Update Python and packages

[tamuri]

WARNING: Don't do this until it's confirmed everything works!

We need to:

1. Update to a recent version of Python (3.11? 3.10?)
2. Update the package dependencies.

We've done this before in #144.

[tamuri]

Steps :

1. Create a new conda environment, specifying version of Python: conda create -n tlo310 python=3.10
2. Activate: conda activate tlo310
3. Install requirements (note: not the file with pinned versions). In TLOmodel directory: pip install -r requirements/dev.in
4. Install TLOmodel: pip install -e .
5. Test:pytest

[tamuri]

Lots of errors because the old way of slicing dataframe to set categorical columns doesn't work. Column dtypes gets coerced to object. e.g. district_of_residence in demography module.

This demonstrates the problem (and possible solution):

df = pd.DataFrame(data={'is_alive':[True, True, True], 'catcol': pd.Categorical([np.nan, np.nan, np.nan], categories=['A', 'B', 'C'])})

# In [54]: df.dtypes
# Out[54]:
# is_alive        bool
# catcol      category
# dtype: object

s = pd.Series(['A', 'A', 'B'])

# this works on current version, but breaks when dependencies are updated:
df.loc[df.is_alive, 'catcol'] = s.values[:]

# gives this warning:
# <ipython-input-51-f84c3c1188d6>:1: FutureWarning: In a future version, `df.iloc[:, i] = newvals` will attempt to set the values inplace instead of always setting a new array. To retain the old behavior, use either `df[df.columns[i]] = newvals` or, if columns are non-unique, `df.isetitem(i, newvals)`

# and breaks dtypes of columns
# In [52]: df.dtypes
# Out[52]:
# is_alive      bool
# catcol      object
# dtype: object

# this way works:
df = pd.DataFrame(data={'is_alive':[True, True, True], 'catcol': pd.Categorical([np.nan, np.nan, np.nan], categories=['A', 'B', 'C'])})
df.loc[df.is_alive, 'catcol'] = s.to_list()
df.dtypes

is_alive        bool
catcol      category
dtype: object

In [56]: df.catcol.cat.categories
Out[56]: Index(['A', 'B', 'C'], dtype='object')

[matt-graham]

1. Update to a recent version of Python (3.11? 3.10?)

I would vote for updating to Python 3.11 if we taking the pain of getting everything working with updated dependencies anyway as Python 3.11 has some performance improvements that can give significant speedups over 3.10 (10-60% depending on task).

[tamuri]

I think we're leaning toward using Anaconda packages. [Once we have this sorted...] I thought we could set up Dependabot to keep us up to date. There is some discussion about how to support conda envs, so might need to think of some alternative (to dependabot).

[matt-graham]

df = pd.DataFrame(data={'is_alive':[True, True, True], 'catcol': pd.Categorical([np.nan, np.nan, np.nan], categories=['A', 'B', 'C'])})

# In [54]: df.dtypes
# Out[54]:
# is_alive        bool
# catcol      category
# dtype: object

s = pd.Series(['A', 'A', 'B'])

# this works on current version, but breaks when dependencies are updated:
df.loc[df.is_alive, 'catcol'] = s.values[:]

# gives this warning:
# <ipython-input-51-f84c3c1188d6>:1: FutureWarning: In a future version, `df.iloc[:, i] = newvals` will attempt to set the values inplace instead of always setting a new array. To retain the old behavior, use either `df[df.columns[i]] = newvals` or, if columns are non-unique, `df.isetitem(i, newvals)`

@tamuri Can you remember which version of Pandas this breaks on? Running this example with Python 3.11 with Pandas 1.5.3 (current latest stable release) I get a deprecation warning (was previously a FutureWarning but was updated in pandas-dev/pandas#50044, see also related discussion in pandas-dev/pandas#48673), but running on Python 3.11 with Pandas 2.0.0rc1 the example runs without a warning or error (and with the dataframe updated as expected and with column datatype retained).

[matt-graham]

Running the non-slow tests on Python 3.11 with Pandas 2.0.0rc1 overall test summary is

273 failed, 487 passed, 149 skipped, 20 warnings, 34 errors in 106.12s

with the main error types causing test failures are

AttributeError: 'Series' object has no attribute 'iteritems'
AttributeError: 'DataFrame' object has no attribute 'append'
TypeError: Categorical input must be list-like
TypeError: Cannot setitem on a Categorical with a new category (A), set the categories first
TypeError: Casting to unit-less dtype 'datetime64' is not supported. Pass e.g. 'datetime64[ns]' instead.

