diff --git a/CHANGELOG.md b/CHANGELOG.md
index 759945a..b00266e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,471 +1,1313 @@
-# Changelog
+# CHANGELOG
+
+
+
+## v5.1.0 (2024-03-05)
+
+### Feature
+
+* feat: allow building pages on demand ([`10259ca`](https://github.com/siemdejong/sclicom/commit/10259cadca2c4ba46b0bd2327ad16813f2421b10))
+
+### Fix
+
+* fix: make toml_version tuple ([`56e0f7a`](https://github.com/siemdejong/sclicom/commit/56e0f7af5d894702fdf32c08836b8ed70b30dcfe))
+
+* fix: deactivate type check
+
+This is to ignore new type errors. Issue is opened to fixe type errors ([`e9eb9a6`](https://github.com/siemdejong/sclicom/commit/e9eb9a6cac7e6994600c3d355e35d7467567c0de))
+
+### Unknown
+
+* Deactivate isort and black in ci ([`8d8cad6`](https://github.com/siemdejong/sclicom/commit/8d8cad60ee7d73e0a745a1dd006110725dbaa79b))
+
+* Update README.md
+
+Name change ([`b2f4eb3`](https://github.com/siemdejong/sclicom/commit/b2f4eb3928d579c7c770e8356e8fd70d1b5ca2db))
 
-<!--next-version-placeholder-->
 
 ## v5.0.1 (2023-07-02)
 
 ### Fix
 
-* Typing ([`e1e60f8`](https://github.com/siemdejong/sclicom/commit/e1e60f849fa8334bb91cdd382c286b5e83c9e74d))
-* Typing ([`beaaf4d`](https://github.com/siemdejong/sclicom/commit/beaaf4d7c59126ade0ae79145cee8356e783d4ca))
+* fix: typing ([`e1e60f8`](https://github.com/siemdejong/sclicom/commit/e1e60f849fa8334bb91cdd382c286b5e83c9e74d))
+
+* fix: typing ([`beaaf4d`](https://github.com/siemdejong/sclicom/commit/beaaf4d7c59126ade0ae79145cee8356e783d4ca))
+
+### Unknown
+
+* version at hand in ([`2205b58`](https://github.com/siemdejong/sclicom/commit/2205b58cdeb385c24b9e10c6d32aef7529dacfe0))
+
 
 ## v5.0.0 (2023-05-07)
-### Fix
-* Do not track out, sbatch, ckpt ([`68d4c55`](https://github.com/siemdejong/dpat/commit/68d4c557ba35da13bcdca11c9a46447292623a6f))
-* Use train stage for setup ([`d0b63b1`](https://github.com/siemdejong/dpat/commit/d0b63b1a7a2e72ffe5d1e8ab337924d049d6ec7c))
-* Update dataloader ([`b166512`](https://github.com/siemdejong/dpat/commit/b1665124193bf2c6832df7f9dcbb9c386f4e8c61))
-* Update defaults ([`5964cc7`](https://github.com/siemdejong/dpat/commit/5964cc758cd0a02cffcf13986bd67549c1a19622))
-* Remove scheduler arg ([`03f60dc`](https://github.com/siemdejong/dpat/commit/03f60dc22a90d7b60ecb3cb20ae8cb2624b4c4fb))
 
 ### Breaking
-* scheduler is unset ([`03f60dc`](https://github.com/siemdejong/dpat/commit/03f60dc22a90d7b60ecb3cb20ae8cb2624b4c4fb))
+
+* fix: remove scheduler arg
+
+BREAKING CHANGE: scheduler is unset ([`03f60dc`](https://github.com/siemdejong/sclicom/commit/03f60dc22a90d7b60ecb3cb20ae8cb2624b4c4fb))
+
+### Fix
+
+* fix: do not track out, sbatch, ckpt ([`68d4c55`](https://github.com/siemdejong/sclicom/commit/68d4c557ba35da13bcdca11c9a46447292623a6f))
+
+* fix: use train stage for setup ([`d0b63b1`](https://github.com/siemdejong/sclicom/commit/d0b63b1a7a2e72ffe5d1e8ab337924d049d6ec7c))
+
+* fix: update dataloader ([`b166512`](https://github.com/siemdejong/sclicom/commit/b1665124193bf2c6832df7f9dcbb9c386f4e8c61))
+
+* fix: update defaults ([`5964cc7`](https://github.com/siemdejong/sclicom/commit/5964cc758cd0a02cffcf13986bd67549c1a19622))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`6385a6a`](https://github.com/siemdejong/sclicom/commit/6385a6a55dfc26f0b33758a2979945e90eede4d6))
+
 
 ## v4.15.0 (2023-04-25)
+
 ### Feature
-* Compute mean and confidence interval ([`da2e834`](https://github.com/siemdejong/dpat/commit/da2e834abaf6bfbb745a356041277db9a34c9769))
+
+* feat: compute mean and confidence interval
+
+Following TrivialAugment&#39;s recommendation to provide how the mean and
+confidence interval are calculated. ([`da2e834`](https://github.com/siemdejong/sclicom/commit/da2e834abaf6bfbb745a356041277db9a34c9769))
 
 ### Fix
-* Add confidence typehint ([`c057652`](https://github.com/siemdejong/dpat/commit/c057652a1023cdfd954720bd84ac42d4635bb2a3))
-* Add typehints ([`cb761f2`](https://github.com/siemdejong/dpat/commit/cb761f2d610ede18c6afeeb13db1c30309e1f642))
-* Revert hidden layers to one hidden layer ([`3139c46`](https://github.com/siemdejong/dpat/commit/3139c46e737138cdae6e375d4432758a68373d72))
-* Add typehint ([`f382d1f`](https://github.com/siemdejong/dpat/commit/f382d1f7506a403304ff8260109e9b405a3d11e3))
-* Ignore missing scipy imports ([`f562790`](https://github.com/siemdejong/dpat/commit/f5627908133aef9d4997988d48a8ef12186d5b88))
+
+* fix: add confidence typehint ([`c057652`](https://github.com/siemdejong/sclicom/commit/c057652a1023cdfd954720bd84ac42d4635bb2a3))
+
+* fix: add typehints ([`cb761f2`](https://github.com/siemdejong/sclicom/commit/cb761f2d610ede18c6afeeb13db1c30309e1f642))
+
+* fix: revert hidden layers to one hidden layer
+
+with dropout. ([`3139c46`](https://github.com/siemdejong/sclicom/commit/3139c46e737138cdae6e375d4432758a68373d72))
+
+* fix: add typehint ([`f382d1f`](https://github.com/siemdejong/sclicom/commit/f382d1f7506a403304ff8260109e9b405a3d11e3))
+
+* fix: ignore missing scipy imports ([`f562790`](https://github.com/siemdejong/sclicom/commit/f5627908133aef9d4997988d48a8ef12186d5b88))
+
 
 ## v4.14.2 (2023-04-25)
+
 ### Fix
-* Remove contrastive collate_fn ([`1811bb5`](https://github.com/siemdejong/dpat/commit/1811bb50cc63742e63563f6aa2f94259abfc0a9b))
+
+* fix: remove contrastive collate_fn
+
+fixes #13 ([`1811bb5`](https://github.com/siemdejong/sclicom/commit/1811bb50cc63742e63563f6aa2f94259abfc0a9b))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of https://github.com/siemdejong/dpat ([`d2acb15`](https://github.com/siemdejong/sclicom/commit/d2acb157ba1dd25c62eeb84a76ea517fdb9ddcc3))
+
 
 ## v4.14.1 (2023-04-24)
+
 ### Fix
-* Don't try to open augmented set if not exists ([`bf33e12`](https://github.com/siemdejong/dpat/commit/bf33e12ca961276f765c6f092f242c5bd919154c))
+
+* fix: don&#39;t try to open augmented set if not exists ([`bf33e12`](https://github.com/siemdejong/sclicom/commit/bf33e12ca961276f765c6f092f242c5bd919154c))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of https://github.com/siemdejong/dpat ([`1eafdef`](https://github.com/siemdejong/sclicom/commit/1eafdefab2aab062a7f54348b6f04c239d747684))
+
 
 ## v4.14.0 (2023-04-24)
+
 ### Feature
-* Do data augmentation in feature space ([`2d0fa05`](https://github.com/siemdejong/dpat/commit/2d0fa058f510ddc0eade62446d9f0a52803c717d))
+
+* feat: do data augmentation in feature space
+
+Following extrapolation from https://arxiv.org/pdf/1702.05538.pdf. ([`2d0fa05`](https://github.com/siemdejong/sclicom/commit/2d0fa058f510ddc0eade62446d9f0a52803c717d))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of https://github.com/siemdejong/dpat ([`6fe7e1e`](https://github.com/siemdejong/sclicom/commit/6fe7e1ef0c32455609a482e25264e446da2e584e))
+
 
 ## v4.13.2 (2023-04-21)
+
 ### Fix
-* Use clinical_context attr for export ([`446bb2b`](https://github.com/siemdejong/dpat/commit/446bb2b87cd12eea5f2dc3024229de13f9ced49d))
+
+* fix: use clinical_context attr for export ([`446bb2b`](https://github.com/siemdejong/sclicom/commit/446bb2b87cd12eea5f2dc3024229de13f9ced49d))
+
 
 ## v4.13.1 (2023-04-21)
+
 ### Fix
-* Alter seed config space ([`e8a652e`](https://github.com/siemdejong/dpat/commit/e8a652e31f250686da0c345131cd863148f0c34c))
-* Use variable splits_dirname ([`f3824e4`](https://github.com/siemdejong/dpat/commit/f3824e41f8086a4c3e8aca29bbd8ef0f2fca57aa))
-* Automatically set_clinical context ([`764b77c`](https://github.com/siemdejong/dpat/commit/764b77cda317e4544b1475e77b57ff6f5f3101c6))
+
+* fix: alter seed config space ([`e8a652e`](https://github.com/siemdejong/sclicom/commit/e8a652e31f250686da0c345131cd863148f0c34c))
+
+* fix: use variable splits_dirname ([`f3824e4`](https://github.com/siemdejong/sclicom/commit/f3824e41f8086a4c3e8aca29bbd8ef0f2fca57aa))
+
+* fix: automatically set_clinical context ([`764b77c`](https://github.com/siemdejong/sclicom/commit/764b77cda317e4544b1475e77b57ff6f5f3101c6))
+
 
 ## v4.13.0 (2023-04-21)
+
 ### Feature
-* Add device to mean and std calc ([`4db5601`](https://github.com/siemdejong/dpat/commit/4db5601044ad3b8e652b6861602cd2d064c22716))
+
+* feat: add device to mean and std calc ([`4db5601`](https://github.com/siemdejong/sclicom/commit/4db5601044ad3b8e652b6861602cd2d064c22716))
 
 ### Fix
-* Add batch size to compile features tool ([`7a13c09`](https://github.com/siemdejong/dpat/commit/7a13c094af585f0abd3b0acd9c88b7cb10663639))
-* Add num_workers to compile features tool ([`018861f`](https://github.com/siemdejong/dpat/commit/018861fc8740b57cd74260793d3113243799af04))
-* Add clinical context to compile features tool ([`8d89607`](https://github.com/siemdejong/dpat/commit/8d896075a73bc95cc08b1655f3e8830708c9d130))
-* Change location dtype to string in hdf5 ([`ef9e5cf`](https://github.com/siemdejong/dpat/commit/ef9e5cf1bd712721b5d9f99ced9a2d5054a1a3d0))
-* Use normalization based on masked tiles ([`6e5e639`](https://github.com/siemdejong/dpat/commit/6e5e639b4511561fa14131fddab465cb302bfb94))
-* Typo ([`cadd918`](https://github.com/siemdejong/dpat/commit/cadd918758f3c78558216e02396fc7ea4eca8279))
+
+* fix: add batch size to compile features tool ([`7a13c09`](https://github.com/siemdejong/sclicom/commit/7a13c094af585f0abd3b0acd9c88b7cb10663639))
+
+* fix: add num_workers to compile features tool ([`018861f`](https://github.com/siemdejong/sclicom/commit/018861fc8740b57cd74260793d3113243799af04))
+
+* fix: add clinical context to compile features tool ([`8d89607`](https://github.com/siemdejong/sclicom/commit/8d896075a73bc95cc08b1655f3e8830708c9d130))
+
+* fix: change location dtype to string in hdf5 ([`ef9e5cf`](https://github.com/siemdejong/sclicom/commit/ef9e5cf1bd712721b5d9f99ced9a2d5054a1a3d0))
+
+* fix: use normalization based on masked tiles ([`6e5e639`](https://github.com/siemdejong/sclicom/commit/6e5e639b4511561fa14131fddab465cb302bfb94))
+
+* fix: typo ([`cadd918`](https://github.com/siemdejong/sclicom/commit/cadd918758f3c78558216e02396fc7ea4eca8279))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of https://github.com/siemdejong/dpat ([`41a1621`](https://github.com/siemdejong/sclicom/commit/41a162128013caef80a70d507db32bca4fa6cf90))
+
 
