Snp-transformer

Fix

* fix: added missing argument to tests ([`1466a33`](https://github.com/KennethEnevoldsen/snp-transformer/commit/1466a3353ac9307ba98e288b7c88d85681318022))

* fix: reformatted and ran linters ([`9b76a26`](https://github.com/KennethEnevoldsen/snp-transformer/commit/9b76a269495bfd8047b36f2f643e133a73e78f4d))

* fix: redid test to take into account new changes ([`43ddb51`](https://github.com/KennethEnevoldsen/snp-transformer/commit/43ddb51256439b5dd199ab7b19bf95afbf706c2f))

* fix: Added a bunch of new experiments ([`cb679ae`](https://github.com/KennethEnevoldsen/snp-transformer/commit/cb679aed16b19832304dd50c0e1040148b8e5e9d))

Style

* style: linting ([`54e9a6f`](https://github.com/KennethEnevoldsen/snp-transformer/commit/54e9a6fddc117a434048daa15b9de9ed846527d2))

* style: formatted ([`0a1e362`](https://github.com/KennethEnevoldsen/snp-transformer/commit/0a1e3620d363cbe1433d8c16d84836356dd1a6c7))

Unknown

* Merge pull request 41 from KennethEnevoldsen/create-100-snp-model

100 SNP experiments ([`cd34e46`](https://github.com/KennethEnevoldsen/snp-transformer/commit/cd34e4607b431d5d5c5251357ae97526f5e387b2))

* Merge branch &39;create-100-snp-model&39; of https://github.com/KennethEnevoldsen/snp-transformer into create-100-snp-model ([`4f2890c`](https://github.com/KennethEnevoldsen/snp-transformer/commit/4f2890c6da7f0434dfdb14e7b0d56a660801640e))

* Added warmup experiments ([`2e8f7e1`](https://github.com/KennethEnevoldsen/snp-transformer/commit/2e8f7e1918e9fbbcf1c6dfdeba6c5e700b0d5591))

* Merge branch &39;create-100-snp-model&39; of https://github.com/KennethEnevoldsen/snp-transformer into create-100-snp-model ([`493f0f4`](https://github.com/KennethEnevoldsen/snp-transformer/commit/493f0f442da8ea6145a762c33b3b3f7ba721f489))

* Added analysis ([`34844f6`](https://github.com/KennethEnevoldsen/snp-transformer/commit/34844f62db7f583d951d44806ec324d48ea80e3a))

* Added script for 100snps experiments ([`e4a8847`](https://github.com/KennethEnevoldsen/snp-transformer/commit/e4a8847abd385d0c0904d8acea899f9a68f85c3a))

* experimenting on multiple phenotypes ([`a7eddbe`](https://github.com/KennethEnevoldsen/snp-transformer/commit/a7eddbe8628f97191874b86fed474c1170d5f7d1))

* Merge pull request 40 from KennethEnevoldsen/dependabot/pip/torch-2.2.1

deps:(deps-dev): bump torch from 2.2.0 to 2.2.1 ([`ecbbf97`](https://github.com/KennethEnevoldsen/snp-transformer/commit/ecbbf97be8663186bb50c8b07aa3b0c22a2c64b8))

* deps:(deps-dev): bump torch from 2.2.0 to 2.2.1

Bumps [torch](https://github.com/pytorch/pytorch) from 2.2.0 to 2.2.1.
- [Release notes](https://github.com/pytorch/pytorch/releases)
- [Changelog](https://github.com/pytorch/pytorch/blob/main/RELEASE.md)
- [Commits](https://github.com/pytorch/pytorch/compare/v2.2.0...v2.2.1)

---
updated-dependencies:
- dependency-name: torch
dependency-type: direct:production
update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <supportgithub.com> ([`055eb42`](https://github.com/KennethEnevoldsen/snp-transformer/commit/055eb4294e8a068b91f225d3cf25390bc050bc2a))

* ran fine_tune_no_pretrain_only_511.cfg ([`aa9ff8a`](https://github.com/KennethEnevoldsen/snp-transformer/commit/aa9ff8a41851dadce7eff1d4047c81cf7d77dd71))

