[med-svn] [python-cobra] 04/10: Remove obsolete patches
Afif Elghraoui
afif-guest at moszumanska.debian.org
Fri Jul 10 04:26:44 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository python-cobra.
commit be6efe5fa474278b9cee832ba79507c976b3e89c
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Thu Jul 9 18:25:27 2015 -0700
Remove obsolete patches
The patch to improve python-3 support was actually not applicable
to the files intended for jython. The files that it was applicable
for have been removed from the source distribution upstream.
---
debian/patches/improve-python3-support.patch | 309 ---------------------------
debian/patches/series | 1 -
2 files changed, 310 deletions(-)
diff --git a/debian/patches/improve-python3-support.patch b/debian/patches/improve-python3-support.patch
deleted file mode 100644
index 6f3c28a..0000000
--- a/debian/patches/improve-python3-support.patch
+++ /dev/null
@@ -1,309 +0,0 @@
-Description: Improve Python3 compatibility
- Some parts of the code had Python2-specific syntax. These instances have
- been changed to work with both Python2 and Python3. It's interesting to
- note that these do not cause build-time errors. The problem becomes
- apparent when trying to install the built python3-cobra package.
-Author: Afif Elghraoui <afif at ghraoui.name>
-Forwarded: https://github.com/opencobra/cobrapy/pull/165
-Last-Update: 2015-06-13
----
-This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- python-cobra.orig/cobra/external/ppmap.py
-+++ python-cobra/cobra/external/ppmap.py
-@@ -30,6 +30,8 @@
- # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- # POSSIBILITY OF SUCH DAMAGE.
-
-+from __future__ import print_function
-+
- """
- Very basic parallel processing support
-
-@@ -105,18 +107,18 @@
- # Immediate evaluation example
- start = time.time()
- results = ppmap(None, busybeaver, range(10))
-- print 'Time to queue the jobs:', time.time() - start
-+ print('Time to queue the jobs: {:f}'.format(time.time() - start))
- start = time.time()
- # Casting the ppmap generator to a list forces each result to be
- # evaluated. When done immediately after the jobs are submitted,
- # our program twiddles its thumbs while the work is finished.
-- print list(results)
-- print 'Time to get the results:', time.time() - start
-+ print(list(results))
-+ print('Time to get the results: {:f}'.format(time.time() - start))
-
- # Delayed evaluation example
- start = time.time()
- results = ppmap(None, busybeaver, range(10))
-- print 'Time to queue the jobs:', time.time() - start
-+ print('Time to queue the jobs: {:f}'.format(time.time() - start))
- # In contrast with the above example, this time we're submitting a
- # batch of jobs then going off to do more work while they're
- # processing. Maybe "time.sleep" isn't the most exciting example,
-@@ -128,24 +130,24 @@
- # results.
- time.sleep(5)
- start = time.time()
-- print list(results)
-- print 'Time to get the first results:', time.time() - start
-+ print(list(results))
-+ print('Time to get the first results: {:f}'.format(time.time() - start))
-
- # Built-in map example
-- print map(add, [1, 2, 3], [4, 5, 6], [7, 8, 9])
-+ print(list(map(add, [1, 2, 3], [4, 5, 6], [7, 8, 9])))
-
- # Trivial ppmap tests
- for i in range(10):
-- print '-' * 30
-+ print('-' * 30)
- start = time.time()
-- print i, 'adders'
-- print ppmap(i, add, [1, 2, 3], [4, 5, 6], [7, 8, 9])
-- print 'Iteration time:', time.time() - start
-+ print('{:d} adders'.format(i))
-+ print(list(ppmap(i, add, [1, 2, 3], [4, 5, 6], [7, 8, 9])))
-+ print('Iteration time: {:f}'.format(time.time() - start))
-
- # Heavier ppmap tests
- for i in range(10):
-- print '-' * 30
-+ print('-' * 30)
- start = time.time()
-- print i, 'beavers'
-- print ppmap(i, busybeaver, range(10))
-- print 'Iteration time:', time.time() - start
-+ print('{:d} beavers'.format(i))
-+ print(list(ppmap(i, busybeaver, range(10))))
-+ print('Iteration time: {:f}'.format(time.time() - start))
---- python-cobra.orig/cobra/mlab/mlab.py
-+++ python-cobra/cobra/mlab/mlab.py
-@@ -1,5 +1,6 @@
- #cobra.mlab.py
- #System modules
-+from __future__ import print_function
