Pyrovelocity

[0.2.0-beta.14](https://github.com/pinellolab/pyrovelocity/compare/v0.2.0-beta.13...v0.2.0-beta.14) (2024-03-29)


Bug Fixes

* **bazel:** update test module list ([f9a38aa](https://github.com/pinellolab/pyrovelocity/commit/f9a38aa2be311cd256d7fbd7c54375b351a5616b))
* **docs:** update badges ([0a84010](https://github.com/pinellolab/pyrovelocity/commit/0a8401094953488ad4e77cd46bb3acf860c11953))
* **gitattributes:** linguist ignore Makefiles ([508bddd](https://github.com/pinellolab/pyrovelocity/commit/508bddd45cd7361f6f4bd4c7e239800a23924a99))
* **gitattributes:** linguist ignore nbs and reproducibility ([7c4f28d](https://github.com/pinellolab/pyrovelocity/commit/7c4f28d5d0eb1a6d449fac93a2b97928ed9be007))

[0.2.0-beta.13](https://github.com/pinellolab/pyrovelocity/compare/v0.2.0-beta.12...v0.2.0-beta.13) (2024-03-26)


Features

* **ci:** check and fast-forward merge PRs ([251e11f](https://github.com/pinellolab/pyrovelocity/commit/251e11f774e726e2afe50d61d31bfa616b561d7b))
* **help:** add help module ([d30f670](https://github.com/pinellolab/pyrovelocity/commit/d30f670a70ed211da06906f9587e12c82b7b5a44))
* **make:** add targets to build and serve nbs ([28e3779](https://github.com/pinellolab/pyrovelocity/commit/28e37793f8242298be7ef46c3da1a1884ee59486))
* **nbs:** add interlinks extension ([dc99563](https://github.com/pinellolab/pyrovelocity/commit/dc99563d00f2daa6170b30a18b7e72910d09a6fe))
* **nbs:** add sn extension ([7e4331c](https://github.com/pinellolab/pyrovelocity/commit/7e4331ce2f2d39fef91eba518e91725229153021))
* **nbs:** add user example to templates ([bbeceaf](https://github.com/pinellolab/pyrovelocity/commit/bbeceaf2e815dcd303936ac4d6b4d2df79198830))
* **nbs:** copy contributing ([c7f84d8](https://github.com/pinellolab/pyrovelocity/commit/c7f84d8b2790b0f132a3be046939b0213a247e63))
* **nbs:** enable api reference docs ([cf4e1a9](https://github.com/pinellolab/pyrovelocity/commit/cf4e1a950ca86aaf78c0a3e31d35a7d7501efcde))
* **nbs:** export ipynb format ([b174e95](https://github.com/pinellolab/pyrovelocity/commit/b174e95c256526a682e1a2d65cb47b08a60a85ae))
* **nbs:** init installation ([258fdc1](https://github.com/pinellolab/pyrovelocity/commit/258fdc1ec064527ca5a681e4eeb75c5df2abfe84))
* **pypi_template:** add workflow execution example ([c69767d](https://github.com/pinellolab/pyrovelocity/commit/c69767d04640e81ea5f1ebba2f193dba029af8a9))
* **pypi_template:** generate and display figure outputs ([a0111e2](https://github.com/pinellolab/pyrovelocity/commit/a0111e2f3765bbd98900229744e0aece8a1c92d4))
* **pypi_template:** include training and summary for two distinct model classes ([217a3fd](https://github.com/pinellolab/pyrovelocity/commit/217a3fdd5fa1ed2ea989ff511872c1ca9302d10a))
* **scripts:** add nbs build script ([59f708f](https://github.com/pinellolab/pyrovelocity/commit/59f708f2a47248ade1613422e628ab733f3dd4f6))
* **scripts:** init pypi template ([5ed5f10](https://github.com/pinellolab/pyrovelocity/commit/5ed5f103fa24f36e4faa60a7bcc4805d2e350a4d))
* **scripts:** pull _freeze from dvc cache during nbs build ([45d191b](https://github.com/pinellolab/pyrovelocity/commit/45d191bd3065d2797df79902f0a53056f572574e))
* **utils:** add class to suppress function output ([76af2cc](https://github.com/pinellolab/pyrovelocity/commit/76af2cc6d10361dfa2483ec6a0cd65d8f8dc4160))
* **utils:** add print_config_tree ([e3546df](https://github.com/pinellolab/pyrovelocity/commit/e3546dff0de4c8d6cf2d25b80b23d9b35561ba2f))
* **workflows:** add medium resources category to configuration ([aad47f4](https://github.com/pinellolab/pyrovelocity/commit/aad47f4e8aadb81d781edbc3003a2164b0caa31f))
* **workflows:** separate summarize cache version ([55ada29](https://github.com/pinellolab/pyrovelocity/commit/55ada29afd4e213f5823b558afa3d307f02c8732))