Chore

* chore: remove unused file ([`3540921`](https://github.com/KennethEnevoldsen/snp-transformer/commit/35409217cf44e624dbb403d3cd3b5445112b09b5))

Fix

* fix: All tests now pass ([`394f85e`](https://github.com/KennethEnevoldsen/snp-transformer/commit/394f85e53e516a5d275cd37d98273566c58c6d29))

* fix: ran ruff and fixed bugs ([`9eaac1d`](https://github.com/KennethEnevoldsen/snp-transformer/commit/9eaac1d9d9a22c9fccfcd3287cbe5ba1d41e6aa7))

Style

* style: ran linters ([`2bc6e1f`](https://github.com/KennethEnevoldsen/snp-transformer/commit/2bc6e1f33757cf627d87751e8ca45cf25129a4c9))

* style: linting ([`f1ea0bb`](https://github.com/KennethEnevoldsen/snp-transformer/commit/f1ea0bb07541e6a9ddeeea14594f6f04079c6163))

* style: linting ([`cd463c8`](https://github.com/KennethEnevoldsen/snp-transformer/commit/cd463c8ef7553796fa6c5f1042fa9359a5201ada))

* style: linting ([`b67569d`](https://github.com/KennethEnevoldsen/snp-transformer/commit/b67569d888e06f3e8c7baafbff9a79718906bcd2))

Unknown

* Merge pull request 39 from KennethEnevoldsen/fine-tune-mdl

Fine tune mdl ([`02e9839`](https://github.com/KennethEnevoldsen/snp-transformer/commit/02e98393d23ecd67cdaf54aebdb26700dae34c55))

* Merge branch &39;fine-tune-mdl&39; of https://github.com/KennethEnevoldsen/snp-transformer into fine-tune-mdl ([`387ba7d`](https://github.com/KennethEnevoldsen/snp-transformer/commit/387ba7de9657693e4581f257b7e4be27b7daadb0))

* Merge branch &39;fine-tune-mdl&39; of https://github.com/KennethEnevoldsen/snp-transformer into fine-tune-mdl ([`a9f6a8d`](https://github.com/KennethEnevoldsen/snp-transformer/commit/a9f6a8da803a843db3a185bb62665050328d23a2))

* Merge branch &39;fine-tune-mdl&39; of https://github.com/KennethEnevoldsen/snp-transformer into fine-tune-mdl ([`1dbb6a1`](https://github.com/KennethEnevoldsen/snp-transformer/commit/1dbb6a19e16150f1d8fd3089e1c074d5bf52da08))

* misc ([`c226b56`](https://github.com/KennethEnevoldsen/snp-transformer/commit/c226b5655b0b668a0cf0b4b3e5a1d50c773ab13c))

* Add current changes ([`21b754d`](https://github.com/KennethEnevoldsen/snp-transformer/commit/21b754d2aa2ae9857d53eca3488e3f0815848ae5))

* Merge pull request 35 from KennethEnevoldsen/dependabot/pip/torch-2.2.0

deps:(deps-dev): bump torch from 2.1.2 to 2.2.0 ([`cc7416c`](https://github.com/KennethEnevoldsen/snp-transformer/commit/cc7416c3efc2315763ffe694bb954f165db507b9))

* deps:(deps-dev): bump torch from 2.1.2 to 2.2.0

Bumps [torch](https://github.com/pytorch/pytorch) from 2.1.2 to 2.2.0.
- [Release notes](https://github.com/pytorch/pytorch/releases)
- [Changelog](https://github.com/pytorch/pytorch/blob/main/RELEASE.md)
- [Commits](https://github.com/pytorch/pytorch/compare/v2.1.2...v2.2.0)

---
updated-dependencies:
- dependency-name: torch
dependency-type: direct:production
update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <supportgithub.com> ([`bf9efe4`](https://github.com/KennethEnevoldsen/snp-transformer/commit/bf9efe4f37a6292f72ee65b2256ed642e62237ef))