Package versions in conda environment conda list

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
adal                      1.2.7                    pypi_0    pypi
asttokens                 2.2.1                    pypi_0    pypi
attrs                     22.2.0                   pypi_0    pypi
azure-batch               13.0.0                   pypi_0    pypi
azure-common              1.1.28                   pypi_0    pypi
azure-core                1.26.3                   pypi_0    pypi
azure-identity            1.12.0                   pypi_0    pypi
azure-keyvault            4.2.0                    pypi_0    pypi
azure-keyvault-certificates 4.7.0                    pypi_0    pypi
azure-keyvault-keys       4.8.0                    pypi_0    pypi
azure-keyvault-secrets    4.7.0                    pypi_0    pypi
azure-storage-file-share  12.11.1                  pypi_0    pypi
backcall                  0.2.0                    pypi_0    pypi
build                     0.10.0                   pypi_0    pypi
bzip2                     1.0.8                h7f98852_4    conda-forge
ca-certificates           2022.12.7            ha878542_0    conda-forge
cachetools                5.3.0                    pypi_0    pypi
certifi                   2022.12.7                pypi_0    pypi
cffi                      1.15.1                   pypi_0    pypi
chardet                   5.1.0                    pypi_0    pypi
charset-normalizer        3.1.0                    pypi_0    pypi
click                     8.1.3                    pypi_0    pypi
colorama                  0.4.6                    pypi_0    pypi
contourpy                 1.0.7                    pypi_0    pypi
cryptography              40.0.1                   pypi_0    pypi
cycler                    0.11.0                   pypi_0    pypi
decorator                 5.1.1                    pypi_0    pypi
distlib                   0.3.6                    pypi_0    pypi
et-xmlfile                1.1.0                    pypi_0    pypi
execnet                   1.9.0                    pypi_0    pypi
executing                 1.2.0                    pypi_0    pypi
filelock                  3.10.6                   pypi_0    pypi
fonttools                 4.39.2                   pypi_0    pypi
gitdb                     4.0.10                   pypi_0    pypi
gitpython                 3.1.31                   pypi_0    pypi
idna                      3.4                      pypi_0    pypi
iniconfig                 2.0.0                    pypi_0    pypi
ipython                   8.11.0                   pypi_0    pypi
isodate                   0.6.1                    pypi_0    pypi
jedi                      0.18.2                   pypi_0    pypi
kiwisolver                1.4.4                    pypi_0    pypi
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgomp                   12.2.0              h65d4601_19    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libsqlite                 3.40.0               h753d276_0    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libzlib                   1.2.13               h166bdaf_4    conda-forge
matplotlib                3.7.1                    pypi_0    pypi
matplotlib-inline         0.1.6                    pypi_0    pypi
msal                      1.21.0                   pypi_0    pypi
msal-extensions           1.0.0                    pypi_0    pypi
msrest                    0.7.1                    pypi_0    pypi
msrestazure               0.6.4                    pypi_0    pypi
ncurses                   6.3                  h27087fc_1    conda-forge
numpy                     1.24.2                   pypi_0    pypi
oauthlib                  3.2.2                    pypi_0    pypi
openpyxl                  3.1.2                    pypi_0    pypi
openssl                   3.1.0                h0b41bf4_0    conda-forge
packaging                 23.0                     pypi_0    pypi
pandas                    2.0.0rc1                 pypi_0    pypi
parso                     0.8.3                    pypi_0    pypi
pexpect                   4.8.0                    pypi_0    pypi
pickleshare               0.7.5                    pypi_0    pypi
pillow                    9.4.0                    pypi_0    pypi
pip                       23.0.1             pyhd8ed1ab_0    conda-forge
pip-tools                 6.12.3                   pypi_0    pypi
platformdirs              3.2.0                    pypi_0    pypi
pluggy                    1.0.0                    pypi_0    pypi
portalocker               2.7.0                    pypi_0    pypi
prompt-toolkit            3.0.38                   pypi_0    pypi
ptyprocess                0.7.0                    pypi_0    pypi
pure-eval                 0.2.2                    pypi_0    pypi
pycparser                 2.21                     pypi_0    pypi
pygments                  2.14.0                   pypi_0    pypi
pyjwt                     2.6.0                    pypi_0    pypi
pyparsing                 3.0.9                    pypi_0    pypi
pyproject-api             1.5.1                    pypi_0    pypi
pyproject-hooks           1.0.0                    pypi_0    pypi
pyshp                     2.3.1                    pypi_0    pypi
pytest                    7.2.2                    pypi_0    pypi
pytest-xdist              3.2.1                    pypi_0    pypi
python                    3.11.0          he550d4f_1_cpython    conda-forge
python-dateutil           2.8.2                    pypi_0    pypi
pytz                      2023.2                   pypi_0    pypi
readline                  8.2                  h8228510_1    conda-forge
requests                  2.28.2                   pypi_0    pypi
requests-oauthlib         1.3.1                    pypi_0    pypi
scipy                     1.10.1                   pypi_0    pypi
setuptools                67.6.0             pyhd8ed1ab_0    conda-forge
six                       1.16.0                   pypi_0    pypi
smmap                     5.0.0                    pypi_0    pypi
squarify                  0.4.3                    pypi_0    pypi
stack-data                0.6.2                    pypi_0    pypi
tk                        8.6.12               h27826a3_0    conda-forge
tlo                       0.1.0                     dev_0    <develop>
tox                       4.4.8                    pypi_0    pypi
traitlets                 5.9.0                    pypi_0    pypi
typing-extensions         4.5.0                    pypi_0    pypi
tzdata                    2023b                h71feb2d_0    conda-forge
urllib3                   1.26.15                  pypi_0    pypi
virtualenv                20.21.0                  pypi_0    pypi
wcwidth                   0.2.6                    pypi_0    pypi
wheel                     0.40.0             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge

Failed tests for pytest tests --skip-slow

ERROR tests/test_alri.py::test_integrity_of_linear_models[83563095832589325021] - TypeError: Categorical input must be list-like
ERROR tests/test_alri.py::test_basic_run[83563095832589325021] - TypeError: Categorical input must be list-like
ERROR tests/test_alri.py::test_alri_polling[83563095832589325021] - TypeError: Categorical input must be list-like
ERROR tests/test_alri.py::test_nat_hist_recovery[83563095832589325021] - TypeError: Categorical input must be list-like
ERROR tests/test_alri.py::test_nat_hist_death[83563095832589325021] - TypeError: Categorical input must be list-like
ERROR tests/test_alri.py::test_nat_hist_cure_if_recovery_scheduled[83563095832589325021] - TypeError: Categorical input must be list-like
ERROR tests/test_alri.py::test_nat_hist_cure_if_death_scheduled[83563095832589325021] - TypeError: Categorical input must be list-like
ERROR tests/test_alri.py::test_immediate_onset_complications[83563095832589325021] - TypeError: Categorical input must be list-like
ERROR tests/test_alri.py::test_no_immediate_onset_complications[83563095832589325021] - TypeError: Categorical input must be list-like
ERROR tests/test_alri.py::test_classification_based_on_symptoms_and_imci[83563095832589325021] - TypeError: Categorical input must be list-like
ERROR tests/test_alri.py::test_do_effects_of_alri_treatment[83563095832589325021] - TypeError: Categorical input must be list-like
ERROR tests/test_dxmanager.py::test_create_dx_test_and_register[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
ERROR tests/test_alri.py::test_severe_pneumonia_referral_from_hsi_first_appts[83563095832589325021] - TypeError: Categorical input must be list-like
ERROR tests/test_dxmanager.py::test_create_duplicate_test_that_should_be_allowed[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
ERROR tests/test_dxmanager.py::test_create_dx_test_and_run[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
ERROR tests/test_dxmanager.py::test_create_dx_tests_with_consumable_useage_given_by_item_code_only[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
ERROR tests/test_dxmanager.py::test_dx_tests_with_optional_consumable[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
ERROR tests/test_dxmanager.py::test_run_batch_of_dx_test_in_one_call[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
ERROR tests/test_dxmanager.py::test_create_tuple_of_dx_tests_which_fail_and_require_chain_execution[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
ERROR tests/test_dxmanager.py::test_create_dx_test_and_run_with_imperfect_sensitivity[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
ERROR tests/test_dxmanager.py::test_create_dx_test_and_run_with_bool_dx_and_imperfect_specificity[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
ERROR tests/test_dxmanager.py::test_create_dx_test_and_run_with_cont_value_and_cutoff[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
ERROR tests/test_dxmanager.py::test_create_dx_test_and_run_with_cont_dx_and_error[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
ERROR tests/test_dxmanager.py::test_dx_with_categorial[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
ERROR tests/test_dxmanager.py::test_dx_with_categorial_multiple_levels_accepted[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
ERROR tests/test_logging_end_to_end.py::TestWriteAndReadLog::test_rows_as_dicts - TypeError: Casting to unit-less dtype 'datetime64' is not supported. Pass e.g. 'datetime64[ns]' instead.
ERROR tests/test_logging_end_to_end.py::TestWriteAndReadLog::test_rows_as_individuals - TypeError: Casting to unit-less dtype 'datetime64' is not supported. Pass e.g. 'datetime64[ns]' instead.
ERROR tests/test_logging_end_to_end.py::TestWriteAndReadLog::test_log_entire_df - TypeError: Casting to unit-less dtype 'datetime64' is not supported. Pass e.g. 'datetime64[ns]' instead.
ERROR tests/test_logging_end_to_end.py::TestWriteAndReadLog::test_fixed_length_list - TypeError: Casting to unit-less dtype 'datetime64' is not supported. Pass e.g. 'datetime64[ns]' instead.
ERROR tests/test_logging_end_to_end.py::TestWriteAndReadLog::test_variable_length_list - TypeError: Casting to unit-less dtype 'datetime64' is not supported. Pass e.g. 'datetime64[ns]' instead.
ERROR tests/test_logging_end_to_end.py::TestWriteAndReadLog::test_string - TypeError: Casting to unit-less dtype 'datetime64' is not supported. Pass e.g. 'datetime64[ns]' instead.
ERROR tests/test_logging_end_to_end.py::TestWriteAndReadLog::test_categorical - TypeError: Casting to unit-less dtype 'datetime64' is not supported. Pass e.g. 'datetime64[ns]' instead.
ERROR tests/test_logging_end_to_end.py::test_parse_log_file - TypeError: Casting to unit-less dtype 'datetime64' is not supported. Pass e.g. 'datetime64[ns]' instead.
ERROR tests/test_logging_end_to_end.py::test_parsed_log_object_pickleable - TypeError: Casting to unit-less dtype 'datetime64' is not supported. Pass e.g. 'datetime64[ns]' instead.
FAILED tests/test_diarrhoea.py::test_do_when_presentation_with_diarrhoea_severe_dehydration[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_bladder_cancer.py::test_initial_config_of_pop_high_prevalence[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_diarrhoea.py::test_do_when_presentation_with_diarrhoea_severe_dehydration_dxtest_notfunctional[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_cardiometabolicdisorders.py::test_no_availability_of_consumables_for_conditions[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_bladder_cancer.py::test_initial_config_of_pop_zero_prevalence[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_diarrhoea.py::test_do_when_presentation_with_diarrhoea_non_severe_dehydration[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_bladder_cancer.py::test_initial_config_of_pop_usual_prevalence[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_cardiometabolicdisorders.py::test_no_availability_of_consumables_for_events[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_diarrhoea.py::test_run_each_of_the_HSI[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_breast_cancer.py::test_initial_config_of_pop_high_prevalence[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_diarrhoea.py::test_does_treatment_prevent_death[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_breast_cancer.py::test_initial_config_of_pop_zero_prevalence[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_diarrhoea.py::test_do_treatment_for_those_that_will_die_if_consumables_available[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_breast_cancer.py::test_initial_config_of_pop_usual_prevalence[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_diarrhoea.py::test_do_treatment_for_those_that_will_die_if_consumables_not_available[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_diarrhoea.py::test_do_treatment_for_those_that_will_not_die[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_cardiometabolicdisorders.py::test_if_health_system_cannot_run[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_diarrhoea.py::test_effect_of_vaccine[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_cardiometabolicdisorders.py::test_hsi_investigation_not_following_symptoms[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_diarrhoea.py::test_check_perfect_treatment_leads_to_zero_risk_of_death[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_cardiometabolicdisorders.py::test_hsi_investigation_following_symptoms[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_analysis.py::test_flattening_and_unflattening_multiindex - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_cardiometabolicdisorders.py::test_hsi_weight_loss_and_medication[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_analysis.py::test_get_treatment_ids - TypeError: Categorical input must be list-like
FAILED tests/test_cardiometabolicdisorders.py::test_hsi_emergency_events[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_analysis.py::test_colormap_short_treatment_id - TypeError: Categorical input must be list-like
