{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from cobra.test import test_all"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "============================= test session starts ==============================\n",
      "platform linux -- Python 3.7.6, pytest-5.4.2, py-1.8.1, pluggy-0.13.1 -- /opt/conda/bin/python\n",
      "cachedir: .pytest_cache\n",
      "benchmark: 3.2.3 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000)\n",
      "rootdir: /work/bio334_spring2020_exam\n",
      "plugins: benchmark-3.2.3\n",
      "collecting ... collected 292 items\n",
      "\n",
      "test/test_manipulation.py::TestManipulation::test_escape_ids PASSED      [  0%]\n",
      "test/test_manipulation.py::TestManipulation::test_rename_gene PASSED     [  0%]\n",
      "test/test_manipulation.py::TestManipulation::test_gene_knockout_computation PASSED [  1%]\n",
      "test/test_manipulation.py::TestManipulation::test_remove_genes PASSED    [  1%]\n",
      "test/test_manipulation.py::TestManipulation::test_sbo_annotation PASSED  [  1%]\n",
      "test/test_manipulation.py::TestManipulation::test_validate_formula_compartment PASSED [  2%]\n",
      "test/test_manipulation.py::TestManipulation::test_validate_mass_balance PASSED [  2%]\n",
      "test/test_manipulation.py::TestManipulation::test_prune_unused_mets_output_type PASSED [  2%]\n",
      "test/test_manipulation.py::TestManipulation::test_prune_unused_mets_functionality PASSED [  3%]\n",
      "test/test_manipulation.py::TestManipulation::test_prune_unused_rxns_output_type PASSED [  3%]\n",
      "test/test_manipulation.py::TestManipulation::test_prune_unused_rxns_functionality PASSED [  3%]\n",
      "test/test_medium.py::TestModelMedium::test_model_medium PASSED           [  4%]\n",
      "test/test_medium.py::TestTypeDetection::test_external_compartment PASSED [  4%]\n",
      "test/test_medium.py::TestTypeDetection::test_multi_external PASSED       [  4%]\n",
      "test/test_medium.py::TestTypeDetection::test_exchange PASSED             [  5%]\n",
      "test/test_medium.py::TestTypeDetection::test_demand PASSED               [  5%]\n",
      "test/test_medium.py::TestTypeDetection::test_sink PASSED                 [  5%]\n",
      "test/test_medium.py::TestTypeDetection::test_sbo_terms PASSED            [  6%]\n",
      "test/test_medium.py::TestMinimalMedia::test_medium_linear PASSED         [  6%]\n",
      "test/test_medium.py::TestMinimalMedia::test_medium_mip PASSED            [  6%]\n",
      "test/test_medium.py::TestMinimalMedia::test_medium_alternative_mip PASSED [  7%]\n",
      "test/test_medium.py::TestMinimalMedia::test_benchmark_medium_linear SKIPPED [  7%]\n",
      "test/test_medium.py::TestMinimalMedia::test_benchmark_medium_mip SKIPPED [  7%]\n",
      "test/test_medium.py::TestMinimalMedia::test_medium_exports PASSED        [  8%]\n",
      "test/test_medium.py::TestMinimalMedia::test_open_exchanges PASSED        [  8%]\n",
      "test/test_medium.py::TestErrorsAndExceptions::test_no_boundary_reactions PASSED [  8%]\n",
      "test/test_medium.py::TestErrorsAndExceptions::test_no_names_or_boundary_reactions PASSED [  9%]\n",
      "test/test_medium.py::TestErrorsAndExceptions::test_bad_exchange PASSED   [  9%]\n",
      "test/test_core/test_configuration.py::test_default_bounds PASSED         [  9%]\n",
      "test/test_core/test_configuration.py::test_bounds PASSED                 [ 10%]\n",
      "test/test_core/test_configuration.py::test_solver PASSED                 [ 10%]\n",
      "test/test_core/test_configuration.py::test_default_tolerance PASSED      [ 10%]\n",
      "test/test_core/test_configuration.py::test_toy_model_tolerance_with_different_default PASSED [ 11%]\n",
      "test/test_core/test_configuration.py::test_tolerance_assignment PASSED   [ 11%]\n",
      "test/test_core/test_core_reaction.py::test_gpr PASSED                    [ 11%]\n",
      "test/test_core/test_core_reaction.py::test_gpr_modification PASSED       [ 12%]\n",
      "test/test_core/test_core_reaction.py::test_gene_knock_out PASSED         [ 12%]\n",
      "test/test_core/test_core_reaction.py::test_str PASSED                    [ 13%]\n",
      "test/test_core/test_core_reaction.py::test_str_from_model PASSED         [ 13%]\n",
      "test/test_core/test_core_reaction.py::test_add_metabolite_from_solved_model[glpk] PASSED [ 13%]\n",
      "test/test_core/test_core_reaction.py::test_add_metabolite_from_solved_model[cplex] SKIPPED [ 14%]\n",
      "test/test_core/test_core_reaction.py::test_add_metabolite_from_solved_model[gurobi] SKIPPED [ 14%]\n",
      "test/test_core/test_core_reaction.py::test_add_metabolite_benchmark[glpk] SKIPPED [ 14%]\n",
      "test/test_core/test_core_reaction.py::test_add_metabolite_benchmark[cplex] SKIPPED [ 15%]\n",
      "test/test_core/test_core_reaction.py::test_add_metabolite_benchmark[gurobi] SKIPPED [ 15%]\n",
      "test/test_core/test_core_reaction.py::test_add_metabolite PASSED         [ 15%]\n",
      "test/test_core/test_core_reaction.py::test_subtract_metabolite_benchmark[glpk] SKIPPED [ 16%]\n",
      "test/test_core/test_core_reaction.py::test_subtract_metabolite_benchmark[cplex] SKIPPED [ 16%]\n",
      "test/test_core/test_core_reaction.py::test_subtract_metabolite_benchmark[gurobi] SKIPPED [ 16%]\n",
      "test/test_core/test_core_reaction.py::test_subtract_metabolite[glpk] PASSED [ 17%]\n",
      "test/test_core/test_core_reaction.py::test_subtract_metabolite[cplex] PASSED [ 17%]\n",
      "test/test_core/test_core_reaction.py::test_subtract_metabolite[gurobi] PASSED [ 17%]\n",
      "test/test_core/test_core_reaction.py::test_mass_balance PASSED           [ 18%]\n",
      "test/test_core/test_core_reaction.py::test_build_from_string PASSED      [ 18%]\n",
      "test/test_core/test_core_reaction.py::test_bounds_setter PASSED          [ 18%]\n",
      "test/test_core/test_core_reaction.py::test_copy PASSED                   [ 19%]\n",
      "test/test_core/test_core_reaction.py::test_iadd PASSED                   [ 19%]\n",
      "test/test_core/test_core_reaction.py::test_add PASSED                    [ 19%]\n",
      "test/test_core/test_core_reaction.py::test_radd PASSED                   [ 20%]\n",
      "test/test_core/test_core_reaction.py::test_mul PASSED                    [ 20%]\n",
      "test/test_core/test_core_reaction.py::test_sub PASSED                    [ 20%]\n",
      "test/test_core/test_core_reaction.py::test_removal_from_model_retains_bounds PASSED [ 21%]\n",
      "test/test_core/test_core_reaction.py::test_set_bounds_scenario_1 PASSED  [ 21%]\n",
      "test/test_core/test_core_reaction.py::test_set_bounds_scenario_3 PASSED  [ 21%]\n",
      "test/test_core/test_core_reaction.py::test_set_bounds_scenario_4 PASSED  [ 22%]\n",
      "test/test_core/test_core_reaction.py::test_set_upper_before_lower_bound_to_0 PASSED [ 22%]\n",
      "test/test_core/test_core_reaction.py::test_set_bounds_scenario_2 PASSED  [ 22%]\n",
      "test/test_core/test_core_reaction.py::test_change_bounds PASSED          [ 23%]\n",
      "test/test_core/test_core_reaction.py::test_make_irreversible PASSED      [ 23%]\n",
      "test/test_core/test_core_reaction.py::test_make_reversible PASSED        [ 23%]\n",
      "test/test_core/test_core_reaction.py::test_make_irreversible_irreversible_to_the_other_side PASSED [ 24%]\n",
      "test/test_core/test_core_reaction.py::test_make_lhs_irreversible_reversible PASSED [ 24%]\n",