 ## v4.12.0 (2023-04-21)
+
 ### Feature
-* Calculate mean and stddev ([`4ddf6d1`](https://github.com/siemdejong/dpat/commit/4ddf6d1315486526885dd22a755e759e79d011e0))
+
+* feat: calculate mean and stddev ([`4ddf6d1`](https://github.com/siemdejong/sclicom/commit/4ddf6d1315486526885dd22a755e759e79d011e0))
 
 ### Fix
-* Raise error if no mask_root_dir is set ([`2fd7157`](https://github.com/siemdejong/dpat/commit/2fd71577137ea13949e724ecd32bbb570418eb68))
-* Allow null as datamodule model ([`77dff7e`](https://github.com/siemdejong/dpat/commit/77dff7e88daeb37f83df6128a7cd40c5b7063498))
+
+* fix: raise error if no mask_root_dir is set
+
+when loading from disk ([`2fd7157`](https://github.com/siemdejong/sclicom/commit/2fd71577137ea13949e724ecd32bbb570418eb68))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of https://github.com/siemdejong/dpat ([`08bf1c9`](https://github.com/siemdejong/sclicom/commit/08bf1c9a221a7b022e5e8c6d8c041b53206f3561))
+
 
 ## v4.11.1 (2023-04-21)
-### Fix
-* Typo ([`a25a251`](https://github.com/siemdejong/dpat/commit/a25a2512d2dc742f67c220b6d13f2c2098c31e79))
 
 ### Documentation
-* Add steps to adding-new-data ([`49f10d5`](https://github.com/siemdejong/dpat/commit/49f10d5d1b303a4e12d1df39808195cae16edcfb))
-* Clarify tensorflow for gpu installation ([`2a8b90d`](https://github.com/siemdejong/dpat/commit/2a8b90d7aed04695171cce1607bacaaad66a5965))
 
-## v4.11.0 (2023-04-20)
-### Feature
-* Add denoising tool ([`ee43414`](https://github.com/siemdejong/dpat/commit/ee434144fdff5becc756f4186fedfa851a49e746))
+* docs: add steps to adding-new-data ([`49f10d5`](https://github.com/siemdejong/sclicom/commit/49f10d5d1b303a4e12d1df39808195cae16edcfb))
 
-### Fix
-* Add mask creation to CLI and update docs ([`0dbdbc4`](https://github.com/siemdejong/dpat/commit/0dbdbc49a89204cc33f114bfe87f338a1472ea95))
+* docs: clarify tensorflow for gpu installation ([`2a8b90d`](https://github.com/siemdejong/sclicom/commit/2a8b90d7aed04695171cce1607bacaaad66a5965))
 
-## v4.10.1 (2023-04-14)
 ### Fix
-* Change defaults ([`7240d9e`](https://github.com/siemdejong/dpat/commit/7240d9e93fa030cd79eb0c1534931e1ac2520f70))
 
-## v4.10.0 (2023-04-13)
-### Feature
-* Allow for CCMIL hparam tuning ([`9e587f8`](https://github.com/siemdejong/dpat/commit/9e587f8765a36bc5e68525c567436ba922eeda31))
+* fix: allow null as datamodule model ([`77dff7e`](https://github.com/siemdejong/sclicom/commit/77dff7e88daeb37f83df6128a7cd40c5b7063498))
 
-### Fix
-* Typing of example array ([`cb98f39`](https://github.com/siemdejong/dpat/commit/cb98f397736e6860e3427cc0ad92bbca303b0387))
-* Make random tensor as example ([`a8d21f0`](https://github.com/siemdejong/dpat/commit/a8d21f0440708b20894a659864a582f82328e072))
-* Move tokenized inputs to device ([`2b75731`](https://github.com/siemdejong/dpat/commit/2b75731c7e4dc5ac8e93ab322c7a8f0d039da54e))
-* Make new example input for lightning ([`a431ab2`](https://github.com/siemdejong/dpat/commit/a431ab2f82f2977900612bcbddbd4acc27ea5c51))
-* Only use one clinical context of the bag ([`82a71df`](https://github.com/siemdejong/dpat/commit/82a71dfd2f25dfa12bebd26755c67e44c8feef75))
+* fix: typo
 
-## v4.9.3 (2023-04-13)
-### Fix
-* Restructure config files ([`35c24a9`](https://github.com/siemdejong/dpat/commit/35c24a965cba5b34c920727bc5f6149f46a32c9a))
-* Revert switch to cpu ([`0bb86e7`](https://github.com/siemdejong/dpat/commit/0bb86e783f67ad25765aa07aabdbd80a38f2f92d))
+wrong number of selected images was displayed ([`a25a251`](https://github.com/siemdejong/sclicom/commit/a25a2512d2dc742f67c220b6d13f2c2098c31e79))
 
-## v4.9.2 (2023-04-12)
-### Fix
-* Switch to clinical tiny BERT ([`ac199c1`](https://github.com/siemdejong/dpat/commit/ac199c152c25761eae3f1755e3c5b599cdde4502))
+### Unknown
 
-## v4.9.1 (2023-04-12)
-### Fix
-* Set llm to eval mode and disable gradient cal ([`1303353`](https://github.com/siemdejong/dpat/commit/1303353b0a59e9e6de9d3d1dc6ff9766c58ef082))
+* Merge branch &#39;main&#39; of https://github.com/siemdejong/dpat ([`466b68c`](https://github.com/siemdejong/sclicom/commit/466b68ca4fd7f04c62c50581b5b6225d0b74530f))
 
-### Documentation
-* Remove _static rom html_static_path ([`d1a1da8`](https://github.com/siemdejong/dpat/commit/d1a1da8fe8bdf79e0fe48e6426e004b45325f80c))
 
-## v4.9.0 (2023-04-12)
+## v4.11.0 (2023-04-20)
+
 ### Feature
-* Add location to splits output ([`4440a53`](https://github.com/siemdejong/dpat/commit/4440a53921d2182f0eed0a7de5ffd0a324795a44))
-* Add CCMIL ([`b0294ce`](https://github.com/siemdejong/dpat/commit/b0294ceb96a52757eebf53566f72b527e9978294))
-* Add clinical context to h5 dataset ([`3197f81`](https://github.com/siemdejong/dpat/commit/3197f8126dc74ba052a005c44fc4bc3b5e661a50))
-* Add clinical context to image dataset ([`e229d1e`](https://github.com/siemdejong/dpat/commit/e229d1ef89d7216f406c94445f3ea7ea73df0e55))
+
+* feat: add denoising tool ([`ee43414`](https://github.com/siemdejong/sclicom/commit/ee434144fdff5becc756f4186fedfa851a49e746))
 
 ### Fix
-* Add typehints ([`486b392`](https://github.com/siemdejong/dpat/commit/486b392c6e4005e80c683a1d9bc057ee6ef0bd5e))
-* Add LLM output last_hidden_state protocol ([`81e5e74`](https://github.com/siemdejong/dpat/commit/81e5e7445957409c1349b64c05cd2be1287b4de5))
-* Ignore transformers missing import ([`5c6806d`](https://github.com/siemdejong/dpat/commit/5c6806d45f620d92db5971409410209dd426c49e))
-* Add transformers dependency ([`8145723`](https://github.com/siemdejong/dpat/commit/8145723ea89f15199985be59a14f316561b1866b))
 
-## v4.8.0 (2023-04-06)
-### Feature
-* Add num_workers to feature compiling ([`0f4ef30`](https://github.com/siemdejong/dpat/commit/0f4ef30378edc9397b74934674f6debd40552078))
+* fix: add mask creation to CLI and update docs ([`0dbdbc4`](https://github.com/siemdejong/sclicom/commit/0dbdbc49a89204cc33f114bfe87f338a1472ea95))
 
-## v4.7.0 (2023-04-06)
-### Feature
-* Attention tiles viz ([`df9f90f`](https://github.com/siemdejong/dpat/commit/df9f90fc734fddc4a6f269d02ca63b1a7422ba55))
-* Change hparam search vars ([`fbd5847`](https://github.com/siemdejong/dpat/commit/fbd584767cee5a0d0bd6f22093df8b85e22db2d0))
+### Unknown
 
-### Fix
-* Explicitly export attention model ([`7aa356d`](https://github.com/siemdejong/dpat/commit/7aa356d98842a681aba398ccecc1ee7e47332b81))
-* Remove argument linking ([`d0d28e6`](https://github.com/siemdejong/dpat/commit/d0d28e6a3a04d9f76d155a226c6b1ff91d8380e1))
-* Change defaults ([`dcdfea6`](https://github.com/siemdejong/dpat/commit/dcdfea6212b251c18bfbe5d4c8bbe06259c2a3ce))
+* Merge pull request #43 from siemdejong/denoise
 
-## v4.6.0 (2023-04-04)
-### Feature
-* Make trials reproducible ([`6fb64c4`](https://github.com/siemdejong/dpat/commit/6fb64c493dba130ab64e4b44ece9a85d62846dd8))
+feat: add denoising tool ([`fb62c1b`](https://github.com/siemdejong/sclicom/commit/fb62c1b04145826ee99be17e5355855e58dd4c23))
 
-## v4.5.0 (2023-04-04)
-### Feature
-* Test model ([`857d2cd`](https://github.com/siemdejong/dpat/commit/857d2cd7e6b11269a73c83a10625250f4229f61d))
+* Merge pull request #42 from siemdejong/mask
 
-## v4.4.0 (2023-03-30)
-### Feature
-* Add hparam tuner ([#31](https://github.com/siemdejong/dpat/issues/31)) ([`b2e4094`](https://github.com/siemdejong/dpat/commit/b2e40942abc3dad0b72499480fe024f56872b6ee))
+fix: add mask creation to CLI and update docs ([`6121500`](https://github.com/siemdejong/sclicom/commit/6121500fd0bfa25bdbf50ef5e793444ca2c0836d))
 
-### Fix
-* Run black ([`619679f`](https://github.com/siemdejong/dpat/commit/619679fa3c808b699b16d79bd915d00bbcabca6b))
 
-## v4.3.2 (2023-03-24)
+## v4.10.1 (2023-04-14)
+
 ### Fix
-* Type error ([`e2af84a`](https://github.com/siemdejong/dpat/commit/e2af84a6474303aec2e2b8d25fdf47468a9cfb3b))
-* Bug with reading from bytes ([`ba1c58e`](https://github.com/siemdejong/dpat/commit/ba1c58e5290c985877f99526936a7465c9244f4b))
-* Give units to fraction logs ([`416749a`](https://github.com/siemdejong/dpat/commit/416749aa03e1c6d9fbee0ca350e9154033d0fc0e))
 
-### Documentation
-* Fix indent ([`2e7ebf1`](https://github.com/siemdejong/dpat/commit/2e7ebf1c03ac3fa04962cc694e6716070b31f0cc))
-* Ignore autosummary ([`e63a009`](https://github.com/siemdejong/dpat/commit/e63a0094dd431241684169aebd858c1a3b92e350))
-* Move docs from readme to gh pages ([`6012ebc`](https://github.com/siemdejong/dpat/commit/6012ebcadbe1315fcb0e010393290f6c1dc99215))
-* Add docs to github pages ([`1f85ef8`](https://github.com/siemdejong/dpat/commit/1f85ef882464c87d89ee7109cb58ede34dccad5d))
+* fix: change defaults ([`7240d9e`](https://github.com/siemdejong/sclicom/commit/7240d9e93fa030cd79eb0c1534931e1ac2520f70))
 
