code: import warnings
  from os import path
  from tempfile import TemporaryDirectory
  import pytest
  from petab.C import *
  from petab.visualize import (plot_data_and_simulation,
                               plot_measurements_by_observable,
                               save_vis_spec)
  import matplotlib.pyplot as plt
  
  
  @pytest.fixture
  def data_file_Fujita():
      return "doc/example/example_Fujita/Fujita_measurementData.tsv"
  
  
  @pytest.fixture
  def condition_file_Fujita():
      return "doc/example/example_Fujita/Fujita_experimentalCondition.tsv"
  
  
  @pytest.fixture
  def data_file_Fujita_wrongNoise():
      return "doc/example/example_Fujita/Fujita_measurementData_wrongNoise.tsv"
  
  
  @pytest.fixture
  def data_file_Fujita_nanData():
      return "doc/example/example_Fujita/Fujita_measurementData_nanData.tsv"
  
  
  @pytest.fixture
  def simu_file_Fujita():
      return "doc/example/example_Fujita/Fujita_simulatedData.tsv"
  
  
  @pytest.fixture
  def data_file_Fujita_minimal():
      return "doc/example/example_Fujita/Fujita_measurementData_minimal.tsv"
  
  
  @pytest.fixture
  def visu_file_Fujita_small():
      return "doc/example/example_Fujita/Fujita_visuSpec_small.tsv"
  
  
  @pytest.fixture
  def visu_file_Fujita_wo_dsid():
      return "doc/example/example_Fujita/visuSpecs/Fujita_visuSpec_1.tsv"
  
  
  @pytest.fixture
  def visu_file_Fujita_minimal():
      return "doc/example/example_Fujita/visuSpecs/Fujita_visuSpec_mandatory.tsv"
  
  
  @pytest.fixture
  def visu_file_Fujita_empty():
      return "doc/example/example_Fujita/visuSpecs/Fujita_visuSpec_empty.tsv"
  
  
  @pytest.fixture
  def data_file_Isensee():
      return "doc/example/example_Isensee/Isensee_measurementData.tsv"
  
  
  @pytest.fixture
  def condition_file_Isensee():
      return "doc/example/example_Isensee/Isensee_experimentalCondition.tsv"
  
  
  @pytest.fixture
  def vis_spec_file_Isensee():
      return "doc/example/example_Isensee/Isensee_visualizationSpecification.tsv"
  
  
  @pytest.fixture
  def simulation_file_Isensee():
      return "doc/example/example_Isensee/Isensee_simulationData.tsv"
  
  
  def test_visualization_with_vis_and_sim(data_file_Isensee,
                                          condition_file_Isensee,
                                          vis_spec_file_Isensee,
                                          simulation_file_Isensee):
      plot_data_and_simulation(data_file_Isensee,
                               condition_file_Isensee,
                               vis_spec_file_Isensee,
                               simulation_file_Isensee)
  
  
  def test_visualization_with_vis(data_file_Isensee,
                                  condition_file_Isensee,
                                  vis_spec_file_Isensee):
      plot_data_and_simulation(data_file_Isensee,
                               condition_file_Isensee,
                               vis_spec_file_Isensee)
  
  
  def test_visualization_small_visu_file_w_datasetid(data_file_Fujita,
                                                     condition_file_Fujita,
                                                     visu_file_Fujita_small):
      """
      Test: visualization spezification file only with few columns in
      particular datasetId
      (optional columns are optional)
      """
      plot_data_and_simulation(data_file_Fujita,
                               condition_file_Fujita,
                               visu_file_Fujita_small)
  
  
  def test_visualization_small_visu_file_wo_datasetid(data_file_Fujita,
                                                      condition_file_Fujita,
                                                      visu_file_Fujita_wo_dsid):
      """
      Test: visualization spezification file only with few columns in
      particular no datasetId column
      (optional columns are optional)
      """
      plot_data_and_simulation(data_file_Fujita,
                               condition_file_Fujita,
                               visu_file_Fujita_wo_dsid)
  
  
  def test_visualization_minimal_visu_file(data_file_Fujita,
                                           condition_file_Fujita,
                                           visu_file_Fujita_minimal):
      """
      Test: visualization spezification file only with mandatory column plotId
      (optional columns are optional)
      """
      plot_data_and_simulation(data_file_Fujita,
                               condition_file_Fujita,
                               visu_file_Fujita_minimal)
  
  
  def test_visualization_empty_visu_file(data_file_Fujita,
                                         condition_file_Fujita,
                                         visu_file_Fujita_empty):
      """
      Test: Empty visualization spezification file should default to routine
      for no file at all
      """
      plot_data_and_simulation(data_file_Fujita,
                               condition_file_Fujita,
                               visu_file_Fujita_empty)
  
  
  def test_visualization_minimal_data_file(data_file_Fujita_minimal,
                                           condition_file_Fujita,
                                           visu_file_Fujita_small):
      """
      Test visualization, with the case: data file only with mandatory columns
      (optional columns are optional)
      """
      plot_data_and_simulation(data_file_Fujita_minimal,
                               condition_file_Fujita,
                               visu_file_Fujita_small)
  
