Warnings emitted when running pytest while cutting release

[lbianchi-lbl]

• The warnings are displayed during the test run
• Normally (i.e. in PRs, when running from a local Git clone, etc) we don't see these, most likely because of options in the pytest CLI invocation and/or pytest.ini (that's not available when running pytest as part of the release process
• Most of the warnings seem straightforward to fix and we should do that
• NOTE the warning about the missing pytest.mark.solver marker was repeated hundreds of times and I had to manually remove it from the log below

============================================================================================================ test session starts =============================================================================================================
platform linux -- Python 3.8.13, pytest-7.1.2, pluggy-1.0.0
rootdir: /tmp/tmp.e0Q8YgKJfs
collected 1983 items                                                                                                                                                                                                                         

core/plugins/tests/test_solvers.py ........................                                                                                                                                                                            [  1%]
core/tests/test_wt_database.py ................                                                                                                                                                                                        [  2%]
core/tests/test_zero_order_base.py ................                                                                                                                                                                                    [  2%]
core/tests/test_zero_order_costing.py .............                                                                                                                                                                                    [  3%]
core/tests/test_zero_order_diso.py .........                                                                                                                                                                                           [  3%]
core/tests/test_zero_order_electricity.py ..............                                                                                                                                                                               [  4%]
core/tests/test_zero_order_properties.py ...........                                                                                                                                                                                   [  5%]
core/tests/test_zero_order_pt.py ......                                                                                                                                                                                                [  5%]
core/tests/test_zero_order_sido.py ..........                                                                                                                                                                                          [  6%]
core/tests/test_zero_order_sido_reactive.py .....................                                                                                                                                                                      [  7%]
core/tests/test_zero_order_siso.py .........                                                                                                                                                                                           [  7%]
core/util/tests/test_infeasible.py .........                                                                                                                                                                                           [  7%]
core/util/tests/test_initialization.py ...............                                                                                                                                                                                 [  8%]
data/techno_economic/tests/test_unit_parameter_files.py ....................................................................................................                                                                           [ 13%]
data/techno_economic/tests/test_water_sources.py .........                                                                                                                                                                             [ 14%]
edb/tests/test_commands.py ......X.....................xxxx.xxxx.XXXX.xxxx                                                                                                                                                             [ 16%]
edb/tests/test_data_model.py ................                                                                                                                                                                                          [ 17%]
edb/tests/test_db_api.py sss....                                                                                                                                                                                                       [ 17%]
edb/tests/test_edb.py ...s                                                                                                                                                                                                             [ 17%]
edb/tests/test_schemas.py ..                                                                                                                                                                                                           [ 18%]
edb/tests/test_validate.py ....                                                                                                                                                                                                        [ 18%]
examples/chemistry/tests/test__fixtures.py .                                                                                                                                                                                           [ 18%]
examples/chemistry/tests/test_chlorination.py ........                                                                                                                                                                                 [ 18%]
examples/chemistry/tests/test_docs.py s                                                                                                                                                                                                [ 18%]
examples/chemistry/tests/test_enrtl_water_pH.py ..............                                                                                                                                                                         [ 19%]
examples/chemistry/tests/test_notebooks.py s                                                                                                                                                                                           [ 19%]
examples/chemistry/tests/test_pH_dependent_solubility.py ..................                                                                                                                                                            [ 20%]
examples/chemistry/tests/test_pure_water_pH.py ................................                                                                                                                                                        [ 22%]
examples/chemistry/tests/test_recarbonation_process.py .......                                                                                                                                                                         [ 22%]
examples/chemistry/tests/test_remineralization.py ...............                                                                                                                                                                      [ 23%]
examples/chemistry/tests/test_seawater_alkalinity.py ................                                                                                                                                                                  [ 23%]
examples/chemistry/tests/test_solids.py .............                                                                                                                                                                                  [ 24%]
examples/chemistry/tests/test_tutorials.py .                                                                                                                                                                                           [ 24%]
