feat: add to_dataframe to dictlist

release-notes/next-release.md

@@ -3,6 +3,7 @@
 ## New features
 
 * View number of genes in model notebook representation.
+* Add progress bar to `flux_variability_analysis`.
 
 ## Fixes
 

setup.cfg

@@ -68,6 +68,7 @@ install_requires =
 	rich >=8.0
 	ruamel.yaml ~=0.16
 	swiglpk
+	tqdm ~=4.0
 tests_require = 
 	tox
 packages = find:

src/cobra/core/dictlist.py

@@ -16,6 +16,7 @@
 )
 
 import numpy as np
+import pandas as pd
 
 from .object import Object
 
@@ -542,3 +543,28 @@ def __dir__(self) -> list:
         attributes.append("_dict")
         attributes.extend(self._dict.keys())
         return attributes
+
+    def to_df(self):
+        """Convert to a pandas dataframe."""
+        item = None
+        columns = []
+
+        if self:
+            item = self[0]
+            columns = [col for col in item._DF_ATTRS if col != "id"]
+
+        data = []
+        ids = []
+
+        for item in self:
+            ids.append(item.id)
+            data.append([getattr(item, attr) for attr in columns])
+
+        df = pd.DataFrame(columns=columns, data=data, index=ids)
+
+        return df
+
+    def _repr_html_(self):
+        """Display as HTML."""
+        df = self.to_df()
+        return df._repr_html_()

src/cobra/core/formula.py

@@ -22,6 +22,8 @@ class Formula(Object):
         A legal formula string contains only letters and numbers.
     """
 
+    _DF_ATTRS = ["formula"]
+
     def __init__(self, formula: Optional[str] = None, **kwargs) -> None:
         """Initialize a formula.
 

src/cobra/core/gene.py

@@ -204,6 +204,8 @@ class Gene(Species):
         used.
     """
 
+    _DF_ATTRS = Species._DF_ATTRS
+
     # noinspection PyShadowingBuiltins
     def __init__(self, id: str = None, name: str = "", functional: bool = True) -> None:
         """Initialize a gene.

src/cobra/core/group.py

@@ -38,6 +38,8 @@ class Group(Object):
         or member is involved in a disease phenotype).
     """
 
+    _DF_ATTRS = ["id", "name", "kind"]
+
     KIND_TYPES = ("collection", "classification", "partonomy")
 
     def __init__(

src/cobra/core/metabolite.py

@@ -44,6 +44,8 @@ class Metabolite(Species):
        Compartment of the metabolite.
     """
 
+    _DF_ATTRS = Species._DF_ATTRS + ["formula", "compartment", "charge"]
+
     # noinspection PyShadowingBuiltins
     def __init__(
         self,

src/cobra/core/object.py

@@ -5,6 +5,7 @@
 
 class Object:
     """Defines common behavior of object in cobra.core."""
+    _DF_ATTRS = ["id", "name", "notes", "annotation"]
 
     def __init__(self, id: Optional[str] = None, name: str = "") -> None:
         """Initialize a simple object with an identifier.

src/cobra/core/reaction.py

@@ -85,6 +85,13 @@ class Reaction(Object):
         Further keyword arguments are passed on to the parent class.
     """
 
+    _DF_ATTRS = Object._DF_ATTRS + [
+        "subsystem",
+        "gene_reaction_rule",
+        "lower_bound",
+        "upper_bound",
+    ]
+
     # noinspection PyShadowingBuiltins
     def __init__(
         self,

src/cobra/core/species.py

@@ -25,6 +25,8 @@ class Species(Object):
        A human readable name.
     """
 
+    _DF_ATTRS = ["id", "name"]
+
     # noinspection PyShadowingBuiltins
     def __init__(
         self, id: Optional[str] = None, name: Optional[str] = None, **kwargs

src/cobra/flux_analysis/variability.py

@@ -17,6 +17,9 @@
 from .loopless import loopless_fva_iter
 from .parsimonious import add_pfba
 
+# from tqdm.auto import tqdm
+from rich.progress import track
+
 
 if TYPE_CHECKING:
     from cobra import Gene, Model, Reaction
@@ -236,18 +239,28 @@ def flux_variability_analysis(
                 # objective direction for all reactions. This creates a
                 # slight overhead but seems the most clean.
                 chunk_size = len(reaction_ids) // processes
+                description = "Performing FVA for %s fluxes" % what
                 with ProcessPool(
                     processes,
                     initializer=_init_worker,
                     initargs=(model, loopless, what[:3]),
                 ) as pool:
-                    for rxn_id, value in pool.imap_unordered(
-                        _fva_step, reaction_ids, chunksize=chunk_size
+                    for rxn_id, value in track(
+                        pool.imap_unordered(
+                            _fva_step, reaction_ids, chunksize=chunk_size
+                        ),
+                        total=num_reactions,
+                        description=description
                     ):
                         fva_result.at[rxn_id, what] = value
             else:
                 _init_worker(model, loopless, what[:3])
-                for rxn_id, value in map(_fva_step, reaction_ids):
+                for rxn_id, value in track(
+                    map(_fva_step, reaction_ids),
+                    total=num_reactions,
+                    description=description
+                ):
+                    fva_result.at[rxn_id, what] = value
                     fva_result.at[rxn_id, what] = value
 
     return fva_result[["minimum", "maximum"]]

tests/test_core/test_dictlist.py

@@ -5,6 +5,7 @@
 from pickle import HIGHEST_PROTOCOL, dumps, loads
 from typing import Tuple
 
+import pandas as pd
 import pytest
 
 from cobra.core import DictList, Object
@@ -468,3 +469,38 @@ def test_union(dict_list: Tuple[Object, DictList]) -> None:
     # Add only 1 element
     assert len(test_list) == 2
     assert test_list.index("test2") == 1
+
+def test_to_df(dict_list: Tuple[Object, DictList]) -> None:
+    """Test to_df for dictlist.
+
+    Parameters
+    ----------
+    dict_list : tuple
+        The fixture for filled dictlist.
+
+    """
+    _, test_list = dict_list
+    test_list.name = "foo"
+    df = test_list.to_df()
+    assert isinstance(df, pd.DataFrame)
+    assert len(df) == 1
+    assert "id" in df.columns
+    assert "test1" in df["id"].values
+    assert "name" in df.columns
+    assert "foo" in df["name"].values
+
+def test__repr_html(dict_list: Tuple[Object, DictList]) -> None:
+    """Test _repr_html_ for dictlist.
+
+    Parameters
+    ----------
+    dict_list : tuple
+        The fixture for filled dictlist.
+
+    """
+    _, test_list = dict_list
+    test_list.name = "foo"
+    html = test_list._repr_html_()
+    assert isinstance(html, str)
+    assert "test1" in html
+    assert "foo" in html