      "test/test_core/test_core_reaction.py::test_model_less_reaction PASSED    [ 25%]\n",
      "test/test_core/test_core_reaction.py::test_knockout PASSED               [ 25%]\n",
      "test/test_core/test_core_reaction.py::test_reaction_without_model PASSED [ 25%]\n",
      "test/test_core/test_core_reaction.py::test_weird_left_to_right_reaction_issue PASSED [ 26%]\n",
      "test/test_core/test_core_reaction.py::test_one_left_to_right_reaction_set_positive_ub PASSED [ 26%]\n",
      "test/test_core/test_core_reaction.py::test_irrev_reaction_set_negative_lb PASSED [ 26%]\n",
      "test/test_core/test_core_reaction.py::test_twist_irrev_right_to_left_reaction_to_left_to_right PASSED [ 27%]\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb PASSED [ 27%]\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub PASSED [ 27%]\n",
      "test/test_core/test_core_reaction.py::test_add_metabolites_combine_true PASSED [ 28%]\n",
      "test/test_core/test_core_reaction.py::test_add_metabolites_combine_false XFAIL [ 28%]\n",
      "test/test_core/test_core_reaction.py::test_reaction_imul PASSED          [ 28%]\n",
      "test/test_core/test_core_reaction.py::test_remove_from_model PASSED      [ 29%]\n",
      "test/test_core/test_core_reaction.py::test_change_id_is_reflected_in_solver PASSED [ 29%]\n",
      "test/test_core/test_core_reaction.py::test_repr_html_ PASSED             [ 29%]\n",
      "test/test_core/test_dictlist.py::test_contains PASSED                    [ 30%]\n",
      "test/test_core/test_dictlist.py::test_index PASSED                       [ 30%]\n",
      "test/test_core/test_dictlist.py::test_independent PASSED                 [ 30%]\n",
      "test/test_core/test_dictlist.py::test_get_by_any PASSED                  [ 31%]\n",
      "test/test_core/test_dictlist.py::test_append PASSED                      [ 31%]\n",
      "test/test_core/test_dictlist.py::test_insert PASSED                      [ 31%]\n",
      "test/test_core/test_dictlist.py::test_extend PASSED                      [ 32%]\n",
      "test/test_core/test_dictlist.py::test_iadd PASSED                        [ 32%]\n",
      "test/test_core/test_dictlist.py::test_add PASSED                         [ 32%]\n",
      "test/test_core/test_dictlist.py::test_sub PASSED                         [ 33%]\n",
      "test/test_core/test_dictlist.py::test_isub PASSED                        [ 33%]\n",
      "test/test_core/test_dictlist.py::test_init_copy PASSED                   [ 33%]\n",
      "test/test_core/test_dictlist.py::test_slice PASSED                       [ 34%]\n",
      "test/test_core/test_dictlist.py::test_copy PASSED                        [ 34%]\n",
      "test/test_core/test_dictlist.py::test_deepcopy PASSED                    [ 34%]\n",
      "test/test_core/test_dictlist.py::test_pickle PASSED                      [ 35%]\n",
      "test/test_core/test_dictlist.py::test_query PASSED                       [ 35%]\n",
      "test/test_core/test_dictlist.py::test_removal PASSED                     [ 35%]\n",
      "test/test_core/test_dictlist.py::test_set PASSED                         [ 36%]\n",
      "test/test_core/test_dictlist.py::test_sort_and_reverse PASSED            [ 36%]\n",
      "test/test_core/test_dictlist.py::test_dir PASSED                         [ 36%]\n",
      "test/test_core/test_dictlist.py::test_union PASSED                       [ 37%]\n",
      "test/test_core/test_gene.py::test_repr_html_ PASSED                      [ 37%]\n",
      "test/test_core/test_group.py::test_group_add_elements PASSED             [ 38%]\n",
      "test/test_core/test_group.py::test_group_kind PASSED                     [ 38%]\n",
      "test/test_core/test_metabolite.py::test_metabolite_formula PASSED        [ 38%]\n",
      "test/test_core/test_metabolite.py::test_formula_element_setting PASSED   [ 39%]\n",
      "test/test_core/test_metabolite.py::test_set_id[glpk] PASSED              [ 39%]\n",
      "test/test_core/test_metabolite.py::test_set_id[cplex] SKIPPED            [ 39%]\n",
      "test/test_core/test_metabolite.py::test_set_id[gurobi] SKIPPED           [ 40%]\n",
      "test/test_core/test_metabolite.py::test_remove_from_model[glpk] PASSED   [ 40%]\n",
      "test/test_core/test_metabolite.py::test_remove_from_model[cplex] SKIPPED [ 40%]\n",
      "test/test_core/test_metabolite.py::test_remove_from_model[gurobi] SKIPPED [ 41%]\n",
      "test/test_core/test_metabolite.py::test_repr_html_ PASSED                [ 41%]\n",
      "test/test_core/test_model.py::test_add_remove_reaction_benchmark[glpk] SKIPPED [ 41%]\n",
      "test/test_core/test_model.py::test_add_remove_reaction_benchmark[cplex] SKIPPED [ 42%]\n",
      "test/test_core/test_model.py::test_add_remove_reaction_benchmark[gurobi] SKIPPED [ 42%]\n",
      "test/test_core/test_model.py::test_add_metabolite PASSED                 [ 42%]\n",
      "test/test_core/test_model.py::test_remove_metabolite_subtractive PASSED  [ 43%]\n",
      "test/test_core/test_model.py::test_remove_metabolite_destructive PASSED  [ 43%]\n",
      "test/test_core/test_model.py::test_compartments PASSED                   [ 43%]\n",
      "test/test_core/test_model.py::test_add_reaction PASSED                   [ 44%]\n",
      "test/test_core/test_model.py::test_add_reaction_context PASSED           [ 44%]\n",
      "test/test_core/test_model.py::test_add_reaction_from_other_model PASSED  [ 44%]\n",
      "test/test_core/test_model.py::test_model_remove_reaction PASSED          [ 45%]\n",
      "test/test_core/test_model.py::test_reaction_remove PASSED                [ 45%]\n",
      "test/test_core/test_model.py::test_reaction_delete PASSED                [ 45%]\n",
      "test/test_core/test_model.py::test_remove_gene PASSED                    [ 46%]\n",
      "test/test_core/test_model.py::test_group_model_reaction_association PASSED [ 46%]\n",
      "test/test_core/test_model.py::test_group_members_add_to_model PASSED     [ 46%]\n",
      "test/test_core/test_model.py::test_group_loss_of_elements PASSED         [ 47%]\n",
      "test/test_core/test_model.py::test_exchange_reactions PASSED             [ 47%]\n",
      "test/test_core/test_model.py::test_add_boundary[exchange-exchange-EX_] PASSED [ 47%]\n",
      "test/test_core/test_model.py::test_add_boundary[demand-demand-DM_] PASSED [ 48%]\n",
      "test/test_core/test_model.py::test_add_boundary[sink-sink-SK_] PASSED    [ 48%]\n",
      "test/test_core/test_model.py::test_add_boundary_context[exchange-exchange-EX_] PASSED [ 48%]\n",
      "test/test_core/test_model.py::test_add_boundary_context[demand-demand-DM_] PASSED [ 49%]\n",
      "test/test_core/test_model.py::test_add_boundary_context[sink-sink-SK_] PASSED [ 49%]\n",
      "test/test_core/test_model.py::test_add_existing_boundary[exchange-exchange] PASSED [ 50%]\n",
      "test/test_core/test_model.py::test_add_existing_boundary[demand-demand] PASSED [ 50%]\n",
      "test/test_core/test_model.py::test_add_existing_boundary[sink-sink] PASSED [ 50%]\n",
      "test/test_core/test_model.py::test_copy_benchmark[glpk] SKIPPED          [ 51%]\n",
      "test/test_core/test_model.py::test_copy_benchmark[cplex] SKIPPED         [ 51%]\n",
      "test/test_core/test_model.py::test_copy_benchmark[gurobi] SKIPPED        [ 51%]\n",
      "test/test_core/test_model.py::test_copy_benchmark_large_model[glpk] SKIPPED [ 52%]\n",
      "test/test_core/test_model.py::test_copy_benchmark_large_model[cplex] SKIPPED [ 52%]\n",
