Implement clinics in TLO - #1617

Merged

tbhallett merged 105 commits into

Dec 4, 2025

Commits on May 5, 2025

Dummy resource file for clinics and additional param in healthsystems
sangeetabhatia03
committed
cf5ed0f
Necessary edits to docstring
sangeetabhatia03
committed
dd0a193

Commits on May 7, 2025

Conditional read in new resource file
sangeetabhatia03
committed
909e069
WIP; read and rescale clinic time
sangeetabhatia03
committed
371ac5e

Commits on May 14, 2025

Update column name
sangeetabhatia03
committed
ab18c46
Redefine daily capabilities down to non-fungible
sangeetabhatia03
committed
d5b690d
Update daily capabilities based on fungible and non-fungible proportions
sangeetabhatia03
committed
d576369

Commits on May 28, 2025

First pass at getting clinic eligibility
sangeetabhatia03
committed
f5402f2
Fix syntax errors
sangeetabhatia03
committed
4c82733

Commits on May 29, 2025

WIP; setter needs to be moved
sangeetabhatia03
committed
2936a15
Moved getters and setters to healthsystem
sangeetabhatia03
committed
d6b43eb

Commits on Jun 6, 2025

Fix typo
sangeetabhatia03
committed
23163e2
Do not rescale if fractions don't add up to 1
sangeetabhatia03
committed
f9c9297

Commits on Jun 9, 2025

Commits on Jun 10, 2025

Use appropriate counters
sangeetabhatia03
committed
6361f32

Commits on Jun 19, 2025

Fix indentation error and add test (wip)
sangeetabhatia03
committed
7c21176
Fix typos and further edits to test
sangeetabhatia03
committed
41cceeb
Fix more typos while reading in resource file
sangeetabhatia03
committed
838dba9

Commits on Jun 20, 2025

Update column name in resource file for consistency. Fix typos
sangeetabhatia03
committed
e1ce587
Fix erroneous parens
sangeetabhatia03
committed
329055d
Retrieve module columns from Resource file before formatting it
sangeetabhatia03
committed
f3f77ff
Use self.parameters not PARAMETERS
sangeetabhatia03
committed
822e492
Allow setter to accept an argument
sangeetabhatia03
committed
812f569
clinic eligibility is a property of the queue item, not healthsystem
sangeetabhatia03
committed
f00f882

Commits on Jun 26, 2025

Commits on Jun 27, 2025

reformat clinic capabilities
sangeetabhatia03
committed
e691217

Commits on Jun 30, 2025

Fix structure of capabilities still available
sangeetabhatia03
committed
0f0d122
Assign population to one district
sangeetabhatia03
committed
9e69a62
Remove debugging
sangeetabhatia03
committed
5627c02

Commits on Jul 1, 2025

Log clinic name when setting is DEBUG
sangeetabhatia03
committed
ce90095
Test on number of clinic events; run ok
sangeetabhatia03
committed
4a7905b
Test fungible runs if capabilities available
sangeetabhatia03
committed
5a0c0f3

Commits on Jul 3, 2025

Fungible/non-fungible/fungible runs ok
sangeetabhatia03
committed
d23f272

Commits on Jul 8, 2025

Set defaults for new arguments to ensure backward compatibility
sangeetabhatia03
committed
272e756

Commits on Jul 9, 2025

Renaming variables for consistency
sangeetabhatia03
committed
1640ec1

Commits on Jul 10, 2025

Test splitting of capabilities
sangeetabhatia03
committed
16fbba4

Commits on Jul 30, 2025

DRY test for clinics
sangeetabhatia03
committed
e015c2c

Commits on Jul 31, 2025

Commits on Aug 1, 2025

Commits on Aug 5, 2025

Commits on Sep 4, 2025

Commits on Sep 11, 2025

Commits on Sep 12, 2025

Commits on Sep 25, 2025

Create linked resource files
sangeetabhatia03
committed
68ce059

Commits on Sep 26, 2025

Resource files mapping clinics to treatment-id
sangeetabhatia03
committed
184dfb2

Commits on Sep 30, 2025

WIP
sangeetabhatia03
committed
67029ec
Reuse old variable names except this is now a dictionary
sangeetabhatia03
committed
1527cef
Single logical strand for using non-other and other clinics in mode2
sangeetabhatia03
committed
b5cbc1d

Commits on Oct 1, 2025

Update tests
sangeetabhatia03
committed
de8d3fe
Fix typos and remove redundant variable
sangeetabhatia03
committed
8e45d23
Edits to deal with nested dictionary of daily capabilities
sangeetabhatia03
committed
8cba450

Commits on Oct 2, 2025

Clinic capabilities split test works
sangeetabhatia03
committed
86e76ed

Commits on Oct 3, 2025

Commits on Oct 4, 2025

All clinics tests pass ok
sangeetabhatia03
committed
3d259cb
Default empty config
sangeetabhatia03
committed
21b3443
Update config in tests
sangeetabhatia03
committed
b2cc86a
Replace fungible with the old variable name
sangeetabhatia03
committed
1302433

Commits on Oct 6, 2025

Commits on Oct 7, 2025

Update clinics test to NOT use an empty dict
sangeetabhatia03
committed
676aa02
Merge master
sangeetabhatia03
committed
ac14311
Add Clinic to expected fields
sangeetabhatia03
committed
1afe44e

Commits on Oct 8, 2025

Consistent datatypes to avoid Inconsistent logger warning
sangeetabhatia03
committed
3e2436e

Commits on Oct 9, 2025

Remove check about level 2 facilities
sangeetabhatia03
committed
a6c6fda

Commits on Oct 13, 2025

Modify setup to split capabilities BEFORE pooling across levels
sangeetabhatia03
committed
d1d24d7

Commits on Oct 14, 2025

Pool capabilities and drop index
sangeetabhatia03
committed
1e61285
Merge branch 'master' into fix-1608
sangeetabhatia03
committed
c790680
Remove fungible terminology
sangeetabhatia03
committed
f95cfd7

Commits on Nov 3, 2025

Re-add files via LFS
tamuri
committed
090c000
Remove file with wildcard in name (unused)
tamuri
committed
99b0b24
Fix names of healthsystem resources subdirectory
tamuri
committed
664e884

Commits on Nov 5, 2025

Fix typo in variable name
sangeetabhatia03
committed
cc9a676

Commits on Nov 11, 2025

Rename OtherClinic to GenericClinic
sangeetabhatia03
committed
e233df1
Rename OtherClinic to GenericClinic in resource files
sangeetabhatia03
committed
1d31f1f

Commits on Nov 12, 2025

Check that clinic names across the two configuration files are consistent
sangeetabhatia03
committed
89ab2f6

Commits on Nov 13, 2025

Remove eligible_clinic property from hsi_event
sangeetabhatia03
committed
9e9c9d7
Changes to ensure clinic eligibility is set and retrieved for HSIEventQueueItem only
sangeetabhatia03
committed
823efad
Fix indentation
sangeetabhatia03
committed
81ca231

Commits on Nov 24, 2025

Merge from master
sangeetabhatia03
committed
88ae07e
Use rescaling factor by facility id and clinic
sangeetabhatia03
committed
83b4615
Iterate over clinics to get rescaling factor for each facility-id
sangeetabhatia03
committed
e161778
Run through ruff
sangeetabhatia03
committed
6e52d97
Some more formatting
sangeetabhatia03
committed
c1ee2fe
Initialise squeeze factor store in pre_initialise_population
sangeetabhatia03
committed
62d8dcc

Commits on Dec 4, 2025

Make clinic_configuration and clinic_mapping an attribute
sangeetabhatia03
committed
247c39c