- import cPickle, numpy, os, cobra, warnings
- from copy import deepcopy
- from scipy.sparse import dok_matrix
-@@ -48,7 +49,7 @@
- break
- if not os.path.isfile(os.path.join(matlab_cobra_path,
- "initCobraToolbox.m")):
-- print "initCobraToolbox not found in given path"
-+ print("initCobraToolbox not found in given path")
- return
- # store the current directory so we can return to it
- curdir = os.path.abspath(os.curdir)
-@@ -83,7 +84,7 @@
- try:
- import mlabwrap
- except ImportError:
-- print 'Could not import mlabwrap: ' + ImportError + '\n'
-+ print('Could not import mlabwrap: ' + ImportError + '\n')
- return False
- #the_list = mlabwrap.mlab.cell_to_string(the_cell).rstrip('\t').split('\t')
- #Because the mlabwrap.mlab.cell_to_string function will end with a tab, it must
-@@ -96,7 +97,7 @@
- try:
- import mlabwrap
- except ImportError:
-- print 'Could not import mlabwrap: ' + ImportError + '\n'
-+ print('Could not import mlabwrap: ' + ImportError + '\n')
- return False
- if mlabwrap.mlab.double(the_logical)[0][0] == 1:
- return True
-@@ -107,7 +108,7 @@
- try:
- import mlabwrap
- except ImportError:
-- print 'Could not load mlabwrap ' + ImportError + '\n'
-+ print('Could not load mlabwrap ' + ImportError + '\n')
- return False
- if hasattr(the_list[0], 'id'):
- the_list = [x.id for x in the_list]
-@@ -124,7 +125,7 @@
- import mlabwrap
- import scipy.sparse
- except ImportError:
-- print 'Could not load mlabwrap or scipy ' + ImportError + '\n'
-+ print('Could not load mlabwrap or scipy ' + ImportError + '\n')
- return False
- [row_indices, column_indices, the_values] = mlabwrap.mlab.find(matlab_sparse_matrix , nout = 3)
- #Change to 0-based indices
-@@ -148,7 +149,7 @@
- try:
- import mlabwrap
- except ImportError:
-- print 'Could not load mlabwrap ' + ImportError + '\n'
-+ print('Could not load mlabwrap ' + ImportError + '\n')
- return False
- return mlabwrap.mlab.sparse(scipy_sparse_matrix.todense())
-
-@@ -157,7 +158,7 @@
- import mlabwrap
- import numpy
- except ImportError:
-- print 'Could not load mlabwrap or numpy ' + ImportError + '\n'
-+ print('Could not load mlabwrap or numpy ' + ImportError + '\n')
- return False
- [row_indices, column_indices, the_values] = mlabwrap.mlab.find(matlab_sparse_matrix , nout = 3)
- #Change to 0-based indices
-@@ -176,7 +177,7 @@
- try:
- import mlabwrap
- except ImportError:
-- print 'Could not load mlabwrap ' + ImportError + '\n'
-+ print('Could not load mlabwrap ' + ImportError + '\n')
- return False
-
- return mlabwrap.mlab.sparse(numpy_array)
-@@ -398,8 +399,8 @@
- matlab_result = matlab.optimizeCbModel(matlab_struct)
- matlab_solution = repr(float(matlab_result.f))
- if py_cobra_solution[:4] == matlab_solution[:4]:
-- print 'SUCCESS: growth rate match between pyCOBRA and COBRA Toolbox: %s ~ %s'%(py_cobra_solution,
-- matlab_solution)
-+ print('SUCCESS: growth rate match between pyCOBRA and COBRA Toolbox: '
-+ '{:s} ~ {:s}'.format(py_cobra_solution, matlab_solution))
- else:
-- print 'FAILURE: pyCOBRA and COBRA Toolbox do not match: %s !~ %s'%(py_cobra_solution,
-- matlab_solution)
-+ print('FAILURE: pyCOBRA and COBRA Toolbox do not match: '
-+ '{:s} !~ {:s}'.format(py_cobra_solution, matlab_solution))
---- python-cobra.orig/cobra/solvers/cplex_solver_java.py
-+++ python-cobra/cobra/solvers/cplex_solver_java.py
-@@ -1,6 +1,7 @@
- #cobra.solvers.cplex_solver
- #Interface to ilog/cplex 12.4 python / jython interfaces
- #QPs are not yet supported under jython
-+from __future__ import print_function
- from os import name as __name
- from copy import deepcopy
- from warnings import warn
-@@ -315,7 +316,7 @@
-
- the_solution = format_solution(lp, cobra_model)
- if status != 'optimal' and error_reporting:
-- print '%s failed: %s'%(solver_name, status)
-+ print('{:s} failed: {:s}'.format(solver_name, status))
- cobra_model.solution = the_solution
- solution = {'the_problem': lp, 'the_solution': the_solution}
- return solution
---- python-cobra.orig/cobra/solvers/glpk_solver_java.py
-+++ python-cobra/cobra/solvers/glpk_solver_java.py
-@@ -1,5 +1,6 @@
- ##cobra.solvers.glpk_solver
