chore(release): 0.2.0-beta.9

CHANGELOG.md

@@ -1,5 +1,75 @@
 # Changelog
 
+## [0.2.0-beta.9](https://github.com/pinellolab/pyrovelocity/compare/v0.2.0-beta.8...v0.2.0-beta.9) (2024-02-03)
+
+
+### Features
+
+* **api:** typecheck train_model and allow path inputs ([fbd34bf](https://github.com/pinellolab/pyrovelocity/commit/fbd34bf949d6c6350ed471413e2747d85ee66772))
+* **conftest:** provide global fixture to file for sample data ([409d96d](https://github.com/pinellolab/pyrovelocity/commit/409d96dc5c8a63a036cb4b2892b5793d23280e4f))
+* **data:** add load_anndata_from_path ([7d43e29](https://github.com/pinellolab/pyrovelocity/commit/7d43e29867de48620a95ee652f0209eb6054c392))
+* **data:** support subsetting during data download ([fa066cd](https://github.com/pinellolab/pyrovelocity/commit/fa066cd4224857f0b409daaf80ccca356c3a5c13))
+* **flake:** update torch >2 ([6b838d3](https://github.com/pinellolab/pyrovelocity/commit/6b838d3e575593be9858d0ad87d239baeb2939f0))
+* **interfaces:** collect dataclass interfaces ([f2c6ea9](https://github.com/pinellolab/pyrovelocity/commit/f2c6ea95aa30da89c96804489e09711782cf84a8))
+* **main_workflow:** add model training task ([4ca67b4](https://github.com/pinellolab/pyrovelocity/commit/4ca67b466160f4c174d42e69d1a146a225fea9f3))
+* **main_workflow:** use dataclass interfaces ([2324654](https://github.com/pinellolab/pyrovelocity/commit/2324654a9b72b5ca9f763732f119235b8b40e1b3))
+* **make:** add cluster-shell target ([23c3d5e](https://github.com/pinellolab/pyrovelocity/commit/23c3d5e2c922c08c712f37e2126ca33fe15b4b4d))
+* **preprocess:** refactor for compatibility with dataclass interface ([19c7b68](https://github.com/pinellolab/pyrovelocity/commit/19c7b6840fbd4e7095f66837e7ace1e8b5924777))
+* **pyproject:** add requests-mock for testing ([42db104](https://github.com/pinellolab/pyrovelocity/commit/42db1046fd595b6a5d0c063c1997a859733d4a39))
+* **pyproject:** upgrade stable dependencies ([7698cf7](https://github.com/pinellolab/pyrovelocity/commit/7698cf717fdc5f58177b7f99d32bb1a008d89fde))
+* **test_data:** add tests for data module methods ([dcd8276](https://github.com/pinellolab/pyrovelocity/commit/dcd8276454caf575af69fdc941372b8e6622e2e0))
+* **train:** add training script for workflow usage ([5fcf4c3](https://github.com/pinellolab/pyrovelocity/commit/5fcf4c3a11b8874cc56f319273c07425ee33ad08))
+* **workflows:** add pbmc68k, pons, and larry data sets ([41c18e2](https://github.com/pinellolab/pyrovelocity/commit/41c18e27145438eed55c961f521727004ac1f8f3))
+
+
+### Bug Fixes
+
+* **api:** discard returned adata in doctest ([78456f8](https://github.com/pinellolab/pyrovelocity/commit/78456f8347180f93c0ba23a037ac9a58db290015))
+* **bazel:** remove unused test modules ([a724853](https://github.com/pinellolab/pyrovelocity/commit/a724853e38ec24130a4f3a8645bec8379bda7bbd))
+* **cid:** enable cachix cache for build-nix-images job ([63e545f](https://github.com/pinellolab/pyrovelocity/commit/63e545f996b8c21f839d6f8fb5e9ad99c55e364a))
+* **cid:** enable cachix for release images ([49075ef](https://github.com/pinellolab/pyrovelocity/commit/49075efec9ef254ad0b7db979545261dfa2cfd83))
+* **cid:** enable cachix for test-nix job ([f533984](https://github.com/pinellolab/pyrovelocity/commit/f5339843df816d6acc2003f6a60f12ed33ced47f))
+* **cid:** increase root reserve and swap ([8035847](https://github.com/pinellolab/pyrovelocity/commit/8035847797377a9aca86ac910493206af3c8c89f))