examples/chemistry/tests/test_water_softening.py ........                                                                                                                                                                              [ 25%]
examples/edb/tests/test__fixtures.py .                                                                                                                                                                                                 [ 25%]
examples/edb/tests/test_edb_examples.py .......                                                                                                                                                                                        [ 25%]
examples/flowsheets/RO_with_energy_recovery/tests/test_RO_with_energy_recovery_simulation.py ........                                                                                                                                  [ 25%]
examples/flowsheets/RO_with_energy_recovery/tests/test_monte_carlo_sampling_RO_ERD.py ...                                                                                                                                              [ 26%]
examples/flowsheets/case_studies/municipal_treatment/tests/test_municipal_treatment.py .                                                                                                                                               [ 26%]
examples/flowsheets/case_studies/seawater_RO_desalination/tests/test_seawater_RO_desalination.py ..                                                                                                                                    [ 26%]
examples/flowsheets/full_treatment_train/analysis/tests/test_flowsheets.py ........                                                                                                                                                    [ 26%]
examples/flowsheets/full_treatment_train/analysis/tests/test_multi_sweep.py ..............                                                                                                                                             [ 27%]
examples/flowsheets/full_treatment_train/flowsheet_components/chemistry/tests/test_posttreatment.py .....                                                                                                                              [ 27%]
examples/flowsheets/full_treatment_train/flowsheet_components/chemistry/tests/test_pretreatment.py ....                                                                                                                                [ 27%]
examples/flowsheets/full_treatment_train/flowsheet_components/examples/test_full_example.py ..                                                                                                                                         [ 27%]
examples/flowsheets/full_treatment_train/flowsheet_components/tests/test_desalination.py .                                                                                                                                             [ 27%]
examples/flowsheets/full_treatment_train/flowsheet_components/tests/test_pretreatment.py .                                                                                                                                             [ 27%]
examples/flowsheets/full_treatment_train/flowsheet_components/tests/test_pretreatment_softening.py ..                                                                                                                                  [ 28%]
examples/flowsheets/full_treatment_train/flowsheet_components/tests/test_translator_block.py .                                                                                                                                         [ 28%]
examples/flowsheets/full_treatment_train/model_components/eNRTL/test_enrtl.py ....                                                                                                                                                     [ 28%]
examples/flowsheets/full_treatment_train/model_components/tests/test_prop_pack.py .........................                                                                                                                            [ 29%]
examples/flowsheets/full_treatment_train/model_components/tests/test_property_models.py ...                                                                                                                                            [ 29%]
examples/flowsheets/full_treatment_train/model_components/tests/test_unit_models.py .......                                                                                                                                            [ 30%]
examples/flowsheets/lsrro/tests/test_lsrro.py ...........................                                                                                                                                                              [ 31%]
property_models/tests/test_NaCl_prop_pack.py ..........................................                                                                                                                                                [ 33%]
property_models/tests/test_coag_prop_pack.py .........                                                                                                                                                                                 [ 33%]
property_models/tests/test_cryst_prop_pack.py .................................................                                                                                                                                        [ 36%]
property_models/tests/test_ion_DSPMDE_prop_pack.py ........                                                                                                                                                                            [ 36%]
property_models/tests/test_seawater_ion_generic.py .                                                                                                                                                                                   [ 36%]
property_models/tests/test_seawater_prop_pack.py .........................................                                                                                                                                             [ 38%]
property_models/tests/test_water_prop_pack.py ......................................                                                                                                                                                   [ 40%]
tests/test_notebooks.py s                                                                                                                                                                                                              [ 40%]
tools/tests/test_parameter_sweep.py ...................                                                                                                                                                                                [ 41%]
tools/tests/test_parameter_sweep_input_parser.py ......                                                                                                                                                                                [ 42%]
unit_models/mvc/components/tests/test_chen_heat_exchanger.py .                                                                                                                                                                         [ 42%]
unit_models/mvc/components/tests/test_complete_condenser.py .                                                                                                                                                                          [ 42%]
unit_models/mvc/components/tests/test_compressor.py .                                                                                                                                                                                  [ 42%]
unit_models/mvc/components/tests/test_evaporator.py .                                                                                                                                                                                  [ 42%]
unit_models/mvc/tests/test_mvc.py .                                                                                                                                                                                                    [ 42%]
unit_models/tests/test_coag_floc_model.py ..............                                                                                                                                                                               [ 43%]
unit_models/tests/test_crystallizer.py .........                                                                                                                                                                                       [ 43%]
unit_models/tests/test_nanofiltration_0D.py .........                                                                                                                                                                                  [ 44%]
