metabOmics 0.1.6__py3-none-any.whl → 0.1.11__py3-none-any.whl

metabomics/__init__.py

@@ -1,8 +1,9 @@
-from . import cobra
-from . import analysis
-from . import extension
+from . import src
 from . import models
+from . import cobra
+from . import utils
 from . import omicNetwork
-from . import scripts
-from . import src
-from . import utils
+from . import extensions
+from . import analysis
+from . import preprocessing
+from . import scripts

metabomics/analysis/analysis.py

@@ -1,18 +1,18 @@
-from metabomics.cobra.flux_analysis.variability import flux_variability_analysis
-from metabomics.cobra.flux_analysis.geometric import geometric_fba
-from metabomics.cobra.flux_analysis.parsimonious import pfba
-from metabomics.cobra.flux_analysis.moma import moma
-from metabomics.cobra.util import fix_objective_as_constraint
-from metabomics.utils import load_network_model
+from ..cobra.flux_analysis.variability import flux_variability_analysis
+from ..cobra.flux_analysis.geometric import geometric_fba
+from ..cobra.flux_analysis.parsimonious import pfba
+from ..cobra.flux_analysis.moma import moma
+from ..cobra.util import fix_objective_as_constraint
+from ..utils import load_network_model
 from sympy.core.singleton import S
-from metabomics.analysis.drugAnalysis import DrugReactionAnalysis
+from .drugAnalysis import DrugReactionAnalysis
 import sys
 import numpy as np
 sys.path.append(r'../omicNetwork')
-from metabomics.omicNetwork.graph import Graph
+from ..omicNetwork.graph import Graph
 from datetime import datetime
 import json
-from metabomics.cobra import Reaction
+from ..cobra import Reaction
 import metabomics.extensions
 import pandas as pd
 

metabomics/analysis/analysis_equal_val.py

@@ -1,18 +1,18 @@
-from metabomics.cobra.flux_analysis.variability import flux_variability_analysis
-from metabomics.cobra.flux_analysis.geometric import geometric_fba
-from metabomics.cobra.flux_analysis.parsimonious import pfba
-from metabomics.cobra.flux_analysis.moma import moma
-from metabomics.cobra.util import fix_objective_as_constraint
-from metabomics.utils import load_network_model
+from ..cobra.flux_analysis.variability import flux_variability_analysis
+from ..cobra.flux_analysis.geometric import geometric_fba
+from ..cobra.flux_analysis.parsimonious import pfba
+from ..cobra.flux_analysis.moma import moma
+from ..cobra.util import fix_objective_as_constraint
+from ..utils import load_network_model
 from sympy.core.singleton import S
 from .drugAnalysis import DrugReactionAnalysis
 import sys
 import numpy as np
 sys.path.append(r'../omicNetwork')
-from metabomics.omicNetwork.graph import Graph
+from ..omicNetwork.graph import Graph
 import json
-from metabomics.cobra import Reaction
-import metabomics.extensions
+from ..cobra import Reaction
+from ..extensions import *
 import pandas as pd
 
 

metabomics/analysis/analysis_firstVersion.py

@@ -1,18 +1,18 @@
-from metabomics.cobra.flux_analysis.variability import flux_variability_analysis
-from metabomics.cobra.flux_analysis.geometric import geometric_fba
-from metabomics.cobra.flux_analysis.parsimonious import pfba
-from metabomics.cobra.flux_analysis.moma import moma
-from metabomics.cobra.util import fix_objective_as_constraint
-from metabomics.utils import load_network_model
+from ..cobra.flux_analysis.variability import flux_variability_analysis
+from ..cobra.flux_analysis.geometric import geometric_fba
+from ..cobra.flux_analysis.parsimonious import pfba
+from ..cobra.flux_analysis.moma import moma
+from ..cobra.util import fix_objective_as_constraint
+from ..utils import load_network_model
 from sympy.core.singleton import S
 from .drugAnalysis import DrugReactionAnalysis
 import sys
 import numpy as np
 sys.path.append(r'../omicNetwork')
-from metabomics.omicNetwork.graph import Graph
+from ..omicNetwork.graph import Graph
 from datetime import datetime
 import json
-from cobra import Reaction
+from ..cobra import Reaction
 import metabomics.extensions
 import pandas as pd
 

metabomics/analysis/analysis_max_trigger.py

@@ -1,17 +1,17 @@
-from metabomics.cobra.flux_analysis.variability import flux_variability_analysis
-from metabomics.cobra.flux_analysis.geometric import geometric_fba
-from metabomics.cobra.flux_analysis.parsimonious import pfba
-from metabomics.cobra.flux_analysis.moma import moma
-from metabomics.cobra.util import fix_objective_as_constraint
-from metabomics.utils import load_network_model
+from ..cobra.flux_analysis.variability import flux_variability_analysis
+from ..cobra.flux_analysis.geometric import geometric_fba
+from ..cobra.flux_analysis.parsimonious import pfba
+from ..cobra.flux_analysis.moma import moma
+from ..cobra.util import fix_objective_as_constraint
+from ..utils import load_network_model
 from sympy.core.singleton import S
 from .drugAnalysis import DrugReactionAnalysis
 import sys
 import numpy as np
 sys.path.append(r'../omicNetwork')
-from metabomics.omicNetwork.graph import Graph
+from ..omicNetwork.graph import Graph
 import json
-from metabomics.cobra import Reaction
+from ..cobra import Reaction
 import metabomics.extensions
 import pandas as pd
 

metabomics/analysis/analysis_total_trig.py

@@ -1,17 +1,17 @@
-from metabomics.cobra.flux_analysis.variability import flux_variability_analysis
-from metabomics.cobra.flux_analysis.geometric import geometric_fba
-from metabomics.cobra.flux_analysis.parsimonious import pfba
-from metabomics.cobra.flux_analysis.moma import moma
-from metabomics.cobra.util import fix_objective_as_constraint
-from metabomics.utils import load_network_model
+from ..cobra.flux_analysis.variability import flux_variability_analysis
+from ..cobra.flux_analysis.geometric import geometric_fba
+from ..cobra.flux_analysis.parsimonious import pfba
+from ..cobra.flux_analysis.moma import moma
+from ..cobra.util import fix_objective_as_constraint
+from ..utils import load_network_model
 from sympy.core.singleton import S
 from .drugAnalysis import DrugReactionAnalysis
 import sys
 import numpy as np
 sys.path.append(r'../omicNetwork')
-from metabomics.omicNetwork.graph import Graph
+from ..omicNetwork.graph import Graph
 import json
-from metabomics.cobra import Reaction
+from ..cobra import Reaction
 import metabomics.extensions
 import pandas as pd
 