      "test/test_core/test_model.py::test_copy_benchmark_large_model[gurobi] SKIPPED [ 52%]\n",
      "test/test_core/test_model.py::test_copy PASSED                           [ 53%]\n",
      "test/test_core/test_model.py::test_copy_with_groups PASSED               [ 53%]\n",
      "test/test_core/test_model.py::test_deepcopy_benchmark SKIPPED            [ 53%]\n",
      "test/test_core/test_model.py::test_deepcopy PASSED                       [ 54%]\n",
      "test/test_core/test_model.py::test_add_reaction_orphans PASSED           [ 54%]\n",
      "test/test_core/test_model.py::test_merge_models PASSED                   [ 54%]\n",
      "test/test_core/test_model.py::test_change_objective_benchmark[glpk] SKIPPED [ 55%]\n",
      "test/test_core/test_model.py::test_change_objective_benchmark[cplex] SKIPPED [ 55%]\n",
      "test/test_core/test_model.py::test_change_objective_benchmark[gurobi] SKIPPED [ 55%]\n",
      "test/test_core/test_model.py::test_get_objective_direction PASSED        [ 56%]\n",
      "test/test_core/test_model.py::test_set_objective_direction PASSED        [ 56%]\n",
      "test/test_core/test_model.py::test_slim_optimize PASSED                  [ 56%]\n",
      "test/test_core/test_model.py::test_optimize[optlang-glpk] PASSED         [ 57%]\n",
      "test/test_core/test_model.py::test_problem_properties PASSED             [ 57%]\n",
      "test/test_core/test_model.py::test_solution_data_frame PASSED            [ 57%]\n",
      "test/test_core/test_model.py::test_context_manager PASSED                [ 58%]\n",
      "test/test_core/test_model.py::test_objective_coefficient_reflects_changed_objective PASSED [ 58%]\n",
      "test/test_core/test_model.py::test_change_objective_through_objective_coefficient PASSED [ 58%]\n",
      "test/test_core/test_model.py::test_transfer_objective PASSED             [ 59%]\n",
      "test/test_core/test_model.py::test_model_from_other_model PASSED         [ 59%]\n",
      "test/test_core/test_model.py::test_add_reactions PASSED                  [ 59%]\n",
      "test/test_core/test_model.py::test_add_reactions_single_existing PASSED  [ 60%]\n",
      "test/test_core/test_model.py::test_add_reactions_duplicate PASSED        [ 60%]\n",
      "test/test_core/test_model.py::test_add_cobra_reaction PASSED             [ 60%]\n",
      "test/test_core/test_model.py::test_all_objects_point_to_all_other_correct_objects PASSED [ 61%]\n",
      "test/test_core/test_model.py::test_objects_point_to_correct_other_after_copy PASSED [ 61%]\n",
      "test/test_core/test_model.py::test_remove_reactions PASSED               [ 61%]\n",
      "test/test_core/test_model.py::test_objective PASSED                      [ 62%]\n",
      "test/test_core/test_model.py::test_change_objective PASSED               [ 62%]\n",
      "test/test_core/test_model.py::test_set_reaction_objective PASSED         [ 63%]\n",
      "test/test_core/test_model.py::test_set_reaction_objective_str PASSED     [ 63%]\n",
      "test/test_core/test_model.py::test_invalid_objective_raises PASSED       [ 63%]\n",
      "test/test_core/test_model.py::test_solver_change SKIPPED                 [ 64%]\n",
      "test/test_core/test_model.py::test_no_change_for_same_solver PASSED      [ 64%]\n",
      "test/test_core/test_model.py::test_invalid_solver_change_raises PASSED   [ 64%]\n",
      "test/test_core/test_model.py::test_change_solver_to_cplex_and_check_copy_works SKIPPED [ 65%]\n",
      "test/test_core/test_model.py::test_copy_preserves_existing_solution[glpk] PASSED [ 65%]\n",
      "test/test_core/test_model.py::test_copy_preserves_existing_solution[cplex] SKIPPED [ 65%]\n",
      "test/test_core/test_model.py::test_copy_preserves_existing_solution[gurobi] SKIPPED [ 66%]\n",
      "test/test_core/test_model.py::test_repr_html_ PASSED                     [ 66%]\n",
      "test/test_core/test_solution.py::test_solution_contains_only_reaction_specific_values[glpk] PASSED [ 66%]\n",
      "test/test_core/test_solution.py::test_solution_contains_only_reaction_specific_values[cplex] SKIPPED [ 67%]\n",
      "test/test_core/test_solution.py::test_solution_contains_only_reaction_specific_values[gurobi] SKIPPED [ 67%]\n",
      "test/test_core/test_summary/test_metabolite_summary.py::test_metabolite_summary_to_table_previous_solution[optlang-glpk-q8_c] FAILED [ 67%]\n",
      "test/test_core/test_summary/test_metabolite_summary.py::test_metabolite_summary_to_frame_previous_solution[optlang-glpk-q8_c] PASSED [ 68%]\n",
      "test/test_core/test_summary/test_metabolite_summary.py::test_metabolite_summary_to_table[optlang-glpk-q8_c-False] FAILED [ 68%]\n",
      "test/test_core/test_summary/test_metabolite_summary.py::test_metabolite_summary_to_table[optlang-glpk-q8_c-True] FAILED [ 68%]\n",
      "test/test_core/test_summary/test_metabolite_summary.py::test_metabolite_summary_to_frame[optlang-glpk-q8_c-False] PASSED [ 69%]\n",
      "test/test_core/test_summary/test_metabolite_summary.py::test_metabolite_summary_to_frame[optlang-glpk-q8_c-True] PASSED [ 69%]\n",
      "test/test_core/test_summary/test_metabolite_summary.py::test_metabolite_summary_to_table_with_fva[optlang-glpk-0.99-fdp_c] PASSED [ 69%]\n",
      "test/test_core/test_summary/test_metabolite_summary.py::test_metabolite_summary_to_frame_with_fva[optlang-glpk-0.99-fdp_c] PASSED [ 70%]\n",
      "test/test_core/test_summary/test_model_summary.py::test_model_summary_to_table_previous_solution[optlang-glpk-False] PASSED [ 70%]\n",
      "test/test_core/test_summary/test_model_summary.py::test_model_summary_to_table_previous_solution[optlang-glpk-True] PASSED [ 70%]\n",
      "test/test_core/test_summary/test_model_summary.py::test_model_summary_to_frame_previous_solution[optlang-glpk-False] PASSED [ 71%]\n",
      "test/test_core/test_summary/test_model_summary.py::test_model_summary_to_frame_previous_solution[optlang-glpk-True] PASSED [ 71%]\n",
      "test/test_core/test_summary/test_model_summary.py::test_model_summary_to_table[optlang-glpk-False] PASSED [ 71%]\n",
      "test/test_core/test_summary/test_model_summary.py::test_model_summary_to_table[optlang-glpk-True] PASSED [ 72%]\n",
      "test/test_core/test_summary/test_model_summary.py::test_model_summary_to_frame[optlang-glpk-False] PASSED [ 72%]\n",
      "test/test_core/test_summary/test_model_summary.py::test_model_summary_to_frame[optlang-glpk-True] PASSED [ 72%]\n",
      "test/test_core/test_summary/test_model_summary.py::test_model_summary_to_table_with_fva[optlang-glpk-0.95] PASSED [ 73%]\n",
      "test/test_core/test_summary/test_model_summary.py::test_model_summary_to_frame_with_fva[optlang-glpk-0.95] PASSED [ 73%]\n",
      "test/test_core/test_summary/test_reaction_summary.py::test_reaction_summary_to_table[ACALD-False] SKIPPED [ 73%]\n",
      "test/test_core/test_summary/test_reaction_summary.py::test_reaction_summary_to_table[ACALD-True] SKIPPED [ 74%]\n",
      "test/test_core/test_summary/test_reaction_summary.py::test_reaction_summary_to_frame[ACALD-False] PASSED [ 74%]\n",
      "test/test_core/test_summary/test_reaction_summary.py::test_reaction_summary_to_frame[FUM-True] PASSED [ 75%]\n",
      "test/test_io/test_annotation.py::test_read_sbml_annotations PASSED       [ 75%]\n",
      "test/test_io/test_annotation.py::test_read_write_sbml_annotations PASSED [ 75%]\n",
      "test/test_io/test_io_order.py::test_io_order[metabolites-minimized_shuffle-read_sbml_model-write_sbml_model-.xml] PASSED [ 76%]\n",
      "test/test_io/test_io_order.py::test_io_order[metabolites-minimized_shuffle-load_json_model-save_json_model-.json] PASSED [ 76%]\n",
      "test/test_io/test_io_order.py::test_io_order[metabolites-minimized_shuffle-load_yaml_model-save_yaml_model-.yml] PASSED [ 76%]\n",
      "test/test_io/test_io_order.py::test_io_order[metabolites-minimized_reverse-read_sbml_model-write_sbml_model-.xml] PASSED [ 77%]\n",
      "test/test_io/test_io_order.py::test_io_order[metabolites-minimized_reverse-load_json_model-save_json_model-.json] PASSED [ 77%]\n",
      "test/test_io/test_io_order.py::test_io_order[metabolites-minimized_reverse-load_yaml_model-save_yaml_model-.yml] PASSED [ 77%]\n",
      "test/test_io/test_io_order.py::test_io_order[reactions-minimized_reverse-read_sbml_model-write_sbml_model-.xml] PASSED [ 78%]\n",
      "test/test_io/test_io_order.py::test_io_order[reactions-minimized_reverse-load_json_model-save_json_model-.json] PASSED [ 78%]\n",
      "test/test_io/test_io_order.py::test_io_order[reactions-minimized_reverse-load_yaml_model-save_yaml_model-.yml] PASSED [ 78%]\n",
      "test/test_io/test_io_order.py::test_io_order[reactions-minimized_shuffle-read_sbml_model-write_sbml_model-.xml] PASSED [ 79%]\n",
      "test/test_io/test_io_order.py::test_io_order[reactions-minimized_shuffle-load_json_model-save_json_model-.json] PASSED [ 79%]\n",
      "test/test_io/test_io_order.py::test_io_order[reactions-minimized_shuffle-load_yaml_model-save_yaml_model-.yml] PASSED [ 79%]\n",
      "test/test_io/test_io_order.py::test_io_order[reactions-minimized_sorted-read_sbml_model-write_sbml_model-.xml] PASSED [ 80%]\n",
      "test/test_io/test_io_order.py::test_io_order[reactions-minimized_sorted-load_json_model-save_json_model-.json] PASSED [ 80%]\n",
      "test/test_io/test_io_order.py::test_io_order[reactions-minimized_sorted-load_yaml_model-save_yaml_model-.yml] PASSED [ 80%]\n",
      "test/test_io/test_io_order.py::test_io_order[metabolites-minimized_sorted-read_sbml_model-write_sbml_model-.xml] PASSED [ 81%]\n",
      "test/test_io/test_io_order.py::test_io_order[metabolites-minimized_sorted-load_json_model-save_json_model-.json] PASSED [ 81%]\n",
      "test/test_io/test_io_order.py::test_io_order[metabolites-minimized_sorted-load_yaml_model-save_yaml_model-.yml] PASSED [ 81%]\n",
      "test/test_io/test_io_order.py::test_io_order[genes-minimized_sorted-read_sbml_model-write_sbml_model-.xml] PASSED [ 82%]\n",
      "test/test_io/test_io_order.py::test_io_order[genes-minimized_sorted-load_json_model-save_json_model-.json] PASSED [ 82%]\n",
      "test/test_io/test_io_order.py::test_io_order[genes-minimized_sorted-load_yaml_model-save_yaml_model-.yml] PASSED [ 82%]\n",
      "test/test_io/test_io_order.py::test_io_order[genes-minimized_reverse-read_sbml_model-write_sbml_model-.xml] PASSED [ 83%]\n",
      "test/test_io/test_io_order.py::test_io_order[genes-minimized_reverse-load_json_model-save_json_model-.json] PASSED [ 83%]\n",
      "test/test_io/test_io_order.py::test_io_order[genes-minimized_reverse-load_yaml_model-save_yaml_model-.yml] PASSED [ 83%]\n",
      "test/test_io/test_io_order.py::test_io_order[genes-minimized_shuffle-read_sbml_model-write_sbml_model-.xml] PASSED [ 84%]\n",
      "test/test_io/test_io_order.py::test_io_order[genes-minimized_shuffle-load_json_model-save_json_model-.json] PASSED [ 84%]\n",
      "test/test_io/test_io_order.py::test_io_order[genes-minimized_shuffle-load_yaml_model-save_yaml_model-.yml] PASSED [ 84%]\n",
      "test/test_io/test_json.py::test_validate_json XFAIL                      [ 85%]\n",
      "test/test_io/test_json.py::test_load_json_model PASSED                   [ 85%]\n",
      "test/test_io/test_json.py::test_save_json_model XFAIL                    [ 85%]\n",
      "test/test_io/test_mat.py::test_load_matlab_model PASSED                  [ 86%]\n",
      "test/test_io/test_mat.py::test_save_matlab_model PASSED                  [ 86%]\n",
      "test/test_io/test_pickle.py::test_read_pickle[load] PASSED               [ 86%]\n",
      "test/test_io/test_pickle.py::test_read_pickle[None] SKIPPED              [ 87%]\n",
      "test/test_io/test_pickle.py::test_write_pickle[dump] PASSED              [ 87%]\n",
      "test/test_io/test_pickle.py::test_write_pickle[None] SKIPPED             [ 88%]\n",
      "test/test_io/test_sbml.py::TestCobraIO::test_read_1[fbc2] PASSED         [ 88%]\n",
      "test/test_io/test_sbml.py::TestCobraIO::test_read_2[fbc2] PASSED         [ 88%]\n",
      "test/test_io/test_sbml.py::TestCobraIO::test_write_1[fbc2] PASSED        [ 89%]\n",
      "test/test_io/test_sbml.py::TestCobraIO::test_write_2[fbc2] PASSED        [ 89%]\n",
      "test/test_io/test_sbml.py::TestCobraIO::test_read_1[fbc2Gz] PASSED       [ 89%]\n",
      "test/test_io/test_sbml.py::TestCobraIO::test_read_2[fbc2Gz] PASSED       [ 90%]\n",
      "test/test_io/test_sbml.py::TestCobraIO::test_write_1[fbc2Gz] PASSED      [ 90%]\n",
      "test/test_io/test_sbml.py::TestCobraIO::test_write_2[fbc2Gz] PASSED      [ 90%]\n",
      "test/test_io/test_sbml.py::TestCobraIO::test_read_1[fbc2Bz2] PASSED      [ 91%]\n",
      "test/test_io/test_sbml.py::TestCobraIO::test_read_2[fbc2Bz2] PASSED      [ 91%]\n",
      "test/test_io/test_sbml.py::TestCobraIO::test_write_1[fbc2Bz2] PASSED     [ 91%]\n",
      "test/test_io/test_sbml.py::TestCobraIO::test_write_2[fbc2Bz2] PASSED     [ 92%]\n",
      "test/test_io/test_sbml.py::TestCobraIO::test_read_1[fbc1] XFAIL          [ 92%]\n",
      "test/test_io/test_sbml.py::TestCobraIO::test_read_2[fbc1] XFAIL          [ 92%]\n",
      "test/test_io/test_sbml.py::TestCobraIO::test_write_1[fbc1] XFAIL         [ 93%]\n",
      "test/test_io/test_sbml.py::TestCobraIO::test_write_2[fbc1] XFAIL         [ 93%]\n",
      "test/test_io/test_sbml.py::TestCobraIO::test_read_1[cobra] PASSED        [ 93%]\n",
      "test/test_io/test_sbml.py::TestCobraIO::test_read_2[cobra] XFAIL         [ 94%]\n",
      "test/test_io/test_sbml.py::TestCobraIO::test_write_1[cobra] PASSED       [ 94%]\n",
      "test/test_io/test_sbml.py::TestCobraIO::test_write_2[cobra] XFAIL        [ 94%]\n",
      "test/test_io/test_sbml.py::test_filehandle PASSED                        [ 95%]\n",
      "test/test_io/test_sbml.py::test_from_sbml_string PASSED                  [ 95%]\n",
      "test/test_io/test_sbml.py::test_model_history SKIPPED                    [ 95%]\n",
      "test/test_io/test_sbml.py::test_groups PASSED                            [ 96%]\n",
      "test/test_io/test_sbml.py::test_missing_flux_bounds1 PASSED              [ 96%]\n",
      "test/test_io/test_sbml.py::test_missing_flux_bounds2 PASSED              [ 96%]\n",
      "test/test_io/test_sbml.py::test_validate PASSED                          [ 97%]\n",
      "test/test_io/test_sbml.py::test_validation_warnings PASSED               [ 97%]\n",
      "test/test_io/test_sbml.py::test_infinity_bounds PASSED                   [ 97%]\n",
      "test/test_io/test_sbml.py::test_boundary_conditions PASSED               [ 98%]\n",
      "test/test_io/test_sbml.py::test_gprs PASSED                              [ 98%]\n",
      "test/test_io/test_sbml.py::test_identifiers_annotation PASSED            [ 98%]\n",
      "test/test_io/test_sbml.py::test_smbl_with_notes PASSED                   [ 99%]\n",
      "test/test_io/test_yaml.py::test_load_yaml_model PASSED                   [ 99%]\n",
      "test/test_io/test_yaml.py::test_save_yaml_model XFAIL                    [100%]\n",