unit_models/tests/test_nanofiltration_DSPMDE_0D.py .........                                                                                                                                                                           [ 44%]
unit_models/tests/test_nanofiltration_ZO.py ............                                                                                                                                                                               [ 45%]
unit_models/tests/test_pressure_exchanger.py .........                                                                                                                                                                                 [ 45%]
unit_models/tests/test_pump_isothermal.py .......                                                                                                                                                                                      [ 45%]
unit_models/tests/test_reverse_osmosis_0D.py ....................                                                                                                                                                                      [ 46%]
unit_models/tests/test_reverse_osmosis_1D.py ......................                                                                                                                                                                    [ 48%]
unit_models/zero_order/tests/test_aeration_basin_zo.py ....................                                                                                                                                                            [ 49%]
unit_models/zero_order/tests/test_air_flotation_zo.py ...................                                                                                                                                                              [ 50%]
unit_models/zero_order/tests/test_anaerobic_digestion_oxidation_zo.py ...................                                                                                                                                              [ 50%]
unit_models/zero_order/tests/test_anaerobic_mbr_mec_zo.py ............                                                                                                                                                                 [ 51%]
unit_models/zero_order/tests/test_backwash_solids_handling_zo.py ..........                                                                                                                                                            [ 52%]
unit_models/zero_order/tests/test_bio_active_filtration_zo.py ...................                                                                                                                                                      [ 53%]
unit_models/zero_order/tests/test_bioreactor_zo.py .........                                                                                                                                                                           [ 53%]
unit_models/zero_order/tests/test_blending_reservoir_zo.py .........                                                                                                                                                                   [ 53%]
unit_models/zero_order/tests/test_brine_concentrator_zo.py ......................                                                                                                                                                      [ 55%]
unit_models/zero_order/tests/test_buffer_tank_zo.py .........                                                                                                                                                                          [ 55%]
unit_models/zero_order/tests/test_cartridge_filtration_zo.py ...................                                                                                                                                                       [ 56%]
unit_models/zero_order/tests/test_chemical_addition_zo.py ...........................                                                                                                                                                  [ 57%]
unit_models/zero_order/tests/test_chlorination_zo.py .................                                                                                                                                                                 [ 58%]
unit_models/zero_order/tests/test_clarifier_zo.py ...................                                                                                                                                                                  [ 59%]
unit_models/zero_order/tests/test_co2_addition_zo.py .........                                                                                                                                                                         [ 60%]
unit_models/zero_order/tests/test_coag_and_floc_zo.py .........                                                                                                                                                                        [ 60%]
unit_models/zero_order/tests/test_cofermentation_zo.py ..........                                                                                                                                                                      [ 61%]
unit_models/zero_order/tests/test_constructed_wetlands_zo.py ........                                                                                                                                                                  [ 61%]
unit_models/zero_order/tests/test_cooling_supply_zo.py .........                                                                                                                                                                       [ 61%]
unit_models/zero_order/tests/test_cooling_tower_zo.py ..........                                                                                                                                                                       [ 62%]
unit_models/zero_order/tests/test_decarbonator_zo.py .................                                                                                                                                                                 [ 63%]
unit_models/zero_order/tests/test_deep_well_injection_zo.py ..........                                                                                                                                                                 [ 63%]
unit_models/zero_order/tests/test_dissolved_air_flotation_zo.py ..................                                                                                                                                                     [ 64%]
unit_models/zero_order/tests/test_dmbr_zo.py ..........                                                                                                                                                                                [ 65%]
unit_models/zero_order/tests/test_dual_media_filtration_zo.py ...................                                                                                                                                                      [ 66%]
unit_models/zero_order/tests/test_electrodialysis_reversal_zo.py ...........                                                                                                                                                           [ 66%]
unit_models/zero_order/tests/test_energy_recovery_zo.py .........                                                                                                                                                                      [ 67%]
unit_models/zero_order/tests/test_evaporation_pond_zo.py ..........                                                                                                                                                                    [ 67%]
unit_models/zero_order/tests/test_feed_water_tank_zo.py .........                                                                                                                                                                      [ 68%]
unit_models/zero_order/tests/test_feed_zo.py ........                                                                                                                                                                                  [ 68%]
unit_models/zero_order/tests/test_filter_press_zo.py ..........                                                                                                                                                                        [ 69%]
unit_models/zero_order/tests/test_fixed_bed_zo.py ....................                                                                                                                                                                 [ 70%]