metabomics/analysis/analysis_update_coeff.py

@@ -1,18 +1,18 @@
-from metabomics.cobra.flux_analysis.variability import flux_variability_analysis
-from metabomics.cobra.flux_analysis.geometric import geometric_fba
-from metabomics.cobra.flux_analysis.parsimonious import pfba
-from metabomics.cobra.flux_analysis.moma import moma
-from metabomics.cobra.util import fix_objective_as_constraint
-from metabomics.utils import load_network_model
+from ..cobra.flux_analysis.variability import flux_variability_analysis
+from ..cobra.flux_analysis.geometric import geometric_fba
+from ..cobra.flux_analysis.parsimonious import pfba
+from ..cobra.flux_analysis.moma import moma
+from ..cobra.util import fix_objective_as_constraint
+from ..utils import load_network_model
 from sympy.core.singleton import S
 from .drugAnalysis import DrugReactionAnalysis
 import sys
 import numpy as np
 sys.path.append(r'../omicNetwork')
-from metabomics.omicNetwork.graph import Graph
+from ..omicNetwork.graph import Graph
 from datetime import datetime
 import json
-from cobra import Reaction
+from ..cobra import Reaction
 import metabomics.extensions
 import pandas as pd
 

metabomics/analysis/analysis_v1.py

@@ -1,18 +1,18 @@
-from metabomics.cobra.flux_analysis.variability import flux_variability_analysis
-from metabomics.cobra.flux_analysis.geometric import geometric_fba
-from metabomics.cobra.flux_analysis.parsimonious import pfba
-from metabomics.cobra.flux_analysis.moma import moma
-from metabomics.cobra.util import fix_objective_as_constraint
-from metabomics.utils import load_network_model
+from ..cobra.flux_analysis.variability import flux_variability_analysis
+from ..cobra.flux_analysis.geometric import geometric_fba
+from ..cobra.flux_analysis.parsimonious import pfba
+from ..cobra.flux_analysis.moma import moma
+from ..cobra.util import fix_objective_as_constraint
+from ..utils import load_network_model
 from sympy.core.singleton import S
 from .drugAnalysis import DrugReactionAnalysis
 import sys
 import numpy as np
 sys.path.append(r'../omicNetwork')
-from metabomics.omicNetwork.graph import Graph
+from ..omicNetwork.graph import Graph
 from datetime import datetime
 import json
-from metabomics.cobra import Reaction
+from ..cobra import Reaction
 import metabomics.extensions
 import pandas as pd
 

metabomics/analysis/analysis_v2.py

@@ -1,18 +1,18 @@
-from metabomics.cobra.flux_analysis.variability import flux_variability_analysis
-from metabomics.cobra.flux_analysis.geometric import geometric_fba
-from metabomics.cobra.flux_analysis.parsimonious import pfba
-from metabomics.cobra.flux_analysis.moma import moma
-from metabomics.cobra.util import fix_objective_as_constraint
-from metabomics.utils import load_network_model
+from ..cobra.flux_analysis.variability import flux_variability_analysis
+from ..cobra.flux_analysis.geometric import geometric_fba
+from ..cobra.flux_analysis.parsimonious import pfba
+from ..cobra.flux_analysis.moma import moma
+from ..cobra.util import fix_objective_as_constraint
+from ..utils import load_network_model
 from sympy.core.singleton import S
 from .drugAnalysis import DrugReactionAnalysis
 import sys
 import numpy as np
 sys.path.append(r'../omicNetwork')
-from metabomics.omicNetwork.graph import Graph
+from ..omicNetwork.graph import Graph
 from datetime import datetime
 import json
-from metabomics.cobra import Reaction
+from ..cobra import Reaction
 import metabomics.extensions
 import pandas as pd
 

metabomics/cobra/core/configuration.py

@@ -11,7 +11,7 @@ from typing import Optional, Tuple, Union
 
 import appdirs
 
-from ..core.singleton import Singleton
+from .singleton import Singleton
 from ..exceptions import SolverNotFound
 from ..util.solver import interface_to_str
 from ..util.solver import solvers as SOLVERS

metabomics/cobra/core/formula.py

@@ -5,7 +5,7 @@ from __future__ import absolute_import
 import re
 from warnings import warn
 
-from ..core.object import Object
+from .object import Object
 
 
 # Numbers are not required because of the |(?=[A-Z])? block. See the

metabomics/cobra/core/gene.py

@@ -8,7 +8,7 @@ from ast import parse as ast_parse
 from keyword import kwlist
 from warnings import warn
 
-from ..core.species import Species
+from .species import Species
 from ..util import resettable
 from ..util.util import format_long_string
 

metabomics/cobra/core/group.py

@@ -6,8 +6,8 @@ from __future__ import absolute_import
 
 from warnings import warn
 
-from ..core.dictlist import DictList
-from ..core.object import Object
+from .dictlist import DictList
+from .object import Object
 
 
 class Group(Object):

metabomics/cobra/core/metabolite.py

@@ -9,8 +9,8 @@ from warnings import warn
 
 from future.utils import raise_from, raise_with_traceback
 
-from ..core.formula import elements_and_molecular_weights
-from ..core.species import Species
+from .formula import elements_and_molecular_weights
+from .species import Species
 from ..exceptions import OptimizationError
 from ..util.solver import check_solver_status
 from ..util.util import format_long_string

metabomics/cobra/core/model.py

@@ -9,14 +9,14 @@ from warnings import warn
 import optlang
 from optlang.symbolics import Basic, Zero
 
-from ..core.configuration import Configuration
-from ..core.dictlist import DictList
-from ..core.gene import Gene
-from ..core.group import Group
-from ..core.metabolite import Metabolite
-from ..core.object import Object
-from ..core.reaction import Reaction
-from ..core.solution import get_solution
+from .configuration import Configuration
+from .dictlist import DictList
+from .gene import Gene
+from .group import Group
+from .metabolite import Metabolite
+from .object import Object
+from .reaction import Reaction
+from .solution import get_solution
 from ..medium import find_boundary_types, find_external_compartment, sbo_terms
 from ..util.context import HistoryManager, get_context, resettable
 from ..util.solver import (

metabomics/cobra/core/reaction.py

@@ -15,10 +15,10 @@ from warnings import warn
 
 from future.utils import raise_from, raise_with_traceback
 
-from ..core.configuration import Configuration
-from ..core.gene import Gene, ast2str, eval_gpr, parse_gpr
-from ..core.metabolite import Metabolite
-from ..core.object import Object
+from .configuration import Configuration
+from .gene import Gene, ast2str, eval_gpr, parse_gpr
+from .metabolite import Metabolite
+from .object import Object
 from ..exceptions import OptimizationError
 from ..util.context import get_context, resettable
 from ..util.solver import (

metabomics/cobra/core/species.py

@@ -4,7 +4,7 @@ from __future__ import absolute_import
 
 from copy import deepcopy
 
-from ..core.object import Object
+from .object import Object
 
 
 class Species(Object):

metabomics/cobra/flux_analysis/fastcc.py

@@ -8,7 +8,7 @@ from .helpers import normalize_cutoff
 
 
 if TYPE_CHECKING:
-    from metabomics.cobra.core import Model, Reaction
+    from ..core import Model, Reaction
 
 
 def _find_sparse_mode(

metabomics/cobra/flux_analysis/gapfilling.py

@@ -12,7 +12,7 @@ from ..util import fix_objective_as_constraint, interface_to_str
 
 
 if TYPE_CHECKING:
-    from metabomics.cobra import Reaction
+    from cobra import Reaction
 
 
 logger = logging.getLogger(__name__)

metabomics/cobra/flux_analysis/geometric.py

@@ -13,7 +13,7 @@ logger = logging.getLogger(__name__)
 
 
 if TYPE_CHECKING:
-    from metabomics.cobra import Model, Solution
+    from cobra import Model, Solution
 
