Snp-transformer

Feature

* feat: Added phenos to embedding module ([`be5f552`](https://github.com/KennethEnevoldsen/snp-transformer/commit/be5f552363806f355934a40fe316726a2a2fbbca))

Fix

* fix: restructured folders ([`90c456f`](https://github.com/KennethEnevoldsen/snp-transformer/commit/90c456f336c77551cefed24e184592826650e441))

Style

* style: linting ([`d832519`](https://github.com/KennethEnevoldsen/snp-transformer/commit/d832519ddbb0aefecdeb8ab507d0301bf45d7172))

Unknown

* Merge pull request 6 from KennethEnevoldsen/pretrain_simple

initial outline for pre-training ([`d2a1a69`](https://github.com/KennethEnevoldsen/snp-transformer/commit/d2a1a695533da40ed0a8400fabbf06c559dbd1d2))

* added phenotypes ([`1ba08ef`](https://github.com/KennethEnevoldsen/snp-transformer/commit/1ba08eff79576a065d206dee924a7b718aff5b83))

* ran a full epoch on on the MHC region ([`7543d7a`](https://github.com/KennethEnevoldsen/snp-transformer/commit/7543d7acca610a43a8e4ef17c105f581bf13b2dc))

Ci

* ci: Updated tests to only run lowest version ([`d737ff0`](https://github.com/KennethEnevoldsen/snp-transformer/commit/d737ff052139c35c07b070e8265d543c0995753b))

Feature

* feat: add 39 support ([`79ccd84`](https://github.com/KennethEnevoldsen/snp-transformer/commit/79ccd84a9119c1deb039c863677a9b7eb0a24c97))

Fix

* fix: added missing test env ([`bd1e157`](https://github.com/KennethEnevoldsen/snp-transformer/commit/bd1e157f55d789eaee1d0051756bfa18f8fa1eb1))

* fix: added fixes from genomedk ([`6500b47`](https://github.com/KennethEnevoldsen/snp-transformer/commit/6500b4793f5d07c6c71b2e1c2d0efd6e443dfdb4))

* fix: ran precommit ([`f889552`](https://github.com/KennethEnevoldsen/snp-transformer/commit/f8895529a3351c7c3c4c10719043045498bd2922))

Style

* style: linting ([`ab3d611`](https://github.com/KennethEnevoldsen/snp-transformer/commit/ab3d611bb020abf608fcea7667340e90717b84fd))

* style: linting ([`1e68d98`](https://github.com/KennethEnevoldsen/snp-transformer/commit/1e68d98c288cbf2a2ca74d797c67519617e94c6f))

* style: linting ([`3be9733`](https://github.com/KennethEnevoldsen/snp-transformer/commit/3be97330051394cb25fe619acf877886c5bf1a9b))

* style: linting ([`0a65559`](https://github.com/KennethEnevoldsen/snp-transformer/commit/0a655599691b99709ed1198ec61085c105c62432))

Unknown

* Merge remote-tracking branch &39;origin&39; into pretrain_simple ([`d8cbc36`](https://github.com/KennethEnevoldsen/snp-transformer/commit/d8cbc36551269110be77d8cf7097865f0ac4e4f2))

* Merge remote-tracking branch &39;origin&39; into pretrain_simple ([`f3404ed`](https://github.com/KennethEnevoldsen/snp-transformer/commit/f3404edfc51303c6f86d8956130f64c4a3301884))

* Merge pull request 16 from KennethEnevoldsen/39-support

feat: add 39 support ([`f0c7a06`](https://github.com/KennethEnevoldsen/snp-transformer/commit/f0c7a0658acd8a16c94967413ee2a17a099767a0))

* Merge branch &39;39-support&39; of https://github.com/KennethEnevoldsen/snp-transformer into 39-support ([`80e306c`](https://github.com/KennethEnevoldsen/snp-transformer/commit/80e306cff5cc62d224e228d5d9b5b1ade4bbdf82))

* Merge branch &39;pretrain_simple&39; of https://github.com/KennethEnevoldsen/snp-transformer into pretrain_simple ([`8ec7701`](https://github.com/KennethEnevoldsen/snp-transformer/commit/8ec770145622d06293947b993a45de52e0094d55))

Feature

* feat: save hyperparameters in checkpoints ([`add3320`](https://github.com/KennethEnevoldsen/snp-transformer/commit/add332045f76eba33396db51ed7810a4bc565e24))