      "\n",
      "=================================== FAILURES ===================================\n",
      "____ test_metabolite_summary_to_table_previous_solution[optlang-glpk-q8_c] _____\n",
      "\n",
      "model = <Model e_coli_core at 0x7f3eae5be610>, opt_solver = 'optlang-glpk'\n",
      "met = 'q8_c'\n",
      "\n",
      "    @pytest.mark.parametrize(\"met\", [\"q8_c\"])\n",
      "    def test_metabolite_summary_to_table_previous_solution(model, opt_solver, met):\n",
      "        \"\"\"Test metabolite summary._to_table() of previous solution.\"\"\"\n",
      "        model.solver = opt_solver\n",
      "        solution = pfba(model)\n",
      "    \n",
      "        expected_entry = ['PRODUCING CYTBD     100    43.6  2.0 h_c + 0.5 o2_c + '\n",
      "                          'q8h2_c --> h2o_c + 2.0 h_...']\n",
      "    \n",
      "        with captured_output() as (out, _):\n",
      "            print(model.metabolites.get_by_id(met).summary(solution))\n",
      ">           check_in_line(out.getvalue(), expected_entry)\n",
      "\n",
      "/opt/conda/lib/python3.7/site-packages/cobra/test/test_core/test_summary/test_metabolite_summary.py:25: \n",
      "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n",
      "\n",
      "output = '                  PERCENT  FLUX                     REACTION_STRING                    \\nRXN_STAT  ID                ...-> 3.0 h_e + nad_c + q8h2_c\\n          SUCDi    11.6    5.06                        q8_c + succ_c --> fum_c + q8h2_c\\n'\n",
      "expected_entries = ['PRODUCING CYTBD     100    43.6  2.0 h_c + 0.5 o2_c + q8h2_c --> h2o_c + 2.0 h_...']\n",
      "pattern = re.compile('\\\\s')\n",
      "\n",
      "    def check_in_line(output, expected_entries,\n",
      "                      pattern=re.compile(r\"\\s\")):\n",
      "        \"\"\"Ensure each expected entry is contained in the output.\"\"\"\n",
      "        output_strip = [pattern.sub(\"\", line) for line in\n",
      "                        output.splitlines()]\n",
      "        for elem in expected_entries:\n",
      "            assert any(\n",
      "                pattern.sub(\"\", elem) in line for line in output_strip), \\\n",
      "                \"Not found: {} in:\\n{}\".format(pattern.sub(\"\", elem),\n",
      ">                                              \"\\n\".join(output_strip))\n",
      "E           AssertionError: Not found: PRODUCINGCYTBD10043.62.0h_c+0.5o2_c+q8h2_c-->h2o_c+2.0h_... in:\n",
      "E           PERCENTFLUXREACTION_STRING\n",
      "E           RXN_STATID\n",
      "E           PRODUCINGCYTBD10043.62.0h_c+0.5o2_c+q8h2_c-->h2o_c+2.0h_e+q8_c\n",
      "E           CONSUMINGNADH1688.438.54.0h_c+nadh_c+q8_c-->3.0h_e+nad_c+q8h2_c\n",
      "E           SUCDi11.65.06q8_c+succ_c-->fum_c+q8h2_c\n",
      "\n",
      "/opt/conda/lib/python3.7/site-packages/cobra/test/test_core/test_summary/__init__.py:43: AssertionError\n",
      "__________ test_metabolite_summary_to_table[optlang-glpk-q8_c-False] ___________\n",
      "\n",
      "model = <Model e_coli_core at 0x7f3eaea13050>, opt_solver = 'optlang-glpk'\n",
      "met = 'q8_c', names = False\n",
      "\n",
      "    @pytest.mark.parametrize(\"met, names\", [\n",
      "        (\"q8_c\", False),\n",
      "        (\"q8_c\", True)\n",
      "    ])\n",
      "    def test_metabolite_summary_to_table(model, opt_solver, met, names):\n",
      "        \"\"\"Test metabolite summary._to_table().\"\"\"\n",
      "        model.solver = opt_solver\n",
      "        model.optimize()\n",
      "    \n",
      "        if names:\n",
      "            expected_entry = ['PRODUCING cytochrome oxidase bd '\n",
      "                              '(ubiquinol-8: 2 protons)    100    43.6  '\n",
      "                              '2.0 H+ + 0.5 O2 + Ubiquinol-8 --> H2O + 2.0 H+...']\n",
      "        else:\n",
      "            expected_entry = ['PRODUCING CYTBD     100    43.6  2.0 h_c + '\n",
      "                              '0.5 o2_c + q8h2_c --> h2o_c + 2.0 h_...']\n",
      "    \n",
      "        with captured_output() as (out, _):\n",
      "            print(model.metabolites.get_by_id(met).summary(names=names))\n",
      ">           check_in_line(out.getvalue(), expected_entry)\n",
      "\n",
      "/opt/conda/lib/python3.7/site-packages/cobra/test/test_core/test_summary/test_metabolite_summary.py:60: \n",
      "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n",
      "\n",
      "output = '                  PERCENT  FLUX                     REACTION_STRING                    \\nRXN_STAT  ID                ...-> 3.0 h_e + nad_c + q8h2_c\\n          SUCDi    11.6    5.06                        q8_c + succ_c --> fum_c + q8h2_c\\n'\n",
      "expected_entries = ['PRODUCING CYTBD     100    43.6  2.0 h_c + 0.5 o2_c + q8h2_c --> h2o_c + 2.0 h_...']\n",
      "pattern = re.compile('\\\\s')\n",
      "\n",
      "    def check_in_line(output, expected_entries,\n",
      "                      pattern=re.compile(r\"\\s\")):\n",
      "        \"\"\"Ensure each expected entry is contained in the output.\"\"\"\n",
      "        output_strip = [pattern.sub(\"\", line) for line in\n",
      "                        output.splitlines()]\n",
      "        for elem in expected_entries:\n",
      "            assert any(\n",
      "                pattern.sub(\"\", elem) in line for line in output_strip), \\\n",
      "                \"Not found: {} in:\\n{}\".format(pattern.sub(\"\", elem),\n",
      ">                                              \"\\n\".join(output_strip))\n",
      "E           AssertionError: Not found: PRODUCINGCYTBD10043.62.0h_c+0.5o2_c+q8h2_c-->h2o_c+2.0h_... in:\n",
      "E           PERCENTFLUXREACTION_STRING\n",
      "E           RXN_STATID\n",
      "E           PRODUCINGCYTBD10043.62.0h_c+0.5o2_c+q8h2_c-->h2o_c+2.0h_e+q8_c\n",
      "E           CONSUMINGNADH1688.438.54.0h_c+nadh_c+q8_c-->3.0h_e+nad_c+q8h2_c\n",
      "E           SUCDi11.65.06q8_c+succ_c-->fum_c+q8h2_c\n",
      "\n",
      "/opt/conda/lib/python3.7/site-packages/cobra/test/test_core/test_summary/__init__.py:43: AssertionError\n",
      "___________ test_metabolite_summary_to_table[optlang-glpk-q8_c-True] ___________\n",
      "\n",
      "model = <Model e_coli_core at 0x7f3eaecf2510>, opt_solver = 'optlang-glpk'\n",
      "met = 'q8_c', names = True\n",
      "\n",
      "    @pytest.mark.parametrize(\"met, names\", [\n",
      "        (\"q8_c\", False),\n",
      "        (\"q8_c\", True)\n",
      "    ])\n",
      "    def test_metabolite_summary_to_table(model, opt_solver, met, names):\n",
      "        \"\"\"Test metabolite summary._to_table().\"\"\"\n",
      "        model.solver = opt_solver\n",
      "        model.optimize()\n",
      "    \n",
      "        if names:\n",
      "            expected_entry = ['PRODUCING cytochrome oxidase bd '\n",
      "                              '(ubiquinol-8: 2 protons)    100    43.6  '\n",
      "                              '2.0 H+ + 0.5 O2 + Ubiquinol-8 --> H2O + 2.0 H+...']\n",
      "        else:\n",
      "            expected_entry = ['PRODUCING CYTBD     100    43.6  2.0 h_c + '\n",
      "                              '0.5 o2_c + q8h2_c --> h2o_c + 2.0 h_...']\n",
      "    \n",
      "        with captured_output() as (out, _):\n",
      "            print(model.metabolites.get_by_id(met).summary(names=names))\n",
      ">           check_in_line(out.getvalue(), expected_entry)\n",
      "\n",
      "/opt/conda/lib/python3.7/site-packages/cobra/test/test_core/test_summary/test_metabolite_summary.py:60: \n",
      "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n",
      "\n",
      "output = '                                                          PERCENT  FLUX                                              ...                                                                 Ubiquinone-8 + Succinate --> Fumarate + Ubiquinol-8\\n'\n",
      "expected_entries = ['PRODUCING cytochrome oxidase bd (ubiquinol-8: 2 protons)    100    43.6  2.0 H+ + 0.5 O2 + Ubiquinol-8 --> H2O + 2.0 H+...']\n",
      "pattern = re.compile('\\\\s')\n",
      "\n",
      "    def check_in_line(output, expected_entries,\n",
      "                      pattern=re.compile(r\"\\s\")):\n",
      "        \"\"\"Ensure each expected entry is contained in the output.\"\"\"\n",
      "        output_strip = [pattern.sub(\"\", line) for line in\n",
      "                        output.splitlines()]\n",
      "        for elem in expected_entries:\n",
      "            assert any(\n",
      "                pattern.sub(\"\", elem) in line for line in output_strip), \\\n",
      "                \"Not found: {} in:\\n{}\".format(pattern.sub(\"\", elem),\n",
      ">                                              \"\\n\".join(output_strip))\n",
      "E           AssertionError: Not found: PRODUCINGcytochromeoxidasebd(ubiquinol-8:2protons)10043.62.0H++0.5O2+Ubiquinol-8-->H2O+2.0H+... in:\n",
      "E           PERCENTFLUXREACTION_STRING\n",
      "E           RXN_STATID\n",
      "E           PRODUCINGcytochromeoxidasebd(ubiquinol-8:2protons)10043.62.0H++0.5O2+Ubiquinol-8-->H2O+2.0H++Ubiquinone-8\n",
      "E           CONSUMINGNADHdehydrogenase(ubiquinone-8&3protons)88.438.54.0H++Nicotinamideadeninedinucleotide-reduced+Ubiquinone-8-->3.0H++Nicotinamideadeninedinucleotide+Ubiquinol-8\n",
      "E           succinatedehydrogenase(irreversible)11.65.06Ubiquinone-8+Succinate-->Fumarate+Ubiquinol-8\n",
      "\n",
      "/opt/conda/lib/python3.7/site-packages/cobra/test/test_core/test_summary/__init__.py:43: AssertionError\n",
      "=============================== warnings summary ===============================\n",
      "test/test_manipulation.py::TestManipulation::test_escape_ids\n",
      "  /opt/conda/lib/python3.7/site-packages/optlang/interface.py:1358 \u001b[1;31mDeprecationWarning\u001b[0m: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3,and in 3.9 it will stop working\n",
      "\n",
      "test/test_manipulation.py: 6 tests with warnings\n",
      "test/test_medium.py: 3 tests with warnings\n",
      "test/test_core/test_core_reaction.py: 2 tests with warnings\n",
      "test/test_core/test_model.py: 5 tests with warnings\n",
      "  cobra/core/model.py:525 \u001b[1;31mDeprecationWarning\u001b[0m: add_reaction deprecated. Use add_reactions instead\n",
      "\n",
      "test/test_medium.py::TestModelMedium::test_model_medium\n",
      "test/test_medium.py::TestModelMedium::test_model_medium\n",
      "  cobra/core/model.py:289 \u001b[1;31mDeprecationWarning\u001b[0m: The 'warn' method is deprecated, use 'warning' instead\n",
      "\n",
      "test/test_medium.py: 11 tests with warnings\n",
      "  cobra/medium/minimal_medium.py:100 \u001b[1;31mDeprecationWarning\u001b[0m: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning.\n",
      "\n",
      "test/test_medium.py::TestErrorsAndExceptions::test_no_names_or_boundary_reactions\n",
      "  cobra/medium/boundary_types.py:50 \u001b[1;31mDeprecationWarning\u001b[0m: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_bounds_scenario_1\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ACALD' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_bounds_scenario_3\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ACALD' to a fixed flux value of -9. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_bounds_scenario_3\n",
      "test/test_core/test_core_reaction.py::test_set_bounds_scenario_4\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ACALD' to a fixed flux value of 2. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_bounds_scenario_3\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ACALD' to a fixed flux value of -10. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_bounds_scenario_3\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ACALD' to a fixed flux value of -11. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_bounds_scenario_4\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ACALD' to a fixed flux value of -2. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_bounds_scenario_2\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ACALD' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_make_irreversible_irreversible_to_the_other_side\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PFK' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_knockout\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ATPM' to a fixed flux value of 8.39. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ACALDt' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ACKr' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ACONTa' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ACONTb' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ACt2r' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ADK1' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'AKGDH' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'AKGt2r' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ALCD2x' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ATPM' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ATPS4r' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'Biomass_Ecoli_core' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'CO2t' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'CS' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'CYTBD' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'D_LACt2' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ENO' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ETOHt2r' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_ac_e' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_acald_e' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_akg_e' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_co2_e' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_etoh_e' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_for_e' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_fru_e' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_fum_e' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_glc__D_e' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_gln__L_e' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_glu__L_e' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_h_e' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_h2o_e' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_lac__D_e' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_mal__L_e' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_nh4_e' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_o2_e' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_pi_e' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_pyr_e' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_succ_e' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'FBA' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'FBP' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