…as equipment in MNH modules

diff --git src/tlo/methods/breast_cancer.py src/tlo/methods/breast_cancer.py
index 402266516..57e842119 100644
--- src/tlo/methods/breast_cancer.py
+++ src/tlo/methods/breast_cancer.py
@@ -646,8 +646,9 @@ class HSI_BreastCancer_Investigation_Following_breast_lump_discernible(HSI_Event
         self.TREATMENT_ID = "BreastCancer_Investigation"
         self.EXPECTED_APPT_FOOTPRINT = self.make_appt_footprint({"Over5OPD": 1, "Mammography": 1})
         self.ACCEPTED_FACILITY_LEVEL = '3'  # Biopsy only available at level 3 and above.
-        # TODO: but the appt footprints suggests mammography to be provided
-        self.EQUIPMENT = {'Slice Master sample processing Unit', 'Paraffin Dispense', 'Whatever used with biopsy'}
+
+        # TODO: Eva's dummy equipment example (not sure if it actually needs to be added and if it is in the RF)
+        #  {'Slice Master sample processing Unit', 'Paraffin Dispense', 'Whatever used with biopsy'}

         # ap_oct23 - Eva, I cannot locate a biopsy needle in the equipment - perhaps it is in consumables
         # the other equipment need is for histology in the lab - there is a whole long list of items needed
@@ -771,8 +772,9 @@ class HSI_BreastCancer_StartTreatment(HSI_Event, IndividualScopeEventMixin):
         df.at[person_id, "brc_date_treatment"] = self.sim.date
         df.at[person_id, "brc_stage_at_which_treatment_given"] = df.at[person_id, "brc_status"]

+        # TODO: Eva's dummy equipment example - it needs to be replaced by real items from the RF
         # Update equipment
-        self.EQUIPMENT.update({'Anything used for mastectomy'})
+        # self.EQUIPMENT.update({'Anything used for mastectomy'})

         # Schedule a post-treatment check for 12 months:
         hs.schedule_hsi_event(
diff --git src/tlo/methods/contraception.py src/tlo/methods/contraception.py
index 6f9e4254b..8c9821b0c 100644
--- src/tlo/methods/contraception.py
+++ src/tlo/methods/contraception.py
@@ -1284,8 +1284,10 @@ class HSI_Contraception_FamilyPlanningAppt(HSI_Event, IndividualScopeEventMixin)

             # Update equipment
             if _new_contraceptive == 'female_sterilization':
+                # TODO: Eva's dummy example - needs to be replaced by real item(s)
                 self.EQUIPMENT.update({'Smt used to sterilize a woman'})
             elif _new_contraceptive == 'IUD':
+                # TODO: Eva's dummy example - needs to be replaced by real item(s)
                 self.EQUIPMENT.update({'Equipment used when performing IUD'})

         else:

diff --git src/tlo/methods/care_of_women_during_pregnancy.py src/tlo/methods/care_of_women_during_pregnancy.py
index 2944ee41f..96a4b6975 100644
--- src/tlo/methods/care_of_women_during_pregnancy.py
+++ src/tlo/methods/care_of_women_during_pregnancy.py
@@ -572,7 +572,7 @@ class CareOfWomenDuringPregnancy(Module):

     def antenatal_care_scheduler(self, individual_id, visit_to_be_scheduled, recommended_gestation_next_anc):
         """
-        This function is responsible for scheduling a womans next ANC contact in the schedule if she chooses to seek
+        This function is responsible for scheduling a woman's next ANC contact in the schedule if she chooses to seek
         care again.  It is called by each of the ANC HSIs.
         :param individual_id: individual_id
         :param visit_to_be_scheduled: Number if next visit in the schedule (2-8)
@@ -1572,8 +1572,8 @@ class HSI_CareOfWomenDuringPregnancy_SecondAntenatalCareContact(HSI_Event, Indiv
                 self.module.antenatal_care_scheduler(person_id, visit_to_be_scheduled=3,
                                                      recommended_gestation_next_anc=gest_age_next_contact)