* feat: Updated loaders to you pyarrow backend ([`9d16f69`](https://github.com/KennethEnevoldsen/snp-transformer/commit/9d16f69dc5257fe3b63499682c6a20cd466c396c))

Fix

* fix: fixed erorrs raised from test ([`c14ae16`](https://github.com/KennethEnevoldsen/snp-transformer/commit/c14ae163cbf82f7edef4299afc8b2bce61b98927))

* fix: minor fixes ([`c551612`](https://github.com/KennethEnevoldsen/snp-transformer/commit/c551612caf4c91d91b130b63b0b7064d2de04663))

* fix: indexing issues with sparse ([`f74fcc5`](https://github.com/KennethEnevoldsen/snp-transformer/commit/f74fcc597640bb572db8d2061b1843c7970f4bb0))

* fix: Updated tests to work with polars ([`e38021b`](https://github.com/KennethEnevoldsen/snp-transformer/commit/e38021bf67258a06ad022853c624cc43b1e6e8ed))

* fix: Added progressbar to convertion script ([`44bd751`](https://github.com/KennethEnevoldsen/snp-transformer/commit/44bd7516d5dd673f0d22c96421b1de6c6f800d9b))

* fix: Added psparse format ([`a418095`](https://github.com/KennethEnevoldsen/snp-transformer/commit/a418095249a69f7e3a0d243046f83d2b3bba66b7))

* fix: Added logging during setup ([`a393683`](https://github.com/KennethEnevoldsen/snp-transformer/commit/a39368303281e2c5af6a4071b481519c8c915adf))

* fix: added missing dependency ([`b2e7fcc`](https://github.com/KennethEnevoldsen/snp-transformer/commit/b2e7fcce8f863cfd89af7df5cf510c1cbc97da7b))

Style

* style: linting ([`664db5e`](https://github.com/KennethEnevoldsen/snp-transformer/commit/664db5ea38e5352858280793f334cce568bcf6ab))

* style: linting ([`026e9ce`](https://github.com/KennethEnevoldsen/snp-transformer/commit/026e9ce001c9dc4df5a6ba6ba6f76b33987bb13e))

* style: linting ([`cd0410c`](https://github.com/KennethEnevoldsen/snp-transformer/commit/cd0410ca6c46a87f6a737bbfc66ddf3175722943))

* style: linting ([`e48e180`](https://github.com/KennethEnevoldsen/snp-transformer/commit/e48e18028875656877f2cafbb5885cff7e39c9f0))

* style: linting ([`ef3b320`](https://github.com/KennethEnevoldsen/snp-transformer/commit/ef3b3209df43ae5d54bb3a87c631751d459416cb))

* style: linting ([`87b3941`](https://github.com/KennethEnevoldsen/snp-transformer/commit/87b39410c17cca11878533b0c195991c8ad0f5f0))

* style: linting ([`e0f6f3d`](https://github.com/KennethEnevoldsen/snp-transformer/commit/e0f6f3db882ef2c149bc3cb9f37da618caab9987))

* style: linting ([`c0dbd39`](https://github.com/KennethEnevoldsen/snp-transformer/commit/c0dbd3937fbff0ce97e8efb4e48663656e386230))

* style: linting ([`15104e8`](https://github.com/KennethEnevoldsen/snp-transformer/commit/15104e8c4dbc681ba30660f0ef62bfd525ade750))

* style: linting ([`77a3359`](https://github.com/KennethEnevoldsen/snp-transformer/commit/77a33594377c5a45eb76d2222445e26fa973c7b9))

* style: linting ([`929981a`](https://github.com/KennethEnevoldsen/snp-transformer/commit/929981a4132026d38d54676e307551f79befdcd9))

* style: linting ([`4f75ac9`](https://github.com/KennethEnevoldsen/snp-transformer/commit/4f75ac9f3952dad793b9663e1024d01244988297))

Unknown

* Merge branch &39;main&39; of https://github.com/KennethEnevoldsen/snp-transformer into pretrain_simple ([`ca26bd5`](https://github.com/KennethEnevoldsen/snp-transformer/commit/ca26bd5e053af8f0f70927b16ad7f8dcc97c47bf))

* Merge pull request 11 from KennethEnevoldsen/add-mlm-accuracy

Add MLM accuracy ([`35b8eb6`](https://github.com/KennethEnevoldsen/snp-transformer/commit/35b8eb626bb76a98b76b41cbbc3764d712e49200))