* Added initial training steps ([`47da8ab`](https://github.com/KennethEnevoldsen/snp-transformer/commit/47da8ab38ad9ad2a98ed4154988ea47c75d6ee32))

* Added pheno_dir as a option to configs. ([`1dfe929`](https://github.com/KennethEnevoldsen/snp-transformer/commit/1dfe92928b90570a272613a0eddf45d5d20cc535))

Feature

* feat: Added callbacks ([`8ea1878`](https://github.com/KennethEnevoldsen/snp-transformer/commit/8ea1878dabc3900bc957e8541c3ebe597d5be6c5))

Fix

* fix: Updated pyright ([`9dfeb23`](https://github.com/KennethEnevoldsen/snp-transformer/commit/9dfeb23a66c40a2cccd8680de51900df1855c577))

* fix: fixes type checks ([`bda6ace`](https://github.com/KennethEnevoldsen/snp-transformer/commit/bda6aced49b1201ed2e0ec5e691fc14ecd3cb555))

* fix: Fixed static typing ([`3fe5aa2`](https://github.com/KennethEnevoldsen/snp-transformer/commit/3fe5aa2715feed96add686e0722569e31c3bf044))

* fix: Update typing for 3.9 ([`1eb6c86`](https://github.com/KennethEnevoldsen/snp-transformer/commit/1eb6c8608ac01f4f8db5d873fd5407fdd699e8c0))

* fix: lint and type check ([`064314b`](https://github.com/KennethEnevoldsen/snp-transformer/commit/064314b04c2546cc2adbb76a3841baeaeb56f63a))

* fix: remove accidentally added newline to split ([`9cdde47`](https://github.com/KennethEnevoldsen/snp-transformer/commit/9cdde4723a8e76c51785613bdbf84d3be34af9ed))

* fix: Added new logo ([`80e6a20`](https://github.com/KennethEnevoldsen/snp-transformer/commit/80e6a2071a6b883090ec10312922c4432ab554b3))

Style

* style: lint ([`5c43095`](https://github.com/KennethEnevoldsen/snp-transformer/commit/5c430954affd2ef2027300a845b0830edef692f3))

Unknown

* Merge pull request 32 from KennethEnevoldsen/fine-tune-mdl

Added functionality for fine-tuning and applying model ([`bddf9f0`](https://github.com/KennethEnevoldsen/snp-transformer/commit/bddf9f001aaa8497d8479cc680e194f2a509ffe3))

* clean: Removed outdated files and updated old configs ([`9f1bb41`](https://github.com/KennethEnevoldsen/snp-transformer/commit/9f1bb41ce0f29839db525275e9b9c6252b7ef476))

* Added encoder checkpoint for tests ([`a4a3c1b`](https://github.com/KennethEnevoldsen/snp-transformer/commit/a4a3c1b2a66ef8f93b98bb1155bf2560ebe94290))

* Test pass for apply ([`337d2eb`](https://github.com/KennethEnevoldsen/snp-transformer/commit/337d2eb606b945ea2968fd6767b5196b5c451169))

* Fix model training and apply bugs ([`3e77844`](https://github.com/KennethEnevoldsen/snp-transformer/commit/3e77844ab70d55dcce5b14aa80baa39b91e65472))

* refactored train to runner to include apply ([`82b9b32`](https://github.com/KennethEnevoldsen/snp-transformer/commit/82b9b32675c24f0dd26e0d697a8fee519278b968))

* Added config ([`4641015`](https://github.com/KennethEnevoldsen/snp-transformer/commit/464101513e5f3b9574730ce109ae837fce3baeda))

* Merge pull request 31 from KennethEnevoldsen/dependabot/pip/torch-2.1.2

deps:(deps-dev): bump torch from 2.1.1 to 2.1.2 ([`0978251`](https://github.com/KennethEnevoldsen/snp-transformer/commit/09782519da7b43acd78a56d7d97d4bb861720778))

