Merge branch 'devel' into fix/group_name

pyproject.toml

@@ -1,24 +1,24 @@
 [build-system]
 requires = [
-  'setuptools>=40.6.0',
-  'wheel'
+  "setuptools>=40.6.0",
+  "wheel"
 ]
 build-backend = "setuptools.build_meta"
 
 [tool.black]
 line-length = 88
-python-version = ['py36']
-include = '\.pyi?$'
-exclude = '''
+target-version = ["py38"]
+include = "\\.pyi?$"
+exclude = """
 
 (
   /(
-      \.eggs         # exclude a few common directories in the
-    | \.git          # root of the project
-    | \.hg
-    | \.mypy_cache
-    | \.tox
-    | \.venv
+      \\.eggs         # exclude a few common directories in the
+    | \\.git          # root of the project
+    | \\.hg
+    | \\.mypy_cache
+    | \\.tox
+    | \\.venv
     | _build
     | buck-out
     | build
@@ -27,4 +27,4 @@ exclude = '''
     | benchmarks
   )/
 )
-'''
+"""

release-notes/next-release.md

@@ -4,7 +4,9 @@
 
 ## Fixes
 
-Fixeed a bug with SBML group parsing that affects the Debian package.
+* Fixes the incorrect bounds in the CycleFree loop removal.
+* Fixes reduced costs and shadow prices not available when using non-convex models.
+* Fixed a bug with SBML group parsing that affects the Debian package.
 
 ## Other
 

src/cobra/core/configuration.py

@@ -1,6 +1,5 @@
 """Provide a global configuration object."""
 
-
 import logging
 import pathlib
 import types

src/cobra/core/solution.py

@@ -174,7 +174,15 @@ def get_solution(
     reduced = np.empty(len(reactions))
     var_primals = model.solver.primal_values
     shadow = np.empty(len(metabolites))
-    if model.solver.is_integer:
+
+    try:
+        var_duals = model.solver.reduced_costs
+        constr_duals = model.solver.shadow_prices
+        duals_available = True
+    except Exception:
+        duals_available = False
+
+    if model.solver.is_integer or not duals_available:
         reduced.fill(np.nan)
         shadow.fill(np.nan)
         for i, rxn in enumerate(reactions):

src/cobra/core/species.py

@@ -1,6 +1,5 @@
 """Define the Species class, used as a base for Gene and Metabolite."""
 
-
 from copy import deepcopy
 from typing import TYPE_CHECKING, FrozenSet, Optional
 

src/cobra/exceptions.py

@@ -1,4 +1,5 @@
 """Module for shared exceptions in the Cobra package."""
+
 import optlang.interface
 
 

src/cobra/flux_analysis/gapfilling.py

@@ -1,6 +1,5 @@
 """Provide the base class and utility function for gap filling."""
 
-
 import logging
 from typing import TYPE_CHECKING, Dict, List, Optional, Union
 

src/cobra/flux_analysis/loopless.py

@@ -1,6 +1,5 @@
 """Provide functions to remove thermodynamically infeasible loops."""
 
-
 from typing import TYPE_CHECKING, Dict, Optional, Union
 
 import numpy as np
@@ -113,10 +112,10 @@ def _add_cycle_free(model: "Model", fluxes: Dict[str, float]) -> None:
             rxn.bounds = (flux, flux)
             continue
         if flux >= 0:
-            rxn.bounds = max(0, rxn.lower_bound), max(flux, rxn.upper_bound)
+            rxn.bounds = max(0, rxn.lower_bound), min(flux, rxn.upper_bound)
             objective_vars.append(rxn.forward_variable)
         else:
-            rxn.bounds = min(flux, rxn.lower_bound), min(0, rxn.upper_bound)
+            rxn.bounds = max(flux, rxn.lower_bound), min(0, rxn.upper_bound)
             objective_vars.append(rxn.reverse_variable)
 
     model.objective.set_linear_coefficients({v: 1.0 for v in objective_vars})

src/cobra/flux_analysis/variability.py

@@ -1,6 +1,5 @@
 """Provide variability based methods such as flux variability or gene essentiality."""
 
-
 import logging
 from typing import TYPE_CHECKING, List, Optional, Set, Tuple, Union
 from warnings import warn

src/cobra/io/__init__.py

@@ -1,6 +1,5 @@
 """Provide functions for loading and saving metabolic models."""
 