-            # Then we administer interventions that are due to be delivered at this womans gestational age, which may be
-            # in addition to intervention delivered in ANC2
+            # Then we administer interventions that are due to be delivered at this woman's gestational age, which may
+            # be in addition to intervention delivered in ANC2
             if mother.ps_gestational_age_in_weeks < 26:
                 self.module.albendazole_administration(hsi_event=self)
                 self.module.iptp_administration(hsi_event=self)
@@ -1621,7 +1621,7 @@ class HSI_CareOfWomenDuringPregnancy_ThirdAntenatalCareContact(HSI_Event, Indivi
     antenatal care contact (ANC3). It is scheduled by the HSI_CareOfWomenDuringPregnancy_SecondAntenatalCareContact for
     women who choose to seek additional ANC after their previous visit. It is recommended that this visit occur at 26
     weeks gestation. This event delivers the interventions to women which are part of ANC3. Additionally interventions
-    that should be delivered according to a womans gestational age and position in her ANC schedule are delivered.
+    that should be delivered according to a woman's gestational age and position in her ANC schedule are delivered.
     Finally scheduling the next ANC contact in the occurs during this HSI along with admission to antenatal inpatient
     ward in the case of complications"""

…' into equipment/integration_in_modules

# Conflicts:
#	resources/healthsystem/infrastructure_and_equipment/ResourceFile_Equipment.csv
#	src/scripts/healthsystem/equipment/equipment_catalogue.py
#	src/tlo/methods/breast_cancer.py
#	src/tlo/methods/care_of_women_during_pregnancy.py
#	src/tlo/methods/contraception.py
#	src/tlo/methods/healthsystem.py
#	src/tlo/methods/newborn_outcomes.py

…e_name before event_name, sorted by indexes; (2) added summary catal. (3) focused - only this cat. without empty equip rows and split by item per row

…e_name before event_name, sorted by indexes; (2) added summary catal. (3) focused - only this cat. without empty equip rows and split by item per row

…ration_in_modules

# Conflicts:
#	src/scripts/healthsystem/equipment/equipment_catalogue.py

… cancer_consumables.py to prevent repeating code blocks

…ated spelling of cystoscopy within bladder_cancer.py and the associated resource file.

diff --git src/tlo/methods/breast_cancer.py src/tlo/methods/breast_cancer.py
index 1ce9ad2bf..56c935fba 100644
--- src/tlo/methods/breast_cancer.py
+++ src/tlo/methods/breast_cancer.py
@@ -666,6 +666,8 @@ class HSI_BreastCancer_Investigation_Following_breast_lump_discernible(HSI_Event

         # Use a biopsy to diagnose whether the person has breast Cancer:
         # todo: request consumables needed for this
+        self.used_equipment = {'Slice Master sample processing Unit', 'Paraffin Dispense', 'Whatever used with biopsy',
+                               'Mammograph maybe?'}

         dx_result = hs.dx_manager.run_dx_test(
             dx_tests_to_run='biopsy_for_breast_cancer_given_breast_lump_discernible',
@@ -759,6 +761,9 @@ class HSI_BreastCancer_StartTreatment(HSI_Event, IndividualScopeEventMixin):
         df.at[person_id, "brc_date_treatment"] = self.sim.date
         df.at[person_id, "brc_stage_at_which_treatment_given"] = df.at[person_id, "brc_status"]

+        # Record used equipment
+        self.used_equipment = 'Anything used for mastectomy as I guess this is about'
+
         # Schedule a post-treatment check for 12 months:
         hs.schedule_hsi_event(
             hsi_event=HSI_BreastCancer_PostTreatmentCheck(

…reate equip. catalogue

Co-authored-by: Tim Hallett <39991060+tbhallett@users.noreply.github.com>

…e for HSI - set in __init__, otherwise updated in apply

diff --git src/tlo/methods/breast_cancer.py src/tlo/methods/breast_cancer.py
index 5d8fabfcb..26155729a 100644
--- src/tlo/methods/breast_cancer.py
+++ src/tlo/methods/breast_cancer.py
@@ -646,6 +646,8 @@ class HSI_BreastCancer_Investigation_Following_breast_lump_discernible(HSI_Event
         self.TREATMENT_ID = "BreastCancer_Investigation"
         self.EXPECTED_APPT_FOOTPRINT = self.make_appt_footprint({"Over5OPD": 1, "Mammography": 1})
         self.ACCEPTED_FACILITY_LEVEL = '3'  # Biopsy only available at level 3 and above.
+        self.EQUIPMENT = {'Slice Master sample processing Unit', 'Paraffin Dispense', 'Whatever used with biopsy'}
+        # biopsy always performed with this HSI

     def apply(self, person_id, squeeze_factor):
         df = self.sim.population.props
@@ -666,8 +668,6 @@ class HSI_BreastCancer_Investigation_Following_breast_lump_discernible(HSI_Event