-## v4.3.1 (2023-03-23)
-### Fix
-* Up default patience to 100 ([`289d7f9`](https://github.com/siemdejong/dpat/commit/289d7f9b3b97702836f34a6f4815324cbad09247))
 
-## v4.3.0 (2023-03-23)
-### Feature
-* Add early stopping ([`7c4eb01`](https://github.com/siemdejong/dpat/commit/7c4eb01e240402c6033fa2b06d802e41b3e90c60))
-* Add dropout_p parameter to varmil ([`6b59e50`](https://github.com/siemdejong/dpat/commit/6b59e50d8b6c5c800ce0bdcadc09025159412dce))
+## v4.10.0 (2023-04-13)
 
-## v4.2.0 (2023-03-23)
 ### Feature
-* Add hidden features and dropout ([`452082c`](https://github.com/siemdejong/dpat/commit/452082cbff5e2f584938b7de84b887c0a035d418))
+
+* feat: allow for CCMIL hparam tuning ([`9e587f8`](https://github.com/siemdejong/sclicom/commit/9e587f8765a36bc5e68525c567436ba922eeda31))
 
 ### Fix
-* Typing ([`5dce7a4`](https://github.com/siemdejong/dpat/commit/5dce7a4bd174fa9e4411e506d11962b1eb495850))
-* Add area under precision recall curve ([`1a2648f`](https://github.com/siemdejong/dpat/commit/1a2648faed30be99050f9d4877530070dffb238b))
-* Remove optimizer/scheduler defaults ([`d2b62e1`](https://github.com/siemdejong/dpat/commit/d2b62e1631c88db8914497a55baf8a45d04a1f3a))
-* Link max_epochs to scheduler T_max ([`1a05932`](https://github.com/siemdejong/dpat/commit/1a059322768140f33668e4481940bc9a94a6d582))
-* Run black ([`db24156`](https://github.com/siemdejong/dpat/commit/db2415632a81eefd91db152848172511e381a4e1))
-* Support lightning 2 ([`b4a822c`](https://github.com/siemdejong/dpat/commit/b4a822c166edf2ac2ff5d5557f3a8e09b8f68588))
 
-## v4.1.0 (2023-03-23)
-### Feature
-* Entropymasker experiment ([`ec70eef`](https://github.com/siemdejong/dpat/commit/ec70eef917c2128d7e34ef50188b422bc262b732))
+* fix: typing of example array ([`cb98f39`](https://github.com/siemdejong/sclicom/commit/cb98f397736e6860e3427cc0ad92bbca303b0387))
 
-## v4.0.1 (2023-03-20)
-### Fix
-* Compiling model doesn't work, rollback ([`e733a24`](https://github.com/siemdejong/dpat/commit/e733a243879b26ebcf87b35a28d56b098db705b4))
+* fix: make random tensor as example ([`a8d21f0`](https://github.com/siemdejong/sclicom/commit/a8d21f0440708b20894a659864a582f82328e072))
 
-## v4.0.0 (2023-03-20)
-### Fix
-* Update mil config to reflect new signature ([`c4dc0ed`](https://github.com/siemdejong/dpat/commit/c4dc0edce0acc9ad2453f874cde3b619e68ca559))
-* Filter h5 dataset by filenames ([`b3e1770`](https://github.com/siemdejong/dpat/commit/b3e177062d58840a69271f323f84fa67d9bf31cc))
-* Safely bypass sigint or sigterm ([`388d368`](https://github.com/siemdejong/dpat/commit/388d36824e27192a104b84f2a2629fea471b733e))
-* Remove trainer arguments for pl2 ([`99194e0`](https://github.com/siemdejong/dpat/commit/99194e09417bd38a1f2c52d61b870199f91ab7db))
+* fix: move tokenized inputs to device ([`2b75731`](https://github.com/siemdejong/sclicom/commit/2b75731c7e4dc5ac8e93ab322c7a8f0d039da54e))
 
-### Breaking
-* train|val|test_path keywords now do not refer to the the target train|val|test paths to output h5 files to, but to the files providing paths_and_targets. file_path is the new target file, containing all images. ([`b3e1770`](https://github.com/siemdejong/dpat/commit/b3e177062d58840a69271f323f84fa67d9bf31cc))
+* fix: make new example input for lightning ([`a431ab2`](https://github.com/siemdejong/sclicom/commit/a431ab2f82f2977900612bcbddbd4acc27ea5c51))
 
-## v3.2.1 (2023-03-17)
-### Fix
-* Remove pl2 removed trainer arguments ([`817beb8`](https://github.com/siemdejong/dpat/commit/817beb85c59ec8ae7bf3f0273f640c7086a12482))
+* fix: only use one clinical context of the bag ([`82a71df`](https://github.com/siemdejong/sclicom/commit/82a71dfd2f25dfa12bebd26755c67e44c8feef75))
 
-## v3.2.0 (2023-03-17)
-### Feature
-* Automate masking with dlup entropy_masker ([`1066ea1`](https://github.com/siemdejong/dpat/commit/1066ea1264a7c56760b1fb4be10a7fced92336b6))
-* Compile the pytorch lightning models ([`c009004`](https://github.com/siemdejong/dpat/commit/c009004acb837a3026cb370b927b461996f8f51c))
+
+## v4.9.3 (2023-04-13)
 
 ### Fix
-* Lightning 2.0 ignore missing type imports ([`08b3e85`](https://github.com/siemdejong/dpat/commit/08b3e85608f0cc3171812f1cd1f5fe6f5e9a3bfa))
-* Ddp default find_unused_parameters=False ([`3e2a15d`](https://github.com/siemdejong/dpat/commit/3e2a15dab7fd127b8f70c1439b2833a20b32ec4a))
-* Use recommended precision ([`6b654e2`](https://github.com/siemdejong/dpat/commit/6b654e2fc26c7c1223529d1a42cd177ea8c95ff8))
-* Rename *_epoch_end to on_*_epoch_end ([`37e0c52`](https://github.com/siemdejong/dpat/commit/37e0c52dc200bd72093c89aabc6016ec44cf7d60))
-* Add torch/lightning v2 deps ([`2afdf05`](https://github.com/siemdejong/dpat/commit/2afdf057726f40caae1cae1f7fae99aa464ae415))
-* Simclr-16-3 update ([`29fdf58`](https://github.com/siemdejong/dpat/commit/29fdf582a8c24a5475a605130c1903e1a5e30520))
 
-### Performance
-* Do not log to progress bar ([`da4e3b4`](https://github.com/siemdejong/dpat/commit/da4e3b487f24d1503fea17feb8280d486a5bdc36))
+* fix: restructure config files
 
-## v3.1.1 (2023-03-15)
-### Fix
-* Pretrained config typo ([`e6a3778`](https://github.com/siemdejong/dpat/commit/e6a37785d9b9ef49bdbf40eb009d83f35edff82e))
+CCMIL is used by default.
+If another model is needed, specify with &#34;--model path/to/varmil.yaml&#34;
+when training the model. ([`35c24a9`](https://github.com/siemdejong/sclicom/commit/35c24a965cba5b34c920727bc5f6149f46a32c9a))
 
-## v3.1.0 (2023-03-15)
-### Feature
-* Add num_subfolds parameter to create_splits ([`dfe7ceb`](https://github.com/siemdejong/dpat/commit/dfe7ceb3380fef3ea595cd3f7e68ed426b33989d))
+* fix: revert switch to cpu ([`0bb86e7`](https://github.com/siemdejong/sclicom/commit/0bb86e783f67ad25765aa07aabdbd80a38f2f92d))
 
-### Fix
-* Splits tests with num_subfolds ([`3a9d44e`](https://github.com/siemdejong/dpat/commit/3a9d44e84ae570e35fc2262a46fe4b467fc97f98))
+### Unknown
 
-## v3.0.1 (2023-03-15)
-### Fix
-* Update viz of untrained model ([`e32d9f5`](https://github.com/siemdejong/dpat/commit/e32d9f5a1bcacf45b3893c94ec3dddf6cd3682c2))
+* Merge branch &#39;main&#39; of https://github.com/siemdejong/dpat ([`47663d2`](https://github.com/siemdejong/sclicom/commit/47663d278a2058468cb5e6119348690d816798b9))
 
-## v3.0.0 (2023-03-15)
-### Feature
-* From torchvision.models to pytorchcv models ([`bb5732d`](https://github.com/siemdejong/dpat/commit/bb5732d3f8b9fc0434720077d37a448df80e8670))
-* Show targets/img_id/case_id distribution ([`c757995`](https://github.com/siemdejong/dpat/commit/c7579958dcb63b2664dc120ba1feac16af208489))
+
+## v4.9.2 (2023-04-12)
 
 ### Fix
-* Pytorchcv not typed ignore missing imports ([`2b33f70`](https://github.com/siemdejong/dpat/commit/2b33f705443d4d2e92eb045f42f63efdba5feb34))
 
-### Breaking
-* in the config files, models must be specified by corresponding pytorchcv models, not torchvision. ([`bb5732d`](https://github.com/siemdejong/dpat/commit/bb5732d3f8b9fc0434720077d37a448df80e8670))
+* fix: switch to clinical tiny BERT
 
-## v2.7.3 (2023-03-14)
-### Performance
-* Speed up feature compilation ([`772a0bd`](https://github.com/siemdejong/dpat/commit/772a0bd38e356b9d6b547e757286c0b973a45c2e))
+Because it is much quicker. ([`ac199c1`](https://github.com/siemdejong/sclicom/commit/ac199c152c25761eae3f1755e3c5b599cdde4502))
 
-## v2.7.2 (2023-03-14)
-### Fix
-* Create feature directory if not exists ([`674c8c4`](https://github.com/siemdejong/dpat/commit/674c8c4eb33ac614d03cee35a0993bec5b50b4e7))
+### Unknown
 
-## v2.7.1 (2023-03-13)
-### Fix
-* Bypass oom error ([`0177032`](https://github.com/siemdejong/dpat/commit/01770320bcae9608d4efc15793a9d53135e764f3))
-* Add ipywidgets dependency ([`3c26dcd`](https://github.com/siemdejong/dpat/commit/3c26dcd0b43e868ff34bf424f0c1bf5c73bdc433))
+* Merge branch &#39;main&#39; of https://github.com/siemdejong/dpat ([`a4d16c2`](https://github.com/siemdejong/sclicom/commit/a4d16c21f51141edd5ea12b4f34600c5afec11e4))
 
-## v2.7.0 (2023-03-10)
-### Feature
-* Visualize embedding distribution using t-sne ([`91c4190`](https://github.com/siemdejong/dpat/commit/91c4190f4477e2cb53fa5e855d1bf64cfd5a6ecf))
+
+## v4.9.1 (2023-04-12)
+
+### Ci
+
+* ci: disable HDF5 version check
+
+To bypass &#34;UserWarning: h5py is running against HDF5 1.14.0 when it was
+built against 1.12.2&#34;. ([`148c8ab`](https://github.com/siemdejong/sclicom/commit/148c8ab37e8c5168dd0ed72df6dea0b44d9abb67))
 
 ### Documentation
-* Change installation order. ([`63d51c8`](https://github.com/siemdejong/dpat/commit/63d51c8b27db4711b141b9c4aa5104bc658aca57))
 
-## v2.6.1 (2023-03-10)
+* docs: remove _static rom html_static_path ([`d1a1da8`](https://github.com/siemdejong/sclicom/commit/d1a1da8fe8bdf79e0fe48e6426e004b45325f80c))
+
 ### Fix
-* Show case distribution ([`e2dcd66`](https://github.com/siemdejong/dpat/commit/e2dcd667eb1f48d00eb4fb2ce5ba653ec7149ebb))
 