-
 from cobra.io.dict import model_from_dict, model_to_dict
 from cobra.io.json import from_json, load_json_model, save_json_model, to_json
 from cobra.io.mat import load_matlab_model, save_matlab_model

src/cobra/io/json.py

@@ -1,4 +1,5 @@
 """Provide functions for I/O in JSON format."""
+
 from pathlib import Path
 from typing import IO, TYPE_CHECKING, Any, Union
 
@@ -72,7 +73,7 @@ def save_json_model(
     filename: Union[str, Path, IO],
     sort: bool = False,
     pretty: bool = False,
-    **kwargs: Any
+    **kwargs: Any,
 ) -> None:
     """Write the cobra model to a file in JSON format.
 

src/cobra/io/mat.py

@@ -213,19 +213,23 @@ def _cell_to_str_list(
     """
     if str_prefix and pattern_split:
         return [
-            [
-                str_prefix + str_found if str_prefix not in str_found else str_found
-                for str_found in pattern_split.findall(str(each_cell[0][0]))
-            ]
-            if np.size(each_cell[0])
-            else empty_value
+            (
+                [
+                    str_prefix + str_found if str_prefix not in str_found else str_found
+                    for str_found in pattern_split.findall(str(each_cell[0][0]))
+                ]
+                if np.size(each_cell[0])
+                else empty_value
+            )
             for each_cell in m_cell
         ]
     elif pattern_split:
         return [
-            pattern_split.findall(str(each_cell[0][0]))
-            if np.size(each_cell[0])
-            else empty_value
+            (
+                pattern_split.findall(str(each_cell[0][0]))
+                if np.size(each_cell[0])
+                else empty_value
+            )
             for each_cell in m_cell
         ]
     else:
@@ -481,9 +485,11 @@ def mat_parse_notes(
             # things like PMC or OMIM, but those are placed as string in notes.
             _notes = _cell_to_str_list(mat_struct[caseunfold[mat_key]][0, 0])
             notes[name] = [
-                _pubmed_re.sub("", x).strip()
-                if x and len(_pubmed_re.sub("", x).strip())
-                else None
+                (
+                    _pubmed_re.sub("", x).strip()
+                    if x and len(_pubmed_re.sub("", x).strip())
+                    else None
+                )
                 for x in _notes
             ]
         elif mat_key == "rxnConfidenceScores".casefold():

src/cobra/io/sbml.py

@@ -614,9 +614,9 @@ def _sbml_to_model(
                 {
                     "familyName": c.getFamilyName() if c.isSetFamilyName() else None,
                     "givenName": c.getGivenName() if c.isSetGivenName() else None,
-                    "organisation": c.getOrganisation()
-                    if c.isSetOrganisation()
-                    else None,
+                    "organisation": (
+                        c.getOrganisation() if c.isSetOrganisation() else None
+                    ),
                     "email": c.getEmail() if c.isSetEmail() else None,
                 }
             )

src/cobra/io/web/__init__.py

@@ -1,6 +1,5 @@
 """Provide functionality to access remote model repositories."""
 
-
 from .abstract_model_repository import AbstractModelRepository
 from .bigg_models_repository import BiGGModels
 from .biomodels_repository import BioModels

src/cobra/io/web/abstract_model_repository.py

@@ -1,6 +1,5 @@
 """Provide an abstract base class that describes a remote model repository."""
 
-
 from abc import ABC, abstractmethod
 from typing import Union
 

src/cobra/io/web/bigg_models_repository.py

@@ -1,6 +1,5 @@
 """Provide a concrete implementation of the BioModels repository interface."""
 
-
 from io import BytesIO
 
 import httpx

src/cobra/io/web/biomodels_repository.py

@@ -1,6 +1,5 @@
 """Provide functions for loading metabolic models over the wire."""
 
-
 import gzip
 from io import BytesIO
 from typing import List

src/cobra/io/web/cobrapy_repository.py

@@ -1,6 +1,5 @@
 """Provide functions for loading metabolic models from local package data."""
 
-
 import importlib_resources
 
 import cobra.data

src/cobra/io/web/load.py

@@ -1,6 +1,5 @@
 """Provide a function ``load_model`` to access remote model repositories."""
 