+* **cid:** increase swap size ([3ea04b7](https://github.com/pinellolab/pyrovelocity/commit/3ea04b7aad945f8cdd70470c5496317f824434f0)), closes [/github.com/actions/runner-images/discussions/7188#discussioncomment-6750749](https://github.com/pinellolab//github.com/actions/runner-images/discussions/7188/issues/discussioncomment-6750749)
+* **cid:** reduce swap ([87cb626](https://github.com/pinellolab/pyrovelocity/commit/87cb626ab1d1bbff9283c01d531543df5dc81de4))
+* **cid:** remove debug ([95a88f3](https://github.com/pinellolab/pyrovelocity/commit/95a88f304718ec437325c8fc9ef7b3ed72d3c291))
+* **cid:** update codecov-action to v4 ([e0dbda3](https://github.com/pinellolab/pyrovelocity/commit/e0dbda36ff820f94c71faeacbc656cf6dc270993))
+* **cid:** update nix-installer to main ([98a0b78](https://github.com/pinellolab/pyrovelocity/commit/98a0b78d51a0881b9bbb984f934229746c1bd9f7))
+* **cspell:** update dictionary ([119f436](https://github.com/pinellolab/pyrovelocity/commit/119f4365e5841d0937c41b5e04807c2626b7d16e))
+* **data:** make var names unique ([8fb44f8](https://github.com/pinellolab/pyrovelocity/commit/8fb44f866c125ac16ef2d8f1b5a7aa3bd12180cc))
+* **dev:** add example security context overrides ([4ac343d](https://github.com/pinellolab/pyrovelocity/commit/4ac343d9873f86a3df35061b10c0aa6018c13a6b))
+* **execution_utils:** construct dataclasses given defaults ([fa95db3](https://github.com/pinellolab/pyrovelocity/commit/fa95db3391d54f83edec43ad877451c5a44bc7a5))
+* **gitignore:** models directory ([f6e4208](https://github.com/pinellolab/pyrovelocity/commit/f6e420818983f657bab04f2197b4767fba275194))
+* **gitignore:** only ignore top-level models directory ([8ad7a6d](https://github.com/pinellolab/pyrovelocity/commit/8ad7a6d86203d7fa9521cd80f9c3eee623368e9c))
+* **interfaces:** use train_dataset from train module ([76b5563](https://github.com/pinellolab/pyrovelocity/commit/76b55638abcf81d8fce115c3951a522179baa0e5))
+* **magic-nix-cache:** revert v3 update ([d1c85f8](https://github.com/pinellolab/pyrovelocity/commit/d1c85f8be3bd240d809be09f0320072d45b81036))
+* **main_workflow:** update docstrings ([e1f726d](https://github.com/pinellolab/pyrovelocity/commit/e1f726dcebb14b0efed4a037b90ac6780309e694))
+* **main_workflow:** use NamedTuple class ([618c430](https://github.com/pinellolab/pyrovelocity/commit/618c430427023ee1c3c79d2c1b5bc95ee78a5497))
+* **make:** exclude additional modules from dep graph ([58850a4](https://github.com/pinellolab/pyrovelocity/commit/58850a4dad16b4eace9080c2741f863f049d801a))
+* **make:** filter io and configuration from pydeps ([ddf6d7d](https://github.com/pinellolab/pyrovelocity/commit/ddf6d7df10d058cc1ef6628a002141608f79c57d))
+* **make:** move pod ID extraction inside cluster-shell target ([7e31b54](https://github.com/pinellolab/pyrovelocity/commit/7e31b54f74fe961504da53d363b86572e3da373f))
+* **make:** remove unused pydeps exclusion ([0df6346](https://github.com/pinellolab/pyrovelocity/commit/0df63464fd78a746b2da6b891aa7a812e03f7f15))
+* **make:** set cachix in gh vars/secrets ([f5098eb](https://github.com/pinellolab/pyrovelocity/commit/f5098eb9746baf8957e473728531efa43148d9cf))
+* **preprocess:** remove completed TODOs ([970ac7a](https://github.com/pinellolab/pyrovelocity/commit/970ac7a44598cffc8cbde7fdcc94731c9f53b732))
+* **pyproject:** pytest ignore reproducibility folder ([434efae](https://github.com/pinellolab/pyrovelocity/commit/434efae8fa78e34c504c78e631e2a0110b02b0a5))