unit_models/zero_order/tests/test_gac_zo.py ......................                                                                                                                                                                     [ 71%]
unit_models/zero_order/tests/test_gas_sparged_membrane.py ...........                                                                                                                                                                  [ 71%]
unit_models/zero_order/tests/test_injection_well_disposal_zo.py .........                                                                                                                                                              [ 72%]
unit_models/zero_order/tests/test_intrusion_mitigation_zo.py .........                                                                                                                                                                 [ 72%]
unit_models/zero_order/tests/test_ion_exchange_zo.py ...........................                                                                                                                                                       [ 73%]
unit_models/zero_order/tests/test_iron_and_manganese_removal_zo.py ..........                                                                                                                                                          [ 74%]
unit_models/zero_order/tests/test_landfill_zo.py ..........                                                                                                                                                                            [ 74%]
unit_models/zero_order/tests/test_mabr_zo.py ..........                                                                                                                                                                                [ 75%]
unit_models/zero_order/tests/test_mbr_zo.py ......................                                                                                                                                                                     [ 76%]
unit_models/zero_order/tests/test_media_filtration_zo.py ...................                                                                                                                                                           [ 77%]
unit_models/zero_order/tests/test_microfiltration_zo.py ..................                                                                                                                                                             [ 78%]
unit_models/zero_order/tests/test_microscreen_filtration_zo.py ...................                                                                                                                                                     [ 79%]
unit_models/zero_order/tests/test_municipal_drinking_zo.py .........                                                                                                                                                                   [ 79%]
unit_models/zero_order/tests/test_municipal_wwtp_zo.py .........                                                                                                                                                                       [ 80%]
unit_models/zero_order/tests/test_nanofiltration_zo.py ..................                                                                                                                                                              [ 81%]
unit_models/zero_order/tests/test_ozone_aop_zo.py ...................                                                                                                                                                                  [ 82%]
unit_models/zero_order/tests/test_ozone_zo.py ..................                                                                                                                                                                       [ 83%]
unit_models/zero_order/tests/test_primary_separator_zo.py ...................                                                                                                                                                          [ 84%]
unit_models/zero_order/tests/test_pump_zo.py ...................                                                                                                                                                                       [ 85%]
unit_models/zero_order/tests/test_screen_zo.py ..........                                                                                                                                                                              [ 85%]
unit_models/zero_order/tests/test_sedimentation_zo.py .................................                                                                                                                                                [ 87%]
unit_models/zero_order/tests/test_settling_pond_zo.py ...................                                                                                                                                                              [ 88%]
unit_models/zero_order/tests/test_sludge_tank_zo.py ...................                                                                                                                                                                [ 89%]
unit_models/zero_order/tests/test_smp_zo.py .........                                                                                                                                                                                  [ 89%]
unit_models/zero_order/tests/test_static_mixer_zo.py .........                                                                                                                                                                         [ 90%]
unit_models/zero_order/tests/test_storage_tank_zo.py .........                                                                                                                                                                         [ 90%]
unit_models/zero_order/tests/test_surface_discharge.py ....................                                                                                                                                                            [ 91%]
unit_models/zero_order/tests/test_sw_onshore_intake_zo.py .........                                                                                                                                                                    [ 91%]
unit_models/zero_order/tests/test_tramp_oil_tank_zo.py ........                                                                                                                                                                        [ 92%]
unit_models/zero_order/tests/test_tri_media_filtration_zo.py ..................                                                                                                                                                        [ 93%]
unit_models/zero_order/tests/test_ultra_filtration_zo.py ...................                                                                                                                                                           [ 94%]
unit_models/zero_order/tests/test_uv_aop_zo.py .................                                                                                                                                                                       [ 95%]
unit_models/zero_order/tests/test_uv_zo.py .................                                                                                                                                                                           [ 95%]
unit_models/zero_order/tests/test_vfa_recovery_zo.py ...................                                                                                                                                                               [ 96%]
unit_models/zero_order/tests/test_waiv_zo.py ..........                                                                                                                                                                                [ 97%]
unit_models/zero_order/tests/test_walnut_shell_filter_zo.py ..........                                                                                                                                                                 [ 97%]
unit_models/zero_order/tests/test_water_pumping_station_zo.py ......................                                                                                                                                                   [ 98%]
unit_models/zero_order/tests/test_well_field_zo.py ....................                                                                                                                                                                [100%]