 
 def geometric_fba(

metabomics/cobra/flux_analysis/helpers.py

@@ -4,7 +4,7 @@ from typing import TYPE_CHECKING, Optional
 
 
 if TYPE_CHECKING:
-    from metabomics.cobra import Model
+    from cobra import Model
 
 
 def normalize_cutoff(model: "Model", zero_cutoff: Optional[float] = None) -> float:

metabomics/cobra/flux_analysis/loopless.py

@@ -12,7 +12,7 @@ from .helpers import normalize_cutoff
 
 
 if TYPE_CHECKING:
-    from metabomics.cobra import Model, Reaction, Solution
+    from cobra import Model, Reaction, Solution
 
 
 def add_loopless(model: "Model", zero_cutoff: Optional[float] = None) -> None:

metabomics/cobra/flux_analysis/moma.py

@@ -9,7 +9,7 @@ from .parsimonious import pfba
 
 
 if TYPE_CHECKING:
-    from metabomics.cobra.core import Model, Solution
+    from ..core import Model, Solution
 
 
 def moma(

metabomics/cobra/flux_analysis/parsimonious.py

@@ -13,7 +13,7 @@ from ..util import solver as sutil
 if TYPE_CHECKING:
     from optlang.interface import Objective
 
-    from metabomics.cobra import Model, Reaction, Solution
+    from cobra import Model, Reaction, Solution
 
 
 def optimize_minimal_flux(

metabomics/cobra/flux_analysis/phenotype_phase_plane.py

@@ -16,7 +16,7 @@ from .variability import flux_variability_analysis as fva
 if TYPE_CHECKING:
     from optlang.interface import Objective
 
-    from metabomics.cobra import Model, Reaction
+    from cobra import Model, Reaction
 
 
 def production_envelope(

metabomics/cobra/flux_analysis/reaction.py

@@ -8,7 +8,7 @@ from ..core import Reaction
 
 
 if TYPE_CHECKING:
-    from metabomics.cobra import Model
+    from cobra import Model
 
 
 def assess(

metabomics/cobra/flux_analysis/room.py

@@ -8,7 +8,7 @@ from .parsimonious import pfba
 
 
 if TYPE_CHECKING:
-    from metabomics.cobra import Model, Solution
+    from cobra import Model, Solution
 
 
 def room(

metabomics/cobra/flux_analysis/variability.py

@@ -19,7 +19,7 @@ from .parsimonious import add_pfba
 
 
 if TYPE_CHECKING:
-    from metabomics.cobra import Gene, Model, Reaction
+    from cobra import Gene, Model, Reaction
 
 
 logger = logging.getLogger(__name__)

metabomics/cobra/io/json.py

@@ -2,7 +2,7 @@
 
 from __future__ import absolute_import
 
-from ..io.dict import model_from_dict, model_to_dict
+from .dict import model_from_dict, model_to_dict
 
 
 try:

metabomics/cobra/io/sbml.py

@@ -40,11 +40,11 @@ from sys import platform
 
 import libsbml
 
-import metabomics.cobra 
-from metabomics.cobra.core import Gene, Group, Metabolite, Model, Reaction
-from metabomics.cobra.core.gene import ast2str, parse_gpr
-from metabomics.cobra.manipulation.validate import check_metabolite_compartment_formula
-from metabomics.cobra.util.solver import linear_reaction_coefficients, set_objective
+import cobra 
+from ..core import Gene, Group, Metabolite, Model, Reaction
+from ..core.gene import ast2str, parse_gpr
+from ..manipulation.validate import check_metabolite_compartment_formula
+from ..util.solver import linear_reaction_coefficients, set_objective
 
 
 try:
@@ -64,7 +64,7 @@ LOGGER = logging.getLogger(__name__)
 # -----------------------------------------------------------------------------
 # Defaults and constants for writing SBML
 # -----------------------------------------------------------------------------
-config = metabomics.cobra.Configuration()  # for default bounds
+config = cobra.Configuration()  # for default bounds
 LOWER_BOUND_ID = "cobra_default_lb"
 UPPER_BOUND_ID = "cobra_default_ub"
 ZERO_BOUND_ID = "cobra_0_bound"

metabomics/cobra/io/yaml.py

@@ -7,7 +7,7 @@ import io
 from ruamel.yaml.compat import StringIO
 from ruamel.yaml.main import YAML
 
-from ..io.dict import model_from_dict, model_to_dict
+from .dict import model_from_dict, model_to_dict
 
 
 YAML_SPEC = "1.2"

metabomics/cobra/manipulation/annotate.py

@@ -4,7 +4,7 @@ from typing import TYPE_CHECKING
 
 
 if TYPE_CHECKING:
-    from metabomics.cobra import Model
+    from cobra import Model
 
 
 def add_SBO(model: "Model") -> None:

metabomics/cobra/manipulation/delete.py

@@ -8,7 +8,7 @@ from ..core.gene import ast2str, eval_gpr, parse_gpr
 
 
 if TYPE_CHECKING:
-    from metabomics.cobra import Gene, Metabolite, Model, Reaction
+    from cobra import Gene, Metabolite, Model, Reaction
 
 
 def prune_unused_metabolites(model: "Model") -> Tuple["Model", List["Metabolite"]]:

metabomics/cobra/manipulation/modify.py

@@ -9,7 +9,7 @@ from .delete import get_compiled_gene_reaction_rules
 
 
 if TYPE_CHECKING:
-    from metabomics.cobra import Gene, Model
+    from cobra import Gene, Model
 
 # Set of tuples of operators and their corresponding textual form
 _renames = (

metabomics/cobra/manipulation/validate.py

@@ -4,7 +4,7 @@ from typing import TYPE_CHECKING, Dict, List
 
 
 if TYPE_CHECKING:
-    from metabomics.cobra import Metabolite, Model, Reaction
+    from cobra import Metabolite, Model, Reaction
 
 
 # Set of mass unbalanced SBO terms

metabomics/cobra/medium/boundary_types.py

@@ -20,7 +20,7 @@ from .annotations import compartment_shortlist, excludes, sbo_terms
 
 
 if TYPE_CHECKING:
-    from metabomics.cobra import Model, Reaction
+    from cobra import Model, Reaction
 
 
 logger = logging.getLogger(__name__)

metabomics/cobra/medium/minimal_medium.py

@@ -11,7 +11,7 @@ from .boundary_types import find_boundary_types
 
 
 if TYPE_CHECKING:
-    from metabomics.cobra import Model, Reaction
+    from cobra import Model, Reaction
 
 
 logger = logging.getLogger(__name__)

metabomics/cobra/sampling/achr.py

@@ -10,7 +10,7 @@ from .hr_sampler import HRSampler
 
 
 if TYPE_CHECKING:
-    from metabomics.cobra import Model
+    from cobra import Model
 
 
 class ACHRSampler(HRSampler):

metabomics/cobra/sampling/hr_sampler.py

@@ -12,11 +12,11 @@ import pandas as pd
 from optlang.interface import OPTIMAL
 from optlang.symbolics import Zero
 
