refactor: change ordering behaviour of dict-like model outputs

.travis.yml

@@ -69,7 +69,7 @@ matrix:
 before_install:
   - if [[ -n "${MB_PYTHON_VERSION}" ]]; then
       (travis_retry git clone https://github.com/matthew-brett/multibuild.git && cd multibuild && git checkout 37040e31b1044468027bd86991c805006a92bf09);
-      TEST_DEPENDS="swiglpk optlang sympy decorator cython codecov coverage numpy scipy jsonschema six pytest pytest-cov pytest-benchmark tabulate";
+      TEST_DEPENDS="swiglpk optlang sympy decorator cython codecov coverage numpy scipy==0.19.1 jsonschema six pytest pytest-cov pytest-benchmark tabulate";
       BUILD_DEPENDS="swiglpk optlang sympy cython numpy scipy";
       source multibuild/common_utils.sh;
       source multibuild/travis_steps.sh;

appveyor.yml

@@ -66,7 +66,7 @@ install:
           conda install -q pip } else {
           python -m pip install pip setuptools>=24.0 wheel --upgrade }
   - if not defined CONDA %WITH_COMPILER% python -m pip install --upgrade pytest
-  - if defined CONDA conda install -q setuptools pytest numpy scipy
+  - if defined CONDA conda install -q setuptools pytest numpy scipy==0.19.1
   - python -m pip install pytest-cov pytest-benchmark pandas swiglpk optlang python-libsbml decorator Cython jsonschema twine pypandoc
   - "%WITH_COMPILER% python appveyor/build_glpk.py"
 

cobra/io/dict.py

@@ -65,6 +65,8 @@ def _fix_type(value):
         return bool(value)
     if isinstance(value, set):
         return list(value)
+    if isinstance(value, dict):
+        return OrderedDict((key, value[key]) for key in sorted(value))
     # handle legacy Formula type
     if value.__class__.__name__ == "Formula":
         return str(value)
@@ -145,13 +147,16 @@ def reaction_from_dict(reaction, model):
     return new_reaction
 
 
-def model_to_dict(model):
+def model_to_dict(model, sort=False):
     """Convert model to a dict.
 
     Parameters
     ----------
     model : cobra.Model
-        The model to reformulate as a dict
+        The model to reformulate as a dict.
+    sort : bool, optional
+        Whether to sort the metabolites, reactions, and genes or maintain the
+        order defined in the model.
 
     Returns
     -------
@@ -166,17 +171,17 @@ def model_to_dict(model):
     cobra.io.model_from_dict
     """
     obj = OrderedDict()
-    obj["reactions"] = sorted(
-        (reaction_to_dict(reaction) for reaction in model.reactions),
-        key=itemgetter("id"))
-    obj["metabolites"] = sorted(
-        (metabolite_to_dict(metabolite) for metabolite in model.metabolites),
-        key=itemgetter("id"))
-    obj["genes"] = sorted(
-        (gene_to_dict(gene) for gene in model.genes), key=itemgetter("id"))
+    obj["metabolites"] = list(map(metabolite_to_dict, model.metabolites))
+    obj["reactions"] = list(map(reaction_to_dict, model.reactions))
+    obj["genes"] = list(map(gene_to_dict, model.genes))
     obj["id"] = model.id
     _update_optional(model, obj, _OPTIONAL_MODEL_ATTRIBUTES,
                      _ORDERED_OPTIONAL_MODEL_KEYS)
+    if sort:
+        get_id = itemgetter("id")
+        obj["metabolites"].sort(key=get_id)
+        obj["reactions"].sort(key=get_id)
+        obj["genes"].sort(key=get_id)
     return obj
 
 

cobra/io/json.py

@@ -15,7 +15,7 @@
 JSON_SPEC = "1"
 
 
-def to_json(model, **kwargs):
+def to_json(model, sort=False, **kwargs):
     """
     Return the model as a JSON document.
 
@@ -25,6 +25,9 @@ def to_json(model, **kwargs):
     ----------
     model : cobra.Model
         The cobra model to represent.
+    sort : bool, optional
+        Whether to sort the metabolites, reactions, and genes or maintain the
+        order defined in the model.
 
