Cervical cancer #1287

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tbhallett merged 381 commits intomasterfrom

cervical_cancer_

Jul 22, 2025

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andrew-phillips-1 commented Mar 4, 2024

Here's a first draft of this module. I need to do another search to try to find additional data for calibration.

I couldn't upload the draft write as it was asking me to use the command line and Git LFS.

andrew-phillips-1 requested review from mnjowe, tbhallett and thewati

March 4, 2024 17:54

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mnjowe commented Apr 2, 2024

Thanks @andrew-phillips-1 for this first draft. I think it looks good. I will be adding some few comments/suggestions for your consideration.

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andrew-phillips-1 commented Apr 2, 2024

Thanks @mnjowe

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tbhallett added 5 commits

June 9, 2025 18:51


          fix script

0d80478


          be explicit about root to be robust to from where script is run

8ed995b


          further fixes

703bb67


          drop men

0e10e33


          Merge branch 'master' into cervical_cancer_

6e3a149

# Conflicts:
#	resources/ResourceFile_Improved_Healthsystem_And_Healthcare_Seeking/main.csv

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tbhallett commented Jun 28, 2025

This will be ready once we have updated version of write-up.

andrew-phillips-1 and others added 2 commits

June 30, 2025 10:14

3b74044


          linting

082ab54

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tbhallett commented Jun 30, 2025

@mnjowe --- I think this is ready to go now and all your comments have been addressed. Please could you approve the PR, and we'll get it merged?

tbhallett removed the request for review from tdm32

June 30, 2025 10:38


          Merge branch 'master' into cervical_cancer_

fd445de

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tamuri commented Jul 9, 2025

test_all_treatment_ids_defined_in_priority_policies in test_healthsystem failed on following line:

assert set(policy) == clean_set_of_filtered_treatment_ids  # Check that all treatment_ids defined are allowed

tbhallett added 8 commits

July 21, 2025 11:24


          Merge branch 'master' into cervical_cancer_

fcd52bc

# Conflicts:
#	resources/ResourceFile_Improved_Healthsystem_And_Healthcare_Seeking/main.csv
#	resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/CVD.csv
#	resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/ClinicallyVulnerable.csv
#	resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/Default.csv
#	resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/EHP_III.csv
#	resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/LCOA_EHP.csv
#	resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/Naive.csv
#	resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/RMNCH.csv
#	resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/Test Mode 1.csv
#	resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/Test.csv
#	resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/VerticalProgrammes.csv


          refactor screening VIA

d58a34b


          refactor screening xpert

9fd0b19


          refactor presentation

f9ad3a5


          refactor CIN

9ad2c97


          refactor treatment

362f719


          update docstring

b0de328


          align HSI names and treatment_ids

e643e5a

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tbhallett commented Jul 21, 2025

test_all_treatment_ids_defined_in_priority_policies in test_healthsystem failed on following line:
assert set(policy) == clean_set_of_filtered_treatment_ids  # Check that all treatment_ids defined are allowed

now fixed!

tbhallett requested review from mnjowe and thewati and removed request for thewati

July 21, 2025 13:09

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tbhallett commented Jul 21, 2025

I think this is ready now, including all of the requested changes by @mnjowe

@mnjowe --- if you're happy please could you approve this updated version?

mnjowe approved these changes

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mnjowe left a comment

Thanks Andrew and all for the amazing work on cervical cancer and for addressing all my comments. This is looking great!

Collaborator Author

andrew-phillips-1 commented Jul 22, 2025

Thanks Emmanuel. It was Tim who got us over the line.

tbhallett merged commit 91e89b4 into master

63 checks passed

tbhallett deleted the cervical_cancer_ branch

July 22, 2025 15:21

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