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commit be6efe5fa474278b9cee832ba79507c976b3e89c Author: Afif Elghraoui <a...@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 <a...@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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-cobra.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit