From 2bb1b1654850ec67d992a49c77e4a9c3babd8502 Mon Sep 17 00:00:00 2001 From: Mark Robinson Date: Fri, 29 May 2020 07:48:26 +0000 Subject: [PATCH] Auto-saving for mark.robinson on branch master from commit dbf813b --- Untitled.ipynb | 1180 ++++++++++++++++++++++++++++++++++ bio334_spring2020_exam.Rproj | 13 + 2 files changed, 1193 insertions(+) create mode 100644 Untitled.ipynb create mode 100644 bio334_spring2020_exam.Rproj diff --git a/Untitled.ipynb b/Untitled.ipynb new file mode 100644 index 0000000..df757ec --- /dev/null +++ b/Untitled.ipynb @@ -0,0 +1,1180 @@ +{ + "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", + 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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 = , 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 = , 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 = , 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: \n", + "SKIPPED [1] /opt/conda/lib/python3.7/site-packages/cobra/test/test_io/test_pickle.py:40: \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": [ + "" + ] + }, + "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 +} diff --git a/bio334_spring2020_exam.Rproj b/bio334_spring2020_exam.Rproj new file mode 100644 index 0000000..8e3c2eb --- /dev/null +++ b/bio334_spring2020_exam.Rproj @@ -0,0 +1,13 @@ +Version: 1.0 + +RestoreWorkspace: Default +SaveWorkspace: Default +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX -- GitLab