     Returns
     -------
@@ -36,7 +39,7 @@ def to_json(model, **kwargs):
     save_json_model : Write directly to a file.
     json.dumps : Base function.
     """
-    obj = model_to_dict(model)
+    obj = model_to_dict(model, sort=sort)
     obj[u"version"] = JSON_SPEC
     return json.dumps(obj, allow_nan=False, **kwargs)
 
@@ -62,7 +65,7 @@ def from_json(document):
     return model_from_dict(json.loads(document))
 
 
-def save_json_model(model, filename, pretty=False, **kwargs):
+def save_json_model(model, filename, sort=False, pretty=False, **kwargs):
     """
     Write the cobra model to a file in JSON format.
 
@@ -75,6 +78,9 @@ def save_json_model(model, filename, pretty=False, **kwargs):
     filename : str or file-like
         File path or descriptor that the JSON representation should be
         written to.
+    sort : bool, optional
+        Whether to sort the metabolites, reactions, and genes or maintain the
+        order defined in the model.
     pretty : bool, optional
         Whether to format the JSON more compactly (default) or in a more
         verbose but easier to read fashion. Can be partially overwritten by the
@@ -85,7 +91,7 @@ def save_json_model(model, filename, pretty=False, **kwargs):
     to_json : Return a string representation.
     json.dump : Base function.
     """
-    obj = model_to_dict(model)
+    obj = model_to_dict(model, sort=sort)
     obj[u"version"] = JSON_SPEC
 
     if pretty:

cobra/io/yaml.py

@@ -12,7 +12,7 @@
 YAML_SPEC = "1"
 
 
-def to_yaml(model, **kwargs):
+def to_yaml(model, sort=False, **kwargs):
     """
     Return the model as a YAML document.
 
@@ -22,6 +22,9 @@ def to_yaml(model, **kwargs):
     ----------
     model : cobra.Model
         The cobra model to represent.
+    sort : bool, optional
+        Whether to sort the metabolites, reactions, and genes or maintain the
+        order defined in the model.
 
     Returns
     -------
@@ -33,7 +36,7 @@ def to_yaml(model, **kwargs):
     save_yaml_model : Write directly to a file.
     ruamel.yaml.dump : Base function.
     """
-    obj = model_to_dict(model)
+    obj = model_to_dict(model, sort=sort)
     obj["version"] = YAML_SPEC
     return yaml.dump(obj, Dumper=yaml.RoundTripDumper, **kwargs)
 
@@ -59,7 +62,7 @@ def from_yaml(document):
     return model_from_dict(yaml.load(document, yaml.RoundTripLoader))
 
 
-def save_yaml_model(model, filename, **kwargs):
+def save_yaml_model(model, filename, sort=False, **kwargs):
     """
     Write the cobra model to a file in YAML format.
 
@@ -72,13 +75,16 @@ def save_yaml_model(model, filename, **kwargs):
     filename : str or file-like
         File path or descriptor that the YAML representation should be
         written to.
+    sort : bool, optional
+        Whether to sort the metabolites, reactions, and genes or maintain the
+        order defined in the model.
 
     See Also
     --------
     to_yaml : Return a string representation.
     ruamel.yaml.dump : Base function.
     """
-    obj = model_to_dict(model)
+    obj = model_to_dict(model, sort=sort)
     obj["version"] = YAML_SPEC
     if isinstance(filename, string_types):
         with io.open(filename, "w") as file_handle:

cobra/test/test_io.py

@@ -185,10 +185,12 @@ def compare_models(cls, name, model1, model2):
     @classmethod
     def extra_comparisons(cls, name, model1, model2):
         assert model1.compartments == model2.compartments
-        assert model1.metabolites[4].annotation == model2.metabolites[
-            4].annotation
-        assert model1.reactions[4].annotation == model2.reactions[4].annotation
-        assert model1.genes[5].annotation == model2.genes[5].annotation
+        assert dict(model1.metabolites[4].annotation) == dict(
+            model2.metabolites[4].annotation)
+        assert dict(model1.reactions[4].annotation) == dict(
+            model2.reactions[4].annotation)
+        assert dict(model1.genes[5].annotation) == dict(
+            model2.genes[5].annotation)
         for attr in ("id", "name"):
             assert getattr(model1.genes[0], attr) == getattr(model2.genes[0],
                                                              attr)

