v0.1.3

Changes

🚀 Features

• fix: run individual summarize stages in parallel (#409) @cameronraysmith
• retrain across all data sets with model 1 (#412) @cameronraysmith
• pin dvc >3.0 (#372) @cameronraysmith
• train model 2 with sample-based enumeration (#370) @cameronraysmith
• add shared time markers to phase portraits (#359) @qinqian
• add pbmc5k data set (#358) @cameronraysmith
• use predictive with one time point and 30 posterior samples from the … (#348) @qinqian
• add bone marrow data set (#344) @cameronraysmith
• compute shared time-distance correlation (#341) @cameronraysmith
• label pbmc10k clusters (#338) @cameronraysmith
• add comparison of angle and magnitude uncertainties (#336) @qinqian
• data set prediction from inferred time (#333) @qinqian
• update gene selection and parameter distribution estimates (#318) @cameronraysmith
• integrate gene selection with parameter distribution estimates (#312) @cameronraysmith
• add parameterized count threshold (#305) @cameronraysmith
• enable rclone in ci (#303) @cameronraysmith
• update figure 3 (#301) @cameronraysmith
• add cluster-conditional distribution plots (#298) @lijc0804
• add script to upload run data to drive (#296) @cameronraysmith
• update figure summary (#289) @qinqian
• add violin plots for uncertainty measurements (#282) @lijc0804
• add pipeline stages for larry auxiliary data (#280) @cameronraysmith
• add hypersphere distribution divergence (#278) @cameronraysmith
• add parallel execution to single-node pipeline (#270) @cameronraysmith
• add draft for distributed pipeline (#264) @cameronraysmith
• build gpu-specific docker image (#262) @cameronraysmith
• Reproduce on all Larry-related datasets and generate figureS3_extra (#259) @lijc0804
• update embedding space comparison (#253) @qinqian
• add differentiated larry (#251) @lijc0804
• add magnitude and pca space uncertainties evaluation (#249) @qinqian
• Add the summarization on PBMC10k (#243) @lijc0804
• preprocess and train model on pbmc10k (#241) @lijc0804
• add shared time uncertainty plot to summarize stages (#216) @qinqian
• train mono / neu / multi subsets of larry (#225) @lijc0804
• build and deploy review application (#223) @cameronraysmith
• preprocess and train with LARRY data (#214) @cameronraysmith
• add function to estimate criticality index (#209) @cameronraysmith
• add raw count data histograms to app (#207) @cameronraysmith
• write h5 files to compressed dfs for app consumption (#203) @cameronraysmith

🪲 Fixes

• fix: pin versions for model1 computations (#408) @cameronraysmith
• use infer_discrete for posterior predictive plots (#375) @qinqian
• use Trace_ELBO (disable exact enumeration) (#367) @qinqian
• update pbmc10k data set download (#244) @lijc0804

🐎 Performance

• retrain across all data sets with model 1 (#412) @cameronraysmith
• compare PCA and UMAP Rayleigh on minimal gene set projection (#335) @qinqian

🚨 Testing

• add single-node pipeline test sandbox (#267) @cameronraysmith
• add pipeline stages for plotting simulated data (#192) @cameronraysmith
• add pipeline stages for training simulated data (#190) @cameronraysmith
• add pipeline stage for preprocessing simulated data (#185) @cameronraysmith
• add pipeline stage for generating simulated data (#182) @cameronraysmith

👷 Continuous Integration

• disable dependabot (#420) @cameronraysmith
• configure renovate (#417) @renovate
• refactor _get_fn_args_from_batch (#397) @cameronraysmith
• add config yaml to drive output (#329) @cameronraysmith
• update pipeline ci timeout (#327) @cameronraysmith
• enable rclone in ci (#303) @cameronraysmith
• build gpu-specific docker image (#262) @cameronraysmith
• automate deployment of review application (#228) @cameronraysmith
• CML PR for master 91df43a (#410) @cameronraysmith
• fix: ignore reports [skip ci] (#326) @cameronraysmith
• CML PR for master 629feb2 (#307) @cameronraysmith

📚 Documentation

• plot angle uncertainty metrics (#236) @qinqian
• add figures for shared time uncertainty (#232) @qinqian
• update demo code in README (#196) @lijc0804

🔨 Refactoring

• refactor _get_fn_args_from_batch (#397) @cameronraysmith
• add DataReview class to app (#212) @cameronraysmith
• add updated pipeline lock; reduce model 1 pkl output (#168) @qinqian