Bug Fixes

* **analyze:** add types to compute_volcano_data ([34885da](https://github.com/pinellolab/pyrovelocity/commit/34885daec571818aba5b6332007f7d30536032b3))
* **conda:** install pytorch from pytorch channel ([750a324](https://github.com/pinellolab/pyrovelocity/commit/750a324c41b0d0294cc7d07d4dcf0204714135fa))
* **containers:** use requirements-main.txt ([25a13dc](https://github.com/pinellolab/pyrovelocity/commit/25a13dcd80c7a68b14494e2998584f76d5eefe6c))
* **cytotrace:** remove a subset of unnecessary print statements ([1847cbd](https://github.com/pinellolab/pyrovelocity/commit/1847cbd63159f9b4925cc531845a5de468fb9b22))
* **dev:** add minimal/testing example config ([c7bd905](https://github.com/pinellolab/pyrovelocity/commit/c7bd905be7c7628a3e802bf69cc3e286aeaf1f01))
* **docs:** migrate history to CHANGELOG ([1204056](https://github.com/pinellolab/pyrovelocity/commit/12040563b33936408c4887346850089e6d4ff61e))
* **docs:** separate cool and warm logos ([b30e041](https://github.com/pinellolab/pyrovelocity/commit/b30e04122e14acc48294c311f4f8b86af10818f1))
* **docs:** sync description ([98fb385](https://github.com/pinellolab/pyrovelocity/commit/98fb385d003930232840d8a4d4b1be1569b26dd4))
* **docs:** update sphinx conf exclude pattern from colab to template ([4363b90](https://github.com/pinellolab/pyrovelocity/commit/4363b90c06a8130b1f46e4a76b7bd8749a8d995d))
* **dvc:** update remote path ([1476bc2](https://github.com/pinellolab/pyrovelocity/commit/1476bc2b002347805313c6c4cb5e6bdc551be8dd))
* **gitignore:** `*.*.md` and `_configuration.yaml` ([ab45036](https://github.com/pinellolab/pyrovelocity/commit/ab45036f0f0b07b9c3e14be60517c97903c86bd0))
* **gitignore:** only ignore top-level data folder by default ([8e9daf5](https://github.com/pinellolab/pyrovelocity/commit/8e9daf56d213698e4638c5856b714179b5b8f07e))
* **init:** reenable workflow-independent public interface ([fc2aae5](https://github.com/pinellolab/pyrovelocity/commit/fc2aae58cdb29db19d6b55c587456210c02bbed4))
* **make:** add passthrough render-notebook target ([465ebaa](https://github.com/pinellolab/pyrovelocity/commit/465ebaab0cc44bb9b68e6c61991d3c1df8af8092))
* **make:** add refresh target to remove cache ([93ccd25](https://github.com/pinellolab/pyrovelocity/commit/93ccd2546fd0375b31cbf86990061cadb968e9cf))
* **make:** add workflow-clean target ([b9c1780](https://github.com/pinellolab/pyrovelocity/commit/b9c1780d409589a8ccdff0d1ba85af99c2ebce7c))
* **make:** print workflow env vars before execution ([823d330](https://github.com/pinellolab/pyrovelocity/commit/823d3300ae121eda37cb86998d2e1363ab4cc733))
* **make:** write requirements-main ([a38380a](https://github.com/pinellolab/pyrovelocity/commit/a38380a4f7427fdcbd036aa8be7ad37127188d87))
* **nbs:** add make target to update `_freeze` directory ([91a7f03](https://github.com/pinellolab/pyrovelocity/commit/91a7f033b02a1999b3d637bf2fc1180a433f71f8))
* **nbs:** add plots to api docs ([d247958](https://github.com/pinellolab/pyrovelocity/commit/d2479580ca3f662ab8f8e7a728e82bd3f97c8a6d))
* **nbs:** add sync-nb make target to upload to gdrive ([9d4d7d0](https://github.com/pinellolab/pyrovelocity/commit/9d4d7d0ed1545421049dd62cc2e29945aad76ac8))
* **nbs:** link numpy ([df49123](https://github.com/pinellolab/pyrovelocity/commit/df49123447f6b58c6547d64ee249b40b1ada42de))
* **nbs:** migrate toc to header ([75bc1ae](https://github.com/pinellolab/pyrovelocity/commit/75bc1ae7463cbbf8748555c327dedbfef7147a0d))
* **nbs:** move introduction to tutorials ([5f02c73](https://github.com/pinellolab/pyrovelocity/commit/5f02c73d14f89a3d5a5da5181b6bdfcd61370a23))
* **nbs:** remove gh pages badge ([3574679](https://github.com/pinellolab/pyrovelocity/commit/3574679f183375b40bdcd53fab81334b05348e34))
* **nbs:** remove reference folder ([77abb60](https://github.com/pinellolab/pyrovelocity/commit/77abb6084ef69918842e736c8b408eace74238a9))
* **nbs:** soft-link to top-level CHANGELOG.md ([15f45ff](https://github.com/pinellolab/pyrovelocity/commit/15f45ffcb44af93e4bc43d120c088f10b3be2ae2))
* **nbs:** static preview port ([928a6cc](https://github.com/pinellolab/pyrovelocity/commit/928a6cc195190ce84b65d67aaa227f0d57dce6b5))
* **nbs:** temporarily link index to readme ([06216f7](https://github.com/pinellolab/pyrovelocity/commit/06216f7027a83f91c63950ab67b5bbce5dba9eff))
* **nbs:** update index ([8945de3](https://github.com/pinellolab/pyrovelocity/commit/8945de3be85f6f8ad5100d0803e39c5307a6f8dc))
* **nbs:** update section contents ([6883231](https://github.com/pinellolab/pyrovelocity/commit/6883231d1c48408d4d6cbc6973313d27b0b86b0a))
* **nbs:** use gdrive notebook in colab link ([fc760e6](https://github.com/pinellolab/pyrovelocity/commit/fc760e6a02b61ada321c7c5b3085450a2fd7f539))
* **plot_gene_ranking:** establish compatibility with adjusttext `1.1.1` ([cf37f8e](https://github.com/pinellolab/pyrovelocity/commit/cf37f8e0949ce4f005f58da146540028c582fd67))
* **plots:** add padding to plot gene ranking ([9b3fa5e](https://github.com/pinellolab/pyrovelocity/commit/9b3fa5e494f8308315d77f5c53d10f62037dfcc0))
* **plots:** add types to plot_gene_ranking ([8ed9a75](https://github.com/pinellolab/pyrovelocity/commit/8ed9a7591316bb6650a797c96d86dec9d0db3b6f))
* **plots:** add types to summarize gene selection ([deeaba5](https://github.com/pinellolab/pyrovelocity/commit/deeaba5d0aca93e418e758fe17675cde5cf85519))
* **plots:** close figure in plot_gene_selection_summary ([099e6fb](https://github.com/pinellolab/pyrovelocity/commit/099e6fbfa483e32e26dc9ca3dd7fa40d946d2eae))
* **plots:** close figure in plot_shared_time_uncertainty ([ea34035](https://github.com/pinellolab/pyrovelocity/commit/ea34035e701ecea897225320a4a36601b2bc5cba))
* **plots:** default to loading data for predictive sampling to cpu ([abcf58b](https://github.com/pinellolab/pyrovelocity/commit/abcf58b2d7a73c455234eb03cdaa77751812e8bd))
* **plots:** enforce types for plot_parameter_posterior_distributions ([8597820](https://github.com/pinellolab/pyrovelocity/commit/8597820f47ea4d79bfe9164809906d3df85f7e07))
* **plots:** enforce types for plot_vector_field_summary ([204db57](https://github.com/pinellolab/pyrovelocity/commit/204db573e3d163feb273b6d2b1b64dac573a4b64))
* **plots:** reenable refactored rainbowplot ([4c130ac](https://github.com/pinellolab/pyrovelocity/commit/4c130acfdee30d8e44140fa9461bc8bb92c00feb))
* **postprocess:** use logger for printing ([18206f7](https://github.com/pinellolab/pyrovelocity/commit/18206f710d3ac0dd413d6b27d248ac87283da9c4))
* **predictive:** use `data_model` input for data set model pairings ([666e48e](https://github.com/pinellolab/pyrovelocity/commit/666e48ec4517308759221d9f684db903b4546722))
* **preprocess:** close figure ([f776c0e](https://github.com/pinellolab/pyrovelocity/commit/f776c0e6a79db13bc4e8f6e55815c8cdd5e3cb82))
* **preprocess:** update docstring ([fc4a8b8](https://github.com/pinellolab/pyrovelocity/commit/fc4a8b817bbf5e605a3d1b59ebe9faaa0e0c64e3))
* **pypi_template:** add blank header cells ([46ecc14](https://github.com/pinellolab/pyrovelocity/commit/46ecc14581dc7b441df0a6499afeec3f6a0574a9))
* **pypi_template:** add exploration section ([1da0a53](https://github.com/pinellolab/pyrovelocity/commit/1da0a53e3b7ff214e0081ce26ed79f6c0d78ed11))
* **pypi_template:** collapse installation instructions in callout note ([266a940](https://github.com/pinellolab/pyrovelocity/commit/266a940632a8807bc06e2057a551e0b873204b84))
* **pypi_template:** remove unnecessary output capture ([562892e](https://github.com/pinellolab/pyrovelocity/commit/562892e33bfe2ae3daf221dd3bbf7fdc4086e338))
* **pypi_template:** sync with library updates ([954d242](https://github.com/pinellolab/pyrovelocity/commit/954d2426093ad8c067e53c5de956c9f50d0e8ed7))
* **pypi_template:** update frontmatter ([f8094b3](https://github.com/pinellolab/pyrovelocity/commit/f8094b3126652b19083d27216c47e620c0a8fd1b))
* **pypi_template:** update gitignore ([78c8447](https://github.com/pinellolab/pyrovelocity/commit/78c844716607eba762f1ac7a6907f5200993deb1))
* **pyrovelocity:** update dunder init ([421c1f4](https://github.com/pinellolab/pyrovelocity/commit/421c1f4ca0f320016f307539ba8a8d5038b7f220))
* **requirements:** rename to requirements-main ([ed50b4d](https://github.com/pinellolab/pyrovelocity/commit/ed50b4dd4eebf77e900ac4a9d59cd63fe236c28f))
* **scripts:** cd with subshell ([90423be](https://github.com/pinellolab/pyrovelocity/commit/90423beff87786e61021738b2d1757dc71ecbecc))
* **scripts:** comment examples authors ([8b48b48](https://github.com/pinellolab/pyrovelocity/commit/8b48b48bd08a85f58c5d6d5bcf37775d46419349))
* **scripts:** disable sudo ([073eeed](https://github.com/pinellolab/pyrovelocity/commit/073eeed0de45521621e1708ec4a8a21a44f911ad))
* **scripts:** use manual installation ([ba68cd0](https://github.com/pinellolab/pyrovelocity/commit/ba68cd06bd165c7cc0d7992d23b21c5a293c03f6))
* **scripts:** use poetry run ([74bc828](https://github.com/pinellolab/pyrovelocity/commit/74bc82829b6b3deffc265076d77fac2b100c22a6))
* **summarize:** check phase portrait cache before exiting ([6692a8a](https://github.com/pinellolab/pyrovelocity/commit/6692a8a0e3c12a5cf4f34167c38e06da4ebf1017))
* **summarize:** include selected genes in summary figure ([16fd344](https://github.com/pinellolab/pyrovelocity/commit/16fd344366f3b728f989d0990f42beebc01a41ed))
* **summarize:** respect typed interface to plot_vector_field_summary ([bac7aad](https://github.com/pinellolab/pyrovelocity/commit/bac7aad5aaf4ec968c160ed59dbe8b171d2cbe69))
* **summarize:** update shared time plot ([8477626](https://github.com/pinellolab/pyrovelocity/commit/84776267b8095b6a816d3174b5b68e2551408f65))
* **summarize:** update shared time plot font ([cdb1f69](https://github.com/pinellolab/pyrovelocity/commit/cdb1f691d501e4d10f40056b3d3d2dc997f64d5d))
* **summary:** support selected genes and marginal histograms ([8d38ccd](https://github.com/pinellolab/pyrovelocity/commit/8d38ccd14e01e6baad8dfd671590e89d45cb69ca))
* **train:** close figure ([31f508b](https://github.com/pinellolab/pyrovelocity/commit/31f508b0435cb2f8d837f7c7a92eda688e269f43))
* **train:** update docstring ([e958c45](https://github.com/pinellolab/pyrovelocity/commit/e958c4570b053735c07e331549871ce0ffb39633))
* **utils:** migrate clear_local_cache to workflows ([08a6463](https://github.com/pinellolab/pyrovelocity/commit/08a646338c6f589745fdbbf4dd8e1abfee365367))
* **workflows:** note migration to CalVer for cache versions ([0e0ac49](https://github.com/pinellolab/pyrovelocity/commit/0e0ac49a9f64b3330f0fc20a33afffed21f5844f))
* **workflows:** read cache flag from env var ([9488074](https://github.com/pinellolab/pyrovelocity/commit/94880740690e6bcda11f16047a0e3dc8c676835f))

