Merge pull request #581 from opencobra/fix-pytest

upgrade memote to be pytest 4.x compatible

HISTORY.rst

@@ -3,6 +3,9 @@ History
 
 Next Release
 ------------
+* Unpin pytest (require >= 4.0) and adjust some internal mechanics accordingly.
+* Display an alternative message if some biomass components do not contain a 
+  formula.
 
 0.8.11 (2019-01-07)
 -------------------

memote/suite/collect.py

@@ -71,30 +71,26 @@ def __init__(self, model, experimental_config=None,
         self._xcld = frozenset() if exclusive is None else frozenset(exclusive)
         self._skip = frozenset() if skip is None else frozenset(skip)
 
-    def pytest_namespace(self):
-        """Insert model information into the pytest namespace."""
-        namespace = dict()
-        namespace["memote"] = memote = dict()
-        memote["biomass_ids"] = [
-            rxn.id for rxn in find_biomass_reaction(self._model)]
-        memote["compartment_ids"] = sorted(self._model.compartments)
-        try:
-            memote["compartment_ids"].remove("c")
-        except ValueError:
-            LOGGER.error(
-                "The model does not contain a compartment ID labeled 'c' for "
-                "the cytosol which is an essential compartment. Many syntax "
-                "tests depend on this being labeled accordingly.")
-        # Add experimental information if there are any.
-        if self._exp_config is None:
-            memote["experimental"] = dict()
-            memote["experimental"]["essentiality"] = list()
-            memote["experimental"]["growth"] = list()
-        else:
-            # Load experimental data.
-            self._exp_config.load_data(self._model)
-            memote["experimental"] = self._exp_config
-        return namespace
+    def pytest_generate_tests(self, metafunc):
+        """Parametrize marked functions at runtime."""
+        if metafunc.definition.get_closest_marker("biomass"):
+            metafunc.parametrize("reaction_id", [
+                rxn.id for rxn in find_biomass_reaction(self._model)])
+            return
+        if metafunc.definition.get_closest_marker("essentiality"):
+            if self._exp_config is None:
+                metafunc.parametrize("experiment", [])
+            else:
+                metafunc.parametrize("experiment",
+                                     self._exp_config.get("essentiality", []))
+            return
+        if metafunc.definition.get_closest_marker("growth"):
+            if self._exp_config is None:
+                metafunc.parametrize("experiment", [])
+            else:
+                metafunc.parametrize("experiment",
+                                     self._exp_config.get("growth", []))
+            return
 
     @pytest.hookimpl(tryfirst=True)
     def pytest_runtest_call(self, item):

memote/suite/tests/test_biomass.py

@@ -36,11 +36,10 @@
 
 
 LOGGER = logging.getLogger(__name__)
-BIOMASS_IDS = pytest.memote.biomass_ids
 
 
 @annotate(title="Biomass Reactions Identified", format_type="count")
-def test_biomass_presence():
+def test_biomass_presence(read_only_model):
     """
     Expect the model to contain at least one biomass reaction.
 
@@ -57,16 +56,16 @@ def test_biomass_presence():
     future.
     """
     ann = test_biomass_presence.annotation
-    ann["data"] = BIOMASS_IDS
+    ann["data"] = [
+        rxn.id for rxn in helpers.find_biomass_reaction(read_only_model)]
     ann["message"] = wrapper.fill(
         """In this model {} the following biomass reactions were
         identified: {}""".format(
             len(ann["data"]), truncate(ann["data"])))
     assert len(ann["data"]) > 0, ann["message"]
 