============================================================================================================== warnings summary ==============================================================================================================
../../opt/conda/envs/test-watertap-0.5.0rc1/lib/python3.8/site-packages/pyomo/contrib/pynumero/sparse/block_matrix.py:25
  /opt/conda/envs/test-watertap-0.5.0rc1/lib/python3.8/site-packages/pyomo/contrib/pynumero/sparse/block_matrix.py:25: DeprecationWarning: Please use `get_index_dtype` from the `scipy.sparse` namespace, the `scipy.sparse.sputils` namespace is deprecated.
    from scipy.sparse.sputils import get_index_dtype

../../opt/conda/envs/test-watertap-0.5.0rc1/lib/python3.8/site-packages/watertap/core/tests/test_zero_order_base.py:200
  /opt/conda/envs/test-watertap-0.5.0rc1/lib/python3.8/site-packages/watertap/core/tests/test_zero_order_base.py:200: DeprecationWarning: invalid escape sequence \(
    " \(index: None\) in database."):

../../opt/conda/envs/test-watertap-0.5.0rc1/lib/python3.8/site-packages/watertap/core/tests/test_zero_order_base.py:219
  /opt/conda/envs/test-watertap-0.5.0rc1/lib/python3.8/site-packages/watertap/core/tests/test_zero_order_base.py:219: DeprecationWarning: invalid escape sequence \(
    " \(index: None\) in database.")

../../opt/conda/envs/test-watertap-0.5.0rc1/lib/python3.8/site-packages/watertap/unit_models/zero_order/tests/test_well_field_zo.py:249
  /opt/conda/envs/test-watertap-0.5.0rc1/lib/python3.8/site-packages/watertap/unit_models/zero_order/tests/test_well_field_zo.py:249: PytestUnknownMarkWarning: Unknown pytest.mark.solver - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
    @pytest.mark.solver

data/techno_economic/tests/test_water_sources.py: 9 warnings
examples/flowsheets/case_studies/municipal_treatment/tests/test_municipal_treatment.py: 1 warning
examples/flowsheets/case_studies/seawater_RO_desalination/tests/test_seawater_RO_desalination.py: 2 warnings
unit_models/mvc/components/tests/test_complete_condenser.py: 1 warning
unit_models/mvc/components/tests/test_compressor.py: 1 warning
unit_models/mvc/components/tests/test_evaporator.py: 2 warnings
unit_models/mvc/tests/test_mvc.py: 3 warnings
unit_models/tests/test_crystallizer.py: 1 warning
unit_models/zero_order/tests/test_cofermentation_zo.py: 2 warnings
unit_models/zero_order/tests/test_feed_zo.py: 2 warnings
  /opt/conda/envs/test-watertap-0.5.0rc1/lib/python3.8/site-packages/idaes/core/unit_model.py:101: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead
    _log.warn(f"DEPRECATION: {str(self.__class__)} has overloaded the "

examples/flowsheets/RO_with_energy_recovery/tests/test_monte_carlo_sampling_RO_ERD.py: 3 warnings
examples/flowsheets/full_treatment_train/analysis/tests/test_multi_sweep.py: 14 warnings
tools/tests/test_parameter_sweep.py: 14 warnings
  /opt/conda/envs/test-watertap-0.5.0rc1/lib/python3.8/site-packages/watertap/tools/parameter_sweep.py:128: UserWarning: Could not import mpi4py from current environment (defaulting to serial).
    warnings.warn("Could not import mpi4py from current environment (defaulting to serial).")