- #This script provides wrappers for libglpk-java 1.0.22 and pyglpk 0.3
-+from __future__ import print_function
- from warnings import warn
- from copy import deepcopy
- ###solver specific parameters
-@@ -83,18 +84,18 @@
- try:
- setattr(self._simplex_parameters, parameter_name,
- parameter_value)
-- except Exception, e1:
-+ except Exception as e1:
- try:
- setattr(self._mip_parameters, parameter_name,
- parameter_value)
-- except Exception, e2:
-+ except Exception as e2:
- if warning:
-- print "Could not set simplex parameter " +\
-- "%s: %s"%(parameter_name, repr(e1))
-+ print("Could not set simplex parameter " +\
-+ "{:s}: {:s}".format(parameter_name, repr(e1)))
-
- if self._mip_parameters is not None:
-- print "Could not set mip parameter " +\
-- "%s: %s"%(parameter_name, repr(e2))
-+ print("Could not set mip parameter " +\
-+ "{:s}: {:s}".format(parameter_name, repr(e2)))
- def get_objective_value(self):
- if self._mip:
- tmp_value = self._g.glp_mip_obj_val(self._lp)
-@@ -222,8 +223,8 @@
- y_dict = dict(zip(cobra_model.metabolites, y))
-
- objective_value = lp.objective_value
-- except Exception, e:
-- print repr(e)
-+ except Exception as e:
-+ print(repr(e))
- y = y_dict = x = x_dict = objective_value = None
- #print status
- else:
-@@ -298,7 +299,7 @@
- lp.solve()
- status = get_status(lp)
- if print_solver_time:
-- print 'optimize time: %f'%(time() - start_time)
-+ print('optimize time: {:f}'.format(time() - start_time))
- return status
-
-
-@@ -359,7 +360,7 @@
-
- the_solution = format_solution(lp, cobra_model)
- if status != 'optimal' and error_reporting:
-- print '%s failed: %s'%(solver_name, status)
-+ print('{:s} failed: {:s}'.format(solver_name, status))
- cobra_model.solution = the_solution
- solution = {'the_problem': lp, 'the_solution': the_solution}
- return solution
---- python-cobra.orig/cobra/solvers/gurobi_solver_java.py
-+++ python-cobra/cobra/solvers/gurobi_solver_java.py
-@@ -1,6 +1,7 @@
- ##cobra.solvers.gurobi_solver
- #Interface to the gurobi 5.0.1 python and java solvers
- #QPs are not yet supported on java
-+from __future__ import print_function
- from warnings import warn
- from os import name as __name
- from copy import deepcopy
-@@ -70,7 +71,7 @@
- else:
- warn("%s is not a DoubleParam, IntParam, StringParam, IntAttr"%parameter_name)
- ## raise Exception("%s is not a DoubleParam, IntParam, StringParam, IntAttr"%parameter_name)
-- except Exception, e:
-+ except Exception as e:
- warn("%s %s didn't work %s"%(parameter_name, parameter_value, e))
-
- def get_objective_value(lp):
-@@ -213,7 +214,7 @@
- lp.optimize()
- status = get_status(lp)
- if print_solver_time:
-- print 'optimize time: %f'%(time() - start_time)
-+ print('optimize time: {:f}'.format(time() - start_time))
- return status
-
-
-@@ -274,7 +275,7 @@
- status = solve_problem(lp, **the_parameters)
- the_solution = format_solution(lp, cobra_model)
- if status != 'optimal' and error_reporting:
-- print '%s failed: %s'%(solver_name, status)
-+ print('{:s} failed: {:s}'.format(solver_name, status))
- cobra_model.solution = the_solution
- solution = {'the_problem': lp, 'the_solution': the_solution}
- return solution
---- python-cobra.orig/cobra/topology/reporter_metabolites.py
-+++ python-cobra/cobra/topology/reporter_metabolites.py
-@@ -1,6 +1,7 @@
- #cobra.topology.reporter_metabolites.py: Module for topological analysis of cobra_models
- #Based on Patil et al 2005 PNAS 102:2685-9
- #TODO: Validate cobra.core compliance
-+from __future__ import print_function
- from copy import deepcopy
- from numpy import array, corrcoef, mean, std, tril, where, unique, zeros
- from scipy.stats import norm, randint
-@@ -162,4 +163,4 @@
- tmp_reps = identify_reporter_metabolites(cobra_model, reaction_scores_dict,
- background_correction=True)
-
-- print 'Need to add in validation for the test'
-+ print('Need to add in validation for the test')
diff --git a/debian/patches/series b/debian/patches/series
index 7d6b773..d86c913 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1 @@
-improve-python3-support.patch
mathjax.patch
--
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