[0.2.0-beta.12](https://github.com/pinellolab/pyrovelocity/compare/v0.2.0-beta.11...v0.2.0-beta.12) (2024-03-16)


Features

* **env:** add pyrovelocity-specific env vars ([6dfa69c](https://github.com/pinellolab/pyrovelocity/commit/6dfa69cc84878be201166c9231c5f800d601288a))
* **scripts:** copy gcs archives to drive ([a4eb5f5](https://github.com/pinellolab/pyrovelocity/commit/a4eb5f57b640204e0e4a7f45aa5ba55cca33190e))
* **workflows:** add upload summary task ([8693728](https://github.com/pinellolab/pyrovelocity/commit/8693728a701dcfde70d32ef3878ce9c36a17892e))
* **workflows:** expose testing and upload flags as environment variables ([9ed24f8](https://github.com/pinellolab/pyrovelocity/commit/9ed24f82f96e5dfbcf56194f56394f56e467d53d))
* **workflows:** use upload_results fields from each WorkflowConfiguration ([fbf4ea3](https://github.com/pinellolab/pyrovelocity/commit/fbf4ea3d0ab388b274262b2ff46532011ef29330))


Bug Fixes

* **cid:** add note on `use-gha-cache` ([6f79f33](https://github.com/pinellolab/pyrovelocity/commit/6f79f3323892eb432b8bb2e60fc4c1fb3d513cc0))
* **cid:** disable `use-gha-cache` ([db6bcda](https://github.com/pinellolab/pyrovelocity/commit/db6bcdade27ed8050bcb05d9136aa066ad91814b))
* **docs:** change feature branch to beta ([e113dcd](https://github.com/pinellolab/pyrovelocity/commit/e113dcd4efeb9ff8ff1068f9c024b80931631efa))
* **gcs:** return file url from upload_file_* ([7d5698e](https://github.com/pinellolab/pyrovelocity/commit/7d5698e670d6a6ec9071d964368ebfd010261d16))
* **readme:** change feature branch to beta ([3ce409a](https://github.com/pinellolab/pyrovelocity/commit/3ce409a7a957ff11d881b7716e2bb32d2d1284dd))
* **scripts:** get colab scripts from beta branch ([15a219b](https://github.com/pinellolab/pyrovelocity/commit/15a219b4c7036265f8896964e0f1bcfb7e16279c))

[0.2.0-beta.11](https://github.com/pinellolab/pyrovelocity/compare/v0.2.0-beta.10...v0.2.0-beta.11) (2024-03-14)