 
-# TODO: Mark this test as skipped if the biomass components lack formulas!
-@pytest.mark.parametrize("reaction_id", BIOMASS_IDS)
+@pytest.mark.biomass
 @annotate(title="Biomass Consistency", format_type="number", data=dict(),
           message=dict(), metric=dict())
 def test_biomass_consistency(read_only_model, reaction_id):
@@ -79,23 +78,32 @@ def test_biomass_consistency(read_only_model, reaction_id):
     defined to be equal to 1 g/mmol. Conforming to this is essential in order
     to be able to reliably calculate growth yields, to cross-compare models,
     and to obtain valid predictions when simulating microbial consortia. A
-    deviation by 1e-03 is accepted.
+    deviation from 1 - 1E-03 to 1 + 1E-06 is accepted.
     """
     ann = test_biomass_consistency.annotation
     reaction = read_only_model.reactions.get_by_id(reaction_id)
-    ann["data"][reaction_id] = biomass.sum_biomass_weight(reaction)
+    try:
+        ann["data"][reaction_id] = biomass.sum_biomass_weight(reaction)
+    except TypeError:
+        ann["data"][reaction_id] = float("nan")
+        ann["message"][reaction_id] = wrapper.fill(
+            """One or more of the biomass components do not have a defined
+            formula or contain unspecified chemical groups."""
+        )
+    else:
+        ann["message"][reaction_id] = wrapper.fill(
+            """The component molar mass of the biomass reaction {} sums up to {}
+            which is outside of the 1e-03 margin from 1 mmol / g[CDW] / h.
+            """.format(reaction_id, ann["data"][reaction_id])
+        )
     ann["metric"][reaction_id] = 1.0  # Placeholder value.
-    ann["message"][reaction_id] = wrapper.fill(
-        """The component molar mass of the biomass reaction {} sums up to {}
-        which is outside of the 1e-03 margin from 1 mmol / g[CDW] / h.
-        """.format(reaction_id, ann["data"][reaction_id]))
-    # To account for numerical innacuracies, a range from 1-1e0-3 to 1+1e-06
-    # is implemented in the assertion check
+    # To account for numerical inaccuracies, a range from 1 - 1e0-3 to 1 + 1e-06
+    # is implemented in the assertion check.
     assert (1 - 1e-03) < ann["data"][reaction_id] < (1 + 1e-06), \
         ann["message"][reaction_id]
 
 
-@pytest.mark.parametrize("reaction_id", BIOMASS_IDS)
+@pytest.mark.biomass
 @annotate(title="Biomass Production In Default Medium", format_type="number",
           data=dict(), message=dict(), metric=dict())
 def test_biomass_default_production(model, reaction_id):
@@ -117,7 +125,7 @@ def test_biomass_default_production(model, reaction_id):
     assert ann["data"][reaction_id] > 0.0, ann["message"][reaction_id]
 
 
-@pytest.mark.parametrize("reaction_id", BIOMASS_IDS)
+@pytest.mark.biomass
 @annotate(title="Biomass Production In Complete Medium", format_type="number",
           data=dict(), message=dict(), metric=dict())
 def test_biomass_open_production(model, reaction_id):
@@ -140,7 +148,7 @@ def test_biomass_open_production(model, reaction_id):
     assert ann["data"][reaction_id] > 0.0, ann["message"][reaction_id]
 
 
-@pytest.mark.parametrize("reaction_id", BIOMASS_IDS)
+@pytest.mark.biomass
 @annotate(title="Blocked Biomass Precursors In Default Medium",
           format_type="count", data=dict(), metric=dict(), message=dict())
 def test_biomass_precursors_default_production(read_only_model, reaction_id):
@@ -173,7 +181,7 @@ def test_biomass_precursors_default_production(read_only_model, reaction_id):
     assert len(ann["data"][reaction_id]) == 0, ann["message"][reaction_id]
 
 
-@pytest.mark.parametrize("reaction_id", BIOMASS_IDS)
+@pytest.mark.biomass
 @annotate(title="Blocked Biomass Precursors In Complete Medium",
           format_type="count", data=dict(), metric=dict(), message=dict())
 def test_biomass_precursors_open_production(model, reaction_id):
@@ -207,7 +215,7 @@ def test_biomass_precursors_open_production(model, reaction_id):
     assert len(ann["data"][reaction_id]) == 0, ann["message"][reaction_id]
 
 
-@pytest.mark.parametrize("reaction_id", BIOMASS_IDS)
+@pytest.mark.biomass
 @annotate(title="Growth-associated Maintenance in Biomass Reaction",
           format_type="raw", data=dict(), message=dict(), metric=dict())
 def test_gam_in_biomass(model, reaction_id):
@@ -229,7 +237,7 @@ def test_gam_in_biomass(model, reaction_id):
     assert ann["data"][reaction_id], ann["message"][reaction_id]
 