         # Use a biopsy to diagnose whether the person has breast Cancer:
         # todo: request consumables needed for this
-        self.used_equipment = {'Slice Master sample processing Unit', 'Paraffin Dispense', 'Whatever used with biopsy',
-                               'Mammograph maybe?'}

         dx_result = hs.dx_manager.run_dx_test(
             dx_tests_to_run='biopsy_for_breast_cancer_given_breast_lump_discernible',
@@ -761,8 +761,9 @@ class HSI_BreastCancer_StartTreatment(HSI_Event, IndividualScopeEventMixin):
         df.at[person_id, "brc_date_treatment"] = self.sim.date
         df.at[person_id, "brc_stage_at_which_treatment_given"] = df.at[person_id, "brc_status"]

-        # Record used equipment
-        self.used_equipment = {'Anything used for mastectomy as I guess this is about'}
+        # Update equipment used with treatment
+        # NB. read only with HSI run and healthsystem.summary logger set at the level INFO or higher
+        self.EQUIPMENT.update({'Anything used for mastectomy as I guess this is about'})

         # Schedule a post-treatment check for 12 months:
         hs.schedule_hsi_event(
diff --git src/tlo/methods/contraception.py src/tlo/methods/contraception.py
index 6ffb0ebc6..15851e1b7 100644
--- src/tlo/methods/contraception.py
+++ src/tlo/methods/contraception.py
@@ -1281,11 +1281,12 @@ class HSI_Contraception_FamilyPlanningAppt(HSI_Event, IndividualScopeEventMixin)

             _new_contraceptive = self.new_contraceptive

-            # Record used equipment when needed
+            # Update equipment when needed
+            # NB. read only with HSI run and healthsystem.summary logger set at the level of logger.INFO or higher
             if _new_contraceptive == 'female_sterilization':
-                self.used_equipment = {'Smt used to sterilize a woman'}
+                self.EQUIPMENT.update({'Smt used to sterilize a woman'})
             elif _new_contraceptive == 'IUD':
-                self.used_equipment = {'Equipment used when performing IUD'}
+                self.EQUIPMENT.update({'Equipment used when performing IUD'})

         else:
             _new_contraceptive = "not_using"
diff --git src/tlo/methods/healthsystem.py src/tlo/methods/healthsystem.py
index c19b0f433..3eb6b9940 100644
--- src/tlo/methods/healthsystem.py
+++ src/tlo/methods/healthsystem.py
@@ -182,7 +182,7 @@ class HSI_Event:
         self._received_info_about_bed_days = None
         self.expected_time_requests = {}
         self.facility_info = None
-        self.used_equipment = set()
+        self.EQUIPMENT = set()

     @Property
     def bed_days_allocated_to_this_event(self):
@@ -1741,7 +1741,7 @@ class HealthSystem(Module):
                 squeeze_factor=_squeeze_factor,
                 did_run=did_run,
                 priority=priority,
-                equipment=hsi_event.used_equipment,
+                equipment=hsi_event.EQUIPMENT,
             )

     def write_to_hsi_log(

diff --git src/tlo/methods/breast_cancer.py src/tlo/methods/breast_cancer.py
index 26155729a..aef476c87 100644
--- src/tlo/methods/breast_cancer.py
+++ src/tlo/methods/breast_cancer.py
@@ -647,7 +647,7 @@ class HSI_BreastCancer_Investigation_Following_breast_lump_discernible(HSI_Event
         self.EXPECTED_APPT_FOOTPRINT = self.make_appt_footprint({"Over5OPD": 1, "Mammography": 1})
         self.ACCEPTED_FACILITY_LEVEL = '3'  # Biopsy only available at level 3 and above.
         self.EQUIPMENT = {'Slice Master sample processing Unit', 'Paraffin Dispense', 'Whatever used with biopsy'}
-        # biopsy always performed with this HSI
+        # biopsy always performed with this HSI, hence always used the same set of equipment

     def apply(self, person_id, squeeze_factor):
         df = self.sim.population.props

…names renamed

…hsi_event_details, counts logged in hsi_event_counts)

diff --git src/tlo/methods/healthsystem.py src/tlo/methods/healthsystem.py
index d14f8f10a..5ecb43368 100644
--- src/tlo/methods/healthsystem.py
+++ src/tlo/methods/healthsystem.py
@@ -2611,7 +2611,7 @@ class HealthSystemScheduler(RegularEvent, PopulationScopeEventMixin):
                     squeeze_factor=0.0,
                     priority=-1,
                     did_run=True,
-                    equipment=set()  # TODO: explore more, should it be non-emtpy in some cases?
+                    equipment=set(),  # TODO: explore more, should it be non-empty in some cases?
                 )

