Code

The Equipment Class#1098

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tbhallett merged 125 commits intomasterUCL/TLOmodel:masterfrom EvaJ/equipment/structure_ToRunSimUCL/TLOmodel:EvaJ/equipment/structure_ToRunSimCopy head branch name to clipboardMay 15, 2024

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Commits on Mar 5, 2024

• TODO: some modules use equipment when talking about consumables

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• breast_cancer: dummy used_equipment added where Andrew requested

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• co: dummy used_equipment added for methods where Emi listed some

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• healthsystem: annual equipment summary log by fac. level

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• breast_cancer: mastectomy dummy equipment fixed

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• equipment_catalogue & utils: new script + a change in utils.py - to create equip. catalogue

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• equipment_catalogue: PEP8

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• healthsystem: sort equipment for log

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• equipment_catalogue: comment updated

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• rti: unified use of consumables/equipment terms

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• hs, brc, co: used_equipment renamed to EQUIPMENT; if equip always same for HSI - set in __init__, otherwise updated in apply

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• brc: comment updated

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• brc & co: rm the dummy examples of equipment from modules

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• RF_Equipment: equipment catalogue - first draft (from Sakshi)

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• RF_Equipment: equipment catalogue - merge duplicates (round 1)

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• RF_Equipment: equipment catalogue - merge duplicates (round 2)

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• hs: debugging Equipment log - rm sorted

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• hs: fix sorting of _equip_by_level

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• RF_Equipment: equipment catalogue - merge duplicates (round 3)

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• RF_Equipment: equipment catalogue - merge duplicates (round 4)

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• RF_Equipment: equipment catalogue - merge duplicates (round 5)

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• RF_Equipment: equipment catalogue - merge duplicates (round 6) + col names renamed

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• RF_Equip: equip item codes added

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• codes_to_items_list: new script created

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• codes_to_items_list: script generalised + PEP 8

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• hs: equipment added to HSIEventDetails

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• equip_catalogue: make catalogues from new logging (equip included in hsi_event_details, counts logged in hsi_event_counts)

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• hs: sort equipment for logging

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• test_hs: assert equipment logging within detailed_hsi_event

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• [no ci] hs: typo; Equipment logging removed

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• equip_catalogue: fix the keys mapping to be done for each run

  EvaJanouskova

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• equip_catalogue: input hsi event details by which to catalog equipment

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• equip_catalogue: input time period by which to catalog equipment

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• equip_catalogue: list of requested details can be empty

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• equip_catalogue: verify inputs as expected & set output file names in 'create_equipment_catalogues' fnc

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• equip_catalogue: (1) detailed - equip set as string in one row, module_name before event_name, sorted by indexes; (2) added summary catal. (3) focused - only this cat. without empty equip rows and …

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• equip_catalogue: suffix (as input) added for output file names

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• hs: structure v2; alri+co: examples to test new structure

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• equip_catalogue: TODO added

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• equip_catalogue: typo

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• equip_catalogue: TODO added

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• equip_catalogue: bug fixed

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• brc: TODO added

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• hs: rm prints

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• hs: rm old code

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• hs: rm/add accidentally added/rmd commas

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• hs & alri+co: rename and correct return of fncs related to equipment

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• hs: log equip item codes instead of names

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• equip_catalogue: updated for logged equip item codes

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• brc: change Andrew suggested

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• hs: updates for better readability; rm unused code

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• hs: PEP8

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• hs: get_equip_item_code_from_item_name fnc updated; ESS.EQUIP as codes

  EvaJanouskova

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• equip_catalogue: add item codes to catalogue by requested details (1 item per row)

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• hs: allow adding equip by pkg name(s)

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• co & RF_Equip: an example of usage of equipment pkg

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• utils: use pandas fnc (instead of make one)

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• hs: ESS_EQUIP as HSI_Event's attribute; if settings of ESS_EQUIP forgotten -> set to empty & warn