* Merge pull request 10 from MartinBernstorff/main

feat: save hyperparameters in checkpoints ([`14983d5`](https://github.com/KennethEnevoldsen/snp-transformer/commit/14983d580bf7567fdd962641e2b454f404e42ff8))

* Merge branch &39;add-mlm-accuracy&39; of https://github.com/KennethEnevoldsen/snp-transformer into add-mlm-accuracy ([`006c71e`](https://github.com/KennethEnevoldsen/snp-transformer/commit/006c71e368f89459d9e062c9bedb27c56bd5147a))

* Added truncation for initial training ([`e959bbf`](https://github.com/KennethEnevoldsen/snp-transformer/commit/e959bbfb8bb570cf81f3ccd6b5d9d78004783599))

* Merge branch &39;pretrain_simple&39; of https://github.com/KennethEnevoldsen/snp-transformer into pretrain_simple ([`2d8e83e`](https://github.com/KennethEnevoldsen/snp-transformer/commit/2d8e83e2ec6b01fbac330eeaeb60211d1de54d48))

* Merge branch &39;pretrain_simple&39; of https://github.com/KennethEnevoldsen/snp-transformer into pretrain_simple ([`efa32b0`](https://github.com/KennethEnevoldsen/snp-transformer/commit/efa32b042aee4073ea189708b7d257ffb7c1a136))

* clean up application scripts ([`7bbc314`](https://github.com/KennethEnevoldsen/snp-transformer/commit/7bbc31471b64e1825218802594b6b56e96e4f64a))

* moved mlm acc into function ([`7ed7247`](https://github.com/KennethEnevoldsen/snp-transformer/commit/7ed7247de9d4d4444caeb1a9fbdc5ebcf67f6496))

* Merge branch &39;pretrain_simple&39; of https://github.com/KennethEnevoldsen/snp-transformer into pretrain_simple ([`12e8c21`](https://github.com/KennethEnevoldsen/snp-transformer/commit/12e8c210fb9695629b66327eea6a8b7614d08a63))

* moved to polars ([`91d24ad`](https://github.com/KennethEnevoldsen/snp-transformer/commit/91d24ad5deb12a4f407bde611aa819844e5fa9fe))

* remove accidental copy paste ([`9bd452c`](https://github.com/KennethEnevoldsen/snp-transformer/commit/9bd452c8c7e25115a000e2014864fe7825fac6ef))

* 0.0.6
Automatically generated by python-semantic-release ([`de54d40`](https://github.com/KennethEnevoldsen/snp-transformer/commit/de54d405cbeefd4c2d7e810e18bacb0bba00a5fc))

* Merge branch &39;pretrain_simple&39; of https://github.com/KennethEnevoldsen/snp-transformer into pretrain_simple ([`497e562`](https://github.com/KennethEnevoldsen/snp-transformer/commit/497e562e76362cd99493ecf8d161efd4dc7394de))

* ran speed test for loading mhc ([`cb3d39b`](https://github.com/KennethEnevoldsen/snp-transformer/commit/cb3d39ba25d9d787b38563c8c4a007559b157dd5))

* Merge branch &39;pretrain_simple&39; of https://github.com/KennethEnevoldsen/snp-transformer into pretrain_simple ([`e2e416d`](https://github.com/KennethEnevoldsen/snp-transformer/commit/e2e416d99e028881933594d6b17d4c0f7b126cf6))

* Added speed test for loading the mhc region ([`9a4df12`](https://github.com/KennethEnevoldsen/snp-transformer/commit/9a4df12567dc9efc523cd4e00f913dc150be1a62))

* Merge branch &39;main&39; of https://github.com/KennethEnevoldsen/snp-transformer into pretrain_simple ([`1c0e00b`](https://github.com/KennethEnevoldsen/snp-transformer/commit/1c0e00b2ec78cf11940da787fb0e3a49292a3b40))

Ci

* ci: removed windows support ([`3be156f`](https://github.com/KennethEnevoldsen/snp-transformer/commit/3be156f2009aa3794631809af0248b016fc87c5d))

Fix

* fix: removed removed poor defaults from config ([`baef699`](https://github.com/KennethEnevoldsen/snp-transformer/commit/baef6998e3be75809c582328d5ae9d1684e7ebdb))

* fix: remove static path in config ([`31dc374`](https://github.com/KennethEnevoldsen/snp-transformer/commit/31dc3742e823ebf724f5d398c9fc15ff3883989c))