-## v2.6.0 (2023-03-10)
-### Feature
-* Nearest neighbours visualization features ([`6239607`](https://github.com/siemdejong/dpat/commit/6239607b792d561a4ca3ce5c424e3ac6b273b1ea))
+* fix: set llm to eval mode and disable gradient cal
 
-## v2.5.2 (2023-03-10)
-### Fix
-* Jsonargparse dependency ([`94242b2`](https://github.com/siemdejong/dpat/commit/94242b2b7654ef4fb015f332a9c256a59c6d5aad))
+unless trainable_llm is set to True. ([`1303353`](https://github.com/siemdejong/sclicom/commit/1303353b0a59e9e6de9d3d1dc6ff9766c58ef082))
 
-## v2.5.1 (2023-03-10)
-### Fix
-* **log:** Log origin of image data ([`1bb50ae`](https://github.com/siemdejong/dpat/commit/1bb50aea5c76849fe9be7b5219abc6f938de9922))
+### Unknown
 
-## v2.5.0 (2023-03-09)
-### Feature
-* **pretrain:** Add SimCLR ([`502bba3`](https://github.com/siemdejong/dpat/commit/502bba37010819a4f0a90292e3e47e721aac8738))
+* Merge branch &#39;main&#39; of https://github.com/siemdejong/dpat ([`cafd5bf`](https://github.com/siemdejong/sclicom/commit/cafd5bfbed0574a7be579c15a066b1189c58ee1b))
 
-## v2.4.2 (2023-03-08)
-### Fix
-* **type:** Fix __iter__ type error ([`d69fb24`](https://github.com/siemdejong/dpat/commit/d69fb24dee31c13cb3cd543b66526a9bdf4d87e9))
-* Use WeightedRandomSampler ([`55334c4`](https://github.com/siemdejong/dpat/commit/55334c4ce402de9d39f49eea0ab39fbf99f98478))
 
-## v2.4.1 (2023-03-08)
-### Performance
-* **varmil:** Set gradients to none instead of 0 ([`b8a850a`](https://github.com/siemdejong/dpat/commit/b8a850a9ce5ae8fe896585ff8eeb3d308049feb7))
+## v4.9.0 (2023-04-12)
 
-## v2.4.0 (2023-03-07)
 ### Feature
-* Train varmil ([`56a3ae9`](https://github.com/siemdejong/dpat/commit/56a3ae9ae1bddf481867ac146322ea9852e1cb2e))
 
-### Fix
-* Some typing issues ([`6a46853`](https://github.com/siemdejong/dpat/commit/6a46853ea016ee8dc8849b4dfb992a7d52cdedff))
-* Bug where M was calculated wrong ([`d3a675b`](https://github.com/siemdejong/dpat/commit/d3a675b7befec145976f9a95774e591ef61ddd9e))
-* Export variables from packages ([`e0db9e3`](https://github.com/siemdejong/dpat/commit/e0db9e3191c2455085ce2671694634cddc3cfde7))
+* feat: add location to splits output ([`4440a53`](https://github.com/siemdejong/sclicom/commit/4440a53921d2182f0eed0a7de5ffd0a324795a44))
 
-## v2.3.3 (2023-03-04)
-### Fix
-* Uncomment feature compilation ([`4e018fe`](https://github.com/siemdejong/dpat/commit/4e018fe2c0760a1292edae65be11effd9c1f0787))
+* feat: add CCMIL ([`b0294ce`](https://github.com/siemdejong/sclicom/commit/b0294ceb96a52757eebf53566f72b527e9978294))
 
-## v2.3.2 (2023-03-04)
-### Fix
-* Fix number of compiled feature vectors ([`b659501`](https://github.com/siemdejong/dpat/commit/b659501ccec8e7521e8c4d61d6e6e200a8956f40))
+* feat: add clinical context to h5 dataset ([`3197f81`](https://github.com/siemdejong/sclicom/commit/3197f8126dc74ba052a005c44fc4bc3b5e661a50))
+
+* feat: add clinical context to image dataset ([`e229d1e`](https://github.com/siemdejong/sclicom/commit/e229d1ef89d7216f406c94445f3ea7ea73df0e55))
 
-## v2.3.1 (2023-03-03)
 ### Fix
-* Concatenate features ([`349b13d`](https://github.com/siemdejong/dpat/commit/349b13d5c0be43dea0ede14cffc65c11089c9154))
-* H5 classmethod return type ([`bc4b24a`](https://github.com/siemdejong/dpat/commit/bc4b24af8dcd40caca4089217a5dd9c98ee2aae8))
 
-## v2.3.0 (2023-03-02)
-### Feature
-* Add h5 dataset ([`0f6cfe2`](https://github.com/siemdejong/dpat/commit/0f6cfe24673dd27c43bd230636d4ad4698813865))
+* fix: add typehints ([`486b392`](https://github.com/siemdejong/sclicom/commit/486b392c6e4005e80c683a1d9bc057ee6ef0bd5e))
 
-## v2.2.0 (2023-03-02)
-### Feature
-* Add feature extraction ([`e71d5be`](https://github.com/siemdejong/dpat/commit/e71d5becd0b1e194c5205d9993813dd74f4bb32d))
+* fix: add LLM output last_hidden_state protocol ([`81e5e74`](https://github.com/siemdejong/sclicom/commit/81e5e7445957409c1349b64c05cd2be1287b4de5))
 
-## v2.1.6 (2023-02-26)
-### Performance
-* Pin memory of dataloaders ([`4afcdf2`](https://github.com/siemdejong/dpat/commit/4afcdf2e59d0dd04aafbe90dfe070a831522d9ad))
-* Zero_grad to non ([`d6d62c7`](https://github.com/siemdejong/dpat/commit/d6d62c759296b478c1038d94c7e103461a86ec5b))
+* fix: ignore transformers missing import ([`5c6806d`](https://github.com/siemdejong/sclicom/commit/5c6806d45f620d92db5971409410209dd426c49e))
 
-## v2.1.5 (2023-02-26)
-### Fix
-* **tests:** Add tests for create_splits ([`780ed07`](https://github.com/siemdejong/dpat/commit/780ed077000f55c0f7b86888c1f9646ec0085864))
+* fix: add transformers dependency ([`8145723`](https://github.com/siemdejong/sclicom/commit/8145723ea89f15199985be59a14f316561b1866b))
 
-## v2.1.4 (2023-02-26)
-### Fix
-* **tests:** Add convert tests ([`819e23d`](https://github.com/siemdejong/dpat/commit/819e23dbdb36824ffbcf5a520e8d43ac42acb0d8))
+### Unknown
 
-## v2.1.3 (2023-02-25)
-### Fix
-* **semantic-release:** Add build command ([`c35a40f`](https://github.com/siemdejong/dpat/commit/c35a40f214390c36a4f377523fc03560f3eb8cfd))
+* tests: add location to splits ([`2a9698a`](https://github.com/siemdejong/sclicom/commit/2a9698aed3ffaf58ca648894aea6d68b93b8eafd))
 
-## v2.1.2 (2023-02-25)
-### Fix
-* **typing:** Add typing ([`0842497`](https://github.com/siemdejong/dpat/commit/0842497f3498bf8f66af5ea917b5ecf012406b51))
+* nb: add clinical context to existing hdf5 files ([`906b370`](https://github.com/siemdejong/sclicom/commit/906b37099d4b11beb72352113a0232f7bacab2e6))
 
-## v2.1.1 (2023-02-23)
-### Fix
-* **swav:** Make swav return a number ([`d21dcce`](https://github.com/siemdejong/dpat/commit/d21dcce5c0590d94c87478b7c7eb8324476328f4))
-* **deps:** Add tensorboard to dependencies ([`5ee3528`](https://github.com/siemdejong/dpat/commit/5ee35280bf5d7e990bcf3c26ae13975e5990b782))
-* **convert:** Only log skip if skip_count>0 ([`0a58791`](https://github.com/siemdejong/dpat/commit/0a587910b9f2fa7b32d05c21aa8b0c3facb671b7))
+* nb: test clinnical text embeddings ([`7a48701`](https://github.com/siemdejong/sclicom/commit/7a48701f9436afad0b9bd79a1e8aad6fb14d66af))
 
-## v2.1.0 (2023-02-22)
-### Feature
-* **data:** Add mean and std calculator ([`e6549f6`](https://github.com/siemdejong/dpat/commit/e6549f681bd0f4500077dd2365afd5a9a231c972))
-* **stage1:** Implement swav with pl and lightly ([`3dcbdca`](https://github.com/siemdejong/dpat/commit/3dcbdcab5c4de8ebd08addb8c0f2ce02fdfa4803))
+* Merge branch &#39;main&#39; of https://github.com/siemdejong/dpat ([`6e56e30`](https://github.com/siemdejong/sclicom/commit/6e56e30a95167122d605d80fc8f3e548c1cd87a4))
 
-### Fix
-* **package:** Add dependencies ([`b3d340c`](https://github.com/siemdejong/dpat/commit/b3d340c046929d3b06f417dc2ae40e61ac173e13))
-* **package:** Package dpat subfolder ([`2fb78ed`](https://github.com/siemdejong/dpat/commit/2fb78ed751908f28a0ca1719018c8a74d114b956))
 
-## v2.0.0 (2023-02-16)
+## v4.8.0 (2023-04-06)
+
 ### Feature
-* **installation:** Remove the need for config.yml ([`bdbed64`](https://github.com/siemdejong/dpat/commit/bdbed641081d0717d97876aa3a76bb0a9f0c216f))
 
-### Fix
-* **dpat:** Only read config.yml if windows ([`f823ccc`](https://github.com/siemdejong/dpat/commit/f823ccca59c966622464f821da158a70e3449469))
-* **logging:** Let the cli configure logging ([`85875fd`](https://github.com/siemdejong/dpat/commit/85875fd6684933dfc01431be8f007c45b266e0ca))
+* feat: add num_workers to feature compiling ([`0f4ef30`](https://github.com/siemdejong/sclicom/commit/0f4ef30378edc9397b74934674f6debd40552078))
 
-### Breaking
-* installation via the config.yml is no longer possible. It is also no longer needed for splits/convert cli operations. For coming deep learning cli applications, it will be needed to fetch the path to vipsbin from a config with deep learning options. ([`bdbed64`](https://github.com/siemdejong/dpat/commit/bdbed641081d0717d97876aa3a76bb0a9f0c216f))
-* logging with the config file is now unsupported. Configure logging in the application using the library. ([`85875fd`](https://github.com/siemdejong/dpat/commit/85875fd6684933dfc01431be8f007c45b266e0ca))
 
-### Documentation
-* **cuda:** Add docs about cuda ([`58ca68f`](https://github.com/siemdejong/dpat/commit/58ca68f97c7c6a956654a3f5cb2a6b694a5c2fdc))
-* **logging:** Remove config.yml logging ([`60e6d90`](https://github.com/siemdejong/dpat/commit/60e6d906e27db69203db389d268ca6e846973db1))
-* **readme:** Clarify log/vips config ([`0e06f66`](https://github.com/siemdejong/dpat/commit/0e06f66875dd5aa3344106d062aeb935f1ab1f02))
+## v4.7.0 (2023-04-06)
 
-## v1.4.0 (2023-02-15)
 ### Feature
-* **logging:** Add logging and log config ([`6c90359`](https://github.com/siemdejong/dpat/commit/6c90359a5d9153555a1c12a9277d6869ce113525))
+
+* feat: attention tiles viz ([`df9f90f`](https://github.com/siemdejong/sclicom/commit/df9f90fc734fddc4a6f269d02ca63b1a7422ba55))
+
+* feat: change hparam search vars ([`fbd5847`](https://github.com/siemdejong/sclicom/commit/fbd584767cee5a0d0bd6f22093df8b85e22db2d0))
 
 ### Fix
-* **cli:** Remove unnecessary __name__=__main__ chk ([`c5f5223`](https://github.com/siemdejong/dpat/commit/c5f5223c4b1a6a5f8432f0406665a5fca35104d6))
 
