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fix more tests
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tests/test_annotations.py

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@@ -1,12 +1,13 @@
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"""Test for pulling out annotations from models."""
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from cobra.io import load_model
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from cobra.io import read_sbml_model
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from .fixtures import community
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import micom
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from micom.annotation import annotate, annotate_metabolites_from_exchanges
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def test_annotation_cobra_reactions():
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mod = load_model("textbook")
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mod = read_sbml_model(micom.data.test_taxonomy().file[0])
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rids = [r.id for r in mod.reactions]
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anns = annotate(rids, mod, what="reaction")
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assert "reaction" in anns.columns
@@ -15,7 +16,7 @@ def test_annotation_cobra_reactions():
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def test_annotation_cobra_metabolites():
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mod = load_model("textbook")
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mod = read_sbml_model(micom.data.test_taxonomy().file[0])
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mids = [m.id for m in mod.metabolites]
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anns = annotate(mids, mod, what="metabolite")
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assert "metabolite" in anns.columns
@@ -44,7 +45,7 @@ def test_annotation_micom_metabolites(community):
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def test_annotations_cobra_exchanges():
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mod = load_model("textbook")
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mod = read_sbml_model(micom.data.test_taxonomy().file[0])
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anns = annotate_metabolites_from_exchanges(mod)
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assert anns.shape[0] == len(mod.exchanges)
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assert all(

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