FAILED tests/test_healthcareseeking.py::test_healthcareseeking_does_occur_from_symptom_that_does_give_healthcareseeking_behaviour[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_healthcareseeking.py::test_healthcareseeking_does_not_occurs_from_symptom_that_do_not_give_healthcareseeking_behaviour[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_healthcareseeking.py::test_healthcareseeking_does_occur_from_symptom_that_does_give_emergency_healthcareseeking_behaviour[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_consumables.py::test_use_get_consumables_by_hsi_method_get_consumables - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_healthcareseeking.py::test_no_healthcareseeking_when_no_spurious_symptoms_and_no_disease_modules[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_consumables.py::test_outputs_to_log - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_healthcareseeking.py::test_healthcareseeking_occurs_with_spurious_symptoms_only[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_healthcareseeking.py::test_healthcareseeking_occurs_with_spurious_symptoms_and_disease_modules[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_healthcareseeking.py::test_one_per_hsi_scheduled_per_day_when_emergency_and_non_emergency_symptoms_are_onset[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_healthcareseeking.py::test_force_healthcare_seeking[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_healthcareseeking.py::test_force_healthcare_seeking_control_of_behaviour_through_parameters_and_arguments[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_enhanced_lifestyle.py::test_properties_and_dtypes[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_find_events_for_person_in_event_queue.py::test_can_look_at_future_events[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_healthcareseeking.py::test_same_day_healthcare_seeking_for_emergency_symptoms[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_healthburden.py::test_run_with_healthburden_with_dummy_diseases[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_healthcareseeking.py::test_same_day_healthcare_seeking_when_using_force_healthcareseeking[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_healthburden.py::test_arithmetic_of_disability_aggregation_calcs[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_healthcareseeking.py::test_everyone_seeks_care_for_symptom_with_high_odds_ratio_of_seeking_care[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_healthburden.py::test_arithmetic_of_dalys_calcs[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_healthcareseeking.py::test_care_seeking_from_symptoms_with_intermediate_level_of_care_seeking_and_emergency[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_healthburden.py::test_airthmetic_of_lifeyearslost[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_contraception.py::test_woman_starting_contraceptive_after_birth[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_healthcareseeking.py::test_care_seeking_from_symptoms_with_different_levels_of_prob_emergency[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_healthcareseeking.py::test_persons_have_maximum_of_one_hsi_scheduled[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_hiv.py::test_art_is_initiated_for_infants[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_healthsystem.py::test_using_parameter_or_argument_to_set_service_availability[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_analysis.py::test_colormap_cause_of_death_label[83563095832589325021] - TypeError: Categorical input must be list-like
FAILED tests/test_healthsystem.py::test_HealthSystemChangeParameters[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_hiv.py::test_hsi_testandrefer_and_circ[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_contraception.py::test_occurrence_of_HSI_for_maintaining_on_and_switching_to_methods[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_hiv.py::test_hsi_testandrefer_and_behavchg[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_hiv.py::test_hsi_testandrefer_and_prep[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_hiv.py::test_hsi_testandrefer_and_art[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_hiv.py::test_hsi_art_stopped_due_to_no_drug_available_and_no_restart[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_contraception.py::test_record_of_appt_footprint_for_switching_to_methods[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_hiv.py::test_hsi_art_stopped_due_to_no_drug_available_but_will_restart[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_hiv.py::test_hsi_art_stopped_if_healthsystem_cannot_run_hsi_and_no_restart[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_antenatal_interventions.py::test_perfect_run_of_anc_contacts_no_constraints[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_healthsystem.py::test_manipulation_of_service_availability[83563095832589325021] - TypeError: Categorical input must be list-like
FAILED tests/test_hiv.py::test_hsi_art_stopped_if_healthsystem_cannot_run_hsi_but_will_restart[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_healthsystem.py::test_hsi_run_on_same_day_if_scheduled_for_same_day[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_hiv.py::test_use_dummy_version[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_contraception.py::test_correct_number_of_live_births_created[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_hiv.py::test_initialisation[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_hiv.py::test_generation_of_new_infection[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_antenatal_interventions.py::test_anc_contacts_that_should_not_run_wont_run[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_hiv.py::test_generation_of_natural_history_process_no_art[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_hiv.py::test_generation_of_natural_history_process_with_art_before_aids[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_labour.py::test_event_scheduling_for_labour_onset_and_home_birth_no_care_seeking[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_contraception.py::test_initial_distribution_of_contraception[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_hiv.py::test_generation_of_natural_history_process_with_art_after_aids[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_antenatal_interventions.py::test_daisy_chain_care_seeking_logic_to_ensure_certain_number_of_contact[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_hiv.py::test_mtct_at_birth[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_hiv.py::test_mtct_during_breastfeeding_if_mother_infected_already[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_labour.py::test_event_scheduling_for_care_seeking_during_home_birth[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_contraception.py::test_contraception_coverage_with_use_healthsystem[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_control_order_of_events.py::test_control_of_ordering_in_the_day[83563095832589325021] - AssertionError: assert () == ('EventForSta...tForEndOfDay')
FAILED tests/test_hiv.py::test_mtct_during_breastfeeding_if_mother_infected_during_breastfeeding[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_hiv.py::test_test_and_refer_event_scheduled_by_main_event_poll[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_antenatal_interventions.py::test_initiation_of_treatment_for_maternal_anaemia_during_antenatal_inpatient_care[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_hiv.py::test_aids_symptoms_lead_to_treatment_being_initiated[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_labour.py::test_event_scheduling_for_labour_onset_and_facility_delivery[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_antenatal_interventions.py::test_initiation_of_treatment_for_hypertensive_disorder_during_antenatal_inpatient_care[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_labour.py::test_event_scheduling_for_admissions_from_antenatal_inpatient_ward_for_caesarean_section[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_control_order_of_events.py::test_control_of_ordering_in_full_model[83563095832589325021] - TypeError: Categorical input must be list-like
FAILED tests/test_core.py::test_categorical - TypeError: Cannot setitem on a Categorical with a new category (A), set the categories first
FAILED tests/test_core.py::TestLoadParametersFromDataframe::test_happy_path - TypeError: Categorical input must be list-like