  
  def test_visualization_with_dataset_list(data_file_Isensee,
                                           condition_file_Isensee,
                                           simulation_file_Isensee):
      datasets = [['JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_ctrl',
                   'JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_Fsk'],
                  ['JI09_160201_Drg453-452_CycNuc__ctrl',
                   'JI09_160201_Drg453-452_CycNuc__Fsk',
                   'JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM']]
      plot_data_and_simulation(data_file_Isensee,
                               condition_file_Isensee,
                               dataset_id_list=datasets)
  
      plot_data_and_simulation(data_file_Isensee,
                               condition_file_Isensee,
                               sim_data=simulation_file_Isensee,
                               dataset_id_list=datasets)
  
  
  def test_visualization_without_datasets(data_file_Fujita,
                                          condition_file_Fujita,
                                          simu_file_Fujita):
      sim_cond_num_list = [[0, 1, 2], [0, 2, 3], [0, 3, 4], [0, 4, 5]]
      sim_cond_id_list = [['model1_data1'], ['model1_data2', 'model1_data3'],
                          ['model1_data4', 'model1_data5'], ['model1_data6']]
      observable_num_list = [[0], [1], [2], [0, 2], [1, 2]]
      observable_id_list = [['pS6_tot'], ['pEGFR_tot'], ['pAkt_tot']]
  
      plot_data_and_simulation(data_file_Fujita, condition_file_Fujita,
                               sim_cond_num_list=sim_cond_num_list,
                               plotted_noise=PROVIDED)
      plot_data_and_simulation(data_file_Fujita, condition_file_Fujita,
                               sim_data=simu_file_Fujita,
                               sim_cond_num_list=sim_cond_num_list,
                               plotted_noise=PROVIDED)
  
      plot_data_and_simulation(data_file_Fujita, condition_file_Fujita,
                               sim_cond_id_list=sim_cond_id_list)
      plot_data_and_simulation(data_file_Fujita, condition_file_Fujita,
                               sim_data=simu_file_Fujita,
                               sim_cond_id_list=sim_cond_id_list)
  
      plot_data_and_simulation(data_file_Fujita, condition_file_Fujita,
                               observable_num_list=observable_num_list)
      plot_data_and_simulation(data_file_Fujita, condition_file_Fujita,
                               sim_data=simu_file_Fujita,
                               observable_num_list=observable_num_list)
  
      plot_data_and_simulation(data_file_Fujita, condition_file_Fujita,
                               observable_id_list=observable_id_list,
                               plotted_noise=PROVIDED)
      plot_data_and_simulation(data_file_Fujita, condition_file_Fujita,
                               sim_data=simu_file_Fujita,
                               observable_id_list=observable_id_list,
                               plotted_noise=PROVIDED)
  
  
  def test_visualization_omit_empty_datasets(data_file_Fujita_nanData,
                                             condition_file_Fujita):
      observable_num_list = [[0, 1]]
      plot_data_and_simulation(data_file_Fujita_nanData, condition_file_Fujita,
                               observable_num_list=observable_num_list)
  
  
  def test_visualization_raises(data_file_Fujita,
                                condition_file_Fujita,
                                data_file_Fujita_wrongNoise):
      sim_cond_num_list = [[0, 1, 2], [0, 2, 3], [0, 3, 4], [0, 4, 5]]
      sim_cond_id_list = [['model1_data1'], ['model1_data2', 'model1_data3'],
                          ['model1_data4', 'model1_data5'], ['model1_data6']]
      observable_num_list = [[0], [1], [2], [0, 2], [1, 2]]
      observable_id_list = [['pS6_tot'], ['pEGFR_tot'], ['pAkt_tot']]
      error_counter = 0
  
      # Combining simulation condition numbers and IDs should not be allowed
      try:
          plot_data_and_simulation(data_file_Fujita, condition_file_Fujita,
                                   sim_cond_num_list=sim_cond_num_list,
                                   sim_cond_id_list=sim_cond_id_list)
      except NotImplementedError as ErrMsg:
          assert(ErrMsg.args[0] == 'Either specify a list of simulation '
                                   'condition IDs or a list of simulation '
                                   'condition numbers, but not both. '
                                   'Stopping.')
          error_counter += 1
      assert (error_counter == 1)
  
      # Combining observable numbers and IDs should not be allowed
      try:
          plot_data_and_simulation(data_file_Fujita, condition_file_Fujita,
                                   observable_num_list=observable_num_list,
                                   observable_id_list=observable_id_list)
      except NotImplementedError as ErrMsg:
          assert(ErrMsg.args[0] == 'Either specify a list of observable IDs or '
                                   'a list of observable numbers, but not both. '
                                   'Stopping.')
          error_counter += 1
      assert (error_counter == 2)
  