📦 Dependencies

• chore(release): v0.1.3 (#428) @cameronraysmith
• chore(deps): update dependency click to v8.1.7 (#422) @renovate
• disable dependabot (#420) @cameronraysmith
• configure renovate (#417) @renovate
• Bump nox-poetry from 1.0.2 to 1.0.3 in /.github/workflows (#373) @dependabot
• Bump actions/checkout from 3 to 4 (#414) @dependabot
• fix: pin versions for model1 computations (#408) @cameronraysmith
• Bump sphinx-autodoc-typehints from 1.23.0 to 1.23.3 in /docs (#360) @dependabot
• Bump pypa/gh-action-pypi-publish from 1.8.6 to 1.8.7 (#361) @dependabot
• Bump release-drafter/release-drafter from 5.23.0 to 5.24.0 (#362) @dependabot
• updates for compatibility with cml 0.19.1 (#365) @cameronraysmith
• Bump codecov/codecov-action from 3.1.3 to 3.1.4 (#258) @dependabot
• Bump nbsphinx from 0.9.1 to 0.9.2 in /docs (#310) @dependabot
• Bump setuptools from 67.6.1 to 67.7.2 (#257) @dependabot
• Bump etils from 1.2.0 to 1.3.0 (#247) @dependabot
• Bump sphinx from 6.2.1 to 7.0.1 in /docs (#255) @dependabot
• Bump myst-parser from 1.0.0 to 2.0.0 in /docs (#347) @dependabot
• Bump gcsfs from 2023.4.0 to 2023.5.0 (#256) @dependabot
• Bump dvc from 2.55.0 to 2.58.0 (#286) @dependabot
• Bump furo from 2023.3.27 to 2023.5.20 in /docs (#284) @dependabot
• Bump pypa/gh-action-pypi-publish from 1.8.5 to 1.8.6 (#240) @dependabot
• Bump importlib-metadata from 6.5.0 to 6.6.0 (#220) @dependabot
• Bump werkzeug from 2.2.3 to 2.3.3 (#239) @dependabot
• Bump ipython from 8.12.0 to 8.13.1 (#238) @dependabot
• Bump alembic from 1.10.3 to 1.10.4 (#235) @dependabot
• Bump identify from 2.5.22 to 2.5.23 (#230) @dependabot
• Bump pynndescent from 0.5.8 to 0.5.10 (#226) @dependabot
• Bump optax from 0.1.4 to 0.1.5 (#219) @dependabot
• Bump dvc from 2.54.0 to 2.55.0 (#231) @dependabot
• Bump sphinx from 6.2.0 to 6.2.1 in /docs (#218) @dependabot
• Bump pip from 23.1.1 to 23.1.2 in /.github/workflows (#217) @dependabot
• Bump sqlalchemy from 2.0.9 to 2.0.10 (#205) @dependabot
• Bump yarl from 1.8.2 to 1.9.1 (#204) @dependabot
• Bump sphinx from 6.1.3 to 6.2.0 in /docs (#200) @dependabot
• Bump nox from 2022.11.21 to 2023.4.22 in /.github/workflows (#199) @dependabot
• Bump pip from 23.1 to 23.1.1 in /.github/workflows (#198) @dependabot
• Bump dvc-studio-client from 0.6.2 to 0.8.0 (#194) @dependabot
• Bump hypothesis from 6.72.0 to 6.72.1 (#195) @dependabot
• Bump soupsieve from 2.4 to 2.4.1 (#188) @dependabot
• Bump codecov/codecov-action from 3.1.2 to 3.1.3 (#193) @dependabot
• Bump tornado from 6.2 to 6.3 (#187) @dependabot
• Bump flax from 0.6.8 to 0.6.9 (#183) @dependabot
• Bump diskcache from 5.5.1 to 5.6.1 (#179) @dependabot
• Bump scmrepo from 1.0.1 to 1.0.2 (#178) @dependabot
• Bump importlib-metadata from 6.3.0 to 6.5.0 (#180) @dependabot
• Bump pytest from 7.3.0 to 7.3.1 (#175) @dependabot
• Bump psutil from 5.9.4 to 5.9.5 (#174) @dependabot
• Bump cryptography from 40.0.1 to 40.0.2 (#173) @dependabot
• Bump attrs from 22.2.0 to 23.1.0 (#172) @dependabot
• Bump hypothesis from 6.71.0 to 6.72.0 (#171) @dependabot
• Bump mizani from 0.8.1 to 0.9.0 (#170) @dependabot
• Bump pip from 23.0.1 to 23.1 in /.github/workflows (#169) @dependabot

Full Changelog: v0.1.2...v0.1.3