  EvaJanouskova

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• hs: fixed saving _hsi_event_names_missing_ess_equip

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• hs: fixed updating _hsi_event_names_missing_ess_equip

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• hs: TODO smt odd going on with hsi_event_names_missing_ess_equip warning

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• hs: sort hsi_event_names_missing_ess_equip warning

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• hs: equip_item_and_package_code_lookups renamed to equip_item_and_package_lookups

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• hs: ignore_unknown_equip_names

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• hs: warning messages shortened

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Commits on Mar 21, 2024

• co: example of setting ess. equip based on condition

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• co: comment updated; TODO added

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• co, hs, RF_Equip, RF_HS_params, test_alri, test_co, test_hs: checking equip availability (before/within HSI); avail switcher; dummy probs by fac_level = 0.5; tests updated; TODOs added

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• Merge branch 'master' into EvaJ/equipment/structure_ToRunSim

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Commits on Mar 25, 2024

• Merge branch 'master' into EvaJ/equipment/structure_ToRunSim

  tbhallett

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• example test suite

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• typo and add todo

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• further tests

  tbhallett

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• [no_ci] RF_Equip: availabilities changed from probs to True/False values (all True for now)

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Commits on Mar 26, 2024

• ac: rm comments

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• hs: rm equip_availability before sim default

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• labour: rm comments

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Commits on Apr 16, 2024

• hs: rm extra line

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• hs: raise error if 1) ess equip not a set of ints, 2) invalid equip_availability

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Commits on May 9, 2024

• Merge branch 'refs/heads/master' into EvaJ/equipment/structure_ToRunSim

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• roll back incidental changes

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• move codes_to_items_list to scripts/data-file-processing

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• roll back parsing script

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• squash - basic outline of Equipment class

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Commits on May 10, 2024

• squash - basic outline of Equipment class

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• linting

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• update call in bed-days

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Commits on May 12, 2024

• use hashable type in HSIEventDetails

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• update logic and add docstring

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Commits on May 13, 2024

• linting

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• linting

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• Merge branch 'master' into EvaJ/equipment/structure_ToRunSim

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• linting

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• linting

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• provide default for 'equip_availability' in test_alri:get_sim()

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• Prevent recomputing of probabilities every time availability is updated

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• Remove commentted-out code and pass back return value

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• small updates following chnages from Will

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• Update src/tlo/methods/hsi_event.py

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• Update src/tlo/methods/hsi_event.py

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• Update src/tlo/methods/equipment.py

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• Update src/tlo/methods/equipment.py

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• Update src/tlo/methods/equipment.py

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• Update src/tlo/methods/equipment.py

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• Update src/tlo/methods/equipment.py

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• Update src/tlo/methods/equipment.py

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• use property syntax and a setter for availability rather than update_availability

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• update typehint and docstring on parse_items to be more accurate

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• fix typo in test_HealthSystemChangeParameters

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Commits on May 14, 2024

• linting

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• remove update_availability

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• use continue rather than nested if/else statment

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• initialise self._EQUIPMENT in the __init__ so that it specific to the instance and not the class

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• Update src/tlo/methods/hsi_event.py

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• Update src/tlo/methods/hsi_event.py

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• Update src/tlo/methods/hsi_event.py

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• Update src/tlo/methods/hsi_event.py

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• Update src/tlo/methods/hsi_event.py

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• make checks in test_core_functionality_of_equipment_class test for exactly the right resonse, rather than truthiness only.

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• Merge remote-tracking branch 'origin/EvaJ/equipment/structure_ToRunSim' into EvaJ/equipment/structure_ToRunSim

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• check logging from multiple HSI_events in test_logging_of_equipment_from_multiple_hsi

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• Merge remote-tracking branch 'refs/remotes/origin/master' into EvaJ/equipment/structure_ToRunSim

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• roll back incidental changes

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• remove codes_to_items_list.py from this PR

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Commits on May 15, 2024

• Merge branch 'master' into EvaJ/equipment/structure_ToRunSim

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