-### Documentation
-* **convert:** Change bulk to batch ([`2272355`](https://github.com/siemdejong/dpat/commit/2272355593294d6b8963616dc02f295b44589be3))
+* fix: explicitly export attention model ([`7aa356d`](https://github.com/siemdejong/sclicom/commit/7aa356d98842a681aba398ccecc1ee7e47332b81))
 
-## v1.3.0 (2023-02-15)
-### Feature
-* **dataset:** Add PMCHHGImageDataset ([`1c65f85`](https://github.com/siemdejong/dpat/commit/1c65f85f4e170171e27c6a104d2a82c9f0771149))
+* fix: remove argument linking ([`d0d28e6`](https://github.com/siemdejong/sclicom/commit/d0d28e6a3a04d9f76d155a226c6b1ff91d8380e1))
 
-## v1.2.2 (2023-02-15)
-### Fix
-* **splits:** Change saved filename to relative ([`5ba6ed9`](https://github.com/siemdejong/dpat/commit/5ba6ed95ce33f92d4a9677af37c1645944b75edb))
+* fix: change defaults ([`dcdfea6`](https://github.com/siemdejong/sclicom/commit/dcdfea6212b251c18bfbe5d4c8bbe06259c2a3ce))
 
-## v1.2.1 (2023-02-15)
-### Fix
-* **convert:** Decompressionbomberror help ([`9ff923d`](https://github.com/siemdejong/dpat/commit/9ff923db4ec297c78daac5e3c8fb294e42072983))
+### Unknown
 
-### Documentation
-* **cli:** Update docs of cli ([`b917e52`](https://github.com/siemdejong/dpat/commit/b917e52856c06a0dbbb094a53d591a971215e150))
+* Update issue templates
 
-## v1.2.0 (2023-02-15)
-### Feature
-* **cli:** Change from argeparse to click ([`470ae65`](https://github.com/siemdejong/dpat/commit/470ae65c54d90bc69cf93f764b3445c94433254d))
+gh: add docs request issue template ([`7d0663c`](https://github.com/siemdejong/sclicom/commit/7d0663cc4985be3273aa1cd6aaa413e545e1c875))
 
-## v1.1.1 (2023-02-14)
-### Fix
-* **splits:** A bug with default include/exclude ([`3f46207`](https://github.com/siemdejong/dpat/commit/3f462075fa6a07adef252454a9069a478e7414d3))
 
-## v1.1.0 (2023-02-14)
+## v4.6.0 (2023-04-04)
+
 ### Feature
-* **splits:** Change split logic ([`5f38156`](https://github.com/siemdejong/dpat/commit/5f38156574a27694cd8d85f00f356bd335b50764))
-* **splits:** Add inclusion and exclusion pattern ([`caa5d2a`](https://github.com/siemdejong/dpat/commit/caa5d2a3d17f01c738dcb6829f0f233cd0cc68cd))
-* **splits:** Add overwrite argument ([`f2a664f`](https://github.com/siemdejong/dpat/commit/f2a664fdeb3c36495570aa452ca74a378861e9f1))
 
-### Documentation
-* **readme:** Change installation heading ([`dd1416d`](https://github.com/siemdejong/dpat/commit/dd1416df319638a642d1d28884c1fd34c81c9bb1))
+* feat: make trials reproducible
 
-## v1.0.0 (2023-02-14)
-### Feature
-* **dpat:** Change project.ini to config.yml ([`f13ed4b`](https://github.com/siemdejong/dpat/commit/f13ed4bcd9e44d7cbbfe74443effc8ff4347d38a))
+by adding a seed
 
-### Breaking
-* project.ini will not be read anymore. PATHS.vips has to be set in config.yml, somewhere near the root of the repository. ([`f13ed4b`](https://github.com/siemdejong/dpat/commit/f13ed4bcd9e44d7cbbfe74443effc8ff4347d38a))
+and reconfigure search space ([`6fb64c4`](https://github.com/siemdejong/sclicom/commit/6fb64c493dba130ab64e4b44ece9a85d62846dd8))
 
-### Documentation
-* **installation:** Clarify where to specify vipsbin ([`643009a`](https://github.com/siemdejong/dpat/commit/643009ad8f01e10da84167df8792dc4baabcc160))
-* **splits:** Add help of splits cli to README ([`e3ef258`](https://github.com/siemdejong/dpat/commit/e3ef25843576de0b9313bb58462d073a0b258a43))
+### Unknown
 
-## v0.4.1 (2023-02-14)
-### Fix
-* **dpat:** Import pyvips before openslide ([`2d25ae0`](https://github.com/siemdejong/dpat/commit/2d25ae00725775c880f7d3c568985f2a76b0c894))
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`86bdd62`](https://github.com/siemdejong/sclicom/commit/86bdd62bb7c90f97a766741c135e19339b2c7775))
 
-## v0.4.0 (2023-02-14)
-### Feature
-* Add pre-commit ([`620dccb`](https://github.com/siemdejong/dpat/commit/620dccba985db8ab86ae6a6ea3fec3775b9aa057))
-* **splits:** Create splits and run isort/black ([`fe8cf25`](https://github.com/siemdejong/dpat/commit/fe8cf25ac3940ea1810b66edea92bdf080eba792))
 
-## v0.3.0 (2023-02-13)
+## v4.5.0 (2023-04-04)
+
 ### Feature
-* Add num-workers and #chunks to cli ([`0f322c4`](https://github.com/siemdejong/dpat/commit/0f322c49bb3cbdaa7ecf961d85bb5c0c44f756f0))
 
-### Documentation
-* Fix typo ([`18971e2`](https://github.com/siemdejong/dpat/commit/18971e22813b39c2b3cb0679918e0f152f334e75))
-* Fix 300fast typo ([`f0ed148`](https://github.com/siemdejong/dpat/commit/f0ed148fc62ad89d387fece03112bcf64c3cb383))
-* Clarify image fn needs scanprogram for tif ([`f0f7384`](https://github.com/siemdejong/dpat/commit/f0f7384e8d548628b882099b2c3faebd380b7cd8))
-* Clarify conda dependency ([`932569f`](https://github.com/siemdejong/dpat/commit/932569f78a459c218366a1d2ee3d6127a1a3323c))
+* feat: test model ([`857d2cd`](https://github.com/siemdejong/sclicom/commit/857d2cd7e6b11269a73c83a10625250f4229f61d))
+
+### Unknown
+
+* Merge pull request #35 from siemdejong/test
+
+Test the model ([`cad0f37`](https://github.com/siemdejong/sclicom/commit/cad0f375e519438e7722615776c4e3dfd2a8633f))
+
+
+## v4.4.0 (2023-03-30)
+
+### Ci
+
+* ci: only run sphinx build when release successful ([`e4d2c53`](https://github.com/siemdejong/sclicom/commit/e4d2c534549c5b7bbd8346f0a038c893a0b3148d))
 
-## v0.2.0 (2023-02-13)
 ### Feature
-* Clarify dlup will be installed with dpat ([`c062884`](https://github.com/siemdejong/dpat/commit/c062884fcd7232db34c8b48a3c72bd06be095589))
 
