Essential update to fix imports on pip installation. Also some import…

… linting.

.gitignore

@@ -8,3 +8,6 @@ dist/
 
 # jupyter checkpoints
 .ipynb_checkpoints
+
+# solver-specific files that might be generated while running tests locally
+gurobi.log

medusa/__init__.py

@@ -1,5 +1,4 @@
-from __future__ import absolute_import
 
-from medusa.core import Ensemble
+
 
 __version__ = "0.1"

medusa/core/__init__.py

@@ -1 +1,3 @@
 from medusa.core.ensemble import Ensemble
+from medusa.core.feature import Feature
+from medusa.core.member import Member

medusa/reconstruct/load_from_file.py

@@ -1,47 +1,11 @@
-from __future__ import print_function
-from __future__ import absolute_import
-
 import medusa
 import cobra
 import cobra.test
-import numpy as np
-import csv
-import glob
-import pickle
-import pandas as pd
 import math
 import copy
-import time
 import random
-import time
-import sys
-import os
-import itertools
-import logging
-LOGGER = logging.getLogger(__name__)
-
-from sys import getsizeof
 from copy import deepcopy
-from collections import defaultdict
-from warnings import warn
-from itertools import chain
-from optlang.symbolics import Zero
-from optlang.interface import OPTIMAL
-from itertools import chain
-
-import cobra.core.model
-from cobra.flux_analysis import sample
-from cobra.core.solution import get_solution
-from cobra.flux_analysis.sampling import OptGPSampler
-from cobra.manipulation.delete import *
-from cobra.medium import find_boundary_types
-from cobra.flux_analysis import pfba
-from cobra.util import solver as sutil
-from cobra.core.solution import get_solution
-from cobra.core import DictList
 
-from medusa.core.ensemble import Ensemble
-from medusa.flux_analysis.flux_balance import optimize_ensemble
 from medusa.core.feature import Feature
 
 def parent_attr_of_base_component(base_comp):
@@ -109,11 +73,11 @@ def batch_load_from_files(model_file_names, identifier='ensemble', batchsize=5,
                 raise AttributeError("Only cobra.core.Model objects supported")
             model_list.append(model)
         if range_list[0] == 0:
-            final_ensemble = medusa.Ensemble(model_list, identifier = identifier)
+            final_ensemble = medusa.core.Ensemble(model_list, identifier = identifier)
             if verbose == True:
                 print("Ensemble 1 finished")
         else:
-            new_ensemble = medusa.Ensemble(model_list)
+            new_ensemble = medusa.core.Ensemble(model_list)
             final_ensemble = add_ensembles(final_ensemble,new_ensemble)
             del new_ensemble
             if verbose == True:
@@ -130,7 +94,7 @@ def add_ensembles(e1,e2,verbose=False):
         Parameters
         ----------
         e1 & e2 : Ensemble Objects
-            Generated using medusa.Ensemble()
+            Generated using medusa.core.Ensemble()
     """
 
     # Deep copy ensembles

medusa/test/test_load_from_file.py

@@ -1,8 +1,7 @@
+import cobra
 from cobra.test import create_test_model
 from medusa.core.ensemble import Ensemble
-from medusa.reconstruct.load_from_file import *
-
-from pickle import load
+from medusa.reconstruct.load_from_file import batch_load_from_files
 
 REACTION_ATTRIBUTES = ['lower_bound', 'upper_bound']
 MISSING_ATTRIBUTE_DEFAULT = {'lower_bound':0,'upper_bound':0}

medusa_cobra.egg-info/SOURCES.txt

@@ -15,9 +15,11 @@ medusa/quality/mass_balance.py
 medusa/reconstruct/__init__.py
 medusa/reconstruct/degrade.py
 medusa/reconstruct/expand.py
+medusa/reconstruct/load_from_file.py
 medusa/test/__init__.py
 medusa/test/test_ensemble.py
 medusa/test/test_flux_balance.py
+medusa/test/test_load_from_file.py
 medusa/test/test_reconstruct.py
 medusa/test/test_variability.py
 medusa/test/data/Staphylococcus aureus.json