      # Combining observable and simulation conditions numbers or IDs should not
      # be allowed
      try:
          plot_data_and_simulation(data_file_Fujita, condition_file_Fujita,
                                   sim_cond_num_list=observable_num_list,
                                   observable_num_list=observable_num_list)
      except NotImplementedError as ErrMsg:
          assert(ErrMsg.args[0] == 'Plotting without visualization specification'
                                   ' file and datasetId can be performed via '
                                   'grouping by simulation conditions OR '
                                   'observables, but not both. Stopping.')
          error_counter += 1
      assert (error_counter == 3)
      try:
          plot_data_and_simulation(data_file_Fujita, condition_file_Fujita,
                                   sim_cond_id_list=observable_id_list,
                                   observable_id_list=observable_id_list)
      except NotImplementedError as ErrMsg:
          assert(ErrMsg.args[0] == 'Plotting without visualization specification'
                                   ' file and datasetId can be performed via '
                                   'grouping by simulation conditions OR '
                                   'observables, but not both. Stopping.')
          error_counter += 1
      assert (error_counter == 4)
  
      # If no numerical noise is provided, it should not work to plot it
      try:
          plot_measurements_by_observable(data_file_Fujita_wrongNoise,
                                          condition_file_Fujita,
                                          plotted_noise='provided')
      except NotImplementedError as ErrMsg:
          assert(ErrMsg.args[0] == "No numerical noise values provided in the "
                                   "measurement table. Stopping.")
          error_counter += 1
  
      assert (error_counter == 5)
  
  
  def test_visualization_warnings(data_file_Isensee, condition_file_Isensee):
      datasets = [['JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_ctrl',
                   'JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_Fsk'],
                  ['JI09_160201_Drg453-452_CycNuc__ctrl',
                   'JI09_160201_Drg453-452_CycNuc__Fsk',
                   'JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM']]
      sim_cond_num_list = [[0, 1, 2], [0, 2, 3], [0, 3, 4], [0, 4, 5]]
      observable_num_list = [[0], [1], [2], [0, 2], [1, 2]]
  
      # close open figures to avoid runtime warnings
      plt.close("all")
  
      with warnings.catch_warnings(record=True) as warnMsg:
          # Cause all warnings to always be triggered.
          warnings.simplefilter("always")
          # plotting with datasetIds and sim conditions should issue a warning
          plot_data_and_simulation(data_file_Isensee,
                                   condition_file_Isensee,
                                   dataset_id_list=datasets,
                                   sim_cond_num_list=sim_cond_num_list)
  
          # plotting with datasetIds and observables should issue a warning
          plot_data_and_simulation(data_file_Isensee,
                                   condition_file_Isensee,
                                   dataset_id_list=datasets,
                                   observable_num_list=observable_num_list)
  
          # plotting with datasetIds and observables and sim conditions should
          # issue a warning
          plot_data_and_simulation(data_file_Isensee,
                                   condition_file_Isensee,
                                   dataset_id_list=datasets,
                                   observable_num_list=observable_num_list,
                                   sim_cond_num_list=sim_cond_num_list)
  
          # plotting grouped by something else than datasetIds should issue a
          # warning if datasetsIDs would have been available
          plot_data_and_simulation(data_file_Isensee,
                                   condition_file_Isensee,
                                   sim_cond_num_list=sim_cond_num_list)
  
          # test correct number of warnings
          warnings_list = [msg for msg in warnMsg if
                           not issubclass(msg.category, DeprecationWarning)]
          assert len(warnings_list) == 4
  
          # test that all warnings were indeed UserWarnings
          for i_warn in warnings_list:
              assert issubclass(i_warn.category, UserWarning)
  
  
  def test_simple_visualization(data_file_Fujita, condition_file_Fujita):
      plot_measurements_by_observable(data_file_Fujita, condition_file_Fujita)
      plot_measurements_by_observable(data_file_Fujita, condition_file_Fujita,
                                      plotted_noise=PROVIDED)
  
  
  def test_save_plots_to_file(data_file_Isensee, condition_file_Isensee,
                              vis_spec_file_Isensee, simulation_file_Isensee):
      with TemporaryDirectory() as temp_dir:
          plot_data_and_simulation(
              data_file_Isensee,
              condition_file_Isensee,
              vis_spec_file_Isensee,
              simulation_file_Isensee,
              subplot_file_path=temp_dir)
  
  
  def test_save_visu_file(data_file_Isensee,
                          condition_file_Isensee):
  
      with TemporaryDirectory() as temp_dir:
          save_vis_spec(data_file_Isensee,
                        condition_file_Isensee,
                        output_file_path=path.join(temp_dir, "visuSpec.tsv"))
  
          datasets = [['JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_ctrl',
                       'JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_Fsk'],
                      ['JI09_160201_Drg453-452_CycNuc__ctrl',
                       'JI09_160201_Drg453-452_CycNuc__Fsk',
                       'JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM']]
  
          save_vis_spec(data_file_Isensee,
                        condition_file_Isensee,
                        dataset_id_list=datasets,
                        output_file_path=path.join(temp_dir, "visuSpec1.tsv"))
  
apis: matplotlib.pyplot.close