Features

* **actions:** add composite action for build_nix_image ([1f621ce](https://github.com/pinellolab/pyrovelocity/commit/1f621ce4361b27f7ada1a7ddd52b35a184d67a2d))
* **cid:** add job to publish nix flake ([5a52753](https://github.com/pinellolab/pyrovelocity/commit/5a52753a5f8df2df3db4afc3bc13096f698d667d))
* **cid:** add python 3.11 to test-python matrix ([1896c0d](https://github.com/pinellolab/pyrovelocity/commit/1896c0db59a364f77d4e9d3f0df70719f3ccd752))
* **flake:** add devCore lightweight devShell ([96fdfe3](https://github.com/pinellolab/pyrovelocity/commit/96fdfe32030d6489f75c8d08713c5d0558a2a993))
* **flake:** add latex and pandoc ([bff7410](https://github.com/pinellolab/pyrovelocity/commit/bff7410f872624ab4aeccd0a871aff518c668bd2))
* **flake:** add quarto to devPackages ([d6e3eca](https://github.com/pinellolab/pyrovelocity/commit/d6e3eca29041d3f830a385e912441a344087712a))
* **flake:** use refactored poetryOverrides ([7f37d36](https://github.com/pinellolab/pyrovelocity/commit/7f37d369baf6d5775f3c4b13b69208adbb93535e))
* **interfaces:** add AcceleratorType Enum for future replacement of `use_gpu` type annotations ([0122307](https://github.com/pinellolab/pyrovelocity/commit/0122307ad7ae2133f5f66d1ae037f671ca8e6ee5))
* **io:** add fsspec interface ([eb3ae02](https://github.com/pinellolab/pyrovelocity/commit/eb3ae020f6a32a19b3278bf7205d76b382757599))
* **io:** add gcs interface ([1491a1b](https://github.com/pinellolab/pyrovelocity/commit/1491a1b642173d9a0d806cacdfa113ca466b7591))
* **io:** add googleapiclient interface ([a7a36b6](https://github.com/pinellolab/pyrovelocity/commit/a7a36b641888c432c6e71be51d06eb7fba82957a))
* **io:** create archive from filtered directory ([814f184](https://github.com/pinellolab/pyrovelocity/commit/814f18469dae48ff09c0b3f276f4fda2665f5ed6))
* **main_configuration:** add dataclasses for outputs ([abdd8e0](https://github.com/pinellolab/pyrovelocity/commit/abdd8e0b1f98b081f5bf5612d839376376b71e7c))
* **make:** add target to build nix default package ([692b4f7](https://github.com/pinellolab/pyrovelocity/commit/692b4f70389ece30129b52faa319b60f0fd39e95))
* **nix-config:** refactor poetryOverrides ([13714f1](https://github.com/pinellolab/pyrovelocity/commit/13714f1a22bca391d7355918bf14e70d750a436c))
* **nix:** add btop to coreDevPackages ([95f060f](https://github.com/pinellolab/pyrovelocity/commit/95f060fc6a2baaa2de49a86dffdd4822ead43403))
* **scripts:** add colab ([3ff98b9](https://github.com/pinellolab/pyrovelocity/commit/3ff98b9a357315046aa45dcb890101fe1eb3d2ba))
* **scripts:** add literate template ([2cfbd4d](https://github.com/pinellolab/pyrovelocity/commit/2cfbd4dd3dff1c4146c67985722113c76d03c134))
* **scripts:** add manuscript template ([ce65847](https://github.com/pinellolab/pyrovelocity/commit/ce658473da8d2930e7ccca4141433aa421680593))
* **scripts:** extract imported packages from library ([8957327](https://github.com/pinellolab/pyrovelocity/commit/8957327b4a7c0fff5fcced91e11061d9bb2f84e2))
* **summarize:** add summarize task module ([4c1adbf](https://github.com/pinellolab/pyrovelocity/commit/4c1adbfbb8ff458cc908ef8cd6b348bd38fe23a3))
* **tests:** add utils package ([d38a219](https://github.com/pinellolab/pyrovelocity/commit/d38a2194940eb6330450e9cb8fd742fbf3d87aa6))
* **utils:** add function to save anndata counts to dataframe file ([f9d6a91](https://github.com/pinellolab/pyrovelocity/commit/f9d6a919e551668c915892f86a6fb9239a9d10f0))
* **vscode:** add debug test launcher for library code ([abef67f](https://github.com/pinellolab/pyrovelocity/commit/abef67f6b3a3d61187d4440dff2c76855c4f5580))
* **workflows:** add model summary task ([1446119](https://github.com/pinellolab/pyrovelocity/commit/1446119665ee3d092f2ee1b79e4cdedab6701144))
* **workflows:** draft notebooks execution workflow ([34b8f47](https://github.com/pinellolab/pyrovelocity/commit/34b8f471877bb6379f2ba1425f898c656da86c42))
* **workflows:** expose `overwrite_cache` via ExecutionContext ([9c1a633](https://github.com/pinellolab/pyrovelocity/commit/9c1a633dc15f9f23eaa87571853264a0fbaeb1e1))