examples/flowsheets/RO_with_energy_recovery/tests/test_monte_carlo_sampling_RO_ERD.py: 15 warnings
examples/flowsheets/full_treatment_train/analysis/tests/test_multi_sweep.py: 90 warnings
tools/tests/test_parameter_sweep.py: 59 warnings
  /opt/conda/envs/test-watertap-0.5.0rc1/lib/python3.8/site-packages/watertap/tools/parameter_sweep.py:375: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    comp_dict["value"] = np.zeros(num_samples, dtype=np.float)

examples/flowsheets/RO_with_energy_recovery/tests/test_monte_carlo_sampling_RO_ERD.py::test_monte_carlo_sampling_with_files
  /opt/conda/envs/test-watertap-0.5.0rc1/lib/python3.8/site-packages/watertap/tools/parameter_sweep_input_parser.py:171: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead
    _log.warn(f"Cannot set value of component {component}")

examples/flowsheets/case_studies/seawater_RO_desalination/tests/test_seawater_RO_desalination.py: 2 warnings
examples/flowsheets/full_treatment_train/analysis/tests/test_flowsheets.py: 2 warnings
examples/flowsheets/full_treatment_train/analysis/tests/test_multi_sweep.py: 2 warnings
examples/flowsheets/full_treatment_train/flowsheet_components/examples/test_full_example.py: 2 warnings
examples/flowsheets/lsrro/tests/test_lsrro.py: 6 warnings
  /opt/conda/envs/test-watertap-0.5.0rc1/lib/python3.8/site-packages/watertap/unit_models/reverse_osmosis_0D.py:376: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead
    init_log.warn("Trouble solving ReverseOsmosis0D unit model, trying one more time")

examples/flowsheets/full_treatment_train/analysis/tests/test_multi_sweep.py::test_multi_sweep[6-1D]
unit_models/tests/test_reverse_osmosis_1D.py::TestReverseOsmosis::test_initialize
  /opt/conda/envs/test-watertap-0.5.0rc1/lib/python3.8/site-packages/watertap/unit_models/reverse_osmosis_1D.py:421: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead
    init_log.warn("Trouble solving ReverseOsmosis1D unit model, trying one more time")

tools/tests/test_parameter_sweep_input_parser.py::TestInputParser::test_set_defaults_from_yaml
  /opt/conda/envs/test-watertap-0.5.0rc1/lib/python3.8/site-packages/watertap/tools/parameter_sweep_input_parser.py:168: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead
    _log.warn(f"Cannot set value of non-mutable Param {component}")

unit_models/tests/test_nanofiltration_DSPMDE_0D.py::TestNanoFiltration::test_initialize
  /opt/conda/envs/test-watertap-0.5.0rc1/lib/python3.8/site-packages/watertap/unit_models/nanofiltration_DSPMDE_0D.py:1036: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead
    init_log.warn("Trouble solving NanofiltrationDSPMDE0D unit model with deactivated constraint.")

unit_models/tests/test_nanofiltration_DSPMDE_0D.py::TestNanoFiltration::test_initialize
  /opt/conda/envs/test-watertap-0.5.0rc1/lib/python3.8/site-packages/watertap/unit_models/nanofiltration_DSPMDE_0D.py:1043: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead
    init_log.warn("Trouble solving NanofiltrationDSPMDE0D unit model. Trying one more time.")

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
============================================================================== 1959 passed, 7 skipped, 12 xfailed, 5 xpassed, 505 warnings in 497.56s (0:08:17) ==============================================================================

[ksbeattie]

Closing this, as this will come up again during the next release.