v0.3.0

0.3.0 (2024-08-16)

What's Changed

• chore(deps): update actions/checkout digest to 692973e by @renovate in #568
• chore(deps): update actions/download-artifact digest to fa0a91b by @renovate in #569
• chore(deps): update actions/cache digest to 0c45773 by @renovate in #567
• chore(deps): update condaforge/mambaforge docker tag to v23.3.1 by @renovate in #434
• chore(deps): update docker/setup-qemu-action digest to 5927c83 by @renovate in #578
• chore(deps): update docker/metadata-action digest to 8e5442c by @renovate in #577
• chore(deps): update docker/build-push-action digest to ca052bb by @renovate in #575
• chore(deps): update codecov/codecov-action digest to e28ff12 by @renovate in #573
• chore(deps): update actions/upload-artifact digest to 0b2256b by @renovate in #571
• chore(deps): update actions/setup-python digest to 39cd149 by @renovate in #570
• chore(deps): update mikefarah/yq digest to ef6fb92 by @renovate in #580
• chore(deps): update google-github-actions/auth digest to 71fee32 by @renovate in #579
• chore(deps): update docker/login-action digest to 0d4c9c5 by @renovate in #576
• chore(deps): update pypa/gh-action-pypi-publish digest to fb9fc6a by @renovate in #581
• chore(deps): update determinatesystems/flakehub-push digest to d3b4b64 by @renovate in #574
• chore(deps): update rlespinasse/github-slug-action digest to 797d688 by @renovate in #582
• chore(bazel): make 3.11 default python by @cameronraysmith in #593
• docs(guides): provide example interactive results review by @cameronraysmith in #592
• feat(deps): make 3.11 default python by @cameronraysmith in #594
• docs: compare gene selection among model configurations by @cameronraysmith in #596
• feat(io): (de)serialize anndata objects by @cameronraysmith in #607
• feat(tasks): generate plots with preprocessing task by @cameronraysmith in #605
• fix(tests): use importlib resources to refer to fixture data by @cameronraysmith in #610
• feat(models): use sparse arrays for posterior samples by @cameronraysmith in #612
• feat(workflows): add dataclass for preprocessing outputs interface by @cameronraysmith in #623
• feat(workflows): track model metrics with results summaries by @cameronraysmith in #624
• chore: release 0.3.0 by @cameronraysmith in #625

Full Changelog: v0.2.0...v0.3.0

Features

• analyze: add function to extract top mae genes (508f1ba)
• flake: make python 3.11 default devshell (c7ed17b)
• io: add (de)serialization functions (6699308)
• io: add cluster module (b98ca30)
• io: add function to add duration to run info formatted json files (86cc9d7)
• io: add function to copy a list of files to a target directory (eb0b9f9)
• io: add module to combine json files (678c95d)
• io: add module to sparsify/densify array dictionaries (c1f15fc)
• io: generate model comparison tables (9582ab2)
• io: sparsify array dictionaries by default (e11412e)
• nbs: add support for model comparison to pancreas notebook (7cb5f77)
• nbs: initialize downsampled pancreas tutorial (f7a0006)
• plots: add interactive count histogram plot (68f3e16)
• 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: add qc plots to preprocessing task (5b40254)
• tasks: save loss data to csv (15c1dc9)
• tasks: save parameter posterior means to dataframe (90813c6)
• utils: add function to save parameter posterior means to dataframe (d3e4537)
• utils: construct anndata string diff (411defe)
• utils: log array data type with shape (eb769b5)
• workflows: add task to collect metrics for all data sets and models (b242f80)
• workflows: enable decks (d89a638)
• workflows: track model metrics with results summary (98f269f)
• workflows: update task interfaces to track metrics (02f4897)
• workflows: use PreprocessOutputs dataclass (1e5a223)

