v0.4.0-beta.4

0.4.0-beta.4 (2024-08-21)

Features

• workflows: add accelerator_type to WorkflowConfiguration (d306c48)
• workflows: use WorkflowConfiguration accelerator_type to override train_model accelerator (1978a25)

Bug Fixes

• io: expose density threshold parameter in CompressedPickle.save (c8b0cf3)
• nix: update ctan packages (028fa53)
• sparsity: decrease default density threshold to 0.3 (9d8eee1)
• workflow: remove manual definition of L4 GPUAccelerator (7d0da7e)
• workflows: add extra large training resource requests and limits (468bc6b)
• workflows: remove unused training arguments (5598ef6)
• workflows: reset constants to default values (70dc44e)
• workflows: reset training configurations list (4f4bb3a)

v0.4.0-beta.3

0.4.0-beta.3 (2024-08-19)

Features

• workflows: enable larry data model selection (57d27d3)
• workflows: enable pbmc68k model selection (8a6c997)

Bug Fixes

• cid: ignore push to reproducibility directory (d2bcf68)
• dvc: specify ignored subdirectory (9359211)
• workflows: increase timeouts for long-running tasks (cda7d32)
• workflows: remove unused imports (21ac5df)

v0.4.0-beta.2

0.4.0-beta.2 (2024-08-18)

Features

• workflows: add human bone marrow configuration (fdda157)
• workflows: add pbmc10k configuration (a36ad8e)
• workflows: add pbmc5k configuration (c11cd9c)
• workflows: enable execution for human bone marrow data (c118a5c)
• workflows: enable execution for pbmc10k data (43e0658)
• workflows: enable execution for pbmc5k data (db73f75)
• workflows: enable execution for pons data (3b2ef4b)

Bug Fixes

• workflows: set dev mode to use dev image tag (8e2037c)

v0.4.0-beta.1

0.4.0-beta.1 (2024-08-17)

Features

• workflows: add larry monocyte precursor configuration (168af3e)
• workflows: add larry multilineage configuration (0232207)
• workflows: add larry neutrophil precursor configuration (055d1e0)
• workflows: enable execution for larry monocyte precursor data (8464429)
• workflows: enable execution for larry multilineage data (d0321ca)
• workflows: enable execution for larry neutrophil precursor data (441d9e9)

Bug Fixes

• cid: set hydra outputs artifact name from set-variables outputs (32e400f)
• io: increase default compression level for posterior samples (160f857)
• io: write data sets modified on download (560e31f)
• workflows: import cache flag from constants (784f276)
• workflows: import contants in configuration (0741330)
• workflows: import contants in workflow (121381c)
• workflows: load dotenv in constants (13a5313)
• workflows: log env from constants (d2ca2fc)
• workflows: log warnings when cluster config files not found (e40270f)
• workflows: reenable simulated and pancreas data (cc59182)
• workflows: use overwrite cache variable to set default value (610d7cc)

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 ([...

v0.3.0-beta.7

0.3.0-beta.7 (2024-08-16)

Features

• 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: generate model comparison tables (9582ab2)
• tasks: save loss data to csv (15c1dc9)
• workflows: add task to collect metrics for all data sets and models (b242f80)
• workflows: track model metrics with results summary (98f269f)
• workflows: update task interfaces to track metrics (02f4897)

Bug Fixes

• interfaces: resolve str | Path union to str (93d1422)
• scripts: include json, html, md, tex in uploads (a157b27)
• tasks: update ticks on loss plot axes (350499f)
• workflows: add CombinedMetricsOutputs dataclass (c6f3e3c)
• workflows: toggle data subset to default false (55ac13a)

v0.3.0-beta.6

0.3.0-beta.6 (2024-08-15)

Features

• workflows: use PreprocessOutputs dataclass (1e5a223)

Bug Fixes

• io: increase default sparsify threshold (6ba43a1)
• tasks: include preprocessing reports directory in outputs (aee79a1)
• tests: account for updated postprocessing outputs interface (ed6a81f)
• workflows: add PreprocessOutputs dataclass (4fed2dd)

v0.3.0-beta.5

0.3.0-beta.5 (2024-08-14)

Features

• io: add module to sparsify/densify array dictionaries (c1f15fc)
• io: sparsify array dictionaries by default (e11412e)
• utils: log array data type with shape (eb769b5)

v0.3.0-beta.4

0.3.0-beta.4 (2024-08-13)

Bug Fixes

• tests: use importlib resources to refer to fixture data (7175c79)

v0.3.0-beta.3

0.3.0-beta.3 (2024-08-13)

Features

• io: add (de)serialization functions (6699308)
• plots: add interactive count histogram plot (68f3e16)
• tasks: add qc plots to preprocessing task (5b40254)
• utils: construct anndata string diff (411defe)

Bug Fixes

• conda: transiently pin scipy <1.14.0 (f8f4e49)
• io: update required fields for serialization (73e4b86)
• nbs: plot mitochondrial and ribosomal percentage histograms in preprocessing guide (a9cde59)
• nbs: update path to preprocessing notebook (682e9a3)
• pyproject: pin conda-lock fmt <11.0 for libmambapy (d78a8f8)
• tests: set tmp path to preprocessing reports (1cfd403)