updated version number

conda-recipe/meta.yaml

@@ -1,4 +1,4 @@
-{% set version = '1.10' %}
+{% set version = '3.11' %}
 
 package:
  name: straindesign

docs/source/conf.py

@@ -21,7 +21,7 @@
 author = "Philipp Schneider"
 
 # The full version, including alpha/beta/rc tags
-release = "1.10"
+release = "3.11"
 
 # -- General configuration ---------------------------------------------------
 

setup.py

@@ -2,7 +2,7 @@
 
 setup(
  name="straindesign",
- version="1.10",
+ version="3.11",
  url="https://github.com/klamt-lab/straindesign.git",
  description="Computational strain design package for the COBRApy framework",
  long_description=
@@ -23,8 +23,8 @@
  classifiers=[
  "Intended Audience :: Science/Research", "Development Status :: 3 - Alpha", "Programming Language :: Python :: 3.7",
  "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10",
- "Programming Language :: Python :: 3.11", "Natural Language :: English", 
- "Operating System :: OS Independent", "Topic :: Scientific/Engineering :: Bio-Informatics"
+ "Programming Language :: Python :: 3.11", "Natural Language :: English", "Operating System :: OS Independent",
+ "Topic :: Scientific/Engineering :: Bio-Informatics"
  ],
  keywords=["metabolism", "constraint-based", "mixed-integer", "strain design"],
  zip_safe=False,

straindesign/networktools.py

@@ -178,7 +178,7 @@ def warning_name_too_long(id, p=""):
  "solver or consider simplifying GPR rules or gene names in your model.")
 
  def truncate(id):
- return id[0:MAX_NAME_LEN-16]+hex(abs(hash(id)))[2:]
+ return id[0:MAX_NAME_LEN - 16] + hex(abs(hash(id)))[2:]
 
  solver = search('(' + '|'.join(avail_solvers) + ')', model.solver.interface.__name__)[0]
 

straindesign/strainDesignProblem.py

@@ -505,7 +505,7 @@ def link_z(self):
  _, max_Ax[i] = worker_compute(i)
 
  # round Ms up to 5 digits
- Ms = [np.ceil(M* 1e5) / 1e5 if not np.isinf(M) else self.M for M in max_Ax]
+ Ms = [np.ceil(M * 1e5) / 1e5 if not np.isinf(M) else self.M for M in max_Ax]
  # fill up M-vector also for notknockable reactions
  Ms = [
  Ms[np.array([i == j

tests/conftest.py

@@ -29,11 +29,13 @@
 except ImportError:
  pass # SCIP is not installed
 
+
 @pytest.fixture(params=solvers, scope="session")
 def curr_solver(request: pytest.FixtureRequest) -> str:
  """Provide session-level fixture for parametrized solver names."""
  return request.param
 
+
 @pytest.fixture(params=[ANY, BEST, POPULATE], scope="session")
 def comp_approach(request: pytest.FixtureRequest) -> str:
  """Provide session-level fixture for computation modes."""

tests/test_01_load_models_and_solvers.py

@@ -40,7 +40,7 @@ def test_solver_loading(curr_solver):
  assert (milp.solve() == ([], 0.0, OPTIMAL))
 
 
-def test_load_solvers(model_small_example,curr_solver):
+def test_load_solvers(model_small_example, curr_solver):
  """Test solver choice."""
 
  # solver selection with no solver specified