-### Documentation
-* Remove logo ([`f932b71`](https://github.com/siemdejong/dpat/commit/f932b714653002ea6b8023d1eb4f49032e90e3ae))
-* Make package and add readme ([`e5fd4a5`](https://github.com/siemdejong/dpat/commit/e5fd4a5c44c160430e7245bc80b185300e6379bb))
+* feat: add hparam tuner (#31)
+
+* feat: add hparam tuner
+
+* docs: add clarification on wprkaround class
+
+* fix: don&#39;t assume self.D is a list
+
+* fix: move parameters to one place
+
+* fix: remove ray_lightning
+
+* fix: use minimum number of epochs
+
+* fix: use multivariate TPE with constant_liar
+
+* fix: report accuracies to ray
+
+* fix: add comments on tpesampler ([`b2e4094`](https://github.com/siemdejong/sclicom/commit/b2e40942abc3dad0b72499480fe024f56872b6ee))
+
+### Fix
+
+* fix: run black ([`619679f`](https://github.com/siemdejong/sclicom/commit/619679fa3c808b699b16d79bd915d00bbcabca6b))
+
+### Unknown
+
+* Optuna (#33)
+
+* feat: add hparam tuner
+
+* docs: add clarification on wprkaround class
+
+* fix: don&#39;t assume self.D is a list
+
+* fix: move parameters to one place
+
+* fix: remove ray_lightning
+
+* fix: use minimum number of epochs
+
+* fix: use multivariate TPE with constant_liar
+
+* fix: report accuracies to ray
+
+* fix: add comments on tpesampler
+
+* fix: run precommit ([`53f16b4`](https://github.com/siemdejong/sclicom/commit/53f16b4576a0b4af7237232e6d123f97c1126a85))
+
+
+## v4.3.2 (2023-03-24)
+
+### Ci
+
+* ci: only build docs if release workflow completed ([`9d49a34`](https://github.com/siemdejong/sclicom/commit/9d49a3413bc698ff4fcec3bc4e0e595e3f8a5b51))
+
+* ci: remove sphinx action ([`b512b35`](https://github.com/siemdejong/sclicom/commit/b512b35851ec923262aba952ead1b54a142bdbf1))
+
+* ci: set bash defaults ([`18bbd18`](https://github.com/siemdejong/sclicom/commit/18bbd182e323ed5c0b6c90d38bbc709399dfbc56))
+
+* ci: activate dpat for docs compilation ([`f459363`](https://github.com/siemdejong/sclicom/commit/f45936357974170c7370e85f2e2176841f0b16e7))
+
+### Documentation
+
+* docs: fix indent ([`2e7ebf1`](https://github.com/siemdejong/sclicom/commit/2e7ebf1c03ac3fa04962cc694e6716070b31f0cc))
+
+* docs: ignore autosummary ([`e63a009`](https://github.com/siemdejong/sclicom/commit/e63a0094dd431241684169aebd858c1a3b92e350))
+
+* docs: move docs from readme to gh pages ([`6012ebc`](https://github.com/siemdejong/sclicom/commit/6012ebcadbe1315fcb0e010393290f6c1dc99215))
+
+* docs: add docs to github pages ([`1f85ef8`](https://github.com/siemdejong/sclicom/commit/1f85ef882464c87d89ee7109cb58ede34dccad5d))
+
+### Fix
+
+* fix: type error ([`e2af84a`](https://github.com/siemdejong/sclicom/commit/e2af84a6474303aec2e2b8d25fdf47468a9cfb3b))
+
+* fix: bug with reading from bytes
+
+Seek first character of a string before reading it in the h5 dataset. ([`ba1c58e`](https://github.com/siemdejong/sclicom/commit/ba1c58e5290c985877f99526936a7465c9244f4b))
+
+* fix: give units to fraction logs ([`416749a`](https://github.com/siemdejong/sclicom/commit/416749aa03e1c6d9fbee0ca350e9154033d0fc0e))
+
+
+## v4.3.1 (2023-03-23)
+
+### Fix
+
+* fix: up default patience to 100 ([`289d7f9`](https://github.com/siemdejong/sclicom/commit/289d7f9b3b97702836f34a6f4815324cbad09247))
+
+
+## v4.3.0 (2023-03-23)
+
+### Feature
+
+* feat: add early stopping ([`7c4eb01`](https://github.com/siemdejong/sclicom/commit/7c4eb01e240402c6033fa2b06d802e41b3e90c60))
+
+* feat: add dropout_p parameter to varmil
+
+To possibly change the amount of dropout ([`6b59e50`](https://github.com/siemdejong/sclicom/commit/6b59e50d8b6c5c800ce0bdcadc09025159412dce))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`73c584b`](https://github.com/siemdejong/sclicom/commit/73c584b2087de41c69dbb9654fbdccf5d85b68a7))
+
+
+## v4.2.0 (2023-03-23)
+
+### Ci
+
+* ci: bypass conda bug
+
+https://stackoverflow.com/a/72178361 ([`83c3991`](https://github.com/siemdejong/sclicom/commit/83c3991fbd94c5d0e767f9ea6b645fb98aa50af6))
+
+### Feature
+
+* feat: add hidden features and dropout ([`452082c`](https://github.com/siemdejong/sclicom/commit/452082cbff5e2f584938b7de84b887c0a035d418))
+
+### Fix
+
+* fix: typing ([`5dce7a4`](https://github.com/siemdejong/sclicom/commit/5dce7a4bd174fa9e4411e506d11962b1eb495850))
+
+* fix: add area under precision recall curve ([`1a2648f`](https://github.com/siemdejong/sclicom/commit/1a2648faed30be99050f9d4877530070dffb238b))
+
+* fix: remove optimizer/scheduler defaults
+
+This was needed to set the optimizer and scheduler via the command line, like
+&#34;--optimizer=Adam --optimizer.lr=0.003&#34; etc. ([`d2b62e1`](https://github.com/siemdejong/sclicom/commit/d2b62e1631c88db8914497a55baf8a45d04a1f3a))
+
+* fix: link max_epochs to scheduler T_max
+
+Because otherwise the cosine annealing doesn&#39;t work and only uses the
+initial amount, regardless of what is set at the command line. ([`1a05932`](https://github.com/siemdejong/sclicom/commit/1a059322768140f33668e4481940bc9a94a6d582))
+
+* fix: run black ([`db24156`](https://github.com/siemdejong/sclicom/commit/db2415632a81eefd91db152848172511e381a4e1))
+
+* fix: support lightning 2 ([`b4a822c`](https://github.com/siemdejong/sclicom/commit/b4a822c166edf2ac2ff5d5557f3a8e09b8f68588))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`6c3e27c`](https://github.com/siemdejong/sclicom/commit/6c3e27c602c2ab3da8e55afe29c910c5ba1860fa))
+
+
+## v4.1.0 (2023-03-23)
+
+### Feature
+
+* feat: entropymasker experiment ([`ec70eef`](https://github.com/siemdejong/sclicom/commit/ec70eef917c2128d7e34ef50188b422bc262b732))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`62e2f10`](https://github.com/siemdejong/sclicom/commit/62e2f10da3790d917616da06e0a88ab8971e10be))
+
+
+## v4.0.1 (2023-03-20)
+
+### Fix
+
+* fix: compiling model doesn&#39;t work, rollback
+
+ref: see snellius output slurm-2473416.out ([`e733a24`](https://github.com/siemdejong/sclicom/commit/e733a243879b26ebcf87b35a28d56b098db705b4))
+
+
+## v4.0.0 (2023-03-20)
+
+### Breaking
+
+* fix: filter h5 dataset by filenames
+
+Using the paths_and_targets keyword, which is equivalent to the similar
+similar keyword in the tile dataset.
+
+BREAKING CHANGE: train|val|test_path keywords now do not refer to the
+the target train|val|test paths to output h5 files to, but to the files
+providing paths_and_targets.
+file_path is the new target file, containing all images. ([`b3e1770`](https://github.com/siemdejong/sclicom/commit/b3e177062d58840a69271f323f84fa67d9bf31cc))
+
+### Fix
+
+* fix: update mil config to reflect new signature ([`c4dc0ed`](https://github.com/siemdejong/sclicom/commit/c4dc0edce0acc9ad2453f874cde3b619e68ca559))
+
+* fix: safely bypass sigint or sigterm
+
+handy for using with slurm for example ([`388d368`](https://github.com/siemdejong/sclicom/commit/388d36824e27192a104b84f2a2629fea471b733e))
+
+* fix: remove trainer arguments for pl2 ([`99194e0`](https://github.com/siemdejong/sclicom/commit/99194e09417bd38a1f2c52d61b870199f91ab7db))
+
+
+## v3.2.1 (2023-03-17)
+
+### Fix
+
+* fix: remove pl2 removed trainer arguments ([`817beb8`](https://github.com/siemdejong/sclicom/commit/817beb85c59ec8ae7bf3f0273f640c7086a12482))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`708e3fb`](https://github.com/siemdejong/sclicom/commit/708e3fbb5a65ab05d63b211a6c4b5635490a6a1f))
+
+
+## v3.2.0 (2023-03-17)
+
+### Feature
+
+* feat: automate masking with dlup entropy_masker ([`1066ea1`](https://github.com/siemdejong/sclicom/commit/1066ea1264a7c56760b1fb4be10a7fced92336b6))
+
+* feat: compile the pytorch lightning models ([`c009004`](https://github.com/siemdejong/sclicom/commit/c009004acb837a3026cb370b927b461996f8f51c))
+
+### Fix
+
+* fix: lightning 2.0 ignore missing type imports ([`08b3e85`](https://github.com/siemdejong/sclicom/commit/08b3e85608f0cc3171812f1cd1f5fe6f5e9a3bfa))
+
+* fix: ddp default find_unused_parameters=False
+
+Lightning 2+ sets find_unused_parameters for the ddp strategy to false.
+Therefore, it is unnecessary to set it to False in the config file. ([`3e2a15d`](https://github.com/siemdejong/sclicom/commit/3e2a15dab7fd127b8f70c1439b2833a20b32ec4a))
+
+* fix: use recommended precision
+
+bf16-mixed has less ambiguity than bf16. bf16-mixed makes it clear
+mixed precision is used. ([`6b654e2`](https://github.com/siemdejong/sclicom/commit/6b654e2fc26c7c1223529d1a42cd177ea8c95ff8))
+
+* fix: rename *_epoch_end to on_*_epoch_end
+
+*_epoch_end is deprecated in lightning 2 ([`37e0c52`](https://github.com/siemdejong/sclicom/commit/37e0c52dc200bd72093c89aabc6016ec44cf7d60))
+
+* fix: add torch/lightning v2 deps ([`2afdf05`](https://github.com/siemdejong/sclicom/commit/2afdf057726f40caae1cae1f7fae99aa464ae415))
+
+* fix: simclr-16-3 update ([`29fdf58`](https://github.com/siemdejong/sclicom/commit/29fdf582a8c24a5475a605130c1903e1a5e30520))
+
+### Performance
+
+* perf: do not log to progress bar
+
+Following the lightning 2.0 recommendation of not logging to
+the progress bar, AUC and F1 are not logged to the process bar anymore.
+They are still logged to the installed logger, e.g. Tensorboard. ([`da4e3b4`](https://github.com/siemdejong/sclicom/commit/da4e3b487f24d1503fea17feb8280d486a5bdc36))
+
+### Unknown
+
+* Mask load from disk (#25)
+
+* feat: mask tiles in pmchhgImageDataset
+
+Using the new entropy_masker mask function from dlup.
+
+* fix: bumpy python version ([`340edde`](https://github.com/siemdejong/sclicom/commit/340eddec2dec6db48f6488caac6315f1400b5653))
+
+* Merge pull request #24 from siemdejong/torchv2
+
+Torchv2 ([`a0ef974`](https://github.com/siemdejong/sclicom/commit/a0ef97466a35a0fc853b2f4af864fbd308744fc6))
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`51c0fad`](https://github.com/siemdejong/sclicom/commit/51c0fadb6794befcec87e5e1b34b676165e23aac))
+
+
+## v3.1.1 (2023-03-15)
+
+### Fix
+
+* fix: pretrained config typo ([`e6a3778`](https://github.com/siemdejong/sclicom/commit/e6a37785d9b9ef49bdbf40eb009d83f35edff82e))
+
+
+## v3.1.0 (2023-03-15)
+
+### Feature
+
+* feat: add num_subfolds parameter to create_splits ([`dfe7ceb`](https://github.com/siemdejong/sclicom/commit/dfe7ceb3380fef3ea595cd3f7e68ed426b33989d))
+
+### Fix
+
+* fix: splits tests with num_subfolds ([`3a9d44e`](https://github.com/siemdejong/sclicom/commit/3a9d44e84ae570e35fc2262a46fe4b467fc97f98))
+
+### Unknown
+
+* Merge pull request #23 from siemdejong/less-folds
+
+feat: add num_subfolds parameter to create_splits
+
+fix #22 ([`5d201d1`](https://github.com/siemdejong/sclicom/commit/5d201d1204b3fb77b8ff74314cc697d9f81914e9))
+
+
+## v3.0.1 (2023-03-15)
+
+### Fix
+
+* fix: update viz of untrained model ([`e32d9f5`](https://github.com/siemdejong/sclicom/commit/e32d9f5a1bcacf45b3893c94ec3dddf6cd3682c2))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`d63095a`](https://github.com/siemdejong/sclicom/commit/d63095af26052f9a4e81944e401473a929584ebf))
+
+
+## v3.0.0 (2023-03-15)
+
+### Breaking
+
+* feat: from torchvision.models to pytorchcv models
+
+Torchvision has less pretrained and prebuilt models available than
+pytorchcv.
+Fort the application of a small dataset, it is nice to have smaller
+resnets available, which torchvision has less support for.
+
+BREAKING CHANGE: in the config files, models must be specified by