-from metabomics.cobra.util import constraint_matrices, create_stoichiometric_matrix, nullspace
+from ..util import constraint_matrices, create_stoichiometric_matrix, nullspace
 
 
 if TYPE_CHECKING:
-    from metabomics.cobra import Model
+    from cobra import Model
 
 
 logger = logging.getLogger(__name__)

metabomics/cobra/sampling/optgp.py

@@ -13,7 +13,7 @@ from .hr_sampler import HRSampler, shared_np_array
 
 
 if TYPE_CHECKING:
-    from metabomics.cobra import Model
+    from cobra import Model
 
 
 __all__ = ("OptGPSampler",)

metabomics/cobra/sampling/sampling.py

@@ -9,7 +9,7 @@ from .optgp import OptGPSampler
 
 
 if TYPE_CHECKING:
-    from metabomics.cobra import Model
+    from cobra import Model
 
 
 def sample(

metabomics/cobra/summary/reaction_summary.py

@@ -12,7 +12,7 @@ from ..summary import Summary
 
 
 if TYPE_CHECKING:
-    from .. import Model, Reaction, Solution
+    from cobra import Model, Reaction, Solution
 
 
 logger = logging.getLogger(__name__)

metabomics/cobra/summary/summary.py

@@ -9,7 +9,7 @@ import pandas as pd
 
 
 if TYPE_CHECKING:
-    from .. import Model, Solution
+    from cobra import Model, Solution
 
 
 logger = logging.getLogger(__name__)

metabomics/main_create_imputer_models.py

@@ -2,7 +2,7 @@ import os
 
 from src.imputer.vae_imputer_model import VAEImputerModel
 from src.dataset_class.metabolite_dataset import MetaboliteDataset
-from metabomics.utils.constants import DATASET_ROOT_PATH, filtered_studies
+from utils.constants import DATASET_ROOT_PATH, filtered_studies
 
 
 def run_vae_imputer_model(fname):

metabomics/omicNetwork/Network_Construction.py

@@ -1,6 +1,6 @@
 import pandas as pd
 import numpy as np
-from metabomics.cobra.io import load_json_model
+from ..cobra.io import load_json_model
 from .graph import Graph
 import time
 import json

metabomics/omicNetwork/main.py

@@ -5,7 +5,7 @@
 import pandas as pd
 import numpy as np
 from numba.cuda import cg
-from metabomics.cobra.io import load_json_model
+from ..cobra.io import load_json_model
 import cobra
 from bioservices import UniProt
 from .graph import Graph

metabomics/omicNetwork/main_local.py

@@ -1,6 +1,6 @@
 import pandas as pd
 import numpy as np
-from metabomics.cobra.io import load_json_model
+from ..cobra.io import load_json_model
 from .graph import Graph
 import time
 import json

metabomics/omicNetwork/main_local_uniprot.py

@@ -1,6 +1,6 @@
 import pandas as pd
 import numpy as np
-from metabomics.cobra.io import load_json_model
+from ..cobra.io import load_json_model
 from .graph import Graph
 import time
 import json

metabomics/preprocessing/metabolite_diff_transformer.py

@@ -1,7 +1,7 @@
 from sklearn.base import TransformerMixin
 
 
-from metabomics.utils import load_network_model
+from ..utils import load_network_model
 
 
 class MetaboliteDiffTransformer(TransformerMixin):

metabomics/preprocessing/metabolitics_pipeline.py

@@ -5,12 +5,12 @@ from sklearn.feature_selection import VarianceThreshold, SelectKBest
 from sklearn.pipeline import Pipeline
 from sklearn_utils.preprocessing import *
 
-from metabomics.preprocessing.metabolitics_transformer import FluxTypes
+from .metabolitics_transformer import FluxTypes
 
-from metabomics.preprocessing.metabolitics_transformer import FluxTypes
+from .metabolitics_transformer import FluxTypes
 
 from . import *
-from metabomics.utils import load_metabolite_mapping
+from ..utils import load_metabolite_mapping
 from .metabolite_diff_transformer import MetaboliteDiffTransformer
 
 

metabomics/preprocessing/metabolitics_transformer.py

@@ -1,7 +1,7 @@
 from joblib import Parallel, delayed
 from sklearn.base import TransformerMixin
 from sklearn_utils.utils import SkUtilsIO, filter_by_label
-from metabomics.analysis import MetaboliticsAnalysis
+from ..analysis import MetaboliticsAnalysis
 from sklearn_utils.preprocessing import FoldChangeScaler
 import pandas as pd
 

metabomics/preprocessing/metabolitics_transformer_second.py

@@ -1,7 +1,7 @@
 from joblib import Parallel, delayed
 from sklearn.base import TransformerMixin
 from sklearn_utils.utils import SkUtilsIO, filter_by_label
-from metabomics.analysis import MetaboliticsAnalysis
+from ..analysis import MetaboliticsAnalysis
 from sklearn_utils.preprocessing import FoldChangeScaler
 import pandas as pd
 

metabomics/preprocessing/pathway_reaction_enrichment.py

@@ -3,7 +3,7 @@ from functional import seq
 from sklearn_utils.preprocessing import FunctionalEnrichmentAnalysis
 
 
-from metabomics.utils import load_network_model
+from ..utils import load_network_model
 
 
 class PathwayReactionEnrichment(FunctionalEnrichmentAnalysis):

metabomics/preprocessing/pathway_transformer.py

@@ -3,7 +3,7 @@ from collections import defaultdict
 from sklearn.base import TransformerMixin
 from sklearn_utils.preprocessing import FeatureMerger
 
-from metabomics.utils import load_network_model
+from ..utils import load_network_model
 
 
 class PathwayTransformer(FeatureMerger):

metabomics/preprocessing/reaction_diff_transformer.py

@@ -1,8 +1,8 @@
 from sklearn.base import TransformerMixin
 from sklearn_utils.utils import average_by_label
 
-from metabomics.utils import load_network_model
-from metabomics.utils.properties import get_file_path
+from ..utils import load_network_model
+from ..utils.properties import get_file_path
 from sklearn_utils.utils import SkUtilsIO
 
 

metabomics/preprocessing/transport_pathway_elimination.py

@@ -1,7 +1,7 @@
 from sklearn.base import TransformerMixin
 
 from sklearn_utils.utils import map_dict_list
-from metabomics.utils.properties import get_file_path
+from ..utils.properties import get_file_path
 from sklearn_utils.utils import SkUtilsIO
 
 

metabomics/tests.py

@@ -1,9 +1,9 @@
 import unittest
 
-from metabolitics.analysis.tests import *
-from metabolitics.extensions.tests import *
-from metabolitics.preprocessing.tests import *
-from metabolitics.utils.tests import *
+from analysis.tests import *
+from extensions.tests import *
+from preprocessing.tests import *
+from utils.tests import *
 
 if __name__ == '__main__':
     unittest.main()

{metabomics-0.1.6.dist-info → metabomics-0.1.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: metabOmics
-Version: 0.1.6
+Version: 0.1.11
 Summary: metabOmics — tools for metabolomics and metabolic network analysis
 Home-page: https://github.com/itu-bioinformatics-database-lab/metabOmics
 Author: itu-bioinformatics-database-lab

{metabomics-0.1.6.dist-info → metabomics-0.1.11.dist-info}/RECORD

@@ -1,5 +1,5 @@
-metabomics/__init__.py,sha256=D_zAGdAVjGAMdhJbaywTtEf30X2XwwBntLRjD9ruxSY,180
-metabomics/main_create_imputer_models.py,sha256=rZlraTuVqb3xxjoWG3do4wYU1kKpCGrQmmyadZGx-w0,1099
+metabomics/__init__.py,sha256=2P_jfRzsk8U-sO0Fef36rCwCD8MDSDUdTRdNeofjtFM,210
+metabomics/main_create_imputer_models.py,sha256=5uF3F2HSfaw8dTb9bUn-wDkRk_O0WMJ7O7209oeWWE8,1088
 metabomics/main_filling.py,sha256=HnDhIIwRmEWMQcTcURsQUD0NZzh6ohDZ-mixoQEDDyk,4734
 metabomics/main_flux_type_performance_test.py,sha256=fBwCENB6pRk2OdsAqOHLKXQ0siUd9UrY87lYc96MDxo,6005
 metabomics/main_metabGene_breast_v0.py,sha256=6xF_z6xhnTFYkjmvQqh2RPWz-h8U0945016gexCNehM,6473
@@ -15,78 +15,78 @@ metabomics/main_workbench_pipeline.py,sha256=yWBNzRdhqLRUQRX0zuLACiisQunp1ct21fy
 metabomics/mean_react_diff_scores.py,sha256=vHr_p2K3nP3r9G1z8Wqdx56N2VDYxrk4eZ0Hl8BM8FY,8144
 metabomics/metabolights_data_pipeline.py,sha256=9JYxpLooWv2nZbEnjv8i2axGLQrH0Dq2tmOXzGwuo_A,42476
 metabomics/metabolights_downloader.py,sha256=Wjd6k6dYHeGpQxAPq05UOGL8jNuRacRuTkCFuXvQ0Ik,2215
-metabomics/tests.py,sha256=9FMhgU42MZcGI_wnCF_rNLGx1PPqGcQmvaeWJOykqMc,246
+metabomics/tests.py,sha256=GfPMC7WPXP-IfkPR2afiR7CfxseksP2J7XLkmkesjW0,194
 metabomics/workbench_data_pipeline.py,sha256=ftmz8MvcHjSClwW5kovN9L8LDH2CROG5199ZgXMc9i0,39141
 metabomics/analysis/__init__.py,sha256=MJ079k7Ozx0yIJwijq0CJ7nSlcbgA4REexxPU0Um8zM,93
-metabomics/analysis/analysis.py,sha256=M9mDyv5RpGxcLXS-sde60gvftt_GHlsIeMAbHU8yc-0,13958
-metabomics/analysis/analysis_equal_val.py,sha256=BiUn7DhcTwv6-C5gWZ-UcjSRW_MWSRsg1WiRkWbM6fs,14847
-metabomics/analysis/analysis_firstVersion.py,sha256=FgF4OnWjI8dsBgZ3bp8ukn2iVTHf6sNlTL6h1CzJ5Tk,15728
-metabomics/analysis/analysis_max_trigger.py,sha256=EX7qRenfnxY6nT4o7sHUcnMcnhfGkXIkQAWj0UhkLdo,15307
-metabomics/analysis/analysis_total_trig.py,sha256=9KxKcvNeRyZQlK854Snp9hywVIN-PYegIbUp_iDXm4M,20037
-metabomics/analysis/analysis_update_coeff.py,sha256=mWn78Y3UyyufanI3kVDHN0zaP4iXtY7LGS2koYqYn40,16871
-metabomics/analysis/analysis_v1.py,sha256=3iPZyV3GAyecWCL_fDFD2O6dQ_xHRQmKc-9lVfoFLho,15159
-metabomics/analysis/analysis_v2.py,sha256=nR0XzHoiXpB79-mOvtrRSZPco5NP1f_4C4HY1xIffC8,15248
+metabomics/analysis/analysis.py,sha256=gyJDdXSjoSjUjfBP03UEPMVlgtYQjzkMcI1hYzDPuMM,13867
+metabomics/analysis/analysis_equal_val.py,sha256=u8nERk-ZndHhmNWdAuU25kmfi1eDU_thdv5mZHhqGA4,14773
+metabomics/analysis/analysis_firstVersion.py,sha256=4QHn4Razf1kBlFCU9peM61tN6PNMbE7SIZx7C2IyBLE,15667
+metabomics/analysis/analysis_max_trigger.py,sha256=PudGyJu-c-qRIgo9kCdWiVnAWkteWhITF0a5EKaXTRM,15235
+metabomics/analysis/analysis_total_trig.py,sha256=DrawCKQrONwOIiO5zU_VJ2FVC1Z0hWJC1fFGMjJYSDk,19965
+metabomics/analysis/analysis_update_coeff.py,sha256=u3Aafjr5BKdIyNmFg1n8aG_Ajh7LafNe43Fn16QUmYU,16810
+metabomics/analysis/analysis_v1.py,sha256=bUZRukvA4DsEN8om_s1nUiUtDfARgrmZIehOck-cxKk,15087
+metabomics/analysis/analysis_v2.py,sha256=KhBNyL1_sHL6aKGv00yagnhIFJxzVOm8UGvpnD3B_XU,15176
 metabomics/analysis/drugAnalysis.py,sha256=ttP7iuKVtJtHPr_I1GYnMhIOEUsy3eoM55A52kjlUBg,1814
 metabomics/analysis/tests.py,sha256=c3ghyd1Z6SHzxCYgvbLpHb2J1oSBpsvJjlVkZk0zCZo,899
 metabomics/cobra/__init__.py,sha256=TKvZJuDuvyzSL1mW8vnQ-L8mkX1E-yUQyBWnmERNknQ,491
 metabomics/cobra/exceptions.py,sha256=FeZsDry_CwgcqFJFBPIeVj_XItTjP1b63Qkb7HVGxdE,1108
 metabomics/cobra/core/__init__.py,sha256=fe-15tp2DfSjDcKm6mPqFdZbeht6OCySM1KUHFCvfJI,398
-metabomics/cobra/core/configuration.py,sha256=Uc6wJVqQjQFZCNbCHcv-llx59uuIRAIIrS0_P32brwQ,8576
+metabomics/cobra/core/configuration.py,sha256=1_JIPKGFzfRXeV1SDxtYJ-hUYepTdEthAQ6wwUK9R8A,8570
 metabomics/cobra/core/dictlist.py,sha256=snA489jJ5jzXj1ozN2bXSEFMzmSHyiHClyHaeu_BS4U,15199
-metabomics/cobra/core/formula.py,sha256=A6gnSHSYZ-O9bpQ_1XGf6lBVLcQnElmQX3IIjJ84C0I,5771
-metabomics/cobra/core/gene.py,sha256=Dz76KHE-BA9puOO2IIVVXMfR5ywyvVGGjEes1W99grA,10065
-metabomics/cobra/core/group.py,sha256=dhQUU0fx7gw7jqOunJAamTN34lT8_8PwIMAlgaReQ1I,3634
-metabomics/cobra/core/metabolite.py,sha256=jkVkDN877gqhAKKkqjWl5G8e9rrxO4rj_vkW35WLC4M,9990
-metabomics/cobra/core/model.py,sha256=0OnNqxFkJV18Bw0RpLK4NCt-IHOKebipmmc-B3l5R8E,51030