-
 import gzip
 import logging
 from typing import TYPE_CHECKING, Iterable

src/cobra/manipulation/delete.py

@@ -1,4 +1,5 @@
 """Provide functions for pruning reactions, metabolites and genes."""
+
 import logging
 from ast import And, BoolOp, Name, NodeTransformer
 from functools import partial

src/cobra/sampling/achr.py

@@ -94,7 +94,7 @@ def __init__(
         thinning: int = 100,
         nproj: Optional[int] = None,
         seed: Optional[int] = None,
-        **kwargs
+        **kwargs,
     ) -> None:
         """Initialize a new ACHRSampler."""
         super().__init__(model, thinning, nproj=nproj, seed=seed, **kwargs)

src/cobra/sampling/optgp.py

@@ -1,6 +1,5 @@
 """Provide the OptGP sampler class and helper functions."""
 
-
 from typing import TYPE_CHECKING, Dict, Optional, Tuple
 
 import numpy as np
@@ -110,10 +109,10 @@ def __init__(
         processes: Optional[int] = None,
         nproj: Optional[int] = None,
         seed: Optional[int] = None,
-        **kwargs
+        **kwargs,
     ) -> None:
         """Initialize a new OptGPSampler."""
-        super().__init__(model, thinning, nproj=nproj, seed=seed, *kwargs)
+        super().__init__(model, thinning, nproj=nproj, seed=seed, **kwargs)
         self.generate_fva_warmup()
 
         if processes is None:

src/cobra/summary/metabolite_summary.py

@@ -1,6 +1,5 @@
 """Provide the metabolite summary class."""
 
-
 import logging
 from operator import attrgetter
 from textwrap import shorten

src/cobra/summary/model_summary.py

@@ -1,6 +1,5 @@
 """Provide the model summary class."""
 
-
 import logging
 from operator import attrgetter
 from typing import TYPE_CHECKING, Dict, List, Optional, Union

src/cobra/summary/reaction_summary.py

@@ -1,6 +1,5 @@
 """Provide the reaction summary class."""
 
-
 import logging
 from textwrap import dedent, shorten
 from typing import TYPE_CHECKING, Optional, Union

src/cobra/summary/summary.py

@@ -1,6 +1,5 @@
 """Provide the abstract base summary class."""
 
-
 import logging
 from abc import ABC, abstractmethod
 from typing import TYPE_CHECKING, Optional, Union

src/cobra/util/process_pool.py

@@ -1,6 +1,5 @@
 """Provide a process pool with enhanced performance on Windows."""
 
-
 import multiprocessing
 import os
 import pickle
@@ -30,7 +29,7 @@ def __init__(
         initializer: Optional[Callable] = None,
         initargs: Tuple = (),
         maxtasksperchild: Optional[int] = None,
-        **kwargs
+        **kwargs,
     ) -> None:
         """
         Initialize a process pool.

tests/test_core/test_gene.py

@@ -1,6 +1,5 @@
 """Test functions of gene.py ."""
 
-
 from cobra.core import Model
 
 

tests/test_core/test_group.py

@@ -1,6 +1,5 @@
 """Test functions of group via model.py."""
 
-
 import pytest
 
 from cobra import Model

tests/test_flux_analysis/test_deletion.py

@@ -1,6 +1,5 @@
 """Test functionalities of reaction and gene deletions."""
 
-
 import math
 import os
 from typing import Callable, List

tests/test_medium/test_boundary_types.py

@@ -1,6 +1,5 @@
 """Test functionalities of boundary type detection functions."""
 
-
 import pytest
 
 from cobra.core import Metabolite, Model, Reaction

tests/test_summary/test_metabolite_summary.py

@@ -1,6 +1,5 @@
 """Unit test the MetaboliteSummary class."""
 
-
 import pytest
 
 from cobra.flux_analysis import flux_variability_analysis, pfba

tests/test_summary/test_model_summary.py

@@ -1,6 +1,5 @@
 """Unit test the model summary."""
 
-
 import pytest
 
 from cobra.flux_analysis import flux_variability_analysis, pfba

tests/test_summary/test_reaction_summary.py

@@ -1,6 +1,5 @@
 """Unit test the ReactionSummary class."""
 
-
 import pytest
 
 from cobra.flux_analysis import flux_variability_analysis, pfba

tests/test_util/test_process_pool.py

@@ -1,6 +1,5 @@
 """Test the behaviour of the ProcessPool class."""
 
-
 import os
 from typing import Iterable, Tuple