+corresponding pytorchcv models, not torchvision. ([`bb5732d`](https://github.com/siemdejong/sclicom/commit/bb5732d3f8b9fc0434720077d37a448df80e8670))
+
+### Feature
+
+* feat: show targets/img_id/case_id distribution ([`c757995`](https://github.com/siemdejong/sclicom/commit/c7579958dcb63b2664dc120ba1feac16af208489))
+
+### Fix
+
+* fix: pytorchcv not typed ignore missing imports ([`2b33f70`](https://github.com/siemdejong/sclicom/commit/2b33f705443d4d2e92eb045f42f63efdba5feb34))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`79c5b72`](https://github.com/siemdejong/sclicom/commit/79c5b7211b9a4cc5933d2b2387730c8ef4483466))
+
+
+## v2.7.3 (2023-03-14)
+
+### Performance
+
+* perf: speed up feature compilation
+
+Fixes part of #16, namely the writing part. ([`772a0bd`](https://github.com/siemdejong/sclicom/commit/772a0bd38e356b9d6b547e757286c0b973a45c2e))
+
+
+## v2.7.2 (2023-03-14)
+
+### Fix
+
+* fix: create feature directory if not exists ([`674c8c4`](https://github.com/siemdejong/sclicom/commit/674c8c4eb33ac614d03cee35a0993bec5b50b4e7))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`0859ba1`](https://github.com/siemdejong/sclicom/commit/0859ba12ca95f65c2481da080ce784892d6bb186))
+
+
+## v2.7.1 (2023-03-13)
+
+### Fix
+
+* fix: bypass oom error ([`0177032`](https://github.com/siemdejong/sclicom/commit/01770320bcae9608d4efc15793a9d53135e764f3))
+
+* fix: add ipywidgets dependency
+
+for tqdm in notebooks ([`3c26dcd`](https://github.com/siemdejong/sclicom/commit/3c26dcd0b43e868ff34bf424f0c1bf5c73bdc433))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`65a9bd1`](https://github.com/siemdejong/sclicom/commit/65a9bd135a59d1c82535f4621e2c303bd26846be))
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`07c8f20`](https://github.com/siemdejong/sclicom/commit/07c8f20146781ce3ceee18f54f5379057dd34d52))
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`120fefb`](https://github.com/siemdejong/sclicom/commit/120fefbff711643c52f4242d46c332d8d87d1ad9))
+
+
+## v2.7.0 (2023-03-10)
+
+### Documentation
+
+* docs: change installation order. ([`63d51c8`](https://github.com/siemdejong/sclicom/commit/63d51c8b27db4711b141b9c4aa5104bc658aca57))
+
+### Feature
+
+* feat: visualize embedding distribution using t-sne ([`91c4190`](https://github.com/siemdejong/sclicom/commit/91c4190f4477e2cb53fa5e855d1bf64cfd5a6ecf))
+
+
+## v2.6.1 (2023-03-10)
+
+### Chore
+
+* chore: remove notebooks from linguist ([`98e5411`](https://github.com/siemdejong/sclicom/commit/98e5411bcc96250b04a792ee026056f3bc8e8fcd))
+
+### Fix
+
+* fix: show case distribution ([`e2dcd66`](https://github.com/siemdejong/sclicom/commit/e2dcd667eb1f48d00eb4fb2ce5ba653ec7149ebb))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`4c2edf3`](https://github.com/siemdejong/sclicom/commit/4c2edf300882335862dd1ba8c108690d39c312e5))
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`28b5398`](https://github.com/siemdejong/sclicom/commit/28b5398feeb75a2709af212662b1b72308a0754c))
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`90a8b81`](https://github.com/siemdejong/sclicom/commit/90a8b8131d4cb6ea277658b6531d999995a2774d))
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`1b81024`](https://github.com/siemdejong/sclicom/commit/1b810244d81e648641e387e0e42510840d51b285))
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`2639798`](https://github.com/siemdejong/sclicom/commit/26397983f1843b69489a5a80f3e13e3582b2a5a1))
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`bdbc689`](https://github.com/siemdejong/sclicom/commit/bdbc6898fff46cb21bb52fa6b3bc8517ca3a1acc))
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`77ef0eb`](https://github.com/siemdejong/sclicom/commit/77ef0ebe48d41698c9de90e5811735d34448c50b))
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`0ca5433`](https://github.com/siemdejong/sclicom/commit/0ca5433aba601fd6f1109758b13c8fe890a46a44))
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`f9152ee`](https://github.com/siemdejong/sclicom/commit/f9152ee0ffcb5aecb9ef06fa09761c4546abaa2b))
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`1cc30c4`](https://github.com/siemdejong/sclicom/commit/1cc30c4727626439e582b722d54d334d91ece9c0))
+
+
+## v2.6.0 (2023-03-10)
+
+### Feature
+
+* feat: nearest neighbours visualization features ([`6239607`](https://github.com/siemdejong/sclicom/commit/6239607b792d561a4ca3ce5c424e3ac6b273b1ea))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`b47b685`](https://github.com/siemdejong/sclicom/commit/b47b685b08b14e4dd44b09e05067f7423e9a021d))
+
+
+## v2.5.2 (2023-03-10)
+
+### Fix
+
+* fix: jsonargparse dependency ([`94242b2`](https://github.com/siemdejong/sclicom/commit/94242b2b7654ef4fb015f332a9c256a59c6d5aad))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`8440021`](https://github.com/siemdejong/sclicom/commit/844002110e4c8ffff34378183ca07610bcafb075))
+
+
+## v2.5.1 (2023-03-10)
+
+### Fix
+
+* fix(log): log origin of image data ([`1bb50ae`](https://github.com/siemdejong/sclicom/commit/1bb50aea5c76849fe9be7b5219abc6f938de9922))
+
+
+## v2.5.0 (2023-03-09)
+
+### Feature
+
+* feat(pretrain): add SimCLR ([`502bba3`](https://github.com/siemdejong/sclicom/commit/502bba37010819a4f0a90292e3e47e721aac8738))
+
+### Unknown
+
+* Merge pull request #21 from siemdejong/simclr
+
+feat(pretrain): add SimCLR ([`c6dc62f`](https://github.com/siemdejong/sclicom/commit/c6dc62fd807dc639f6fea911ee15190d41625450))
+
+
+## v2.4.2 (2023-03-08)
+
+### Ci
+
+* ci: run mypy in the dpat directory at pre-commit ([`662276e`](https://github.com/siemdejong/sclicom/commit/662276e9450f0c7af6d2818f1d2e3461d5f7bc10))
+
+### Fix
+
+* fix(type): fix __iter__ type error ([`d69fb24`](https://github.com/siemdejong/sclicom/commit/d69fb24dee31c13cb3cd543b66526a9bdf4d87e9))
+
+* fix: use WeightedRandomSampler
+
+Because the training dataset could be imbalanced. ([`55334c4`](https://github.com/siemdejong/sclicom/commit/55334c4ce402de9d39f49eea0ab39fbf99f98478))
+
+### Unknown
+
+* Merge pull request #20 from siemdejong/oversampling-minority
+
+fix: use WeightedRandomSampler
+
+Fixes #19 ([`f20f57e`](https://github.com/siemdejong/sclicom/commit/f20f57e5e1d152e323eb7bc1f93fab81eb72f764))
+
+
+## v2.4.1 (2023-03-08)
+
+### Performance
+
+* perf(varmil): set gradients to none instead of 0 ([`b8a850a`](https://github.com/siemdejong/sclicom/commit/b8a850a9ce5ae8fe896585ff8eeb3d308049feb7))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`a344d8f`](https://github.com/siemdejong/sclicom/commit/a344d8fc82ee5c1a1c32ebd53993ee3a8a067a9c))
+
+
+## v2.4.0 (2023-03-07)
+
+### Ci
+
+* ci: rm arch name from ci cache ([`488edfa`](https://github.com/siemdejong/sclicom/commit/488edfa54f1086d8108634fa864a70aeff5861d8))
+
+### Feature
+
+* feat: train varmil ([`56a3ae9`](https://github.com/siemdejong/sclicom/commit/56a3ae9ae1bddf481867ac146322ea9852e1cb2e))
+
+### Fix
+
+* fix: some typing issues ([`6a46853`](https://github.com/siemdejong/sclicom/commit/6a46853ea016ee8dc8849b4dfb992a7d52cdedff))
+
+* fix: bug where M was calculated wrong ([`d3a675b`](https://github.com/siemdejong/sclicom/commit/d3a675b7befec145976f9a95774e591ef61ddd9e))
+
+* fix: export variables from packages ([`e0db9e3`](https://github.com/siemdejong/sclicom/commit/e0db9e3191c2455085ce2671694634cddc3cfde7))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`fcaa977`](https://github.com/siemdejong/sclicom/commit/fcaa977a9ddaa6a17637aa0e679fac0ddb56de36))
+
+
+## v2.3.3 (2023-03-04)
+
+### Ci
+
+* ci: add env caching ([`c8bef7e`](https://github.com/siemdejong/sclicom/commit/c8bef7eb8358de4603bc849d418e7f556cab9f36))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`fca3841`](https://github.com/siemdejong/sclicom/commit/fca3841293aa381c545c752ab4857fea7bc1fb46))
+
+
+## v2.3.2 (2023-03-04)
+
+### Ci
+
+* ci: flake8 for extract_features pkg ([`c84b6da`](https://github.com/siemdejong/sclicom/commit/c84b6daebedfd17ccd867d0e286b6b041c735fcd))
+
+### Fix
+
+* fix: uncomment feature compilation ([`4e018fe`](https://github.com/siemdejong/sclicom/commit/4e018fe2c0760a1292edae65be11effd9c1f0787))
+
+* fix: fix number of compiled feature vectors
+
+Fix #17 ([`b659501`](https://github.com/siemdejong/sclicom/commit/b659501ccec8e7521e8c4d61d6e6e200a8956f40))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`dbb61cf`](https://github.com/siemdejong/sclicom/commit/dbb61cf71d8b716b1853aec18ac51d7ca12198bd))
+
+
+## v2.3.1 (2023-03-03)
+
+### Fix
+
+* fix: concatenate features
+
+Feature vectors of tiles belonging to the same image will be concatenated and
+stored in the belonging image group along with their metadata in datasets
+instead of h5-attrs.
+
+This allows for MIL to use batch size=1bag
+and load one dataset at a time. ([`349b13d`](https://github.com/siemdejong/sclicom/commit/349b13d5c0be43dea0ede14cffc65c11089c9154))
+
+* fix: h5 classmethod return type ([`bc4b24a`](https://github.com/siemdejong/sclicom/commit/bc4b24af8dcd40caca4089217a5dd9c98ee2aae8))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`05dc1e9`](https://github.com/siemdejong/sclicom/commit/05dc1e92d720737e5b98da8e2106ed07f3126637))
+
+
+## v2.3.0 (2023-03-02)
+
+### Feature
+
+* feat: add h5 dataset
+
+Multi instance learning in stage 2 is easier on tensors obtained from an
+hdf5 file with datasets embedded. ([`0f6cfe2`](https://github.com/siemdejong/sclicom/commit/0f6cfe24673dd27c43bd230636d4ad4698813865))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`87ce747`](https://github.com/siemdejong/sclicom/commit/87ce747197f8229f907f16668137e68595b8995f))
+
+
+## v2.2.0 (2023-03-02)
+
+### Feature
+
+* feat: add feature extraction
+
+Add feature extractor training.
+Add feature vector compilation to HDF5.
+Add config files to be used with pl.Trainer.
+Refactor.
+Add float32 matmul precision setting.
+Add cudnn auto tuner setting.
+Add Omegaconf &#34;now&#34; interpolation.
+Require lightning[extra] and h5py as deps.
+Run pre-commit also on dpat/extract_features.
+Link pl CLI to pl Trainers. ([`e71d5be`](https://github.com/siemdejong/sclicom/commit/e71d5becd0b1e194c5205d9993813dd74f4bb32d))
+
+
+## v2.1.6 (2023-02-26)
+
+### Performance
+
+* perf: pin memory of dataloaders ([`4afcdf2`](https://github.com/siemdejong/sclicom/commit/4afcdf2e59d0dd04aafbe90dfe070a831522d9ad))
+
+* perf: zero_grad to non ([`d6d62c7`](https://github.com/siemdejong/sclicom/commit/d6d62c759296b478c1038d94c7e103461a86ec5b))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`df2974e`](https://github.com/siemdejong/sclicom/commit/df2974e41d371d964d7abf6ecb1d9a9ef7f7093c))
+
+
+## v2.1.5 (2023-02-26)
+
+### Ci
+
+* ci: use conda shell ([`65d7e00`](https://github.com/siemdejong/sclicom/commit/65d7e00f52e5bfb1ae1162da05138c034d5db4c7))
+
+* ci: fix conda python version ([`9ab509d`](https://github.com/siemdejong/sclicom/commit/9ab509d991eedd3e7019c0c9740032ef3bf254ea))
+
+* ci: deps and release needs test ([`fe5e2ed`](https://github.com/siemdejong/sclicom/commit/fe5e2ed8472b18207b7f0cc8efe94983ce8de22a))
+
+### Fix
+
+* fix(tests): add tests for create_splits ([`780ed07`](https://github.com/siemdejong/sclicom/commit/780ed077000f55c0f7b86888c1f9646ec0085864))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of github.com:siemdejong/dpat ([`c015208`](https://github.com/siemdejong/sclicom/commit/c01520824d0c279d847e0f1d21a27f3278822de8))