Bug Fixes

* **actions:** nix store gc 5 -> 3G ([59f74bf](https://github.com/pinellolab/pyrovelocity/commit/59f74bff4f2ba41c44211a92d4445e90995735a8))
* **actions:** reenable post-build garbage collection ([37f1d78](https://github.com/pinellolab/pyrovelocity/commit/37f1d78ddf41d264fc69d746eebba0218f4b4948))
* **actions:** restrict nix gc ([d8c68e9](https://github.com/pinellolab/pyrovelocity/commit/d8c68e9c34c290d6e89b893f49442eb43ebc3e04))
* **actions:** use skopeo instead of docker ([b5b908e](https://github.com/pinellolab/pyrovelocity/commit/b5b908ed5aa34ad211f64b6b15a39b554a848f30))
* **app:** update action versions ([283d6c6](https://github.com/pinellolab/pyrovelocity/commit/283d6c62d3f0b487fbff5449b6206ec7059c1bf4))
* **cid:** add clean nix store to publish release images ([a2daf9a](https://github.com/pinellolab/pyrovelocity/commit/a2daf9a7d3522a1348ff4cb0f7cc96b838fdfebc))
* **cid:** add GAR env to publish release images ([790045a](https://github.com/pinellolab/pyrovelocity/commit/790045a45cdfb5ba106d23d24bb7249d73e2f68a))
* **cid:** add names to test-nix job steps ([ad25df9](https://github.com/pinellolab/pyrovelocity/commit/ad25df94e6c2e4f1f96045f23bfb192bf32d4606))
* **cid:** do not rerun on draft submission ([5314c8d](https://github.com/pinellolab/pyrovelocity/commit/5314c8d76aae3a6a154abfd10cef6a0ff984e425))
* **cid:** ignore changes to colab workflow ([3c36296](https://github.com/pinellolab/pyrovelocity/commit/3c36296dfe7ec71f308f858320755b64cfeda986))
* **cid:** ignore explicit lock files ([1552086](https://github.com/pinellolab/pyrovelocity/commit/155208612c776f95a6bad65b6efe661db66be12b))
* **cid:** image builds condition on NOT dev mode ([947bfa0](https://github.com/pinellolab/pyrovelocity/commit/947bfa0b2dbe19a0f118610dc5dd96d102ee3120))
* **cid:** include python version in test-python concurrency group ([9411e8f](https://github.com/pinellolab/pyrovelocity/commit/9411e8f1f41e71fb84401ff7ca618f35a690b28d))
* **cid:** publish flake on release ([72c0841](https://github.com/pinellolab/pyrovelocity/commit/72c08415db3d1ca4dc59ef2a2389aba8f8590a2e))
* **cid:** reduce root reserve ([94ec314](https://github.com/pinellolab/pyrovelocity/commit/94ec31467c48d701ab1ee5fe203abbe3c8622b40))
* **cid:** reenable restriction to x86_64-linux ([1d0320e](https://github.com/pinellolab/pyrovelocity/commit/1d0320ea36a2358ec0f37e1fdff046f152815f80))
* **cid:** remove deprecated nix image build matrix ([1aa74f0](https://github.com/pinellolab/pyrovelocity/commit/1aa74f09eb58ce295b69ffdf83a31db497eb4426))
* **cid:** test-nix maximize build space ([43600cb](https://github.com/pinellolab/pyrovelocity/commit/43600cb334879c73376596a6c97824c866fba9c7))
* **cid:** update test-nix nix build comments ([e054a60](https://github.com/pinellolab/pyrovelocity/commit/e054a60f9b9f3772545a150b7c3bcee7a28d1f34))
* **cid:** use dev-mode label ([2a4f469](https://github.com/pinellolab/pyrovelocity/commit/2a4f469179fac1589557f615a4143d713f7510f8))
* **cid:** use local nix cache ([ba638f6](https://github.com/pinellolab/pyrovelocity/commit/ba638f6893c13d5fe4410d5ca64a34eb07d68444))
* **cid:** use local nix cache ([f929dbd](https://github.com/pinellolab/pyrovelocity/commit/f929dbd0b20c570c4b54a7ffe7e8dc682982211e))
* **colab:** set cuda 12.2 ([f8c6a73](https://github.com/pinellolab/pyrovelocity/commit/f8c6a7334f9875a4974e59aa7811dd421079f2e1))
* **colab:** set unique path for constructor script ([aeff7c6](https://github.com/pinellolab/pyrovelocity/commit/aeff7c66c3e0d78b009d5e462fac11e44317bf70))
* **colab:** update action versions ([88bd978](https://github.com/pinellolab/pyrovelocity/commit/88bd978c70bdd423ffb1a702defd7a561e2ae34c))
* **conda:** default to python 3.10 ([c093849](https://github.com/pinellolab/pyrovelocity/commit/c093849bf372cc7b9eac269a53bccd258a6d9da3))
* **conda:** move python version to top ([fec219b](https://github.com/pinellolab/pyrovelocity/commit/fec219b7a1ab1350277bb2c31906c413ef0154ca))
* **data:** lint f-strings ([6324327](https://github.com/pinellolab/pyrovelocity/commit/63243273ad01e57362d5d4c3c58b99886b0cd946))
* **data:** remove call to copy method ([979110a](https://github.com/pinellolab/pyrovelocity/commit/979110a790df5fad6dd0e561834ff9edc75d407e))
* **data:** set default adata None and handle ([2a267e0](https://github.com/pinellolab/pyrovelocity/commit/2a267e00ef17116f2f01cb0927b8ec88d9425f75))
* **direnv:** update containers watch_path ([4e622d3](https://github.com/pinellolab/pyrovelocity/commit/4e622d3bbbfb15af3c2a786f3d89d184cc12f556))
* **direnv:** update pkgs watch_path ([84b526c](https://github.com/pinellolab/pyrovelocity/commit/84b526c624a892e93908283f45afb05bd36f42ed))
* **direnv:** update poetry watch_file path ([ae3db70](https://github.com/pinellolab/pyrovelocity/commit/ae3db70fe7fbc1d7f7ca1d329419d37d3e44e1a9))
* **examples:** add install-tinytex make target ([f1f7523](https://github.com/pinellolab/pyrovelocity/commit/f1f7523fee44f897ed1912a4b20eaaf4fd8d1977))
* **examples:** force removal of _files dir ([518567f](https://github.com/pinellolab/pyrovelocity/commit/518567f7d03a4c102dca139508cee4611e615d59))
* **examples:** ignore .quarto ([bc4d21a](https://github.com/pinellolab/pyrovelocity/commit/bc4d21a65e19a89948ec419780c37bd947469602))
* **examples:** set html font ([3df5652](https://github.com/pinellolab/pyrovelocity/commit/3df5652aceb79c63933c5c1e11f2587e9ca38850))
* **examples:** set install-extensions deps ([e034add](https://github.com/pinellolab/pyrovelocity/commit/e034addbc636142359d694a444addfcceafe50eb))
* **examples:** support render without execution ([9b6458e](https://github.com/pinellolab/pyrovelocity/commit/9b6458e825857c7c6d8bd1536df361cd0205e0c3))
* **execute:** add random suffix to remote prod execution version ([4553adf](https://github.com/pinellolab/pyrovelocity/commit/4553adff706d388ed67428732d767ca7c5c46d8d))
* **flake:** add extraEnv vars to makeContainerConfig ([1219d86](https://github.com/pinellolab/pyrovelocity/commit/1219d869a81b392c2c9c33212d54ff501ea08495))
* **flake:** enable ssl for default build ([b832d65](https://github.com/pinellolab/pyrovelocity/commit/b832d65fe7d94b237a2b87df77981dbfcfe712ab))
* **flake:** preferWheel for tensorstore ([29118fb](https://github.com/pinellolab/pyrovelocity/commit/29118fbeac06c00f9752c6840970a80a8f278b17))
* **flake:** provide required tex packages ([535d4c4](https://github.com/pinellolab/pyrovelocity/commit/535d4c475012cac848a51fe9a85e06ec70efe98e))
* **flake:** reenable train_model test on Linux ([e748df3](https://github.com/pinellolab/pyrovelocity/commit/e748df3e29b846886a390b465a3daf58df52051a))
* **flake:** remove texliveSmall from devPackages ([01f12b4](https://github.com/pinellolab/pyrovelocity/commit/01f12b448e5fcdc89a459a09563301aba0b2609a))
* **flake:** reset appBuildInputs to none ([d172d09](https://github.com/pinellolab/pyrovelocity/commit/d172d09aff71e9ad71e20e78169074af8634e2c5))
* **flake:** restrict nvitop to x86_64-linux ([d84dc84](https://github.com/pinellolab/pyrovelocity/commit/d84dc8419bc9741b8ce8e998513cd483a01dc629))
* **flake:** restrict torch nvidia overrides to x86_64-linux systems ([7877359](https://github.com/pinellolab/pyrovelocity/commit/7877359ad63db198f8bbc334822a37517df39933))
* **flake:** revert unstable code-server unavailable for aarch64-darwin ([647cc10](https://github.com/pinellolab/pyrovelocity/commit/647cc107c3379420b4412c67e5bea83325c36fd1))
* **flake:** set QUARTO_PYTHON var in devshell ([e368179](https://github.com/pinellolab/pyrovelocity/commit/e368179b12fb435dee52c6d264627840aaa7ed2b))
* **flake:** switch to unstable for code-server ([70096cd](https://github.com/pinellolab/pyrovelocity/commit/70096cdf387ca391f8c5ad6b291d95bbc1abdf12))
* **flake:** tensorstore requires setuptools ([24522eb](https://github.com/pinellolab/pyrovelocity/commit/24522eb0f63bae687fe6caf4ca49f38da832e2e5))
* **flake:** update checkPhase noting Darwin failure ([980a0fd](https://github.com/pinellolab/pyrovelocity/commit/980a0fddcdc459c0976547000c8d83f871c248a9))
* **flake:** use `./nix/poetry` ([736a757](https://github.com/pinellolab/pyrovelocity/commit/736a757d46ef22fda77b4cc12702a745f6184870))
* **genes:** update logging ([5a80f86](https://github.com/pinellolab/pyrovelocity/commit/5a80f86d68b9c42debd0d0b1f9bc407ff3a4d8b4))
* **gitignore:** ignore top-level reports dir ([94d42c6](https://github.com/pinellolab/pyrovelocity/commit/94d42c6b267dc038559a41245d02c1fe4b90b894))
* **gitignore:** move sample dev pod configs ([f77416e](https://github.com/pinellolab/pyrovelocity/commit/f77416eae6e36d9dfc491c9ca817cd8ef39490bd))
* **interfaces:** declare dataclasses when TYPE_CHECKING ([7576b4d](https://github.com/pinellolab/pyrovelocity/commit/7576b4d745a1bcdf327dbfa4fbb1dec09d0406a3))
* **io:** declare interface ([44b6006](https://github.com/pinellolab/pyrovelocity/commit/44b6006d9125faed6974942b9c4a3d9dd3ce4fb9))
* **io:** use PathLike and Path objects for paths ([6593afd](https://github.com/pinellolab/pyrovelocity/commit/6593afd35aec2b02ec3ea5afff06383564aa6c8d))
* **labels:** change workflow-mode-dev to dev-mode ([c0c7d8f](https://github.com/pinellolab/pyrovelocity/commit/c0c7d8f5929e4fe1ec876d942cd1ca4d51306660))
* **main_workflow:** update logging ([3f162e1](https://github.com/pinellolab/pyrovelocity/commit/3f162e1f9149868a54847b47f3e2fb46863599f8))
* **make:** add docs-clean ([430940a](https://github.com/pinellolab/pyrovelocity/commit/430940a81aac9f05917d50c118a5e2db0ce9aba4))
* **make:** add target to call make in subdirs ([d09b4db](https://github.com/pinellolab/pyrovelocity/commit/d09b4dbda503c264f6fe2398d75f5bd49a6b550a))