+metabomics/cobra/core/formula.py,sha256=korxv87dOLaFqpzrmQglj949fPWQPDxqw4ckxCRNjfs,5765
+metabomics/cobra/core/gene.py,sha256=1A2AhRzQkbVubULZpGSIb63Sa0ggDSVwDxjD27cqBuI,10059
+metabomics/cobra/core/group.py,sha256=1gFmDjfXxMoyY4PKXjeQiZ87LuKnV_olmyqudRdT4y4,3622
+metabomics/cobra/core/metabolite.py,sha256=etCU0kfQ8bBLI_rbbfZTwt0bK_7LFSgs8UKbYmUdPug,9978
+metabomics/cobra/core/model.py,sha256=tOPWG01tmF5Bo-dtYYkhqatvEv1sJA_nQu1UH8gf6GA,50982
 metabomics/cobra/core/object.py,sha256=1GRnLYhUHtXFTt1luxisfgA6LIDMA1hpGrpOSxMVQls,1665
-metabomics/cobra/core/reaction.py,sha256=Dn9YbQtsDx_qJzJHGoLwstTqqMEXDJE6RxEjc3bX-6E,42998
+metabomics/cobra/core/reaction.py,sha256=fxAI2PZQHLLQkYYf64cTopEVc22ruRdCAm-BEXZy8Is,42974
 metabomics/cobra/core/singleton.py,sha256=BqzRgzo_8c8cUuFtmSxC_RD8sh-kptGAD2m-zFhYNwM,480
 metabomics/cobra/core/solution.py,sha256=NOrh3Hq7e2ieiot9tTuXIjlE33VgPjLH3_tYxFi10w8,8693
-metabomics/cobra/core/species.py,sha256=UKhelbEu5VIDBUU5lb_LjkB_DO9d9NfsMLDYEfJhoCQ,1385
+metabomics/cobra/core/species.py,sha256=XqRmauvu6h16LYMklzSmE9eKTTTqmk6ri6bp4jtXQB0,1379
 metabomics/cobra/flux_analysis/__init__.py,sha256=B2ASpNVfwWAdToJ5X3-ZwWTMkyEL7SSLRZB9b1Jpkqo,604
 metabomics/cobra/flux_analysis/deletion.py,sha256=y33rSHcmaOvz-t19pVxeI0OfcFA5kCpyh6bZXnGSJIo,20941
-metabomics/cobra/flux_analysis/fastcc.py,sha256=rry1RVI6trcwpSI88VTzGePNM3fgl05qWudMpW8SSGo,6067
-metabomics/cobra/flux_analysis/gapfilling.py,sha256=xI2rBDY8LrZHqPh3C2HDzfSrevEVAaGXDvhI95GI6nU,16079
-metabomics/cobra/flux_analysis/geometric.py,sha256=OJH3zh_0DBp9qWbCU3dMC6zSj_DEGUOHhPnmmDCQ5fA,4901
-metabomics/cobra/flux_analysis/helpers.py,sha256=AZ9wjvKWTxvmG3rmuDjvuNAhGeE1zLfweyFZVkIcKhM,1065
-metabomics/cobra/flux_analysis/loopless.py,sha256=5cUqJHqGBxNKIekBhWaFSjemFtEA83ToAsNYNsFW8Uk,10452
-metabomics/cobra/flux_analysis/moma.py,sha256=KHrLRP48VQszmfcc5Rmk__1irfzYRcWEITLQ5qGUM0M,6103
-metabomics/cobra/flux_analysis/parsimonious.py,sha256=p5iPkFHqYGOI8km6EX_rjDGEmTQfVRUHgkdSD6Cz9Gk,5228
-metabomics/cobra/flux_analysis/phenotype_phase_plane.py,sha256=IJ8y3qJsqNc1on-3ka9X7c-UYblUeO5gKiMYkTNp9cM,13517
-metabomics/cobra/flux_analysis/reaction.py,sha256=ZPJ2E3G43DdTqi5LPEI0SNux2Td3730WqSDOghvN4DI,10225
-metabomics/cobra/flux_analysis/room.py,sha256=xrKtOowzN7d4-io7qOFJt5zPJOysukhlpp2dLV59OkI,5529
-metabomics/cobra/flux_analysis/variability.py,sha256=KViotXzAmESpmlBGQSjIm-WJtfg7mbik00kwXq8Gfng,15511
+metabomics/cobra/flux_analysis/fastcc.py,sha256=surB0zijZqHzywbnwjEU1nSPuMdtNX_U06bZfMgUBk8,6052
+metabomics/cobra/flux_analysis/gapfilling.py,sha256=27hwgnQ_zbLBGoKkN-Ozs6kADyP6pi-z4AT2PBTLjfA,16068
+metabomics/cobra/flux_analysis/geometric.py,sha256=NdgYQIhOUtY4lG7i6zZCkb0XqSwcFPpwU6ujXbTBk3c,4890
+metabomics/cobra/flux_analysis/helpers.py,sha256=1oFKh-39saZMLXJRrJzR3sIB6-4tOlsDy2PM0JQrF3k,1054
+metabomics/cobra/flux_analysis/loopless.py,sha256=OXX6xcOW4-skBWVdHZ5OB-cncl9j37Bj1GnAbmvIjMo,10441
+metabomics/cobra/flux_analysis/moma.py,sha256=FGc6979BYZ0DCgnbrgr6i0kJzojncV97e39TJip4MxY,6088
+metabomics/cobra/flux_analysis/parsimonious.py,sha256=HMFdzwAQ-jDzyPgt4M1n8NGibY0LtPXl-KtypbOdIWE,5217
+metabomics/cobra/flux_analysis/phenotype_phase_plane.py,sha256=2CbDo6hRQB9IegODsOWQ8djP-Q93tgN4r8Y1SjRGI1s,13506
+metabomics/cobra/flux_analysis/reaction.py,sha256=UpdWKjMWGorKjJPcW0BngVcj3EqrHnpyKzAXDJM-WIs,10214
+metabomics/cobra/flux_analysis/room.py,sha256=O-4vHfB0bJ5u5arhwy5Tb4JyIiCE2Rqh7rVCvAyWk_Y,5518
+metabomics/cobra/flux_analysis/variability.py,sha256=sRWReZ3ASr7sggbivfEH_tz-OJujrFvsHjgM2bH_VRo,15500
 metabomics/cobra/io/__init__.py,sha256=GMfmp6gRsZ4FSPNpaiW4o5loa-tIbtfUJp3U73UQUoQ,494
 metabomics/cobra/io/dict.py,sha256=7e1Occ79HsXeBgEhOwTeUj7BPZn0zojdV1yTCRtpigo,8074
-metabomics/cobra/io/json.py,sha256=nsQlmKCzQZQ2XQkx-L5nDjkEn-uaX2QNUS_AyxuFfDE,3622
+metabomics/cobra/io/json.py,sha256=UqfOMblGQ2twQHvBCuejetEsu3nfqmWCjH2ZrFH6SyY,3618
 metabomics/cobra/io/mat.py,sha256=Opv0iZ0kwu_j0MzUePkk1Z7WN-KdDVglXKYzUk7gn_o,11422
-metabomics/cobra/io/sbml.py,sha256=GymBLgvAH8KISgjb37tAHkvKF80RbkJcrojZObg3MzM,67244
-metabomics/cobra/io/yaml.py,sha256=FxYRDuYLRk6VKYdRmAItzOO_3HdOvKakBI6PPgBfGnQ,3388
+metabomics/cobra/io/sbml.py,sha256=kO2QqevhwOsCHS_ZQrhxdVVpT5IyL_wCYajLIlFY1TQ,67162