* deps:(deps-dev): bump torch from 2.1.1 to 2.1.2

Bumps [torch](https://github.com/pytorch/pytorch) from 2.1.1 to 2.1.2.
- [Release notes](https://github.com/pytorch/pytorch/releases)
- [Changelog](https://github.com/pytorch/pytorch/blob/main/RELEASE.md)
- [Commits](https://github.com/pytorch/pytorch/compare/v2.1.1...v2.1.2)

---
updated-dependencies:
- dependency-name: torch
dependency-type: direct:production
update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <supportgithub.com> ([`0d78696`](https://github.com/KennethEnevoldsen/snp-transformer/commit/0d78696023e19fdf3c406f47775a9a8637dd81ae))

* fine-tune on icd 100 ([`0628e82`](https://github.com/KennethEnevoldsen/snp-transformer/commit/0628e82c3dd35363646f633497f530973af500c2))

* training works ([`e5bfa5f`](https://github.com/KennethEnevoldsen/snp-transformer/commit/e5bfa5f951eaefa38db2452f82085fd81c59d247))

* Refactor dataset filtering and sparse conversion ([`2467a1c`](https://github.com/KennethEnevoldsen/snp-transformer/commit/2467a1cbe55d1142e6ca37cfd5484a3a08a93659))

* Added new splits ([`75c749f`](https://github.com/KennethEnevoldsen/snp-transformer/commit/75c749fff4fcebdbb0bb81d4a25708d93d42a794))

Feature

* feat: fixed bug for pheno embedding, added masking
for clf model ([`981ea37`](https://github.com/KennethEnevoldsen/snp-transformer/commit/981ea37144974005aff368f972a37c530b004b09))

Fix

* fix: Minor fixes in phenotype logging ([`bb21908`](https://github.com/KennethEnevoldsen/snp-transformer/commit/bb219080e1a747c8adf224e8c24b41f67596b078))

* fix: ran linters ([`89aa4ed`](https://github.com/KennethEnevoldsen/snp-transformer/commit/89aa4ede1eb5bac611cd88845c0b8c8b49b1e936))

* fix: Added test for encoder for clf ([`f10863f`](https://github.com/KennethEnevoldsen/snp-transformer/commit/f10863fc7ebfd6d480dcaef321766cf7bb790ab9))

* fix: Added dataset filtering ([`5bf0a06`](https://github.com/KennethEnevoldsen/snp-transformer/commit/5bf0a067309f08e150aff322dc62d2865411fe8e))

Style

* style: linting ([`6a877b4`](https://github.com/KennethEnevoldsen/snp-transformer/commit/6a877b4974522ed15e2bc74add0b8a697c94fca6))

* style: linting ([`bab895a`](https://github.com/KennethEnevoldsen/snp-transformer/commit/bab895a6e672c9e653ab73fa6b34d0e5782bfe03))

* style: linting ([`b2f5cc7`](https://github.com/KennethEnevoldsen/snp-transformer/commit/b2f5cc7037d8932e9dc282fbb53f5461d63d181e))

* style: linting ([`2d3876a`](https://github.com/KennethEnevoldsen/snp-transformer/commit/2d3876ab900276370e0d653dfa0724aaa3830e8c))

Unknown

* Merge pull request 28 from KennethEnevoldsen/KennethEnevoldsen/issue-Add-fine-tuning-task-based-on-a-pre-trained-model

Add fine-tuning task ([`872a4cf`](https://github.com/KennethEnevoldsen/snp-transformer/commit/872a4cfbfdc16aa452180cd148a3cc65a5572c4e))

* Merge branch &39;KennethEnevoldsen/issue-Add-fine-tuning-task-based-on-a-pre-trained-model&39; of https://github.com/KennethEnevoldsen/snp-transformer into KennethEnevoldsen/issue-Add-fine-tuning-task-based-on-a-pre-trained-model ([`d52cd10`](https://github.com/KennethEnevoldsen/snp-transformer/commit/d52cd107de3fd241d74cc658f098d83dc0483bba))

* Ran linter ([`31efba8`](https://github.com/KennethEnevoldsen/snp-transformer/commit/31efba808c511b85745ea8a5477a9c195a9eb5bf))