FAILED tests/test_core.py::TestLoadParametersFromDataframe::test_string_stripping - TypeError: Categorical input must be list-like
FAILED tests/test_core.py::TestLoadParametersFromDataframe::test_parameter_df_not_in_class - AttributeError: 'DataFrame' object has no attribute 'append'
FAILED tests/test_core.py::TestLoadParametersFromDataframe::test_invalid_list[[1, 2, 3] - TypeError: Categorical input must be list-like
FAILED tests/test_core.py::TestLoadParametersFromDataframe::test_invalid_list[[1 2, 3]] - TypeError: Categorical input must be list-like
FAILED tests/test_core.py::TestLoadParametersFromDataframe::test_invalid_list[['a' 'b', 'c']] - TypeError: Categorical input must be list-like
FAILED tests/test_core.py::TestLoadParametersFromDataframe::test_invalid_list[a] - TypeError: Categorical input must be list-like
FAILED tests/test_core.py::TestLoadParametersFromDataframe::test_invalid_list[2] - TypeError: Categorical input must be list-like
FAILED tests/test_core.py::TestLoadParametersFromDataframe::test_invalid_date[[1, 2, 3]] - TypeError: Categorical input must be list-like
FAILED tests/test_core.py::TestLoadParametersFromDataframe::test_invalid_date[monday] - TypeError: Categorical input must be list-like
FAILED tests/test_core.py::TestLoadParametersFromDataframe::test_invalid_date[False] - TypeError: Categorical input must be list-like
FAILED tests/test_core.py::TestLoadParametersFromDataframe::test_skip_dataframe_and_series - TypeError: Categorical input must be list-like
FAILED tests/test_demography.py::test_run_dtypes_and_mothers_female[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_demography.py::test_storage_of_cause_of_death[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_antenatal_interventions.py::test_initiation_of_treatment_for_gestational_diabetes_during_antenatal_inpatient_care[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_maternal_health_helper_and_analysis_functions.py::test_analysis_events_circumnavigates_sf_and_competency_parameters[83563095832589325021] - TypeError: Categorical input must be list-like
FAILED tests/test_demography.py::test_py_calc[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_demography.py::test_py_calc_w_mask[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_demography.py::test_max_age_initial[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_measles.py::test_single_person[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_demography.py::test_ageing_of_old_people_up_to_max_age[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-HealthBurden] - Failed: Module HealthBurden appears to be missing dependency declarations required to run initialise_population and initialise_...
FAILED tests/test_labour.py::test_application_of_risk_of_complications_in_intrapartum_and_postpartum_phases[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-HealthSeekingBehaviour] - Failed: Module HealthSeekingBehaviour appears to be missing dependency declarations required to run initialise_population and i...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-Alri] - Failed: Module Alri appears to be missing dependency declarations required to run initialise_population and initialise_simulati...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-AlriPropertiesOfOtherModules] - Failed: Module AlriPropertiesOfOtherModules appears to be missing dependency declarations required to run initialise_population...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-HealthSystem] - Failed: Module HealthSystem appears to be missing dependency declarations required to run initialise_population and initialise_...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-DummyHivModule] - Failed: Module DummyHivModule appears to be missing dependency declarations required to run initialise_population and initialis...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-BladderCancer] - Failed: Module BladderCancer appears to be missing dependency declarations required to run initialise_population and initialise...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-BreastCancer] - Failed: Module BreastCancer appears to be missing dependency declarations required to run initialise_population and initialise_...
FAILED tests/test_antenatal_interventions.py::test_initiation_of_treatment_for_prom_with_or_without_chorioamnionitis_during_antenatal_inpatient_care[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_labour.py::test_logic_within_death_and_still_birth_events[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_antenatal_interventions.py::test_initiation_of_treatment_for_antepartum_haemorrhage_during_antenatal_inpatient_care[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_labour.py::test_bemonc_treatments_are_delivered_correctly_with_no_cons_or_quality_constraints_via_functions[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-Hiv] - Failed: Module Hiv appears to be missing dependency declarations required to run initialise_population and initialise_simulatio...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-CardioMetabolicDisorders] - Failed: Module CardioMetabolicDisorders appears to be missing dependency declarations required to run initialise_population and...
FAILED tests/test_antenatal_interventions.py::test_scheduling_and_treatment_effect_of_post_abortion_care[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_labour.py::test_cemonc_event_and_treatments_are_delivered_correct_with_no_cons_or_quality_constraints[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_antenatal_interventions.py::test_scheduling_and_treatment_effect_of_ectopic_pregnancy_case_management[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-Deviance] - Failed: Module Deviance appears to be missing dependency declarations required to run initialise_population and initialise_simu...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-CareOfWomenDuringPregnancy] - Failed: Module CareOfWomenDuringPregnancy appears to be missing dependency declarations required to run initialise_population a...
FAILED tests/test_antenatal_interventions.py::test_focused_anc_scheduling[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_basic_sims.py::test_make_test_property[83563095832589325021] - AssertionError: Series are different
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-ChronicSyndrome] - Failed: Module ChronicSyndrome appears to be missing dependency declarations required to run initialise_population and initiali...
FAILED tests/test_basic_sims.py::test_birth_and_death - AttributeError: 'DataFrame' object has no attribute 'append'
FAILED tests/test_beddays.py::test_beddays_in_isolation[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_beddays.py::test_bed_days_basics[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_beddays.py::test_bed_days_property_is_inpatient[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_beddays.py::test_bed_days_released_on_death[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_beddays.py::test_bed_days_basics_with_healthsystem_disabled[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_beddays.py::test_the_use_of_beds_from_multiple_facilities[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_beddays.py::test_bed_days_allocation_to_HSI[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_beddays.py::test_bed_days_allocation_information_is_provided_to_HSI[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_beddays.py::test_in_patient_appt_included_and_logged[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-Labour] - Failed: Module Labour appears to be missing dependency declarations required to run initialise_population and initialise_simula...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-Contraception] - Failed: Module Contraception appears to be missing dependency declarations required to run initialise_population and initialise...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-Demography] - Failed: Module Demography appears to be missing dependency declarations required to run initialise_population and initialise_si...