'FORt2' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'FORti' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'FRD7' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'FRUpts2' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'FUM' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'FUMt2_2' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'G6PDH2r' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'GAPD' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'GLCpts' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'GLNS' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'GLNabc' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'GLUDy' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'GLUN' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'GLUSy' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'GLUt2r' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'GND' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'H2Ot' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ICDHyr' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ICL' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'LDH_D' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'MALS' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'MALt2_2' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'MDH' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ME1' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ME2' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'NADH16' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'NADTRHD' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'NH4t' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'O2t' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PDH' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PFK' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PFL' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PGI' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PGK' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PGL' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PGM' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PIt2r' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PPC' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PPCK' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PPS' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PTAr' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PYK' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PYRt2' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'RPE' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'RPI' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'SUCCt2_2' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'SUCCt3' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'SUCDi' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'SUCOAS' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'TALA' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'THD2' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'TKT1' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'TKT2' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb\n",
      "  cobra/core/reaction.py:246 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'TPI' to a fixed flux value of 1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ACALDt' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ACKr' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ACONTa' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ACONTb' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ACt2r' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ADK1' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'AKGDH' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'AKGt2r' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ALCD2x' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ATPM' to a fixed flux value of -91.61. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ATPS4r' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'Biomass_Ecoli_core' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'CO2t' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'CS' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'CYTBD' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'D_LACt2' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ENO' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ETOHt2r' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_ac_e' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_acald_e' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_akg_e' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_co2_e' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_etoh_e' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_for_e' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_fru_e' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_fum_e' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_glc__D_e' to a fixed flux value of -110.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_gln__L_e' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_glu__L_e' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_h_e' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_h2o_e' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_lac__D_e' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_mal__L_e' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_nh4_e' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_o2_e' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_pi_e' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_pyr_e' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'EX_succ_e' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'FBA' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'FBP' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'FORt2' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'FORti' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'FRD7' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'FRUpts2' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'FUM' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'FUMt2_2' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'G6PDH2r' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'GAPD' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'GLCpts' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'GLNS' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'GLNabc' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'GLUDy' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'GLUN' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'GLUSy' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'GLUt2r' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'GND' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'H2Ot' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ICDHyr' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ICL' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'LDH_D' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'MALS' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'MALt2_2' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'MDH' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ME1' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'ME2' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'NADH16' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'NADTRHD' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'NH4t' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'O2t' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PDH' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PFL' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PGI' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PGK' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PGL' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PGM' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PIt2r' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PPC' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PPCK' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PPS' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PTAr' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PYK' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'PYRt2' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'RPE' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'RPI' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'SUCCt2_2' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'SUCCt3' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'SUCDi' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'SUCOAS' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'TALA' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'THD2' to a fixed flux value of -100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'TKT1' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'TKT2' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub\n",
      "  cobra/core/reaction.py:276 \u001b[1;31mDeprecationWarning\u001b[0m: You are constraining the reaction 'TPI' to a fixed flux value of -1100.0. Did you intend to do this? We are planning to remove this behavior in a future release. Please let us know your opinion at https://github.com/opencobra/cobrapy/issues/793.\n",
      "\n",
      "test/test_core/test_model.py::test_reaction_delete\n",
      "test/test_core/test_model.py::test_reaction_delete\n",
      "  cobra/core/reaction.py:599 \u001b[1;31mDeprecationWarning\u001b[0m: delete is deprecated. Use reaction.remove_from_model instead\n",
      "\n",
      "test/test_core/test_model.py::test_group_loss_of_elements\n",
      "  cobra/core/group.py:109 \u001b[1;31mUserWarning\u001b[0m: need to pass in a list\n",
      "\n",
      "test/test_core/test_model.py::test_group_loss_of_elements\n",
      "  cobra/core/gene.py:237 \u001b[1;31mUserWarning\u001b[0m: Use cobra.manipulation.remove_genes instead\n",
      "\n",
      "test/test_core/test_model.py::test_merge_models\n",
      "  cobra/core/model.py:307 \u001b[1;31mDeprecationWarning\u001b[0m: use model.merge instead\n",
      "\n",
      "test/test_core/test_model.py::test_merge_models\n",
      "  cobra/core/model.py:317 \u001b[1;31mDeprecationWarning\u001b[0m: use model.merge instead\n",
      "\n",
      "test/test_core/test_summary/test_metabolite_summary.py::test_metabolite_summary_to_table_previous_solution[optlang-glpk-q8_c]\n",
      "test/test_core/test_summary/test_metabolite_summary.py::test_metabolite_summary_to_table[optlang-glpk-q8_c-False]\n",
      "test/test_core/test_summary/test_metabolite_summary.py::test_metabolite_summary_to_table[optlang-glpk-q8_c-True]\n",
      "test/test_core/test_summary/test_metabolite_summary.py::test_metabolite_summary_to_table_with_fva[optlang-glpk-0.99-fdp_c]\n",
      "test/test_core/test_summary/test_model_summary.py::test_model_summary_to_table_previous_solution[optlang-glpk-False]\n",
      "test/test_core/test_summary/test_model_summary.py::test_model_summary_to_table_previous_solution[optlang-glpk-True]\n",
      "test/test_core/test_summary/test_model_summary.py::test_model_summary_to_table[optlang-glpk-False]\n",
      "test/test_core/test_summary/test_model_summary.py::test_model_summary_to_table[optlang-glpk-True]\n",
      "test/test_core/test_summary/test_model_summary.py::test_model_summary_to_table_with_fva[optlang-glpk-0.95]\n",
      "  cobra/core/summary/summary.py:206 \u001b[1;31mUserWarning\u001b[0m: Setting float_format to anything other than None will cause nan to be present in the output.\n",
      "\n",
      "test/test_core/test_summary/test_reaction_summary.py::test_reaction_summary_to_frame[ACALD-False]\n",
      "test/test_core/test_summary/test_reaction_summary.py::test_reaction_summary_to_frame[FUM-True]\n",
      "  cobra/core/summary/reaction_summary.py:82 \u001b[1;31mFutureWarning\u001b[0m: The pandas.np module is deprecated and will be removed from pandas in a future version. Import numpy directly instead\n",
      "\n",
      "test/test_io/test_sbml.py::TestCobraIO::test_write_1[cobra]\n",
      "  cobra/util/solver.py:416 \u001b[1;31mUserWarning\u001b[0m: solver status is 'infeasible'\n",
      "\n",
      "-- Docs: https://docs.pytest.org/en/latest/warnings.html\n",
      "=========================== short test summary info ============================\n",
      "SKIPPED [21] /opt/conda/lib/python3.7/site-packages/pytest_benchmark/plugin.py:395: Benchmarks are skipped (--benchmark-skip was used).\n",
      "SKIPPED [1] ../../opt/conda/lib/python3.7/site-packages/cobra/test/test_core/test_core_reaction.py:109: No CPLEX found on PYTHONPATH\n",
      "SKIPPED [1] ../../opt/conda/lib/python3.7/site-packages/cobra/test/test_core/test_core_reaction.py:109: No Gurobi found on PYTHONPATH\n",
      "SKIPPED [1] ../../opt/conda/lib/python3.7/site-packages/cobra/test/test_core/test_metabolite.py:27: No CPLEX found on PYTHONPATH\n",
      "SKIPPED [1] ../../opt/conda/lib/python3.7/site-packages/cobra/test/test_core/test_metabolite.py:27: No Gurobi found on PYTHONPATH\n",
      "SKIPPED [1] ../../opt/conda/lib/python3.7/site-packages/cobra/test/test_core/test_metabolite.py:40: No CPLEX found on PYTHONPATH\n",
      "SKIPPED [1] ../../opt/conda/lib/python3.7/site-packages/cobra/test/test_core/test_metabolite.py:40: No Gurobi found on PYTHONPATH\n",
      "SKIPPED [1] ../../opt/conda/lib/python3.7/site-packages/cobra/test/test_core/test_model.py:934: need cplex\n",
      "SKIPPED [1] ../../opt/conda/lib/python3.7/site-packages/cobra/test/test_core/test_model.py:964: no cplex\n",
      "SKIPPED [1] ../../opt/conda/lib/python3.7/site-packages/cobra/test/test_core/test_model.py:978: No CPLEX found on PYTHONPATH\n",
      "SKIPPED [1] ../../opt/conda/lib/python3.7/site-packages/cobra/test/test_core/test_model.py:978: No Gurobi found on PYTHONPATH\n",
      "SKIPPED [1] ../../opt/conda/lib/python3.7/site-packages/cobra/test/test_core/test_solution.py:10: No CPLEX found on PYTHONPATH\n",
      "SKIPPED [1] ../../opt/conda/lib/python3.7/site-packages/cobra/test/test_core/test_solution.py:10: No Gurobi found on PYTHONPATH\n",
      "SKIPPED [2] ../../opt/conda/lib/python3.7/site-packages/cobra/test/test_core/test_summary/test_reaction_summary.py:14: has some weird formatting issue\n",
      "SKIPPED [1] /opt/conda/lib/python3.7/site-packages/cobra/test/test_io/test_pickle.py:28: <Skipped instance>\n",
      "SKIPPED [1] /opt/conda/lib/python3.7/site-packages/cobra/test/test_io/test_pickle.py:40: <Skipped instance>\n",
      "SKIPPED [1] ../../opt/conda/lib/python3.7/site-packages/cobra/test/test_io/test_sbml.py:204: Model history currently not written\n",
      "===== 3 failed, 241 passed, 38 skipped, 10 xfailed, 249 warnings in 59.74s =====\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<ExitCode.TESTS_FAILED: 1>"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "test_all()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.6"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}