* Merge branch &39;KennethEnevoldsen/issue-Add-fine-tuning-task-based-on-a-pre-trained-model&39; of https://github.com/KennethEnevoldsen/snp-transformer into KennethEnevoldsen/issue-Add-fine-tuning-task-based-on-a-pre-trained-model ([`9d581f8`](https://github.com/KennethEnevoldsen/snp-transformer/commit/9d581f8e4f069eaf5ad08568be09a0cbd891264e))

* Refactor code and fix validation bug in
TrainableModule ([`52be6a3`](https://github.com/KennethEnevoldsen/snp-transformer/commit/52be6a3075b73156a8795b4244eaa42863fafb3a))

* Merge pull request 29 from KennethEnevoldsen/dependabot/pip/torch-2.1.1

deps:(deps-dev): bump torch from 2.0.1 to 2.1.1 ([`da29d90`](https://github.com/KennethEnevoldsen/snp-transformer/commit/da29d9016c42ba288c7409a7f31e1cac00454d62))

* deps:(deps-dev): bump torch from 2.0.1 to 2.1.1

Bumps [torch](https://github.com/pytorch/pytorch) from 2.0.1 to 2.1.1.
- [Release notes](https://github.com/pytorch/pytorch/releases)
- [Changelog](https://github.com/pytorch/pytorch/blob/main/RELEASE.md)
- [Commits](https://github.com/pytorch/pytorch/compare/v2.0.1...v2.1.1)

---
updated-dependencies:
- dependency-name: torch
dependency-type: direct:production
update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <supportgithub.com> ([`3f5eb5f`](https://github.com/KennethEnevoldsen/snp-transformer/commit/3f5eb5ffed8ca1f3f39bc78f63d59a9991a648b1))

* started bugfixing ([`59c9b29`](https://github.com/KennethEnevoldsen/snp-transformer/commit/59c9b298a51def3597107df44690407bfa360c02))

* Add tests for fine-tuning task ([`1221bb5`](https://github.com/KennethEnevoldsen/snp-transformer/commit/1221bb5f37d05fae1a9b6c4065b02736368dc7fa))

Chore

* chore: remove unused code from pr ([`d457b43`](https://github.com/KennethEnevoldsen/snp-transformer/commit/d457b43b98c4e7fa66105b7c03a05d9711646348))

* chore: clean up ([`2aba044`](https://github.com/KennethEnevoldsen/snp-transformer/commit/2aba044d09e33fe24fa907f4809b81f3622d8a0f))

Fix

* fix: Updated pre-commit hooks ([`1f80415`](https://github.com/KennethEnevoldsen/snp-transformer/commit/1f8041549a27a442c2e3febed2c1ca8b9d667e26))

* fix: comparison operator in EncoderForMaskedLM ([`8c6f3b4`](https://github.com/KennethEnevoldsen/snp-transformer/commit/8c6f3b425ce33f6a2ce447d8bf45b317dc9cbcdf))

* fix: set phenotypes to be first in the masked prediction ([`7db01f9`](https://github.com/KennethEnevoldsen/snp-transformer/commit/7db01f94108f3ff9427293d7415be986274a1f39))

* fix: errors in tests ([`7a1149b`](https://github.com/KennethEnevoldsen/snp-transformer/commit/7a1149bc00f313bad0835081626ad40403d80c13))

* fix: fix invalid syntax in makefile ([`aa4c551`](https://github.com/KennethEnevoldsen/snp-transformer/commit/aa4c551bb047ab70f51a523681d324f4a8113111))

* fix: updated test to only run on cpu ([`dd142ec`](https://github.com/KennethEnevoldsen/snp-transformer/commit/dd142ec08bdb9a58d6aa58815bf8c78713edd87d))

* fix: Convert path from pheno to phenos when looking for dataset ([`4643b62`](https://github.com/KennethEnevoldsen/snp-transformer/commit/4643b62f769c15bbc858d85e580fca4991c47e60))

Style

* style: linting ([`27aef42`](https://github.com/KennethEnevoldsen/snp-transformer/commit/27aef42d9f5c863e1fcd0cb682a60ed9efa8577c))