         # Restart the total footprint of all calls today, beginning with those due to existing in-patients.
@@ -2666,7 +2666,6 @@ class HealthSystemSummaryCounter:
         self._appts = defaultdict(int)  # Running record of the Appointments of `HSI_Event`s that have run
         self._appts_by_level = {_level: defaultdict(int) for _level in ('0', '1a', '1b', '2', '3', '4')}
         # <--Same as `self._appts` but also split by facility_level
-        self._equip_by_level = {_level: set() for _level in ('0', '1a', '1b', '2', '3', '4')}

         # Log HSI_Events that never ran to monitor shortcoming of Health System
         self._never_ran_treatment_ids = defaultdict(int)  # As above, but for `HSI_Event`s that never ran
@@ -2683,8 +2682,7 @@ class HealthSystemSummaryCounter:
                          hsi_event_name: str,
                          squeeze_factor: float,
                          appt_footprint: Counter,
-                         level: str,
-                         equipment: set
+                         level: str
                          ) -> None:
         """Add information about an `HSI_Event` to the running summaries."""

@@ -2701,9 +2699,6 @@ class HealthSystemSummaryCounter:
             self._appts[appt_type] += number
             self._appts_by_level[level][appt_type] += number

-        # Update used equipment by level
-        self._equip_by_level[level].update(equipment)
-
     def record_never_ran_hsi_event(self,
                                    treatment_id: str,
                                    hsi_event_name: str,
@@ -2766,17 +2761,6 @@ class HealthSystemSummaryCounter:
             },
         )

-        # Sort equipment within levels, and log them
-        for key in self._equip_by_level:
-            self._equip_by_level[key] = sorted(self._equip_by_level[key])
-        logger_summary.info(
-            key="Equipment",
-            description="Sets of used equipment for each facility level in this calendar year.",
-            data={
-                "Equipment_By_Level": self._equip_by_level,
-            },
-        )
-
         self._reset_internal_stores()

… 'create_equipment_catalogues' fnc

…e_name before event_name, sorted by indexes; (2) added summary catal. (3) focused - only this cat. without empty equip rows and split by item per row

diff --git src/tlo/methods/alri.py src/tlo/methods/alri.py
index e4b0b46d1..c211e3317 100644
--- src/tlo/methods/alri.py
+++ src/tlo/methods/alri.py
@@ -2290,6 +2290,8 @@ class HSI_Alri_Treatment(HSI_Event, IndividualScopeEventMixin):
         self._treatment_id_stub = 'Alri_Pneumonia_Treatment'
         self._facility_levels = ("0", "1a", "1b", "2")  # Health facility levels at which care may be provided
         assert facility_level in self._facility_levels
+        self.set_essential_equipment({'Pulse oximeter'})
+        # TODO: CORRECT --- an example with ess. equipm. set (which may or may not be used at the end)
         self.is_followup_following_treatment_failure = is_followup_following_treatment_failure

         if not inpatient:
@@ -2596,6 +2598,8 @@ class HSI_Alri_Treatment(HSI_Event, IndividualScopeEventMixin):
                  'cough_or_cold'                    (symptoms-based assessment)
          }."""

+        self.update_equipment({'Pulse oximeter'})
+
         child_is_younger_than_2_months = age_exact_years < (2.0 / 12.0)

         imci_classification_based_on_symptoms = self._get_imci_classification_based_on_symptoms(
diff --git src/tlo/methods/contraception.py src/tlo/methods/contraception.py
index f86e342c8..d6786dd39 100644
--- src/tlo/methods/contraception.py
+++ src/tlo/methods/contraception.py
@@ -353,7 +353,7 @@ class Contraception(Module):
             # Increase prob of 'female_sterilization' in older women accordingly
             probs_30plus = probs.copy()
             probs_30plus['female_sterilization'] = (
-                probs.loc['female_sterilization'] /
+                probs.loc['female_sterilization'] /
                 self.ratio_n_females_30_49_to_15_49_in_2010
             )
             # Scale so that the probability of all outcomes sum to 1.0
@@ -633,7 +633,7 @@ class Contraception(Module):
             # Increase prob of 'female_sterilization' in older women accordingly
             probs_30plus = probs.copy()
             probs_30plus['female_sterilization'] = (
-                probs.loc['female_sterilization'] /
+                probs.loc['female_sterilization'] /
                 self.ratio_n_females_30_49_to_15_49_in_2010
             )
             # Scale so that the probability of all outcomes sum to 1.0
@@ -1194,6 +1194,7 @@ class HSI_Contraception_FamilyPlanningAppt(HSI_Event, IndividualScopeEventMixin)

         self.TREATMENT_ID = "Contraception_Routine"
         self.ACCEPTED_FACILITY_LEVEL = _facility_level
+        self.set_essential_equipment({''})

