Mus mus Cox map, try two

[peterdfields]

@igronau I'm not quite sure what happened but when I tried to merge recent changes to main into the older branch for creating the map things went awry. So, picking up from #1452, I followed you advice to use msprime.RateMap function to create the rates for each chromosome. The tarball of all genetic map files can be accessed using the following link. Please let me know if any other information or changes are needed.

[igronau]

The genetic map files look good. @andrewkern , can you pick it up from here and copy them over to AWS? Anything else @peterdfields needs to do?

[petrelharp]

LGTM! We just need the maps uploaded, looks like.

[peterdfields]

@igronau @petrelharp Maps uploaded by @andrewkern, so I think this should be all set!

[petrelharp]

I've rebased this.

[petrelharp]

Looks like the files are not there:

ERROR tests/test_genetic_maps.py::TestGetChromosomeMap::test_one_chrom_from_each_map - 
urllib.error.HTTPError: HTTP Error 404: Not Found: 
https://stdpopsim.s3-us-west-2.amazonaws.com/genetic_maps/dir/cox.tar.gz

... and, I think the filename needs changing anyhow (to include a version number); see note at the end of the docs.

[peterdfields]

@petrelharp I can change the filename but I'm not sure what it should be. @andrewkern do you know what the file is named on amazon? I received the message that the map had been uploaded on April 5, 2024.

[andrewkern]

this tar ball in AWS is named cox.tar.gz

individual files in there are named like Cox_etal_2009_v3_GRCm39_*

[petrelharp]

Hm well

ERROR tests/test_genetic_maps.py::TestGetChromosomeMap::test_one_chrom_from_each_map - urllib.error.HTTPError: HTTP Error 404: Not Found: https://stdpopsim.s3-us-west-2.amazonaws.com/genetic_maps/dir/cox.tar.gz

[petrelharp]

Let's see if that works...

[andrewkern]

looks like tests failed but try this @petrelharp

ERROR tests/test_genetic_maps.py::TestGetChromosomeMap::test_one_chrom_from_each_map - 
AssertionError: SHA256 for _test_cache/tarballs/Cox_etal_2009_v3_GRCm39.tar.gz doesn't match the SHA256 for 
Cox_etal_2009_v3_GRCm39. If you didn't add this SHA256 yourself, try deleting 
_test_cache/tarballs/Cox_etal_2009_v3_GRCm39.tar.gz and restarting the tests.

[petrelharp]

CI should not have a cache, I think? I'll leave @peterdfields to figure out what's going on?