* style: linting ([`dddeabe`](https://github.com/KennethEnevoldsen/snp-transformer/commit/dddeabeee1ba4655d1f6fc6575f1c6c72947bccd))

* style: linting ([`b9c9bea`](https://github.com/KennethEnevoldsen/snp-transformer/commit/b9c9bea6148219b88cf0b757a117b9b91c69a54b))

* style: linting ([`b1321f0`](https://github.com/KennethEnevoldsen/snp-transformer/commit/b1321f0798bbc83a3bdab45799fd091c79040265))

* style: linting ([`b95dc59`](https://github.com/KennethEnevoldsen/snp-transformer/commit/b95dc59f9ff04bd6a8febfd85a9757d54c8b62fa))

Unknown

* Merge pull request 22 from KennethEnevoldsen/pretraining_w_pos

Pretraining w pos ([`afe5b04`](https://github.com/KennethEnevoldsen/snp-transformer/commit/afe5b049ec1e76c386685db265ea204f4f6d0039))

* Merge branch &39;main&39; into pretraining_w_pos ([`e4377ab`](https://github.com/KennethEnevoldsen/snp-transformer/commit/e4377ab7dd1133edd3d10d40a8f71332ed3487c5))

* Merge pull request 27 from KennethEnevoldsen/add-train-test-split

Add train/test split functionality to IndividualsDataset ([`ec9a24b`](https://github.com/KennethEnevoldsen/snp-transformer/commit/ec9a24b1480facfde6773cfd416a869acdee8073))

* Added train/test split to dataset ([`1f57d9f`](https://github.com/KennethEnevoldsen/snp-transformer/commit/1f57d9f88fbc8ab1491e82e81f6599a4e0354c44))

* merge ([`1ccf494`](https://github.com/KennethEnevoldsen/snp-transformer/commit/1ccf494de806c79caeba579e8a4f423584dfdbf1))

* Fix nan loss calculation in EncoderForMaskedLM ([`8086139`](https://github.com/KennethEnevoldsen/snp-transformer/commit/8086139fb08b6775dfd5acb7b53d9fc2f61681a4))

* Merge branch &39;pretraining_w_pos&39; of https://github.com/KennethEnevoldsen/snp-transformer into pretraining_w_pos ([`6852ccc`](https://github.com/KennethEnevoldsen/snp-transformer/commit/6852ccc1b090910d4564cd504f5879aec7a66044))

* Merge branch &39;pretraining_w_pos&39; of https://github.com/KennethEnevoldsen/snp-transformer into pretraining_w_pos ([`6ea9419`](https://github.com/KennethEnevoldsen/snp-transformer/commit/6ea941925a4a51f37a11d2d526e4f2c6df53c8ce))

* Update config.cfg with new values ([`d940374`](https://github.com/KennethEnevoldsen/snp-transformer/commit/d94037450c75b5c651fab28a990ea4a44889f0aa))

* Merge branch &39;pretraining_w_pos&39; of https://github.com/KennethEnevoldsen/snp-transformer into pretraining_w_pos ([`cafb663`](https://github.com/KennethEnevoldsen/snp-transformer/commit/cafb66302eebabe765d7f38ee12e3e6abce5352b))

* Merge branch &39;main&39; into pretraining_w_pos ([`242b096`](https://github.com/KennethEnevoldsen/snp-transformer/commit/242b096d8601aa8e7505432b9f54170addf05753))

* Update configuration and model modules ([`d3da163`](https://github.com/KennethEnevoldsen/snp-transformer/commit/d3da163b9bbc6edbaa29db1d80ea210988240264))

* Merge branch &39;main&39; into pretraining_w_pos ([`9cdaf6d`](https://github.com/KennethEnevoldsen/snp-transformer/commit/9cdaf6de54a4868b32f94b35bc58db6b09eeccec))

* Refactor InputIds dataclass constructor to include
data validation. ([`8011bde`](https://github.com/KennethEnevoldsen/snp-transformer/commit/8011bdea22e01d9a59bd7cc8a4efed2c4ca76b95))