     @Property
     def EXPECTED_APPT_FOOTPRINT(self):
@@ -1229,6 +1230,11 @@ class HSI_Contraception_FamilyPlanningAppt(HSI_Event, IndividualScopeEventMixin)
         # Record the date that Family Planning Appointment happened for this person
         self.sim.population.props.at[person_id, "co_date_of_last_fp_appt"] = self.sim.date

+        # Measure weight, height and BP even if contraception not administrated
+        self.update_equipment({
+            'Weighing scale', 'Height Pole (Stadiometer)', 'Blood pressure machine'
+        })
+
         # Determine essential and optional items
         # TODO: we don't distinguish essential X optional for contraception methods yet, will need to update once we do
         items_essential = self.module.cons_codes[self.new_contraceptive]
@@ -1255,7 +1261,8 @@ class HSI_Contraception_FamilyPlanningAppt(HSI_Event, IndividualScopeEventMixin)
         items_all = {**items_essential, **items_optional}

         # Determine whether the contraception is administrated (ie all essential items are available),
-        # if so do log the availability of all items, if not set the contraception to "not_using":
+        # if so do log the availability of all items and update used equipment if any, if not set the contraception to
+        # "not_using":
         co_administrated = all(v for k, v in cons_available.items() if k in items_essential)

         if co_administrated:
@@ -1280,6 +1287,16 @@ class HSI_Contraception_FamilyPlanningAppt(HSI_Event, IndividualScopeEventMixin)

             _new_contraceptive = self.new_contraceptive

+            # Update equipment if any needed for the method
+            if _new_contraceptive == 'female_sterilization':
+                self.update_equipment({
+                    'Cusco’s/ bivalved Speculum (small, medium, large)', 'Lamp, Anglepoise'
+                })
+            elif _new_contraceptive == 'IUD':
+                self.update_equipment({
+                    'Cusco’s/ bivalved Speculum (small, medium, large)', 'Sponge Holding Forceps'
+                })
+
         else:
             _new_contraceptive = "not_using"

diff --git src/tlo/methods/healthsystem.py src/tlo/methods/healthsystem.py
index 5ecb43368..1ad875f67 100644
--- src/tlo/methods/healthsystem.py
+++ src/tlo/methods/healthsystem.py
@@ -183,6 +183,7 @@ class HSI_Event:
         self._received_info_about_bed_days = None
         self.expected_time_requests = {}
         self.facility_info = None
+        # self.set_essential_equipment({''})  # HSI needs this attribute, but it is not defined in the Base class
         self.EQUIPMENT = set()

     @Property
@@ -339,6 +340,37 @@ class HSI_Event:
             "values"
         )

+    def set_essential_equipment(self, set_of_equip):
+        """Helper function to set essential equipment.
+
+        Should be passed a set of equipment items names (strings) or an empty set.
+        """
+        # Set EQUIPMENT if the given set_of_equip in correct format, ie a set of strings or an empty set
+        if isinstance(set_of_equip, set) and all(isinstance(item, str) for item in set_of_equip):
+            self.ESSENTIAL_EQUIPMENT  = set_of_equip
+            return 0
+
+        raise ValueError(
+            "Argument to set_essential_equipment should be an empty set or a set of strings of equipment item names "
+            "from ResourceFile_Equipment.csv."
+        )
+
+    def update_equipment(self, set_of_equip):
+        """Helper function to update equipment.
+
+        Should be passed a set of equipment item names (strings).
+        """
+        # Update EQUIPMENT if the given set_of_equip in correct format, ie a non-empty set of strings
+        if isinstance(set_of_equip, set) and (all(isinstance(item, str) for item in set_of_equip)) and \
+           (set_of_equip not in [set(), None, {''}]):
+            self.EQUIPMENT.update(set_of_equip)
+            return self.EQUIPMENT.discard('')
+
+        raise ValueError(
+            "Argument to update_equipment should be a non-empty set of strings of equipment item names "
+            "from ResourceFile_Equipment.csv."
+        )
+
     def initialise(self):
         """Initialise the HSI:
         * Set the facility_info

… if essen. consumbales avail.

…item per row)

…otten -> set to empty & warn