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It would be more logical, with respect to the timeline of events in reality, to update VMMC after HIV testing so that people about to undergo VMMC are tested first. This way we can rely on testing and…
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https://www.insider.co.uk/news/scottish-hiv-charity-fined-10000-25293836
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Whereas, the test script and the initial scenario run showed that the HTM scale-up was working as expected, it appears that the in practice they do not (see [here](https://github.com/UCL/TLOmodel/pull…
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### Setup
I am reporting a problem with Biopython version, Python version, and operating
system as follows:
```python
import sys; print(sys.version)
import platform; print(platform.python_imp…
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Repeat the analysis done in https://www.nature.com/articles/s41598-021-82673-8#Sec2 . In particular, steps 1 and 3 of the phylogenetic analysis are connected.
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Add preview of alignment state/QC/mutations, similar to LANL HIV database
![image](https://github.com/loculus-project/loculus/assets/8379168/ad05132b-e361-4769-9e96-3fda21f2ab19)
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For each of possible activities:
1. How many activities in total were shown.
2. How many activities from those shown were completed.
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It's a bit confusing that users pass in modules in `pars.diseases.hiv`, but during `Sim` initialization, the modules are all popped from the `pars` dict and then added back to the pars via `Module.ini…
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When deploying for the first time, the target user doesn't know about the foreign repository's host name, and this will bail out unless you get it added to `known_hosts` manually. For example:
```b…