v0.3.0-beta.2

0.3.0-beta.2 (2024-08-08)

Features

• analyze: add function to extract top mae genes (508f1ba)
• io: add cluster module (b98ca30)
• nbs: add support for model comparison to pancreas notebook (7cb5f77)
• nbs: initialize downsampled pancreas tutorial (f7a0006)
• plots: add normalized data to rainbow plot (7ddc5f0)
• plots: add option to plot log spliced data to rainbow plot (6226003)
• summarize: save gene ranking table to csv (98f5bd6)
• tasks: save parameter posterior means to dataframe (90813c6)
• utils: add function to save parameter posterior means to dataframe (d3e4537)

Bug Fixes

• analysis: get top mae genes by correlation bin (be165a7)
• analysis: remove cell marker comments (1b70c45)
• bazel: add marker to args (63e0c5b)
• bazel: migrate tests <5 min to size medium (404025f)
• bazel: remove small/large duplicate test module (547af88)
• cid: set sha-specific concurrency groups for workflow execution (30ad7ce)
• io: add doctest for get_remote_task_results (f4d8e7f)
• io: allow specification of a download filename prefix (d0d5439)
• io: include csv files in default model summary archive (8b7c809)
• io: use tmp dir fixture for compressedpickle doctests (f678036)
• make: run slow tests with test-cov-xml target (bc58fed)
• models: remove unused branching in generate_posterior_samples method (4a924e3)
• nbs: add parameter posterior estimates to pancreas results (65246de)
• nbs: add stub for preprocessing notebook (cf23251)
• nbs: separate references to preprocessing and results (afc6bc9)
• nbs: use subdirectory for pancreas tutorial (94427a8)
• nix: add workflows to check groups (be3645e)
• plots: add option to save gene ranking plot (50a71cf)
• plots: add option to save rainbow plot (ffdd829)
• plots: default to highest and lowest shared time correlation genes in summary plot (d5aae5c)
• plots: disable normalized data on summary plot (443ac27)
• plots: enable offset parameters in posterior distribution plots (fe25b4c)
• plots: ensure data is a dense array before flattening (feaa936)
• plots: ensure path for posterior predictive phase portraits (68493c2)
• plots: make parameter names an argument of posterior plot function (c2c35f5)
• plots: use cividis in plot posterior time (68c90ef)
• pyproject: note intention to exclude markers associated with slow tests (057af3d)
• pyproject: temporarily pin yanked matplotlib 3.9.1 (2dedb66)
• summarize: pareto_frontier_genes -> top_mae_genes (d5c3896)
• summarize: use mae percentiles and min genes per bin in marker gene selection (0dfef1e)
• tasks: declare skip preprocess doctest once (49be02f)
• tasks: download_dataset accepts Path type (846d5a7)
• tasks: enable nested mlflow runs (fcbbede)
• tasks: enable Path objects where applicable (4096175)
• tasks: remove ad hoc modification of posterior samples (7738f5c)
• tasks: remove manual figure write (29de76b)
• tasks: remove redundant logic to save rainbow plot in summarize task (591e759)
• tasks: remove unused t0 from model1 posterior samples (583f786)
• tasks: skip postprocess dataset xdoctest (d8a8fc1)
• tasks: update args and examples for summarize dataset (4a51e02)
• tests: add in-memory fixtures used by plotting modules (41176ff)
• tests: remove gene number specification (32008d6)
• workflows: disable flyte decks causing type error (5ca26ff)
• workflows: disable upload summary cache (c8b8548)
• workflows: explicitly include csv in model summary archive (22de101)
• workflows: toggle data subset flag on (ceb7524)