cobra/test/test_io_order.py

@@ -0,0 +1,92 @@
+# -*- coding: utf-8 -*-
+
+from __future__ import absolute_import
+
+import logging
+from operator import attrgetter
+from os.path import join
+from random import sample
+
+import pytest
+
+import cobra.io as cio
+from cobra import DictList, Model
+
+LOGGER = logging.getLogger(__name__)
+
+
+@pytest.fixture(scope="module")
+def tmp_path(tmpdir_factory):
+    return str(tmpdir_factory.mktemp("model_order"))
+
+
+@pytest.fixture(scope="module")
+def minimized_shuffle(small_model):
+    model = small_model.copy()
+    chosen = sample(list(set(model.reactions) - set(model.exchanges)), 10)
+    new = Model("minimized_shuffle")
+    new.add_reactions(chosen)
+    LOGGER.debug("'%s' has %d metabolites, %d reactions, and %d genes.",
+                 new.id, new.metabolites, new.reactions, new.genes)
+    return new
+
+
+@pytest.fixture(scope="module")
+def minimized_sorted(minimized_shuffle):
+    model = minimized_shuffle.copy()
+    model.id = "minimized_sorted"
+    model.metabolites = DictList(
+        sorted(model.metabolites, key=attrgetter("id")))
+    model.genes = DictList(sorted(model.genes, key=attrgetter("id")))
+    model.reactions = DictList(sorted(model.reactions, key=attrgetter("id")))
+    return model
+
+
+@pytest.fixture(scope="module")
+def minimized_reverse(minimized_shuffle):
+    model = minimized_shuffle.copy()
+    model.id = "minimized_reverse"
+    model.metabolites = DictList(
+        sorted(model.metabolites, key=attrgetter("id"), reverse=True))
+    model.genes = DictList(
+        sorted(model.genes, key=attrgetter("id"), reverse=True))
+    model.reactions = DictList(
+        sorted(model.reactions, key=attrgetter("id"), reverse=True))
+    return model
+
+
+@pytest.fixture(scope="module", params=[
+    "minimized_shuffle", "minimized_reverse", "minimized_sorted"])
+def template(request, minimized_shuffle, minimized_reverse, minimized_sorted):
+    return locals()[request.param]
+
+
+@pytest.fixture(scope="module", params=["metabolites", "reactions", "genes"])
+def attribute(request):
+    return request.param
+
+
+def get_ids(iterable):
+    return [x.id for x in iterable]
+
+
+@pytest.mark.parametrize("read, write, ext", [
+    ("read_sbml_model", "write_sbml_model", ".xml"),
+    pytest.mark.skip(("read_legacy_sbml", "write_legacy_sbml", ".xml"),
+                     reason="Order for legacy SBML I/O is uninteresting."),
+    pytest.mark.skip(("load_matlab_model", "save_matlab_model", ".mat"),
+                     reason="Order for Matlab model I/O is uninteresting."),
+    ("load_json_model", "save_json_model", ".json"),
+    ("load_yaml_model", "save_yaml_model", ".yml"),
+])
+def test_io_order(attribute, read, write, ext, template, tmp_path):
+    read = getattr(cio, read)
+    write = getattr(cio, write)
+    filename = join(tmp_path, "template" + ext)
+    write(template, filename)
+    model = read(filename)
+    model_elements = get_ids(getattr(model, attribute))
+    template_elements = get_ids(getattr(template, attribute))
+    assert len(model_elements) == len(template_elements)
+    assert set(model_elements) == set(template_elements)
+    assert model_elements == template_elements

setup.py

@@ -114,7 +114,7 @@ def build_extension(self, ext):
 extras = {
     'matlab': ["pymatbridge"],
     'sbml': ["python-libsbml", "lxml"],
-    'array': ["scipy>=0.11.0"],
+    'array': ["scipy==0.19.1"],
     'display': ["matplotlib", "palettable"]
 }