Merge pull request #30 from SystemsBioinformatics/dev

Added requirement dependency files

Author: bgoli

.gitignore

@@ -1,3 +1,5 @@
 .svn
 cbmpy.egg-info
 __pycache__
+wing-cbmpy.wpr 
+wing-cbmpy.wpu

cbmpy/CBCPLEX.py

@@ -788,7 +788,7 @@ def cplx_writeLPsolution(fba_sol, objf_name, fname, Dir=None, separator=','):
         assert os.path.exists(Dir), '\nPath does not exist'
         fname = os.path.join(Dir, fname)
     fname += '.csv'
-    F = file(fname, 'w')
+    F = open(fname, 'w')
     F.write('%s%s%s\n' % ('ObjectiveFunction', separator, objf_name))
     for r in fba_sol:
         F.write('%s%s%f\n' % (r, separator, fba_sol[r]))
@@ -799,11 +799,14 @@ def cplx_writeLPsolution(fba_sol, objf_name, fname, Dir=None, separator=','):
 
 def cplx_getShadowPrices(c):
     """
-    Returns a dictionary of shadow prices containing 'Rid' : (lb, rhs, ub)
+    Returns a dictionary of shadow prices containing 'N_row_id' : (lb, rhs, ub)
 
      - *c* a cplex LP object
 
     """
+    print(
+        'cplx_getShadowPrices: This function returns a RHS sensitivity and may or may not be realted to what is known as a shadow price.'
+    )
     c_names = c.linear_constraints.get_names()
     rhs_sense = c.solution.sensitivity.rhs()
     rhs_val = c.linear_constraints.get_rhs()

cbmpy/CBConfig.py

@@ -39,7 +39,7 @@
 
 __VERSION_MAJOR__ = 0
 __VERSION_MINOR__ = 8
-__VERSION_MICRO__ = 0
+__VERSION_MICRO__ = 1
 
 __CBCONFIG__ = {
     'VERSION_MAJOR': __VERSION_MAJOR__,

environment.yml

@@ -0,0 +1,23 @@
+name: cbmpy
+channels:
+  - bgoli
+  - sbmlteam
+  - defaults
+dependencies:
+  - biopython>=1.78
+  - ipython
+  - nose
+  - numpy
+  - matplotlib
+  - python-libsbml>=5.18.0
+  - scipy
+  - jedi==0.17.2
+  - setuptools
+  - sympy>=1.7.1
+  - xlsxwriter>=1.3.7
+  - xlwt
+  - cbmpy
+  - pip
+  - pip:
+    - swiglpk==4.65.1
+prefix: C:\Anaconda3\envs\cbmpy

requirements.txt

@@ -0,0 +1,14 @@
+biopython
+jedi==0.17.2
+ipython
+nose
+numpy
+matplotlib
+python-libsbml
+scipy
+swiglpk==4.65.1
+sympy
+xlrd
+XlsxWriter
+xlwt
+cbmpy>=0.8.0