Add testing of EpiAware to CI

[seabbs]

This PR adds unit testing as a CI action. It also reorganises the .toml files to follow the recommended Julia style of having a nested test environment for all testing dependencies.

This PR has been locally tested using act and passes all checks.

_Note: The use of a special temporary environment when tests are called may not work correctly with caching. However, I think resolving this is probably not worth the lift if we can instead wait until julia-actions are enabled.

[SamuelBrand1]

act is failing for me.

So the first failure running act locally from bash with act --container-architecture linux/amd64

[Test EpiAware/test-EpiAware] ⭐ Run Main actions/cache@v3
[Test EpiAware/test-EpiAware]   🐳  docker cp src=/Users/samandfi/.cache/act/actions-cache@v3/ dst=/var/run/act/actions/actions-cache@v3/
[pre-commit/pre-commit      ]   🐳  docker exec cmd=[node /var/run/act/workflow/hashfiles/index.js] user= workdir=
[Test EpiAware/test-EpiAware]   🐳  docker exec cmd=[node /var/run/act/actions/actions-cache@v3/dist/restore/index.js] user= workdir=
[Test EpiAware/test-EpiAware]   💬  ::debug::Resolved Keys:
[Test EpiAware/test-EpiAware]   💬  ::debug::["julia-1.10.0-310dd69f39ec4ba5882e8507dd218d1d143ca697aa9af89d76e91f0e8ce4ce4f"]
[Test EpiAware/test-EpiAware]   💬  ::debug::Checking zstd --quiet --version
[Test EpiAware/test-EpiAware]   💬  ::debug::1.4.8
[Test EpiAware/test-EpiAware]   💬  ::debug::zstd version: 1.4.8
[Test EpiAware/test-EpiAware]   💬  ::debug::Resource Url: http://192.168.0.66:50477/_apis/artifactcache/cache?keys=julia-1.10.0-310dd69f39ec4ba5882e8507dd218d1d143ca697aa9af89d76e91f0e8ce4ce4f&version=3971121c6fff6d6a8e35c7a73fb7ab8e8701d96e94026f2b0cd51c32618257da
[Test EpiAware/test-EpiAware]   💬  ::debug::Failed to delete archive: Error: ENOENT: no such file or directory, unlink ''
| Cache not found for input keys: julia-1.10.0-310dd69f39ec4ba5882e8507dd218d1d143ca697aa9af89d76e91f0e8ce4ce4f