+
+
+## v2.1.4 (2023-02-26)
+
+### Fix
+
+* fix(tests): add convert tests ([`819e23d`](https://github.com/siemdejong/sclicom/commit/819e23dbdb36824ffbcf5a520e8d43ac42acb0d8))
+
+
+## v2.1.3 (2023-02-25)
+
+### Fix
+
+* fix(semantic-release): add build command
+
+setup.py is not available, so python setup.py ... does not work.
+build_command installs &#39;build&#39; en builds distributions. ([`c35a40f`](https://github.com/siemdejong/sclicom/commit/c35a40f214390c36a4f377523fc03560f3eb8cfd))
+
+
+## v2.1.2 (2023-02-25)
+
+### Fix
+
+* fix(typing): add typing ([`0842497`](https://github.com/siemdejong/sclicom/commit/0842497f3498bf8f66af5ea917b5ecf012406b51))
+
+
+## v2.1.1 (2023-02-23)
+
+### Ci
+
+* ci: update psr repo name ([`4ccf2e8`](https://github.com/siemdejong/sclicom/commit/4ccf2e8d35c166b8d9c4269b50b79f1b04ae1e54))
+
+### Fix
+
+* fix(swav): make swav return a number
+
+Fix #7
+
+SwAV by Lightly apparently needs the user to not use a datamodule.
+If using the datamodule, call setup() on it and use
+datamodule.x_dataloader() to pass to trainer.fit along with the model. ([`d21dcce`](https://github.com/siemdejong/sclicom/commit/d21dcce5c0590d94c87478b7c7eb8324476328f4))
+
+* fix(deps): add tensorboard to dependencies ([`5ee3528`](https://github.com/siemdejong/sclicom/commit/5ee35280bf5d7e990bcf3c26ae13975e5990b782))
+
+* fix(convert): only log skip if skip_count&gt;0 ([`0a58791`](https://github.com/siemdejong/sclicom/commit/0a587910b9f2fa7b32d05c21aa8b0c3facb671b7))
+
+
+## v2.1.0 (2023-02-22)
+
+### Ci
+
+* ci: add workflow dispatch ([`10da34a`](https://github.com/siemdejong/sclicom/commit/10da34a559aeafd43055b210e744f3be7ae82b9e))
+
+* ci: docformat, no-opt, print, ssort, black, flake8 ([`50e8ef4`](https://github.com/siemdejong/sclicom/commit/50e8ef4c9249cb03e71bfad8d589b625cf9ffc11))
+
+* ci: add continuous integration
+
+Move setup.py to pyproject.toml.
+Add semantic-release github ci.
+Add flake8 and yesqa to pre-commit. ([`81e50a0`](https://github.com/siemdejong/sclicom/commit/81e50a08299dee8ceb7754e4adcf45943dbd3cf7))
+
+### Feature
+
+* feat(data): add mean and std calculator ([`e6549f6`](https://github.com/siemdejong/sclicom/commit/e6549f681bd0f4500077dd2365afd5a9a231c972))
+
+* feat(stage1): Implement swav with pl and lightly ([`3dcbdca`](https://github.com/siemdejong/sclicom/commit/3dcbdcab5c4de8ebd08addb8c0f2ce02fdfa4803))
+
+### Fix
+
+* fix(package): add dependencies ([`b3d340c`](https://github.com/siemdejong/sclicom/commit/b3d340c046929d3b06f417dc2ae40e61ac173e13))
+
+* fix(package): package dpat subfolder ([`2fb78ed`](https://github.com/siemdejong/sclicom/commit/2fb78ed751908f28a0ca1719018c8a74d114b956))
+
+### Unknown
+
+* Update issue templates ([`7eb8142`](https://github.com/siemdejong/sclicom/commit/7eb8142a481dfaba4a61cb6d82e66d287579bbcf))
+
+
+## v2.0.0 (2023-02-16)
+
+### Breaking
+
+* feat(installation): remove the need for config.yml
+
+To install dpat in a script to use as api on windows, it is able
+to achieve that with
+import dpat
+dpat.install_windows(&#34;path/to/vips/bin&#34;)
+
+BREAKING CHANGE: installation via the config.yml is no longer possible.
+It is also no longer needed for splits/convert cli operations.
+For coming deep learning cli applications, it will be needed to fetch
+the path to vipsbin from a config with deep learning options. ([`bdbed64`](https://github.com/siemdejong/sclicom/commit/bdbed641081d0717d97876aa3a76bb0a9f0c216f))
+
+* fix(logging): let the cli configure logging
+
+This allows for a user using the library to configure logging, e.g. use
+`logging.getLogger(&#39;dpat&#39;).propagate = False`, if logging is not needed.
+The cli will always log to the terminal.
+
+BREAKING CHANGE: logging with the config file is now unsupported.
+Configure logging in the application using the library. ([`85875fd`](https://github.com/siemdejong/sclicom/commit/85875fd6684933dfc01431be8f007c45b266e0ca))
+
+### Documentation
+
+* docs(cuda): add docs about cuda ([`58ca68f`](https://github.com/siemdejong/sclicom/commit/58ca68f97c7c6a956654a3f5cb2a6b694a5c2fdc))
+
+* docs(logging): remove config.yml logging
+
+Previous commit disabled logging config with config.yml. ([`60e6d90`](https://github.com/siemdejong/sclicom/commit/60e6d906e27db69203db389d268ca6e846973db1))
+
+* docs(readme): clarify log/vips config
+
+Add examples for `config.yml` for logging.
+Show how to turn off logging propagation when using as a library. ([`0e06f66`](https://github.com/siemdejong/sclicom/commit/0e06f66875dd5aa3344106d062aeb935f1ab1f02))
+
+### Fix
+
+* fix(dpat): only read config.yml if windows
+
+Linux users should be able to install vips with conda. ([`f823ccc`](https://github.com/siemdejong/sclicom/commit/f823ccca59c966622464f821da158a70e3449469))
+
+
+## v1.4.0 (2023-02-15)
+
+### Documentation
+
+* docs(convert): change bulk to batch ([`2272355`](https://github.com/siemdejong/sclicom/commit/2272355593294d6b8963616dc02f295b44589be3))
+
+### Feature
+
+* feat(logging): add logging and log config
+
+Logging is done to the NullHandler.
+However, the user can turn logging on by setting the handler and
+level in config.yml, like
+LOGGING:
+  handler: StreamHandler
+  level: INFO ([`6c90359`](https://github.com/siemdejong/sclicom/commit/6c90359a5d9153555a1c12a9277d6869ce113525))
+
+### Fix
+
+* fix(cli): remove unnecessary __name__=__main__ chk ([`c5f5223`](https://github.com/siemdejong/sclicom/commit/c5f5223c4b1a6a5f8432f0406665a5fca35104d6))
+
+
+## v1.3.0 (2023-02-15)
+
+### Feature
+
+* feat(dataset): add PMCHHGImageDataset
+
+Add a dataset to loop through all tiles create from images
+in an image directory. ([`1c65f85`](https://github.com/siemdejong/sclicom/commit/1c65f85f4e170171e27c6a104d2a82c9f0771149))
+
+
+## v1.2.2 (2023-02-15)
+
+### Fix
+
+* fix(splits): change saved filename to relative
+
+Fixes #1. ([`5ba6ed9`](https://github.com/siemdejong/sclicom/commit/5ba6ed95ce33f92d4a9677af37c1645944b75edb))
+
+
+## v1.2.1 (2023-02-15)
+
+### Documentation
+
+* docs(cli): update docs of cli ([`b917e52`](https://github.com/siemdejong/sclicom/commit/b917e52856c06a0dbbb094a53d591a971215e150))
+
+### Fix
+
+* fix(convert): decompressionbomberror help ([`9ff923d`](https://github.com/siemdejong/sclicom/commit/9ff923db4ec297c78daac5e3c8fb294e42072983))
+
+
+## v1.2.0 (2023-02-15)
+
+### Feature
+
+* feat(cli): change from argeparse to click ([`470ae65`](https://github.com/siemdejong/sclicom/commit/470ae65c54d90bc69cf93f764b3445c94433254d))
+
+
+## v1.1.1 (2023-02-14)
+
+### Fix
+
+* fix(splits): a bug with default include/exclude
+
+Argparse&#39;s action &#39;append&#39; appends arguments to the default.
+Postprocessing the arguments fixes this. ([`3f46207`](https://github.com/siemdejong/sclicom/commit/3f462075fa6a07adef252454a9069a478e7414d3))
+
+
+## v1.1.0 (2023-02-14)
+
+### Documentation
+
+* docs(readme): change installation heading ([`dd1416d`](https://github.com/siemdejong/sclicom/commit/dd1416df319638a642d1d28884c1fd34c81c9bb1))
+
+### Feature
+
+* feat(splits): change split logic
+
+Create 5 stratified train-test folds. For every fold, randomly create
+5 subfolds, dividing the training set into train-val (0.8/0.2).
+Save every filename of every fold to a file with a unique filename,
+denoting the set type, and subfold and fold id. ([`5f38156`](https://github.com/siemdejong/sclicom/commit/5f38156574a27694cd8d85f00f356bd335b50764))
+
+* feat(splits): add inclusion and exclusion pattern
+
+Some images might be needed to exclude by filename.
+E.g. images with 300fast inside it.
+Otherwise, only images with 200slow may be included. ([`caa5d2a`](https://github.com/siemdejong/sclicom/commit/caa5d2a3d17f01c738dcb6829f0f233cd0cc68cd))
+
+* feat(splits): add overwrite argument ([`f2a664f`](https://github.com/siemdejong/sclicom/commit/f2a664fdeb3c36495570aa452ca74a378861e9f1))
+
+
+## v1.0.0 (2023-02-14)
+
+### Breaking
+
+* feat(dpat): change project.ini to config.yml
+
+YAML files are better structured.
+
+BREAKING CHANGE: project.ini will not be read anymore.
+PATHS.vips has to be set in config.yml, somewhere near the root
+of the repository. ([`f13ed4b`](https://github.com/siemdejong/sclicom/commit/f13ed4bcd9e44d7cbbfe74443effc8ff4347d38a))
+
+### Documentation
+
+* docs(installation): clarify where to specify vipsbin ([`643009a`](https://github.com/siemdejong/sclicom/commit/643009ad8f01e10da84167df8792dc4baabcc160))
+
+* docs(splits): add help of splits cli to README ([`e3ef258`](https://github.com/siemdejong/sclicom/commit/e3ef25843576de0b9313bb58462d073a0b258a43))
+
+### Unknown
+
+* Create LICENSE ([`d9f55dd`](https://github.com/siemdejong/sclicom/commit/d9f55dd719438612596f1a11398880c5cc0fbae3))
+
+
+## v0.4.1 (2023-02-14)
+
+### Fix
+
+* fix(dpat): import pyvips before openslide ([`2d25ae0`](https://github.com/siemdejong/sclicom/commit/2d25ae00725775c880f7d3c568985f2a76b0c894))
+
+
+## v0.4.0 (2023-02-14)
+
+### Feature
+
+* feat: add pre-commit
+
+Make sure black and isort are ran. ([`620dccb`](https://github.com/siemdejong/sclicom/commit/620dccba985db8ab86ae6a6ea3fec3775b9aa057))
+
+* feat(splits): create splits and run isort/black ([`fe8cf25`](https://github.com/siemdejong/sclicom/commit/fe8cf25ac3940ea1810b66edea92bdf080eba792))
+
+
+## v0.3.0 (2023-02-13)
+
+### Documentation
+
+* docs: fix typo ([`18971e2`](https://github.com/siemdejong/sclicom/commit/18971e22813b39c2b3cb0679918e0f152f334e75))
+
+* docs: fix 300fast typo ([`f0ed148`](https://github.com/siemdejong/sclicom/commit/f0ed148fc62ad89d387fece03112bcf64c3cb383))
+
+* docs: clarify image fn needs scanprogram for tif ([`f0f7384`](https://github.com/siemdejong/sclicom/commit/f0f7384e8d548628b882099b2c3faebd380b7cd8))
+
+* docs: clarify conda dependency ([`932569f`](https://github.com/siemdejong/sclicom/commit/932569f78a459c218366a1d2ee3d6127a1a3323c))
+
+### Feature
+
+* feat: add num-workers and #chunks to cli ([`0f322c4`](https://github.com/siemdejong/sclicom/commit/0f322c49bb3cbdaa7ecf961d85bb5c0c44f756f0))
+
+
+## v0.2.0 (2023-02-13)
+
+### Documentation
+
+* docs: remove logo ([`f932b71`](https://github.com/siemdejong/sclicom/commit/f932b714653002ea6b8023d1eb4f49032e90e3ae))
+
+* docs: make package and add readme
+
+Add docs on how to build the package.
+Add README.md to document usage of bulk convert. ([`e5fd4a5`](https://github.com/siemdejong/sclicom/commit/e5fd4a5c44c160430e7245bc80b185300e6379bb))
+
+### Feature
+
+* feat: clarify dlup will be installed with dpat ([`c062884`](https://github.com/siemdejong/sclicom/commit/c062884fcd7232db34c8b48a3c72bd06be095589))
+
+
+## v0.1.0 (2023-02-13)
+
+### Feature
+
+* feat: initial commit
+
+Add dlup and its dependencies, resolved for Windows.
+Add any (e.g. bmp) to TIFF converter. ([`5d2fc3a`](https://github.com/siemdejong/sclicom/commit/5d2fc3a4371298d8de84eb296a735c80b55980f3))
diff --git a/pyproject.toml b/pyproject.toml
index a4f03c5..d311441 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "dpat"
-version = "5.0.1"
+version = "5.1.0"
 authors = [
   {name="Siem de Jong", email="siem.dejong@hotmail.nl"},
 ]