* Merge branch &39;pretraining_w_pos&39; of https://github.com/KennethEnevoldsen/snp-transformer into pretraining_w_pos ([`fc17006`](https://github.com/KennethEnevoldsen/snp-transformer/commit/fc170066ffef2854a106f1ab56b14cc6690f99c4))

* debugging ([`381eb6e`](https://github.com/KennethEnevoldsen/snp-transformer/commit/381eb6e289a63a4a5a82a8eca4384ba4e98ca0eb))

* still debugging ([`02f1f20`](https://github.com/KennethEnevoldsen/snp-transformer/commit/02f1f20646e980c54e2a00f0f2cb4fcc57838f84))

* still debugging ([`ab835f0`](https://github.com/KennethEnevoldsen/snp-transformer/commit/ab835f0d36756f8231923b06fa07acb1c1ff993f))

* started to debug ([`988363c`](https://github.com/KennethEnevoldsen/snp-transformer/commit/988363c608dba978356770636590d76bfdb9307c))

* Added pretrain command to makefile ([`dadf983`](https://github.com/KennethEnevoldsen/snp-transformer/commit/dadf9838db7cc32749496064ec8d1a3877584266))

Ci

* ci: update cruft ([`86dae70`](https://github.com/KennethEnevoldsen/snp-transformer/commit/86dae70698164a6ad04e3b05b0e16b5ebb519d01))

Fix

* fix: ran linting ([`6760456`](https://github.com/KennethEnevoldsen/snp-transformer/commit/676045640a0cfc8b788dabdeff0573da77a38c2a))

Style

* style: linting ([`2621aec`](https://github.com/KennethEnevoldsen/snp-transformer/commit/2621aec3d37eff3ac40f68122cd4fb0b16cc4155))

* style: linting ([`3363715`](https://github.com/KennethEnevoldsen/snp-transformer/commit/3363715d2d95758defeb7ff4c1ca6f61d6e04af0))

Unknown

* Merge pull request 20 from KennethEnevoldsen/pos_enc

Add makefile with static type checking, testing, and linting commands; refactor positional encoding calculation; add positional embedding to SNPEmbedder ([`b614fb0`](https://github.com/KennethEnevoldsen/snp-transformer/commit/b614fb052a1cdf23a72e7683b2d13ed5d1c187e6))

* Merge pull request 21 from KennethEnevoldsen/update-cruft

ci - update cruft ([`29790b4`](https://github.com/KennethEnevoldsen/snp-transformer/commit/29790b44b546909cbca4a9537dc0902290f5adca))

* Merge branch &39;pos_enc&39; of https://github.com/KennethEnevoldsen/snp-transformer into pos_enc ([`a4cedfc`](https://github.com/KennethEnevoldsen/snp-transformer/commit/a4cedfc515abdeb41701f5b2e8508213e2e21ee7))

* Add positional embedding to SNPEmbedder ([`092482d`](https://github.com/KennethEnevoldsen/snp-transformer/commit/092482de861c977b073916ccba01350de7b1815a))

* Refactor positional encoding calculation ([`86cfafc`](https://github.com/KennethEnevoldsen/snp-transformer/commit/86cfafc825355ca27e34898a992e006668686507))

* Add makefile with static type checking, testing,
and linting commands ([`160da71`](https://github.com/KennethEnevoldsen/snp-transformer/commit/160da71a290a73e34588cabe9df7bccb7c7d0c74))

* Added SNPTransformer presentation key ([`6917091`](https://github.com/KennethEnevoldsen/snp-transformer/commit/6917091aa8282849d592e185f8d1da0e2bf45f35))

* Merge branch &39;main&39; of https://github.com/KennethEnevoldsen/snp-transformer into main ([`bb70af0`](https://github.com/KennethEnevoldsen/snp-transformer/commit/bb70af07bddcc6026d7353aa1a6a50006c32a747))

* Add absolute and relative positional encodings for
SNP transformer model ([`a07b5f7`](https://github.com/KennethEnevoldsen/snp-transformer/commit/a07b5f74b0637b086b6d9eaed37e0f3ef8e84f73))