* **make:** add target to get source archive hash ([95768f9](https://github.com/pinellolab/pyrovelocity/commit/95768f9a43ca6d6e6cbc54cfb52dcb9e2846efd5))
* **make:** add targets to clear local cache ([f588cfe](https://github.com/pinellolab/pyrovelocity/commit/f588cfe6ed3da2b0d3ead97db082602ebb1d9a03))
* **make:** clear local cache for parameterized dataset name ([dc0d9bd](https://github.com/pinellolab/pyrovelocity/commit/dc0d9bd7986506661f6eec12d6f7adb499335a9c))
* **make:** remove reports with workflow-clean-outputs ([7f78b46](https://github.com/pinellolab/pyrovelocity/commit/7f78b4602a6f776583e745efb3eed1393df6cd6a))
* **make:** update ratchet `0.7.0` ([5337a8b](https://github.com/pinellolab/pyrovelocity/commit/5337a8b1332864367b57d864374eaa36e351c44a))
* **make:** use pyrovelocity cache ([c1bf2b4](https://github.com/pinellolab/pyrovelocity/commit/c1bf2b45ba856c3b7719793802ceb0b8224b62db))
* **mergify:** update bot account for merge ([17ac41a](https://github.com/pinellolab/pyrovelocity/commit/17ac41a73ce4caf3010c5cc6888067d8928f1277))
* **mergify:** update condition check names ([8457594](https://github.com/pinellolab/pyrovelocity/commit/845759498dd6ce55bf537a6f773120af4c41b346))
* **nix:** reenable impure rev from GIT_SHA var ([a028a02](https://github.com/pinellolab/pyrovelocity/commit/a028a0286e82e2dc770f2cb3cecec3df4c0614ba))
* **nix:** refactor pkgs to support lightweight devCore devShell ([712b044](https://github.com/pinellolab/pyrovelocity/commit/712b044d46e3ef61d5c936f3e4cc5cd468712a1f))
* **notebooks:** remove deprecated system calls ([ccd5e65](https://github.com/pinellolab/pyrovelocity/commit/ccd5e65d90093dc5f494e512b6c3d373535a25f5))
* **parameters:** comment verbose print statements ([3e3f79f](https://github.com/pinellolab/pyrovelocity/commit/3e3f79f85361b85bf334cba6cd747da3648191a9))
* **plots:** address use of deprecated `draw_all` ([1631655](https://github.com/pinellolab/pyrovelocity/commit/1631655694db1940353d10d359b7876fa391ae10))
* **plots:** transform integer names to strings ([40fc653](https://github.com/pinellolab/pyrovelocity/commit/40fc65319aabcf7dbbeda1eef4966e5ec1bd4411))
* **postprocess:** add types for multiple outputs ([0523e73](https://github.com/pinellolab/pyrovelocity/commit/0523e73fa87db2eac3078dd731f56c2f03a7f5f7))
* **postrpocess:** lint imports ([b55e373](https://github.com/pinellolab/pyrovelocity/commit/b55e37317c95a4b4d24905f032e880bb1b8e5f9a))
* **predictive:** comment verbose print statements ([d5160b6](https://github.com/pinellolab/pyrovelocity/commit/d5160b633ead51b6ede22c33ea5899d75525e4e1))
* **preprocess:** make log-transformation explicit ([ce489dd](https://github.com/pinellolab/pyrovelocity/commit/ce489dd40ab8da826a53df47d6bd05d7b36bd36e))
* **preprocess:** update logging ([32c42d8](https://github.com/pinellolab/pyrovelocity/commit/32c42d839a32289efdd95c74244ad890760fabb9))
* **pyproject:** add workflows deps ([687e8c2](https://github.com/pinellolab/pyrovelocity/commit/687e8c2b676d39462cff28a615824647d57be5a4))
* **pyproject:** allow python 3.11 installs ([5f42c26](https://github.com/pinellolab/pyrovelocity/commit/5f42c26743e64e668d8b7937f5426cb4ef81e141))
* **pyproject:** annotate lint rules ([75f6431](https://github.com/pinellolab/pyrovelocity/commit/75f643180a82f761720014eb1ee17ee460f5bd17))
* **pyproject:** convert all pins to lower bounds ([8a5db53](https://github.com/pinellolab/pyrovelocity/commit/8a5db53042c7ff2182bba60f0856a140fb5c1529))
* **pyproject:** downgrade flax to remove tensorstore ([6c86994](https://github.com/pinellolab/pyrovelocity/commit/6c86994f5df2f761a6ad013c1ad2322368bba86b))
* **pyproject:** pin conda-lock output to python 3.10 ([8558b3e](https://github.com/pinellolab/pyrovelocity/commit/8558b3e8ab279f28139f889721c7ac9fe56084ec))
* **pyproject:** remove desert ([92bdd92](https://github.com/pinellolab/pyrovelocity/commit/92bdd92032512cd396845b8196a94bc4243a7b65))
* **pyproject:** remove marshmallow ([e650341](https://github.com/pinellolab/pyrovelocity/commit/e650341923b227b6075eacb4b2b7100bc03eec0a))
* **pyproject:** remove unused deps ([e6f66a9](https://github.com/pinellolab/pyrovelocity/commit/e6f66a9c54b8d8ddfea22356862af2f46872e620))
* **pyproject:** update extras ([5d6063a](https://github.com/pinellolab/pyrovelocity/commit/5d6063a9f0bedd4c624c685b78cf0d93c5256636))
* **pyproject:** update flax ([6b664bf](https://github.com/pinellolab/pyrovelocity/commit/6b664bf8c79ede2ddf653a2e998dce095e95cdf6))
* **summarize:** save anndata dataframe in models directory ([e2078e3](https://github.com/pinellolab/pyrovelocity/commit/e2078e3031a665ee93230b85ac82fd8e7596ae8b))
* **summarize:** update interface and add types for multiple outputs ([0dddefd](https://github.com/pinellolab/pyrovelocity/commit/0dddefd149a7d04914e71cb7e50a876e9eceedb6))
* **test_data:** test failure of mocked download ([f18c159](https://github.com/pinellolab/pyrovelocity/commit/f18c1599539feaeffa01902842e4e2a845b9e602))
* **time:** remove unused comments ([3b7eab8](https://github.com/pinellolab/pyrovelocity/commit/3b7eab83eb36b0317a7b6378f339dbd5356b9787))
* **train:** `use_gpu` with lightning AcceleratorRegistry keywords ([0d708b6](https://github.com/pinellolab/pyrovelocity/commit/0d708b6ab8b6ae7115eed2b07958809b1d278d4c))
* **trainer:** migrate epoch-end hooks for lightning >2 ([3b68fff](https://github.com/pinellolab/pyrovelocity/commit/3b68fff956b8f8e1ac5b10d8611613dd7474deb6)), closes [/www.github.com/Lightning-AI/pytorch-lightning/pull/16800#discussion_r1110256813](https://github.com/pinellolab//www.github.com/Lightning-AI/pytorch-lightning/pull/16800/issues/discussion_r1110256813)
* **trainer:** update logging ([66db9d3](https://github.com/pinellolab/pyrovelocity/commit/66db9d328f2a207cda716071d8177a011a5de70b))
* **train:** log anndata contents before and after training ([96ec859](https://github.com/pinellolab/pyrovelocity/commit/96ec8591b206cb126c9ea5f0661abe6c42d0eecf))
* **uncertainty:** comment verbose print statements ([f776b80](https://github.com/pinellolab/pyrovelocity/commit/f776b807a0e3b4e266473a536b40d63329ed8828))
* **uncertainty:** transform integer names to strings ([cb65bff](https://github.com/pinellolab/pyrovelocity/commit/cb65bffe8c11f0541c481eae8ea8a8ac0ef1d1a2))
* **utils:** remove deprecated print output from doctest ([9443192](https://github.com/pinellolab/pyrovelocity/commit/9443192dc9e46711d2b4525a248a00867059468a))
* **utils:** remove unused function ([7bf4ffd](https://github.com/pinellolab/pyrovelocity/commit/7bf4ffddd1ca5361fdd5fa9fd34180da2e7cd78a))
* **utils:** temporarily reenable initialization function ([5d4d6dc](https://github.com/pinellolab/pyrovelocity/commit/5d4d6dc79ffa660129df461358c1951c640f781a))
* **utils:** update logging ([107e2c1](https://github.com/pinellolab/pyrovelocity/commit/107e2c1979e00fe953f33fa7f2019c54609d35e4))
* **utils:** use numbers ABCs in output types ([9d28080](https://github.com/pinellolab/pyrovelocity/commit/9d28080c56f3678f274d6b2342b1908ac52efc3b))
* **vector_fields:** comment verbose print statements ([b455e85](https://github.com/pinellolab/pyrovelocity/commit/b455e85afe5cf4acbea189a9fee9eedda14d9ded))
* **velocity_module:** `use_gpu` with lightning AcceleratorRegistry keywords ([2871370](https://github.com/pinellolab/pyrovelocity/commit/28713703db6b4d2a6d6de8f1eac7d00b5d45843f))
* **velocity_module:** remove deprecated print output from doctest ([d283a00](https://github.com/pinellolab/pyrovelocity/commit/d283a0015b6a8baf34716607a392804e079a6c5f))
* **velocity_module:** update logging ([ba81901](https://github.com/pinellolab/pyrovelocity/commit/ba819019b2a721495ac9c156f05cf82a3cee232b))
* **velocity:** `use_gpu` with lightning AcceleratorRegistry keywords ([b53a3c4](https://github.com/pinellolab/pyrovelocity/commit/b53a3c43ce19502a78034b03060c4e2ad621d64c))
* **velocity:** update logging ([21699b3](https://github.com/pinellolab/pyrovelocity/commit/21699b3f96d4988ad6f22e770eec55e476966e69))
* **workflows:** add dunder main to cli ([d0aabe6](https://github.com/pinellolab/pyrovelocity/commit/d0aabe6107f5d8e6a2fc5d432181034c0e6c6759))
* **workflows:** add flag to test exclusively with simulated data ([dc261fd](https://github.com/pinellolab/pyrovelocity/commit/dc261fd12cbd374d0e430a03b12157e7383b9f6f))
* **workflows:** add summarizing task resources to configuration ([45cd18a](https://github.com/pinellolab/pyrovelocity/commit/45cd18a71a5a4aef07ec624d58e5b9bce08c807d))
* **workflows:** append configurations ([a68270e](https://github.com/pinellolab/pyrovelocity/commit/a68270ebdca42fcf1a083533e948a77ad331ded6))
* **workflows:** lint docstring ([ae7b3f4](https://github.com/pinellolab/pyrovelocity/commit/ae7b3f463e4ce134839a02aa80192f1bed7608cf))
* **workflows:** reenable CACHE_FLAG on summarize task ([f563b24](https://github.com/pinellolab/pyrovelocity/commit/f563b242cd8bb2bfa72ff558e10c497901948a0a))
* **workflows:** set git refs logging to debug level ([fc13152](https://github.com/pinellolab/pyrovelocity/commit/fc13152fdf587508ad20e8a72add60b8bee67e67))
* **workflows:** set number of posterior samples in testing mode to 4 ([25c8bd9](https://github.com/pinellolab/pyrovelocity/commit/25c8bd9590a164fc98083d197130fb5ccfea4b17))
* **workflows:** simplify simulated-only selection ([ba3baeb](https://github.com/pinellolab/pyrovelocity/commit/ba3baeb5db93fc20ea845af79b0c3d059937aeda))
* **workflows:** use new outputs dataclasses ([120f70f](https://github.com/pinellolab/pyrovelocity/commit/120f70ffcb022af12c16a713428353e1ebd8d77d))