 
-@pytest.mark.parametrize("reaction_id", BIOMASS_IDS)
+@pytest.mark.biomass
 @annotate(title="Unrealistic Growth Rate In Default Medium",
           format_type="raw", data=dict(), message=dict(), metric=dict())
 def test_fast_growth_default(model, reaction_id):
@@ -251,7 +259,7 @@ def test_fast_growth_default(model, reaction_id):
     assert ann["data"][reaction_id] <= 10.3972, ann["message"][reaction_id]
 
 
-@pytest.mark.parametrize("reaction_id", BIOMASS_IDS)
+@pytest.mark.biomass
 @annotate(title="Ratio of Direct Metabolites in Biomass Reaction",
           format_type="percent", data=dict(), message=dict(), metric=dict())
 def test_direct_metabolites_in_biomass(model, reaction_id):
@@ -303,7 +311,7 @@ def test_direct_metabolites_in_biomass(model, reaction_id):
     assert ann["metric"][reaction_id] < 0.5, ann["message"][reaction_id]
 
 
-@pytest.mark.parametrize("reaction_id", BIOMASS_IDS)
+@pytest.mark.biomass
 @annotate(title="Number of Missing Essential Biomass Precursors",
           format_type="count", data=dict(), message=dict(), metric=dict())
 def test_essential_precursors_not_in_biomass(model, reaction_id):

memote/suite/tests/test_essentiality.py

@@ -30,12 +30,8 @@
 from memote.utils import annotate, wrapper
 from memote.support.essentiality import confusion_matrix
 
-ESSENTIALITY_DATA = list(pytest.memote.experimental.essentiality)
 
-
-@pytest.mark.skipif(len(ESSENTIALITY_DATA) == 0,
-                    reason="No essentiality data found.")
-@pytest.mark.parametrize("experiment", ESSENTIALITY_DATA)
+@pytest.mark.essentiality
 @annotate(title="Gene Essentiality Prediction", format_type="percent",
           data=dict(), message=dict(), metric=dict())
 def test_gene_essentiality_from_data_qualitative(model, experiment,

memote/suite/tests/test_growth.py

@@ -30,12 +30,8 @@
 from memote.utils import annotate, wrapper
 from memote.support.essentiality import confusion_matrix
 
-GROWTH_DATA = list(pytest.memote.experimental.growth)
 
-
-@pytest.mark.skipif(len(GROWTH_DATA) == 0,
-                    reason="No growth data found.")
-@pytest.mark.parametrize("experiment", GROWTH_DATA)
+@pytest.mark.growth
 @annotate(title="Growth Prediction", format_type="percent",
           data=dict(), message=dict(), metric=dict())
 def test_growth_from_data_qualitative(model, experiment, threshold=0.95):

setup.cfg

@@ -7,7 +7,7 @@ parse = (?P<major>\d+)
 	\.(?P<minor>\d+)
 	\.(?P<patch>\d+)
 	(?P<release>[a]?)(?P<num>\d*)
-serialize = 
+serialize =
 	{major}.{minor}.{patch}{release}{num}
 	{major}.{minor}.{patch}
 
@@ -17,7 +17,7 @@ url = https://github.com/opencobra/memote
 download_url = https://pypi.org/pypi/memote/
 author = Moritz E. Beber
 author_email = morbeb@biosustain.dtu.dk
-classifiers = 
+classifiers =
 	Development Status :: 5 - Production/Stable
 	Intended Audience :: Developers
 	Intended Audience :: Science/Research
@@ -33,7 +33,7 @@ classifiers =
 license = Apache Software License Version 2.0
 description = the genome-scale metabolic model test suite
 long_description = file: README.rst
-keywords = 
+keywords =
 	memote
 	metabolic
 	constrained-based
@@ -45,13 +45,13 @@ keywords =
 