+metabomics/cobra/io/yaml.py,sha256=52pNua11oh1Bj1uyzfO4i2vHjsQQ-PosIHcD5aQ-hdo,3384
 metabomics/cobra/io/web/__init__.py,sha256=FE7bZPCw8IC9AXZ6o3s8aNbmnd-5JgxBYirZQk4lXKo,257
 metabomics/cobra/io/web/abstract_model_repository.py,sha256=QlWObIHewiAfMSZMJcLsCATjvZqe6lIwOndfyHx1wNA,2047
 metabomics/cobra/io/web/bigg_models_repository.py,sha256=wMIp5VybF60OLDPcKtRPf_OEFE8KF-GcFKW_QJLLkzo,2071
 metabomics/cobra/io/web/biomodels_repository.py,sha256=xNkSi4X6pFX8KQ8Cj-ggVNl4tXeFi8gcQdTaJyUPqQU,2867
 metabomics/cobra/io/web/load.py,sha256=lBqAiVfqJ03oJPsfWUN8Qf1Ymoh0tIHgm6NVVW37Waw,5570
 metabomics/cobra/manipulation/__init__.py,sha256=vkiLlzYdnkESGjxfo9hKWtlrmmDhsLs4bYA5nPdmVAE,419
-metabomics/cobra/manipulation/annotate.py,sha256=6focvZLu--EtjWOUZ6_qY0JS_0vMyLMLSDQEmiqhNds,1162
-metabomics/cobra/manipulation/delete.py,sha256=RNbJA74zOzei4Uo8H7PyRqw_Xbc6yoxV64w5g2x41n8,11471
-metabomics/cobra/manipulation/modify.py,sha256=Yfrb8wz3VTEkuTazUt4njEtYJKjltbIB5FVfGzxgCD0,5538
-metabomics/cobra/manipulation/validate.py,sha256=hubqAGqE7h7GzoQdQOEgnreQk3p6D8QA2kGx86c1vDY,1789
+metabomics/cobra/manipulation/annotate.py,sha256=66c90gHiAvKoq7QxObsH_1N2gCesoVanM9LeMY05vmw,1151
+metabomics/cobra/manipulation/delete.py,sha256=DUqwrqPmIoxgexqnmJvfvIVJPmGYgVn_onenSOJp7ug,11460
+metabomics/cobra/manipulation/modify.py,sha256=oiEravnEdujOrwFWtdCXUD8L7OU9lxlC8Z8X53O9TIU,5527
+metabomics/cobra/manipulation/validate.py,sha256=Y3DnBfu2ARGwg6JEyQMT30HAIPvxBl-4cE_okE8pDQY,1778
 metabomics/cobra/medium/__init__.py,sha256=A3uxPU5oTIlS8uAqPqrMpxDXv1955TRmBCTf3KZgK1s,175
 metabomics/cobra/medium/annotations.py,sha256=VqZu7BBeKvwCJeuxEFMBUXJO0n-r8zQ0axhwyowpBRg,2300
-metabomics/cobra/medium/boundary_types.py,sha256=kX8DvpbFVRvwXZNGOxPG1gFDDPfzZ7kz-cSxSzNscfM,6361
-metabomics/cobra/medium/minimal_medium.py,sha256=BvyCWMmZidMxoO7X5QCCpEGdl5AeYrwDAbDYsLZ2iNA,9979
+metabomics/cobra/medium/boundary_types.py,sha256=jrwm_PxH0REMg0vHiT9jhYa2cpj0bKcPWL_qYLKBE8I,6350
+metabomics/cobra/medium/minimal_medium.py,sha256=dKhZWQl0fF6DAqAEUk3fuqaec7ZP7PF8X2lB8RX2C5M,9968
 metabomics/cobra/sampling/__init__.py,sha256=uwRVl1ivVQCfAj4f2HEpgPeu6DOspq9f48yGjPNjuog,170
-metabomics/cobra/sampling/achr.py,sha256=ZbxD-j-ruf_lp-lslqrE_R8rO6spSKYJ9GvbQocmON0,6141
+metabomics/cobra/sampling/achr.py,sha256=KGISHgfoe-povVzhd6m0EEnQ3Fj6mt49BXBTKKsnkQY,6130
 metabomics/cobra/sampling/core.py,sha256=lldwsMIvQTwyCGk20Xwz0HnPSCKfujucuwGMdUEKlms,3749
-metabomics/cobra/sampling/hr_sampler.py,sha256=blMPsMVnb9iWwPuB-aU4OY0lX0fgA5jvJO2zikdXRgI,21107
-metabomics/cobra/sampling/optgp.py,sha256=5Q0L371KpOv59Ooigm8Pmox66TBRGuzFuyQbtZYxA-g,9147
-metabomics/cobra/sampling/sampling.py,sha256=hnnJiJNT4fjsy9FA2c6KO_RtS9xKelXm3BIZq-0aXKg,3457
+metabomics/cobra/sampling/hr_sampler.py,sha256=PeskEEQNWZK2muu5Rsyj-yjvvjQiVbLEoBHFGBocFvU,21081
+metabomics/cobra/sampling/optgp.py,sha256=XrifkeNwEArb4aYKVYlMe9ukFpz36bbk0qk0lyS3m2o,9136
+metabomics/cobra/sampling/sampling.py,sha256=aMfRk-7Uhcx8Y9CMki50wKf2JGTAgtYmZJSa861Uoc8,3446
 metabomics/cobra/summary/__init__.py,sha256=B7OlMjMZ5_fZaseTB_9dEQisdD-M-4qKNKvE-5buiK4,169
 metabomics/cobra/summary/metabolite_summary.py,sha256=Lvgukd0pFWHvc0M3nERNv3aPnTnGyca3XApKi50mGCw,14467
 metabomics/cobra/summary/model_summary.py,sha256=Mx_rv01EZ9ZR7sXKFHM1m0hFJ7wEHOo_J5A4o6w5hR4,16478
-metabomics/cobra/summary/reaction_summary.py,sha256=-nvyH4SpDOtiHeiDCHxtUILauiokZvYmwHlhH4AiBrw,8134
-metabomics/cobra/summary/summary.py,sha256=iw7NR_4tM5EUAI3m7GeLyPb1Kdq7oTez2FpJLZO4-G0,4933
+metabomics/cobra/summary/reaction_summary.py,sha256=tm3YJpu0fWBdZLzDAvXVjITjS77rtLCMYuecXf6taxQ,8137
+metabomics/cobra/summary/summary.py,sha256=1e6KYeaAzNQMB-fhAre3kDgoRp6SssFLZTEDHv23JKk,4936
 metabomics/cobra/test/__init__.py,sha256=V_XtrXUJqMlBsw2RRfH6XY8M2aWCbC1l0BNIJ58FAJ0,1773
 metabomics/cobra/test/conftest.py,sha256=oJWhYwXC9tHJlNYQ86YqPjqm7zgnSGOWK9B_w02on1k,3096
 metabomics/cobra/test/data/update_pickles.py,sha256=UL6D4mzARzerxkqRCikxgAAD54LGMNn_NZZ9iRLFUWw,4418
@@ -155,27 +155,27 @@ metabomics/extensions/tests.py,sha256=iaefiYznsaoycJu3xG-FJpPOMiA2t7h2hEXKm5qxMh
 metabomics/models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 metabomics/models/gomari_vae_keras.py,sha256=mwVOuCZ3WP6WsU2Q_TXYHIlVFeztHhsI13uOsBULyig,6538