FAILED tests/test_malaria.py::test_dx_algorithm_for_malaria_outcomes[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-Malaria] - Failed: Module Malaria appears to be missing dependency declarations required to run initialise_population and initialise_simul...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-Measles] - Failed: Module Measles appears to be missing dependency declarations required to run initialise_population and initialise_simul...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-Mockitis] - Failed: Module Mockitis appears to be missing dependency declarations required to run initialise_population and initialise_simu...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-Depression] - Failed: Module Depression appears to be missing dependency declarations required to run initialise_population and initialise_si...
FAILED tests/test_malaria.py::test_dx_algorithm_for_non_malaria_outcomes[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-Diarrhoea] - Failed: Module Diarrhoea appears to be missing dependency declarations required to run initialise_population and initialise_sim...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-DiarrhoeaPropertiesOfOtherModules] - Failed: Module DiarrhoeaPropertiesOfOtherModules appears to be missing dependency declarations required to run initialise_popul...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-Lifestyle] - Failed: Module Lifestyle appears to be missing dependency declarations required to run initialise_population and initialise_sim...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-Epi] - Failed: Module Epi appears to be missing dependency declarations required to run initialise_population and initialise_simulatio...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-Epilepsy] - Failed: Module Epilepsy appears to be missing dependency declarations required to run initialise_population and initialise_simu...
FAILED tests/test_malaria.py::test_severe_malaria_deaths_perfect_treatment[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_malaria.py::test_severe_malaria_deaths_treatment_failure[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-NewbornOutcomes] - Failed: Module NewbornOutcomes appears to be missing dependency declarations required to run initialise_population and initiali...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-OesophagealCancer] - Failed: Module OesophagealCancer appears to be missing dependency declarations required to run initialise_population and initia...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-OtherAdultCancer] - Failed: Module OtherAdultCancer appears to be missing dependency declarations required to run initialise_population and initial...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-Tb] - Failed: Module Tb appears to be missing dependency declarations required to run initialise_population and initialise_simulation...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-Wasting] - Failed: Module Wasting appears to be missing dependency declarations required to run initialise_population and initialise_simul...
FAILED tests/test_other_adult_cancers.py::test_initial_config_of_pop_high_prevalence[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_newborn_outcomes.py::test_to_check_babies_delivered_in_facility_receive_post_birth_care[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_other_adult_cancers.py::test_initial_config_of_pop_zero_prevalence[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_maternal_health_helper_and_analysis_functions.py::test_analysis_analysis_events_run_as_expected_and_update_parameters[83563095832589325021] - TypeError: Categorical input must be list-like
FAILED tests/test_other_adult_cancers.py::test_initial_config_of_pop_usual_prevalence[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_other_adult_cancers.py::test_check_progression_through_stages_is_blocked_by_treatment[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-PostnatalSupervisor] - Failed: Module PostnatalSupervisor appears to be missing dependency declarations required to run initialise_population and init...
FAILED tests/test_newborn_outcomes.py::test_to_check_babies_delivered_at_home_dont_receive_post_birth_care[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_postnatal.py::test_antenatal_disease_is_correctly_carried_over_to_postnatal_period_on_birth[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_newborn_outcomes.py::test_care_seeking_for_babies_delivered_at_home_who_develop_complications[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_maternal_health_helper_and_analysis_functions.py::test_analysis_events_force_availability_of_consumables_when_scheduled_in_anc[83563095832589325021] - TypeError: Categorical input must be list-like
FAILED tests/test_postnatal.py::test_application_of_maternal_complications_and_care_seeking_postnatal_week_one_event[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-PregnancySupervisor] - Failed: Module PregnancySupervisor appears to be missing dependency declarations required to run initialise_population and init...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-ProstateCancer] - Failed: Module ProstateCancer appears to be missing dependency declarations required to run initialise_population and initialis...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-RTI] - Failed: Module RTI appears to be missing dependency declarations required to run initialise_population and initialise_simulatio...
FAILED tests/test_newborn_outcomes.py::test_twin_and_single_twin_still_birth_logic_for_twins[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-Schisto] - Failed: Module Schisto appears to be missing dependency declarations required to run initialise_population and initialise_simul...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-SimplifiedBirths] - Failed: Module SimplifiedBirths appears to be missing dependency declarations required to run initialise_population and initial...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-Stunting] - Failed: Module Stunting appears to be missing dependency declarations required to run initialise_population and initialise_simu...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-StuntingPropertiesOfOtherModules] - Failed: Module StuntingPropertiesOfOtherModules appears to be missing dependency declarations required to run initialise_popula...
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-SymptomManager] - Failed: Module SymptomManager appears to be missing dependency declarations required to run initialise_population and initialis...
FAILED tests/test_postnatal.py::test_application_of_neonatal_complications_and_care_seeking_postnatal_week_one_event[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_module_dependencies.py::test_module_dependencies_allow_initialisation[83563095832589325021-DummyTbModule] - Failed: Module DummyTbModule appears to be missing dependency declarations required to run initialise_population and initialise...
FAILED tests/test_newborn_outcomes.py::test_care_seeking_for_twins_delivered_at_home_who_develop_complications[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_maternal_health_helper_and_analysis_functions.py::test_analysis_events_force_availability_of_consumables_for_sba_analysis[83563095832589325021] - TypeError: Categorical input must be list-like
FAILED tests/test_postnatal.py::test_application_of_risk_of_death_to_mothers_postnatal_week_one_event[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_pregnancy_supervisor.py::test_store_dalys_in_mni_function_and_daly_calculations[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_newborn_outcomes.py::test_on_birth_applies_risk_of_complications_and_death_in_term_newborns_delivered_at_home_correctly[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_postnatal.py::test_application_of_risk_of_death_to_neonates_postnatal_week_one_event[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_pregnancy_supervisor.py::test_calculation_of_gestational_age[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_newborn_outcomes.py::test_on_birth_applies_risk_of_complications_and_death_in_preterm_newborns_delivered_at_home_correctly[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_maternal_health_helper_and_analysis_functions.py::test_analysis_events_force_availability_of_consumables_for_pnc_analysis[83563095832589325021] - TypeError: Categorical input must be list-like