Bug Fixes

• analysis: get top mae genes by correlation bin (be165a7)
• analysis: remove cell marker comments (1b70c45)
• analyze: disable progress bar (44e7e41)
• bazel: add marker to args (63e0c5b)
• bazelignore: local venv (e5fa894)
• bazel: migrate tests <5 min to size medium (404025f)
• bazel: remove small/large duplicate test module (547af88)
• bazelversion: 7.0.2 -> 7.2.1 (d1a2ebe)
• cid: include MODULE.bazel in requirements cache key (9ec2174)
• cid: reenable bazel cache restore-keys (809370d)
• cid: set python versions to 3.11 (ef7a62e)
• cid: set sha-specific concurrency groups for workflow execution (30ad7ce)
• conda: transiently pin scipy <1.14.0 (f8f4e49)
• flake: python310 -> python311 (c5b609c)
• gcs: add function to download blob from uri (c20b5d1)
• gcs: add function to download path from uri (10f71d2)
• interfaces: resolve str | Path union to str (93d1422)
• 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: increase default sparsify threshold (6ba43a1)
• io: skip doctests that require gcp credentials (455e941)
• io: update required fields for serialization (73e4b86)
• 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 interactive review to guides contents (7e33abf)
• nbs: add parameter posterior estimates to pancreas results (65246de)
• nbs: add stub for preprocessing notebook (cf23251)
• nbs: auto-hide navigation (4d94b0b)
• nbs: disable ipynb (79a74df)
• nbs: escape apostrophes (420872c)
• nbs: flesh out interactive review (a827c71)
• nbs: indicate explicit output (6628265)
• nbs: move interactive guide to subfolder (eb6419a)
• nbs: move interactive review to 2nd guide (873a0f6)
• nbs: plot mitochondrial and ribosomal percentage histograms in preprocessing guide (a9cde59)
• nbs: pygments -> gruvbox syntax highlighting (ee9b6dc)
• nbs: separate md, mdx, and site configs (9c0f193)
• nbs: separate references to preprocessing and results (afc6bc9)
• nbs: set default syntax highlighter (f30c2b3)
• nbs: sync freeze (810286e)
• nbs: update dark css (261cdcf)
• nbs: update path to preprocessing notebook (682e9a3)
• nbs: use mathjax (81f4808)
• nbs: use subdirectory for pancreas tutorial (94427a8)
• nix: add workflows to check groups (be3645e)
• nix: explicit preferwheel for deps (06320e5)
• nix: make 3.11 default python in container images (4e95dbd)
• 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)
• pre-commit: remove pyupgrade (e3780dd)
• preprocess: disable progress bar (d3a5770)
• preprocess: remove unsupported kwarg (db44ae1)
• pyproject: disable slow tests and print durations (05e6507)
• pyproject: flytekit 1.13 (6ad23e7)
• pyproject: note intention to exclude markers associated with slow tests (057af3d)
• pyproject: pin conda-lock fmt <11.0 for libmambapy (d78a8f8)
• pyproject: shift python version bounds to 3.11 and 3.12 (fe1d4a8)
• pyproject: temporarily pin yanked matplotlib 3.9.1 (2dedb66)
• scripts: include json, html, md, tex in uploads (a157b27)
• scripts: update nbs build (fe20d09)
• 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: include preprocessing reports directory in outputs (aee79a1)
• 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)
• tasks: update ticks on loss plot axes (350499f)
• tests: account for updated postprocessing outputs interface (ed6a81f)
• tests: add in-memory fixtures used by plotting modules (41176ff)
• tests: mark slow tests in determinstic inference module (d3a5254)
• tests: remove gene number specification (32008d6)
• tests: set tmp path to preprocessing reports (1cfd403)
• tests: use importlib resources to refer to fixture data (7175c79)
• utils: use shape of ArrayLike in pretty printing dicts (918378c)
• workflows: add CombinedMetricsOutputs dataclass (c6f3e3c)
• workflows: add PreprocessOutputs dataclass (4fed2dd)
• workflows: disable flyte decks causing type error (5ca26ff)
• workflows: disable upload summary cache (c8b8548)
• workflows: explicitly include csv in model summary archive (22de101)
• workflows: remove top-level wrapper workflow (0ac37df)
• workflows: toggle data subset flag on (ceb7524)
• workflows: toggle data subset to default false (55ac13a)