 [options]
 zip_safe = False
-install_requires = 
+install_requires =
 	click <7.0
 	click-configfile
 	click-log
 	six
 	future
-	pytest >=3.1,<4.1
+	pytest >=4.0
 	gitpython
 	pandas >=0.20.1
 	Jinja2
@@ -72,35 +72,30 @@ install_requires =
 	depinfo
 	equilibrator_api;python_version>='3.5'
 python_requires = >=2.7,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*
-tests_require = 
-	pytest>=3.1
-	pytest-raises
-	pytest-cov
-	codecov
-	xlwt
-	XlsxWriter
+tests_require =
+    tox
 packages = find:
 
 [options.package_data]
-memote.experimental.schemata = 
+memote.experimental.schemata =
 	*.json
-memote.suite = 
+memote.suite =
 	tests/*.py
-memote.suite.templates = 
+memote.suite.templates =
 	*.html
 	*.yml
-memote.support.data = 
+memote.support.data =
 	*.csv
 	*.json
 
 [options.entry_points]
-console_scripts = 
+console_scripts =
 	memote = memote.suite.cli.runner:cli
 
 [bumpversion:part:release]
 optional_value = placeholder
 first_value = placeholder
-values = 
+values =
 	placeholder
 	a
 
@@ -128,7 +123,7 @@ universal = 1
 
 [flake8]
 max-line-length = 80
-exclude = 
+exclude =
 	__init__.py
 	docs
 
@@ -137,7 +132,7 @@ match_dir = memote
 
 [tool:pytest]
 testpaths = tests
-filterwarnings = 
+filterwarnings =
 	ignore::DeprecationWarning:libsbml
 
 [isort]

tests/test_for_experimental/test_for_config.py

@@ -42,8 +42,10 @@ def test_configuration_schema():
 
 
 @pytest.mark.parametrize("filename", [
-    pytest.mark.raises("empty.yml", exception=ValidationError),
-    pytest.mark.raises("invalid.yml", exception=ValidationError),
+    pytest.param("empty.yml",
+                 marks=pytest.mark.raises(exception=ValidationError)),
+    pytest.param("invalid.yml",
+                 marks=pytest.mark.raises(exception=ValidationError)),
     "valid.yml",
     "medium_only.yml"
 ])

tests/test_for_suite/test_for_results/test_for_models.py

@@ -101,7 +101,8 @@ def test_insert(self, session):
 
     @pytest.mark.parametrize("name_a, name_b", [
         ("abcdef", "ghijkl"),
-        pytest.mark.raises(("same", "same"), exception=IntegrityError)
+        pytest.param("same", "same",
+                     marks=pytest.mark.raises(exception=IntegrityError))
     ])
     def test_unique_hexsha(self, session, name_a, name_b):
         timestamp = datetime.now()

tests/test_for_support/test_for_biomass.py

@@ -96,6 +96,27 @@ def sum_outside_of_deviation(base):
     return base
 
 
+@register_with(MODEL_REGISTRY)
+def sum_missing_formula(base):
+    """Define a biomass reaction whose components lack a formula."""
+    met_a = cobra.Metabolite("lipid_c", "H744")
+    met_b = cobra.Metabolite("protein_c", "H119")
+    met_c = cobra.Metabolite("rna_c")
+    met_d = cobra.Metabolite("dna_c")
+    met_e = cobra.Metabolite("ash_c", None)
+    # Reactions
+    rxn_1 = cobra.Reaction("BIOMASS_TEST")
+    rxn_1.add_metabolites({
+        met_a: -0.2,
+        met_b: -0.2,
+        met_c: -0.2,
+        met_d: -0.2,
+        met_e: -0.2
+    })
+    base.add_reactions([rxn_1])
+    return base
+
+
 @register_with(MODEL_REGISTRY)
 def precursors_producing(base):
     met_a = cobra.Metabolite("lipid_c", compartment='c')
@@ -474,6 +495,7 @@ def essential_not_in_model(base):
 @pytest.mark.parametrize("model, expected", [
     ("sum_within_deviation", True),
     ("sum_outside_of_deviation", False),
+    ("sum_missing_formula", False),
 ], indirect=["model"])
 def test_biomass_weight_production(model, expected):
     """