 metabomics/models/gomari_vae_pytorch.py,sha256=EtErIvpsHVQx3cwGymiQpw1b6T-oZf9tmQUaOokQgOU,5098
-metabomics/omicNetwork/Network_Construction.py,sha256=YoMrtvV_3hQEm47mY89OUNoVn2V3mkYsgXn1pCLHxSw,12085
+metabomics/omicNetwork/Network_Construction.py,sha256=lQTjLqRiMrjUlhzz8mVSk5RDwIrE4sYYi7GP5YYZudQ,12076
 metabomics/omicNetwork/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 metabomics/omicNetwork/edge.py,sha256=k2epDeHuUjhc2IQ5Ro17RS82R58gJYn9mJ5xhq3bBxk,1512
 metabomics/omicNetwork/graph.py,sha256=lI4rVEmzZUHE2U6lo_zy54yNuMu-BCXEMRiAyeJ3YR0,5106
 metabomics/omicNetwork/graph_visualizer.py,sha256=uGw68iiZ74eSjogOPih2GF9cOWFvnRqR66uRLxAbZYs,1770
 metabomics/omicNetwork/helper.py,sha256=hkAG4gcDhCW3gHAmu9CeHjlNhu6zsl-6HzGqU7v-aNQ,439
-metabomics/omicNetwork/main.py,sha256=Qrk7CI9n2EaDpCgwQGo6q40uKo0o_6-aujFFz4uY0_I,8184
-metabomics/omicNetwork/main_local.py,sha256=AjnBkT8gT4A7POBMpRcoOtreg_Gecs3T4acToiP7IdE,8167
-metabomics/omicNetwork/main_local_uniprot.py,sha256=M8HSnGjyYCcyCNQch-0ohoT_l_Obhvtpnh4i0rSmm4o,16315
+metabomics/omicNetwork/main.py,sha256=O25LvAgV4AwCok5ELJ9MaFrahMxWnouIHMskJPskb58,8175
+metabomics/omicNetwork/main_local.py,sha256=1M1f5wiaFx_gS4H_ossjc2fcJ8o8Fru58EHruKf1rCk,8158
+metabomics/omicNetwork/main_local_uniprot.py,sha256=mx_xtML8Nj6dt6PxcgqFxs01ikcIwiXmodt3Pl-YR_I,16306
 metabomics/omicNetwork/prepareData.py,sha256=74ukdLKMOMbQOiKRT84B_np6_mo6e-jFYDWbV0WkV2g,6463
 metabomics/omicNetwork/vertex.py,sha256=UDLf9J-vFVIhITHnDcIsQnYr2aQmfpbrpNjGNCH8Hds,2214
 metabomics/preprocessing/__init__.py,sha256=mbZEvznJLMFMl-iv9xYUNmj1F7oFsENG0624vqKuoIA,670
-metabomics/preprocessing/metabolite_diff_transformer.py,sha256=vwQmk10n78_2qk8hULm4lVWZqNsEwUG9F07LugeYaac,804
-metabomics/preprocessing/metabolitics_pipeline.py,sha256=GJPHir9PsoFnkq956yQmPNCRIHY1CBm3Ry6qPtnnbvM,2383
-metabomics/preprocessing/metabolitics_transformer.py,sha256=bwjbyCTYPwxRm-OoYDUIqqZe7tgh8M1HCQ_6nFEeSZw,4255
-metabomics/preprocessing/metabolitics_transformer_second.py,sha256=8TWL-rlLeM-N0v6JCS4KeO_I71X-84Hs8MkPieCPprw,4285
-metabomics/preprocessing/pathway_reaction_enrichment.py,sha256=Bb2CXmjXmWyIPZAbKVxaVO-GhyhwjPnsfu8Ovog9jPQ,1022
-metabomics/preprocessing/pathway_transformer.py,sha256=w0BhEZF4lvKaJbdfdlQ2rkw1n_Kx1K2RP2dt5uKITn0,585
-metabomics/preprocessing/reaction_diff_transformer.py,sha256=-FJgHXuFDqpE6aXtdTF27DXgInm2oyoFt9_CwKRqtQs,3389
+metabomics/preprocessing/metabolite_diff_transformer.py,sha256=5CN9EWB_eBT-XOwlASJYd5kGQtu1W-0nhQxM5TSCj04,795
+metabomics/preprocessing/metabolitics_pipeline.py,sha256=W7xzNeiyVv3UGMgihe1n-um3XKU4NBY2g1aaezFRuWU,2326
+metabomics/preprocessing/metabolitics_transformer.py,sha256=WgeRjpugzoz16aPShPzGmu3Vx-fyumAWj8-WXFnxMKA,4246
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+metabomics/preprocessing/pathway_reaction_enrichment.py,sha256=gJgmjg3sl5119w-KD3UqmuzbbPh3onwAES9U1GOnSyU,1013
+metabomics/preprocessing/pathway_transformer.py,sha256=hyENOwwmPTKRTPSqcrAQrrwz7MtLjzWKDYvtpcYGN2s,576
+metabomics/preprocessing/reaction_diff_transformer.py,sha256=HMrEnq_jWh7y10ngVk8tnA0NDca1ddmnUQP6ZR31g_U,3371
 metabomics/preprocessing/tests.py,sha256=b-PMtEK7423oJen8KA-GW2HjVTrSzvICskeud4wjpXo,3660
-metabomics/preprocessing/transport_pathway_elimination.py,sha256=CvahzjoHTpZ2ZBSqCt0Jei85dn2V-9sRCohsS0tWlyc,577
+metabomics/preprocessing/transport_pathway_elimination.py,sha256=PRhNsrrClgU2PLGJ8_VGE3jrpqgshFsF-H36Lzyu35w,568
 metabomics/scripts/python_scripts/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 metabomics/scripts/python_scripts/metabolite_mapper.py,sha256=-BcxQTRl_koCEtLJQ302XMSiO6_QaFwAt_-FddrLPXo,1298
 metabomics/src/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -2346,8 +2346,8 @@ test_env/Lib/site-packages/sympy/vector/tests/test_operators.py,sha256=KexUWvc_N
 test_env/Lib/site-packages/sympy/vector/tests/test_parametricregion.py,sha256=OfKapF9A_g9X6JxgYc0UfxIhwXzRERzaj-EijQCJONw,4009
 test_env/Lib/site-packages/sympy/vector/tests/test_printing.py,sha256=3BeW55iQ4qXdfDTFqptE2ufJPJIBOzdfIYVx84n_EwA,7708
 test_env/Lib/site-packages/sympy/vector/tests/test_vector.py,sha256=Mo88Jgmy3CuSQz25WSH34EnZSs_JBY7E-OKPO2SjhPc,7861
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