Co2+
-M9[-O2]	M9 minimal medium (anaerobic)	cu2	Cu2+
-M9[-O2]	M9 minimal medium (anaerobic)	fe2	Fe2+
-M9[-O2]	M9 minimal medium (anaerobic)	fe3	Fe3+
-M9[-O2]	M9 minimal medium (anaerobic)	glc__D	D-Glucose
-M9[-O2]	M9 minimal medium (anaerobic)	h2o	H2O
-M9[-O2]	M9 minimal medium (anaerobic)	h	H+
-M9[-O2]	M9 minimal medium (anaerobic)	k	K+
-M9[-O2]	M9 minimal medium (anaerobic)	mg2	Mg
-M9[-O2]	M9 minimal medium (anaerobic)	mn2	Mn2+
-M9[-O2]	M9 minimal medium (anaerobic)	mobd	Molybdate
-M9[-O2]	M9 minimal medium (anaerobic)	na1	Na+
-M9[-O2]	M9 minimal medium (anaerobic)	nh4	Ammonium
-M9[-O2]	M9 minimal medium (anaerobic)	ni2	Ni2+
-M9[-O2]	M9 minimal medium (anaerobic)	pi	Phosphate
-M9[-O2]	M9 minimal medium (anaerobic)	so4	Sulfate
-M9[-O2]	M9 minimal medium (anaerobic)	zn2	Zn2+
-M9[glyc]	M9 minimal medium (glycerol)	ca2	Ca2+
-M9[glyc]	M9 minimal medium (glycerol)	cl	Cl-
-M9[glyc]	M9 minimal medium (glycerol)	cobalt2	Co2+
-M9[glyc]	M9 minimal medium (glycerol)	cu2	Cu2+
-M9[glyc]	M9 minimal medium (glycerol)	fe2	Fe2+
-M9[glyc]	M9 minimal medium (glycerol)	fe3	Fe3+
-M9[glyc]	M9 minimal medium (glycerol)	glyc	Glycerol
-M9[glyc]	M9 minimal medium (glycerol)	h2o	H2O
-M9[glyc]	M9 minimal medium (glycerol)	h	H+
-M9[glyc]	M9 minimal medium (glycerol)	k	K+
-M9[glyc]	M9 minimal medium (glycerol)	mg2	Mg
-M9[glyc]	M9 minimal medium (glycerol)	mn2	Mn2+
-M9[glyc]	M9 minimal medium (glycerol)	mobd	Molybdate
-M9[glyc]	M9 minimal medium (glycerol)	na1	Na+
-M9[glyc]	M9 minimal medium (glycerol)	nh4	Ammonium
-M9[glyc]	M9 minimal medium (glycerol)	ni2	Ni2+
-M9[glyc]	M9 minimal medium (glycerol)	o2	O2
-M9[glyc]	M9 minimal medium (glycerol)	pi	Phosphate
-M9[glyc]	M9 minimal medium (glycerol)	so4	Sulfate
-M9[glyc]	M9 minimal medium (glycerol)	zn2	Zn2+

tests/output/test_detailed.tsv

@@ -0,0 +1,12 @@
+community	medium	receiver	donor	compound	scs	mus	mps	smetana
+all	M9	ec_glc_ko	ec_nh4_ko	M_ac_e	1.0	0.11	1	0.11
+all	M9	ec_glc_ko	ec_nh4_ko	M_acald_e	1.0	0.28	1	0.28
+all	M9	ec_glc_ko	ec_nh4_ko	M_akg_e	1.0	0.25	1	0.25
+all	M9	ec_glc_ko	ec_nh4_ko	M_co2_e	1.0	0.02	1	0.02
+all	M9	ec_glc_ko	ec_nh4_ko	M_etoh_e	1.0	0.31	1	0.31
+all	M9	ec_glc_ko	ec_nh4_ko	M_lac__D_e	1.0	0.37	1	0.37
+all	M9	ec_glc_ko	ec_nh4_ko	M_pyr_e	1.0	0.24	1	0.24
+all	M9	ec_glc_ko	ec_nh4_ko	M_succ_e	1.0	0.09	1	0.09
+all	M9	ec_nh4_ko	ec_glc_ko	M_glu__L_e	1.0	1.0	1	1.0
+all	M9	ec_nh4_ko	ec_glc_ko	M_lac__D_e	1.0	0.08333333333333333	1	0.08333333333333333
+all	M9	ec_nh4_ko	ec_glc_ko	M_pyr_e	1.0	0.08333333333333333	1	0.08333333333333333

tests/output/test_global.tsv

@@ -0,0 +1,3 @@
+community	medium	size	mip	mro
+all	M9	2	n/a	0.0
+all	LB	2	1	0.8

tests/test_smetana.py

@@ -2,33 +2,22 @@
 # -*- coding: utf-8 -*-
 
 import unittest
+from smetana.interface import main
+import pandas as pd
 
 
-class TestMIP(unittest.TestCase):
-    """Test SBML import / export."""
-
-    def setUp(self):
-        pass
-
-    def test_mip(self):
-        raise NotImplementedError("Unit tests are not yet implemented.")
-
-
-class TestMRO(unittest.TestCase):
-    """Test SBML import / export."""
-
-    def setUp(self):
-        pass
-
-    def test_mro(self):
-        raise NotImplementedError("Unit tests are not yet implemented.")
+class TestGlobal(unittest.TestCase):
+    def test_global(self):
+        main(["tests/data/ec_*_ko.xml"], mode="global", output="tests/output/test", media="M9,LB",
+             mediadb="tests/data/media_db.tsv", ext_comp_id="e", exclude="tests/data/inorganic.txt")
+        df = pd.read_csv("tests/output/test_global.tsv")
+        self.assertEqual(df.shape[0], 2)
 
 
 class TestDetailed(unittest.TestCase):
-    """Test SBML import / export."""
 
-    def setUp(self):
-        pass
-
-    def test_global(self):
-        raise NotImplementedError("Unit tests are not yet implemented.")
+    def test_detailed(self):
+        main(["tests/data/ec_*.xml"], mode="detailed", output="tests/output/test", media="M9,LB",
+             mediadb="tests/data/media_db.tsv", ext_comp_id="e", exclude="tests/data/inorganic.txt")
+        df = pd.read_csv("tests/output/test_detailed.tsv")
+        self.assertEqual(df.shape[0], 11)

tox.ini

@@ -0,0 +1,12 @@
+[tox]
+envlist = py36
+
+[travis]
+python =
+    3.6: py36
+
+[testenv]
+setenv =
+    PYTHONPATH = {toxinidir}
+
+commands = python setup.py test