FAILED tests/test_postnatal.py::test_application_of_risk_of_infection_and_sepsis_postnatal_supervisor_event[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_pregnancy_supervisor.py::test_application_of_risk_of_twin_pregnancy[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_newborn_outcomes.py::test_newborn_sba_hsi_deliveries_resuscitation_treatment_as_expected[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_postnatal.py::test_application_of_risk_of_spph_postnatal_supervisor_event[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_pregnancy_supervisor.py::test_spontaneous_abortion_ends_pregnancies_as_expected[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_newborn_outcomes.py::test_newborn_postnatal_check_hsi_delivers_treatment_as_expected[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_oesophagealcancer.py::test_initial_config_of_pop_high_prevalence[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_maternal_health_helper_and_analysis_functions.py::test_analysis_events_force_availability_of_consumables_for_newborn_hsi[83563095832589325021] - TypeError: Categorical input must be list-like
FAILED tests/test_oesophagealcancer.py::test_initial_config_of_pop_zero_prevalence[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_postnatal.py::test_application_of_risk_of_anaemia_postnatal_supervisor_event[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_oesophagealcancer.py::test_initial_config_of_pop_usual_prevalence[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_pregnancy_supervisor.py::test_induced_abortion_ends_pregnancies_as_expected[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_prostate_cancer.py::test_initial_config_of_pop_high_prevalence[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_prostate_cancer.py::test_initial_config_of_pop_zero_prevalence[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_prostate_cancer.py::test_initial_config_of_pop_usual_prevalence[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_prostate_cancer.py::test_check_progression_through_stages_is_blocked_by_treatment[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_simplified_births.py::test_pregnancy_and_birth_for_one_woman[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_simplified_births.py::test_no_pregnancy_among_in_ineligible_populations[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_simplified_births.py::test_no_births_if_no_one_is_pregnant[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_stunting.py::test_models[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_postnatal.py::test_application_of_risk_of_hypertensive_disorders_postnatal_supervisor_event[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_pregnancy_supervisor.py::test_abortion_complications[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_stunting.py::test_polling_event_onset[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_stunting.py::test_polling_event_recovery[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_pregnancy_supervisor.py::test_pregnancy_supervisor_placental_conditions_and_antepartum_haemorrhage[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_stunting.py::test_polling_event_progression[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_stunting.py::test_routine_assessment_for_chronic_undernutrition_if_stunted_and_correctly_diagnosed[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_stunting.py::test_routine_assessment_for_chronic_undernutrition_if_stunted_but_no_checking[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_stunting.py::test_routine_assessment_for_chronic_undernutrition_if_not_stunted[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_stunting.py::test_math_of_incidence_calcs[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_postnatal.py::test_application_of_risk_of_late_onset_neonatal_sepsis[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_symptommanager.py::test_no_symptoms_if_no_diseases[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_pregnancy_supervisor.py::test_still_births_ends_pregnancies_as_expected[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_symptommanager.py::test_spurious_symptoms_during_simulation[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_symptommanager.py::test_adding_quering_and_removing_symptoms[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_symptommanager.py::test_disease_module_in_recognised_module_names[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_symptommanager.py::test_baby_born_has_no_symptoms[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_symptommanager.py::test_disease_module_symptoms_registered[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_symptommanager.py::test_auto_onset_symptom[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_pregnancy_supervisor.py::test_pregnancy_supervisor_pre_eclampsia_and_progression[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_symptommanager.py::test_who_has_single_symptom[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_symptommanager.py::test_who_has_multiple_symptoms[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_symptommanager.py::test_have_what[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_symptommanager.py::test_who_not_have[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_symptommanager.py::test_causes_of[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_symptommanager.py::test_has_what[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_symptommanager.py::test_clear_symptoms_individual[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_symptommanager.py::test_has_what_disease_module[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_symptommanager.py::test_clear_symptoms_multiple_persons[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_pregnancy_supervisor.py::test_run_all_births_end_ectopic_no_care_seeking[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_symptommanager.py::test_add_symptom_individual_single_symptom[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_symptommanager.py::test_remove_symptom_individual_single_symptom[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_symptommanager.py::test_add_symptom_multiple_persons_single_symptom[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_symptommanager.py::test_remove_symptom_multiple_persons_single_symptom[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_symptommanager.py::test_change_symptom_individual_multiple_symptoms[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_pregnancy_supervisor.py::test_pregnancy_supervisor_gestational_hypertension_and_progression[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_symptommanager.py::test_change_symptom_multiple_persons_multiple_symptoms[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_tb.py::test_natural_history[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_tb.py::test_basic_run[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_tb.py::test_treatment_schedule[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_tb.py::test_treatment_failure[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_pregnancy_supervisor.py::test_preterm_labour_logic[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_tb.py::test_relapse_risk[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_tb.py::test_children_referrals[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_tb.py::test_ipt_to_child_of_tb_mother[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_pregnancy_supervisor.py::test_pregnancy_supervisor_gdm[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_tb.py::test_mdr[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_tb.py::test_cause_of_death[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_utils.py::test_logs_parsing - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_tb.py::test_active_tb_linear_model[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_pregnancy_supervisor.py::test_check_first_anc_visit_scheduling[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_pregnancy_supervisor.py::test_pregnancy_supervisor_chorio_and_prom[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_pregnancy_supervisor.py::test_pregnancy_supervisor_anaemia[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'
FAILED tests/test_pregnancy_supervisor.py::test_induction_of_labour_logic[83563095832589325021] - AttributeError: 'Series' object has no attribute 'iteritems'