[0.2.0-beta.10](https://github.com/pinellolab/pyrovelocity/compare/v0.2.0-beta.9...v0.2.0-beta.10) (2024-02-24)


Features

* **cid:** skip image build if one with commit sha tag already exists ([cba38e4](https://github.com/pinellolab/pyrovelocity/commit/cba38e47b91536c3c5274f6c83f118e8ed2a8873))
* **containers:** add dyngen container ([de3abae](https://github.com/pinellolab/pyrovelocity/commit/de3abae66fb03893dfc70e5a0e6e46b4ff8641e1))
* **containers:** add script to generate simulated data ([05b49c2](https://github.com/pinellolab/pyrovelocity/commit/05b49c2683f88d5a080b471846055b311892d65c))
* **dev:** add hpa config ([dadb4d1](https://github.com/pinellolab/pyrovelocity/commit/dadb4d195eb321995140af9f89476e5e79aa14bf))
* **dev:** add job config ([da03a27](https://github.com/pinellolab/pyrovelocity/commit/da03a275db2510394153fdfb56db6fb147435818))
* **dev:** update example config for job ([c956103](https://github.com/pinellolab/pyrovelocity/commit/c95610374ab983f5eaafc29aa88b87d7ab2c892a))
* **execution_utils:** support nested dataclasses ([a382204](https://github.com/pinellolab/pyrovelocity/commit/a382204ffda4eb79cb1759495500944bc3ab9c79))
* **flake:** add GAR images ([eaaddfe](https://github.com/pinellolab/pyrovelocity/commit/eaaddfe68f0430e98b413c9244399b7750ac3488))
* **flake:** add time to sysPackages ([8d1c994](https://github.com/pinellolab/pyrovelocity/commit/8d1c99469a585bab821508d95b6e5d555127656d))
* **make:** add target to build dyngen image ([1c46950](https://github.com/pinellolab/pyrovelocity/commit/1c4695029040768d936a62f47c16aba5695ce896))
* **make:** add target to copy file to cluster pod ([7d22b0c](https://github.com/pinellolab/pyrovelocity/commit/7d22b0c0390c2340406a2634f05b8d8ef00fd66a))
* **make:** add target to disable zsh `time` reserved word ([be99bd9](https://github.com/pinellolab/pyrovelocity/commit/be99bd92183613252c73e2c601001856b34dd29e))
* **make:** add target to forward port from dev pod ([f9cff22](https://github.com/pinellolab/pyrovelocity/commit/f9cff2243194228ed5ce0f6db4e3a552c4d0b7a3))
* **make:** add target to toggle local virtualenvs ([b96691d](https://github.com/pinellolab/pyrovelocity/commit/b96691d087766dfb7d8ba39ac466e0f2ebb2f31b))
* **postprocess:** add postprocess module ([d565e27](https://github.com/pinellolab/pyrovelocity/commit/d565e27d0008a42b2a82707890a612cdb86276ac))
* **preprocess:** allow subsets of obs and vars ([93a0465](https://github.com/pinellolab/pyrovelocity/commit/93a04657ec681ab40a9e44a7ca7906e52c05413a))
* **utils:** add function to generate public api candidates ([402259e](https://github.com/pinellolab/pyrovelocity/commit/402259ef2aa05dbcec741bb4a20fdb291437fb9a))
* **workflows:** add postprocessing task ([5654b6c](https://github.com/pinellolab/pyrovelocity/commit/5654b6cf0c29e48d25b20b8bc1e336684adef319))


