Releases: kipoi/models
Releases · kipoi/models
v2022-07-11
What's Changed
- Updating container urls by @haimasree in #341
- Add a2z-chromatin models by @twrightsman in #343
- Update container jsons by @haimasree in #344
- Few additional changes for a2z-chromatin by @haimasree in #345
- fix missing reverse-complement in reference sequence fetching for APARENT by @Hoeze in #336
- Update container jsons by @haimasree in #347
- Removing hdf5 installation from circleci config by @haimasree in #348
Full Changelog: v2022-06-17...v2022-07-11
v2022-06-17
What's Changed
- Upgrade python version from 3.6 to 3.7 in model dependencies by @haimasree in #310
- Update json by @haimasree in #311
- Add test predictions for model groups by @haimasree in #312
- Updated singularity containers by @haimasree in #313
- Upgrading python 3.7 to python 3.8 for a subset of the models and the shared environment by @haimasree in #314
- Adding a new shared env by @haimasree in #315
- Updated singularity containers to their slim versions by @haimasree in #316
- Updating apptainer version by @haimasree in #317
- add scBasset model to model zoo by @hy395 in #318
- Adding scbasset test predictions by @haimasree in #319
- Updating json with container information about newly added model group scabasset by @haimasree in #322
- Updating container json by @haimasree in #323
- Sync common environment models with kipoi-containers by @haimasree in #324
- updated scbasset model by @hy395 in #325
- Updating test predictions for scbasset by @haimasree in #326
- Fixed issues with new release of sorted-nearest and protobuf by @haimasree in #328
- Fixed FactorNet by @haimasree in #329
- First attempt at adding TREDNet model by @okurman in #330
- Updated singularity containers by @haimasree in #331
- Adding prediction files for TREDNet by @haimasree in #332
- Adding trednet container info by @haimasree in #333
- Move tensorflow and keras dendencies to conda from pip by @haimasree in #334
- Removing pinned sorted nearest by @haimasree in #335
- Fixing issues with triggering sync-containers workflow of kipoi-containers repo from this repo by @haimasree in #337
- Updated container json by @haimasree in #338
- Updating container urls by @haimasree in #339
- Shared env update (moving tensorflow, keras) to conda from pip where ever possible by @haimasree in #340
New Contributors
Full Changelog: v2022-04-26...v2022-06-17
v2022-04-26
Announcement
This would be the last release with models with python=3.6. Most of the models (except KipoiSplice and SeqVec) will be upgraded to python 3.7 as python 3.6 has been EOL-ed. Although Kipoi still supports python=3.6, in future if that changes, kipoi version also must be pinned in model.yaml(s) in KipoiSplice and SeqVec.
What's Changed
- Increased parallelism to avoid build timeout error by @haimasree in #279
- Adding postprocessing back to maintain compatibiliy with kipoi-veff by @haimasree in #281
- Fixed ci by @haimasree in #282
- Fixed ci by @haimasree in #283
- Remove postprocessing from DeepSEA by @haimasree in #284
- Fix APARENT/site_probabilities output labels by @twrightsman in #285
- Add more parallelism to avoid frequent circleci issue with context deadline by @haimasree in #286
- Updated links to singularity containers by @haimasree in #287
- Adding a way to sync with kipoi-containers by @haimasree in #288
- Fix sync workflow by @haimasree in #289
- Added DeepSTARR by @bernardo-de-almeida in #290
- Adding precision for cross platform testing by @haimasree in #291
- Adding DeepSTARR containers by @haimasree in #292
- Adjust APARENT model by @Hoeze in #293
- Update container jsons by @haimasree in #294
- Removing ambiguity for model class definition by @haimasree in #295
- Fixed ci by @haimasree in #296
- Aparent update by @Hoeze in #297
- add variant to APARENT metadata by @Hoeze in #298
- Update container jsons by @haimasree in #299
- Update container jsons by @haimasree in #300
- Update json by @haimasree in #302
- Update container jsons by @haimasree in #303
- Update container jsons by @haimasree in #304
- Updating ci by @haimasree in #305
- Add apptainer by @haimasree in #306
- singularity container images with updated links by @haimasree in #307
- Fixed ci and added conda-libmamba-solver by @haimasree in #308
- Fixed ci by @haimasree in #309
New Contributors
- @twrightsman made their first contribution in #285
- @bernardo-de-almeida made their first contribution in #290
Full Changelog: v2021-11-15...v2022-04-26
v2021-11-15
What's Changed
- Fixed folder structure for epidermal_basset by @haimasree in #248
- Fixed ci by @haimasree in #249
- SeqVec removed by @haimasree in #250
- Parallelized CI by @haimasree in #253
- Attempting to add seqvec back to ci by @haimasree in #254
- Added xpresso dataloader by @haimasree in #255
- Update model-template.yaml of Xpresso to use recent version of kipoiseq by @haimasree in #256
- Adding cython by @haimasree in #257
- Added default arguments to Xpresso's yaml representation by @haimasree in #258
- Unpin kipoi packages and upgrade python 3.5 to 3.6 by @haimasree in #259
- Fixed ci by @haimasree in #260
- Added DeepFlyBrain by @itaskiran in #261
- Fixed ci by @haimasree in #262
- Pinning deepfly dependencies by @haimasree in #263
- Fixed ci by @haimasree in #264
- Upgrading base docker image of ci by @haimasree in #265
- Machine executor added by @haimasree in #266
- Fixed date_release job by @haimasree in #267
- Add seqvec back to ci by @haimasree in #268
- Fixed kipoisplice by @haimasree in #270
- Add APARENT model by @Hoeze in #269
- Improved aparent dependencies by @haimasree in #271
- Updating preprocessing-variant-effects to reflect the current status in kipoi-veff2 intead of kipoi-veff by @haimasree in #272
- Adding resource class to machine instance by @haimasree in #273
- Fixed ci by @haimasree in #274
- Removing postprocessing field from model.yaml by @haimasree in #275
- Fixed ci by @haimasree in #276
- Adding singularity and docker container info by @haimasree in #277
- Add tests with singularity containers by @haimasree in #278
Full Changelog: v2021-06-02...v2021-11-15
epidermal_basset added
Merge pull request #246 from kipoi/fix-ci Fixed CI
Models' dependencies pinned
- Pinned pip version for all of the model groups
- Removal of unused packages from models.yaml (DeepBind)
- Removal of inactive models from rbp
- Updated notebook and documentation in Framepool
v2021-03-12
- DeepMEL has two new models
- DeepSEA/beluga variant effect scoring now has a new scoring function
v2021-03-02
All CIs fixed
v2019-09-01
Release of version 2019-09-01
v2019-08-25
Release of version 2019-08-25