[tamuri]

I get a deprecation warning (was previously a FutureWarning

Sorry, I didn't know pandas version at that time but, yes, must have been an older version. I'm getting deprecation warning too now.

[matt-graham]

@tamuri and I discussed this issue in a meeting today (2023/03/27). The initial plan is to target getting both all tests passing with updated dependencies plus exact reproducibility (in terms of elementwise equality of final population data frame) of a run of the src/scripts/profiling/scale_run.py script compared to running with the current dependency versions. We will aim to target Python 3.11 (which has been out since October 2022 and now has relatively good support in downstream Python packages) given there are quite significant performance gains out of the box compared to previous Python versions. For Pandas, the current latest stable release is v1.5.3, with a v2.0.0 release candidate available but no stable version yet (tracking issue pandas-dev/pandas#46776 suggests there may be a stable release in the next week or two). For now we will aim to test any changes against both v1.5.3 and v2.0.0 with the aim of being able to run against v2.0.0 when it's released given this also has some major performance improvements.

In terms of managing the transition, as a rough plan we may create a 'meta' branch / PR to track the changes needed to run successfully on the updated dependencies, with smaller PRs being made against this branch to deal with fixes for individual issues / failing tests, to facilitate splitting the work up. Similarly we will probably use this issue as meta-issue to track overall progress but create a task list / sub issues for specific changes.

[tamuri]

Another factor: how do we plan to roll this out? Will the updates be such that one will need the new environment as soon as they merge master? Or is there a grace period? I guess this is somewhat related to which versions we target. Do we make the necessary changes to allow updating the stack, whilst letting the code still run on existing version (e.g. v1.2.2 & v2 on pandas).

That might not be desirable, in which case we need to have a "move day"

[matt-graham]

/run python3.11-pandas2.0-all-tests

[matt-graham]

/run python3.11-pandas2.0-all-tests

[ucl-comment-bot]

Run of all tests on Python v3.11 with Pandas v2.0 failed ❌

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