* fix: updated error message ([`5ebd81a`](https://github.com/KennethEnevoldsen/snp-transformer/commit/5ebd81a8f29afab7cf008e5234bcc306154db11d))

* fix: added missing dependency ([`d44edd0`](https://github.com/KennethEnevoldsen/snp-transformer/commit/d44edd0c1a8ab7e5b5841fbad32720ce5311bfac))

* fix: Updated configs ([`ac467b3`](https://github.com/KennethEnevoldsen/snp-transformer/commit/ac467b3dc7629c217085f9d2df821d8c90ca76d4))

* fix: tests ([`5081a3e`](https://github.com/KennethEnevoldsen/snp-transformer/commit/5081a3e24f9300e143b149668241a0402649a985))

* fix: ensure that logging works as intended ([`3f51073`](https://github.com/KennethEnevoldsen/snp-transformer/commit/3f5107309e12695a334467776f5ebcafa24ce000))

Style

* style: linting ([`0773f52`](https://github.com/KennethEnevoldsen/snp-transformer/commit/0773f525e9bbc69a7a64531203f8067fe08e5111))

Unknown

* Merge branch &39;pretrain_simple&39; of https://github.com/KennethEnevoldsen/snp-transformer into pretrain_simple ([`182b1bc`](https://github.com/KennethEnevoldsen/snp-transformer/commit/182b1bc1133288faaee06ae0b8efa2ca62dd92de))

* initial outline for pretraining ([`914062b`](https://github.com/KennethEnevoldsen/snp-transformer/commit/914062b532fe41c7f762aa9340a81b9237d69aab))

* ran ruff ([`23f0198`](https://github.com/KennethEnevoldsen/snp-transformer/commit/23f01981b3a727db0fdfd11b1f90a96291e55e40))

* Merge branch &39;main&39; of https://github.com/KennethEnevoldsen/snp-transformer ([`b69f98c`](https://github.com/KennethEnevoldsen/snp-transformer/commit/b69f98c9daad22fe828b0b79b7cab9c25a56ea15))

* minor ([`fd66009`](https://github.com/KennethEnevoldsen/snp-transformer/commit/fd66009481180afbe3697aa51e29437482fc2238))

* restructured repo ([`c9a32d1`](https://github.com/KennethEnevoldsen/snp-transformer/commit/c9a32d127c47f3b8bb63164c7dca4568aea6f3d9))

* added training config ([`136fa40`](https://github.com/KennethEnevoldsen/snp-transformer/commit/136fa4077d0bd837eb7a3b9bc0378fba41ac2440))

* added keynote presentation ([`272d7be`](https://github.com/KennethEnevoldsen/snp-transformer/commit/272d7be368adbcfdaca92504dfe472cf1207e055))

Fix

* fix: Added working model ([`41fe4c9`](https://github.com/KennethEnevoldsen/snp-transformer/commit/41fe4c91ed43e9256f663a916f9c7f2c2687036a))

Unknown

* Merge branch &39;main&39; of https://github.com/KennethEnevoldsen/snp-transformer ([`4242b31`](https://github.com/KennethEnevoldsen/snp-transformer/commit/4242b317c66383cc9598e4f320acd5e778ac33de))

* Changed task modules to ligthning ([`2065cb3`](https://github.com/KennethEnevoldsen/snp-transformer/commit/2065cb39e3e7474d68bbe3c083eaafa838a44cd0))

Fix

* fix: refactor ([`1b47546`](https://github.com/KennethEnevoldsen/snp-transformer/commit/1b475460d3a4af13311c9c886c3f9eb7bacbed32))

* fix: Added working test for the embedding module ([`d568eee`](https://github.com/KennethEnevoldsen/snp-transformer/commit/d568eee82937701412c3ef83b5578e14b454ff49))

* fix: added embedding module ([`b6bbb22`](https://github.com/KennethEnevoldsen/snp-transformer/commit/b6bbb22d1f7b6bad32067121551bd3b4b5c312b0))

Unknown

* Merge branch &39;main&39; of https://github.com/KennethEnevoldsen/snp-transformer ([`bed0bc7`](https://github.com/KennethEnevoldsen/snp-transformer/commit/bed0bc7813cfc38f02f5ecf6a4bc24c5b7e57a68))

* Merge branch &39;main&39; into add-embedding-module ([`203beb9`](https://github.com/KennethEnevoldsen/snp-transformer/commit/203beb9fb9dd41df28db3d46aa9dad8c95ad78b8))