Bug Fixes

* **analyze:** define public interface ([0ee8e58](https://github.com/pinellolab/pyrovelocity/commit/0ee8e58ab190bcde6f3f91c4409317d4fe1e1e4b))
* **cid:** add nix envs for GAR images ([5fda3ee](https://github.com/pinellolab/pyrovelocity/commit/5fda3ee2183608ed82fcb79581d03776a20e855e))
* **cid:** set build volume mount path `/nix` ([d542fa6](https://github.com/pinellolab/pyrovelocity/commit/d542fa68932872aaff52b70cf6e0c20355335774))
* **cid:** use base64 encoded SA creds ([29af74e](https://github.com/pinellolab/pyrovelocity/commit/29af74ea40ccacca23ccd8e0750a4cf126f0dc0d))
* **colab:** add maximize build space ([9d014b1](https://github.com/pinellolab/pyrovelocity/commit/9d014b1d383912e584a21f01d5ea2cd94f68e5b3))
* **colab:** increase root reserve ([37058af](https://github.com/pinellolab/pyrovelocity/commit/37058afd140e3988c0e74f2ef7ef7d25a5fcdbf8))
* **conda:** remove redundant cuda installation ([d61866b](https://github.com/pinellolab/pyrovelocity/commit/d61866b95beb93a3c29a7e5fc37172e0cda857dc))
* **data:** update public interface ([54932e6](https://github.com/pinellolab/pyrovelocity/commit/54932e6ca879193d56d37a1a16fd44a2adc59bb5))
* **dev:** config pvc name ([2d1d08b](https://github.com/pinellolab/pyrovelocity/commit/2d1d08becbb4f5306edabeb11e23218cf5eab7c0))
* **dev:** remove default latest tag from image spec [no ci] ([24a1ff4](https://github.com/pinellolab/pyrovelocity/commit/24a1ff48a81cafc7fbe0f4df86bc2f7e581f4fd7))
* **dev:** set default pvc name to dev ([0a656eb](https://github.com/pinellolab/pyrovelocity/commit/0a656eb4ffa00edca19a303559c898e4f26e2a84))
* **dev:** set update strategy to recreate ([f79a958](https://github.com/pinellolab/pyrovelocity/commit/f79a9583af7dc86cee7ebbd15a1c67e4c2e1e7ac))
* **dev:** update config to use job vs deployment ([cd7537f](https://github.com/pinellolab/pyrovelocity/commit/cd7537f8477fabac423ce0a70c47318dff268727))
* **dev:** use config pvc name in deployment ([3027f0f](https://github.com/pinellolab/pyrovelocity/commit/3027f0f15b1bf096886ba5e3b4ab24e9cc5902f2))
* **dev:** use config pvc name in job ([77e0ca5](https://github.com/pinellolab/pyrovelocity/commit/77e0ca55fe19ab5c7e05324482f400cfda76dcae))
* **dev:** use config pvc name in pvc ([57310ca](https://github.com/pinellolab/pyrovelocity/commit/57310ca7c7222a873941facb1df1cd552ca35d2b))
* **execute:** print fallback logger exceptions ([2f98d2e](https://github.com/pinellolab/pyrovelocity/commit/2f98d2eab103c66301148e59c74e3d37631ba7ea))
* **execute:** remove unused comments ([1dbd3f8](https://github.com/pinellolab/pyrovelocity/commit/1dbd3f8d2fa135fa4d2eae81852f26edc6addafd))
* **flake:** use base64 encoded SA creds ([1dea556](https://github.com/pinellolab/pyrovelocity/commit/1dea556377879a7de0d1e4c547649a8c6b94a519))
* **gitignore:** *-sa.json ([9bd3132](https://github.com/pinellolab/pyrovelocity/commit/9bd3132ab52c064c9089e7592cb7c18f7634bc05))
* **gitignore:** all *dev.cue ([08c0108](https://github.com/pinellolab/pyrovelocity/commit/08c010872d8edfe127cbed34a2edef9fd5f31d01))
* **interfaces:** define public interface ([28113b6](https://github.com/pinellolab/pyrovelocity/commit/28113b6267cb655378f2db0520921e63d5c4cf33))
* **logging:** set local log level ([8ee8513](https://github.com/pinellolab/pyrovelocity/commit/8ee85138c525228f3fd803a0bbd805b46b721738))
* **main_configuration:** enable testing of primary data sets ([5912daf](https://github.com/pinellolab/pyrovelocity/commit/5912daf989adb85d5ab0a2103c3fd2019bc33bbf))
* **main_configuration:** remove `list[DataClass]` fields from `WorkflowConfiguration` ([016d885](https://github.com/pinellolab/pyrovelocity/commit/016d885aa120f9a06a945250fe35eddd7f68cb8c))
* **main_configuration:** remove resource tuples ([36fe9dd](https://github.com/pinellolab/pyrovelocity/commit/36fe9dd987b919bc3fdd9df6ce78c4a24c874c67))
* **main_workflow:** construct training configurations explicitly ([3f9f12c](https://github.com/pinellolab/pyrovelocity/commit/3f9f12c4e8532c24936a6364fc5dad0b68cf5aca))
* **main_workflow:** reenable testing for primary data sets ([5f04a8c](https://github.com/pinellolab/pyrovelocity/commit/5f04a8c1796a6857155f0bd3a2cd9820aedc3d3a))
* **main_workflow:** set cache parameters from constants ([d247c75](https://github.com/pinellolab/pyrovelocity/commit/d247c75000d9d10ade59faeb2bc3d3c6a13ebae4))
* **main_workflow:** specify accelerator type constant ([d93d863](https://github.com/pinellolab/pyrovelocity/commit/d93d8633bf4e032d56566dfdc49568359ad6a7aa))
* **make:** comment ghsecrets for encoded GAR SA creds ([ed954dc](https://github.com/pinellolab/pyrovelocity/commit/ed954dc20a97804750f0909c57e860c55b516375))
* **models:** use tmp_path fixture for model data ([e17bf9b](https://github.com/pinellolab/pyrovelocity/commit/e17bf9beb209c3e0ae4613bde77c3048a98960bc))
* **postprocess:** ensure `data_model_path` exists ([3cff34f](https://github.com/pinellolab/pyrovelocity/commit/3cff34ff599e58b816ca484d9e78479ccf412b9b))
* **preprocess:** add pca rep if not present ([96afc5b](https://github.com/pinellolab/pyrovelocity/commit/96afc5b11171825223566fbf2067a57771a10e84))
* **preprocess:** ensure n_vars > n_pcs ([a892487](https://github.com/pinellolab/pyrovelocity/commit/a8924876525c2b580b9cfff3dcc024fb8cb6e66e))
* **preprocess:** host data set parameters in interface ([f51a098](https://github.com/pinellolab/pyrovelocity/commit/f51a0989b1664a876b408d71280675fa1a98f4d8))
* **preprocess:** specify public api ([4114d9d](https://github.com/pinellolab/pyrovelocity/commit/4114d9d0c4d0434258f71a5982ea63ccecfd38ba))
* **pyrovelocity:** add dunder main to launch cli as module ([ff5b553](https://github.com/pinellolab/pyrovelocity/commit/ff5b553e75928259840d2125214fc3144e594616))
* **train:** move data set parameters to preprocess ([0a0ea5f](https://github.com/pinellolab/pyrovelocity/commit/0a0ea5fc9c83c8c02d604e821d691f835003a71f))
* **train:** update interface ([52e33da](https://github.com/pinellolab/pyrovelocity/commit/52e33da9b42630f32d8c673705a6a688185a7603))
* **train:** use tmp_path fixture for loss plot ([6af93ea](https://github.com/pinellolab/pyrovelocity/commit/6af93eaee91fc49640259050e6daff8b9d2ccbad))
* **utils:** specify public api ([5e325d9](https://github.com/pinellolab/pyrovelocity/commit/5e325d98411612d6716a5eaa4d7d096237b1b7f4))
* **velocity_model:** remove debug logging of plate sizes ([4ea3f4c](https://github.com/pinellolab/pyrovelocity/commit/4ea3f4c60c9f9ecfc188613c5e612c6ee205f727))
* **workflows:** update training parameters in main configuration ([984255b](https://github.com/pinellolab/pyrovelocity/commit/984255ba0816077bb004e8df278794da5169411c))

[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))