+* **requirements-cpu:** remove outdated hashed version ([3a36c6e](https://github.com/pinellolab/pyrovelocity/commit/3a36c6e36c4111d09cc3e1340c7da3b166c33980))
+* **setup_environment:** update setup-pandoc pin ([24a8ef4](https://github.com/pinellolab/pyrovelocity/commit/24a8ef417e1582cc2afa8ceb4f04cf15d3797314))
+* **trainer:** cast categorical/integers as floats for log-transformation ([62e7fd5](https://github.com/pinellolab/pyrovelocity/commit/62e7fd5491cbfafd1115539504fc51f05001dd56))
+* **train:** update import path in doctest ([a8f50d0](https://github.com/pinellolab/pyrovelocity/commit/a8f50d051dd6a398dceb43589a4b7c83603a773c))
+* **transcription_dynamics:** enable type-checking ([88e496c](https://github.com/pinellolab/pyrovelocity/commit/88e496c78eb92f171803984b6463c69977c646c7))
+* **utils:** comment unused functions ([1c05fa2](https://github.com/pinellolab/pyrovelocity/commit/1c05fa243ae875c712d06a874d2870aa04cd338b))
+* **utils:** update AnnData type import ([42d21d9](https://github.com/pinellolab/pyrovelocity/commit/42d21d98bf5fdb392b09401be701cd566b3cfeeb))
+* **velocity_model:** handle likelihood not implemented ([e5d06d2](https://github.com/pinellolab/pyrovelocity/commit/e5d06d2a57025ca7b48dd125d4701119cdae5236))
+* **velocity_model:** remove optional type defaults for observations ([7b3a9bd](https://github.com/pinellolab/pyrovelocity/commit/7b3a9bdd77782f11642b798d6075a727e377c1f8))
+* **velocity_model:** set u0/s0 types to RNAInputType ([d12e0dd](https://github.com/pinellolab/pyrovelocity/commit/d12e0dd1394a8cdaa26f3b8f4a116a88de293a96))
+* **velocity_model:** update imports ([87386a1](https://github.com/pinellolab/pyrovelocity/commit/87386a1204e2a9d58d0c4b251fbff8ce9dedefd6))
+* **velocity:** cast categorical/integers as floats for log-transformation ([6e1ab7f](https://github.com/pinellolab/pyrovelocity/commit/6e1ab7fe9cc0f455fb6de396a7a83ed202f66835))
+* **vscode:** disable coverage to respect debugging breakpoints ([48dd4b8](https://github.com/pinellolab/pyrovelocity/commit/48dd4b8bd8a70967f649e990255ed028b4d147f8)), closes [/github.com/microsoft/vscode-python/issues/693#issuecomment-367848085](https://github.com/pinellolab//github.com/microsoft/vscode-python/issues/693/issues/issuecomment-367848085)
+* **workflows:** enable cache for training tasks ([86b9333](https://github.com/pinellolab/pyrovelocity/commit/86b9333c2e35be693c4945afb713530384c54d54))
+* **workflows:** increase resources for preprocessing and training tasks ([b0e81b1](https://github.com/pinellolab/pyrovelocity/commit/b0e81b1e3449132d7e5efcbe1fb2a3b0a34aee95))
+* **workflows:** set preprocess data path ([ecde0fa](https://github.com/pinellolab/pyrovelocity/commit/ecde0fa7b4585dee175bcb58b92058ec695e1947))
+* **workflows:** set task resource limits ([7416521](https://github.com/pinellolab/pyrovelocity/commit/7416521d8178783e573de4e4646027b45e60bb8b))
+
 ## [0.2.0-beta.8](https://github.com/pinellolab/pyrovelocity/compare/v0.2.0-beta.7...v0.2.0-beta.8) (2024-01-26)
 
 ### Features

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyrovelocity"
-version = "0.2.0b8"
+version = "0.2.0b9"
 packages = [{ include = "pyrovelocity", from = "src" }]
 description = "A multivariate RNA Velocity model to estimate future cell states with uncertainty using probabilistic modeling with pyro."
 authors = ["pyrovelocity team"]