then we get some SEGFAULTS

[Test EpiAware/test-EpiAware] ⭐ Run Main actions/cache@v3
[Test EpiAware/test-EpiAware]   🐳  docker cp src=/Users/samandfi/.cache/act/actions-cache@v3/ dst=/var/run/act/actions/actions-cache@v3/
[pre-commit/pre-commit      ]   🐳  docker exec cmd=[node /var/run/act/workflow/hashfiles/index.js] user= workdir=
[Test EpiAware/test-EpiAware]   🐳  docker exec cmd=[node /var/run/act/actions/actions-cache@v3/dist/restore/index.js] user= workdir=
[Test EpiAware/test-EpiAware]   💬  ::debug::Resolved Keys:
[Test EpiAware/test-EpiAware]   💬  ::debug::["julia-1.10.0-310dd69f39ec4ba5882e8507dd218d1d143ca697aa9af89d76e91f0e8ce4ce4f"]
[Test EpiAware/test-EpiAware]   💬  ::debug::Checking zstd --quiet --version
[Test EpiAware/test-EpiAware]   💬  ::debug::1.4.8
[Test EpiAware/test-EpiAware]   💬  ::debug::zstd version: 1.4.8
[Test EpiAware/test-EpiAware]   💬  ::debug::Resource Url: http://192.168.0.66:50477/_apis/artifactcache/cache?keys=julia-1.10.0-310dd69f39ec4ba5882e8507dd218d1d143ca697aa9af89d76e91f0e8ce4ce4f&version=3971121c6fff6d6a8e35c7a73fb7ab8e8701d96e94026f2b0cd51c32618257da
[Test EpiAware/test-EpiAware]   💬  ::debug::Failed to delete archive: Error: ENOENT: no such file or directory, unlink ''
| Cache not found for input keys: julia-1.10.0-310dd69f39ec4ba5882e8507dd218d1d143ca697aa9af89d76e91f0e8ce4ce4f
[Test EpiAware/test-EpiAware]   ✅  Success - Main actions/cache@v3
[Test EpiAware/test-EpiAware]   ✅  Success - Main ./.github/actions/install-julia
[Test EpiAware/test-EpiAware] ⭐ Run Main Run unit tests for EpiAware
[Test EpiAware/test-EpiAware]   🐳  docker exec cmd=[bash --noprofile --norc -e -o pipefail /var/run/act/workflow/2] user= workdir=
[pre-commit/pre-commit      ] ⭐ Run Main actions/cache@v3
[pre-commit/pre-commit      ]   🐳  docker cp src=/Users/samandfi/.cache/act/actions-cache@v3/ dst=/var/run/act/actions/actions-cache@v3/
[pre-commit/pre-commit      ]   🐳  docker exec cmd=[node /var/run/act/actions/actions-cache@v3/dist/restore/index.js] user= workdir=
[pre-commit/pre-commit      ]   💬  ::debug::Resolved Keys:
[pre-commit/pre-commit      ]   💬  ::debug::["julia-1.10.0-310dd69f39ec4ba5882e8507dd218d1d143ca697aa9af89d76e91f0e8ce4ce4f"]
[pre-commit/pre-commit      ]   💬  ::debug::Checking zstd --quiet --version
| 
| [111] signal (11.1): Segmentation fault
| in expression starting at none:0
[pre-commit/pre-commit      ]   💬  ::debug::1.4.8
[pre-commit/pre-commit      ]   💬  ::debug::zstd version: 1.4.8
[pre-commit/pre-commit      ]   💬  ::debug::Resource Url: http://192.168.0.66:50477/_apis/artifactcache/cache?keys=julia-1.10.0-310dd69f39ec4ba5882e8507dd218d1d143ca697aa9af89d76e91f0e8ce4ce4f&version=3971121c6fff6d6a8e35c7a73fb7ab8e8701d96e94026f2b0cd51c32618257da
| get_item_for_reloc at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/staticdata.c:1730 [inlined]
| jl_read_reloclist at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/staticdata.c:1874
| jl_restore_system_image_from_stream_ at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/staticdata.c:2996
| jl_restore_system_image_from_stream at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/staticdata.c:3458 [inlined]
| ijl_restore_system_image_data at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/staticdata.c:3523
| jl_load_sysimg_so at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/staticdata.c:586 [inlined]
| ijl_restore_system_image at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/staticdata.c:3494
| _finish_julia_init at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/init.c:859
| julia_init at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/init.c:844
| jl_repl_entrypoint at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/jlapi.c:725
| main at julia (unknown line)
| unknown function (ip: 0x400087bd8f)
| __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
| unknown function (ip: 0x4010b8)
| Allocations: 0 (Pool: 0; Big: 0); GC: 0
| 
| [111] signal (11.1): Segmentation fault
| in expression starting at none:0
| get_item_for_reloc at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/staticdata.c:1730 [inlined]
| jl_read_reloclist at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/staticdata.c:1874
| jl_restore_system_image_from_stream_ at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/staticdata.c:2996
| jl_restore_system_image_from_stream at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/staticdata.c:3458 [inlined]
| ijl_restore_system_image_data at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/staticdata.c:3523
| jl_load_sysimg_so at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/staticdata.c:586 [inlined]
| ijl_restore_system_image at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/staticdata.c:3494
| _finish_julia_init at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/init.c:859
| julia_init at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/init.c:844
| jl_repl_entrypoint at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/jlapi.c:725
| main at julia (unknown line)
| unknown function (ip: 0x400087bd8f)
| __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
| unknown function (ip: 0x4010b8)
| Allocations: 0 (Pool: 0; Big: 0); GC: 0
| qemu: uncaught target signal 11 (Segmentation fault) - core dumped
[pre-commit/pre-commit      ]   💬  ::debug::Failed to delete archive: Error: ENOENT: no such file or directory, unlink ''
| Cache not found for input keys: julia-1.10.0-310dd69f39ec4ba5882e8507dd218d1d143ca697aa9af89d76e91f0e8ce4ce4f
| /var/run/act/workflow/2: line 2:   111 Segmentation fault      julia --project=EpiAware -e 'using Pkg; Pkg.test()'
[Test EpiAware/test-EpiAware]   ❌  Failure - Main Run unit tests for EpiAware

[seabbs]

Not ideal but I think the thing we likely want to review here is if it works on CI which it appears to? I imagine the issue here is that the CI is targeting a version of Julia your computer can't install because of the different silicon?

https://github.com/CDCgov/Rt-without-renewal/pull/19/checks

I think for the Mac silicon macs you can run some kind of virtualiser to get this all working but I am not sure you really need to have locally working actions given all the functionality inside of them can be run sandboxed by Julia quite well.