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)

v0.3.0-beta.1

0.3.0-beta.1 (2024-07-30)

Features

• flake: make python 3.11 default devshell (c7ed17b)
• workflows: enable decks (d89a638)

Bug Fixes

• analyze: disable progress bar (44e7e41)
• cid: set python versions to 3.11 (ef7a62e)
• flake: python310 -> python311 (c5b609c)
• nbs: disable ipynb (79a74df)
• nbs: escape apostrophes (420872c)
• nbs: indicate explicit output (6628265)
• nbs: set default syntax highlighter (f30c2b3)
• nbs: sync freeze (810286e)
• nbs: use mathjax (81f4808)
• nix: explicit preferwheel for deps (06320e5)
• nix: make 3.11 default python in container images (4e95dbd)
• 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: shift python version bounds to 3.11 and 3.12 (fe1d4a8)
• scripts: update nbs build (fe20d09)
• tests: mark slow tests in determinstic inference module (d3a5254)
• workflows: remove top-level wrapper workflow (0ac37df)

v0.2.1-beta.1

0.2.1-beta.1 (2024-07-28)

Bug Fixes

• bazelignore: local venv (e5fa894)
• bazelversion: 7.0.2 -> 7.2.1 (d1a2ebe)
• cid: include MODULE.bazel in requirements cache key (9ec2174)
• cid: reenable bazel cache restore-keys (809370d)
• gcs: add function to download blob from uri (c20b5d1)
• gcs: add function to download path from uri (10f71d2)
• io: skip doctests that require gcp credentials (455e941)
• nbs: add interactive review to guides contents (7e33abf)
• nbs: auto-hide navigation (4d94b0b)
• nbs: flesh out interactive review (a827c71)
• nbs: move interactive guide to subfolder (eb6419a)
• nbs: move interactive review to 2nd guide (873a0f6)
• nbs: pygments -> gruvbox syntax highlighting (ee9b6dc)
• nbs: separate md, mdx, and site configs (9c0f193)
• nbs: update dark css (261cdcf)
• utils: use shape of ArrayLike in pretty printing dicts (918378c)

v0.2.0

What's Changed

• chore(deps): update dependency dparse to v0.6.3 by @renovate in #424
• chore(deps): update pypa/gh-action-pypi-publish action to v1.8.10 by @renovate in #433
• chore(deps): update crazy-max/ghaction-github-labeler action to v4.2.0 by @renovate in #440
• chore(deps): update dependency typeguard to v4 by @renovate in #426
• chore(deps): update dependency nbsphinx to v0.9.3 by @renovate in #430
• feat: add merge queue configuration by @cameronraysmith in #470
• chore(deps): update docker/build-push-action action to v5 by @renovate in #472
• chore(deps): update docker/metadata-action action to v5 by @renovate in #474
• chore(deps): update docker/login-action action to v3 by @renovate in #473
• chore(deps): update crazy-max/ghaction-github-labeler action to v5 by @renovate in #471
• refactor: update dev container and pod by @cameronraysmith in #477
• feat: add nix devshell and update ci by @cameronraysmith in #485
• feat: setup workflow execution by @cameronraysmith in #492
• feat(bazel): add test caching by @cameronraysmith in #499
• feat(ci): add shared test cache by @cameronraysmith in #501
• feat(workflows): setup data download tasks by @cameronraysmith in #502
• feat(workflows): map core workflow over multiple data sets by @cameronraysmith in #510
• feat(workflows): enable preprocessing tasks by @cameronraysmith in #512
• feat(workflows): create model training tasks by @cameronraysmith in #513
• feat(workflows): create postprocessing tasks by @cameronraysmith in #518
• feat(workflows): create model summary tasks by @cameronraysmith in #521
• feat(workflows): upload shareable summary archive by @cameronraysmith in #531
• docs: use local workflow execution in template notebooks by @cameronraysmith in #532
• refactor(tasks): migrate tasks modules to package by @cameronraysmith in #535
• feat(data): generate transcriptome db and simulate deterministic data by @cameronraysmith in #537
• fix(flake): push images to artifact registry by @cameronraysmith in #541
• feat(argo): enable ARC build for oci images by @cameronraysmith in #543
• fix(images): use layer compression and composition to speed up builds by @cameronraysmith in #544
• chore: release 0.2.0 by @cameronraysmith in #545

Full Changelog: v0.1.3...v0.2.0

v0.2.0-beta.22

0.2.0-beta.22 (2024-07-12)

Bug Fixes

• argo: set provisioning mode and retry strategy (e4165ef)
• cid: disable building dev image (5a2e678)
• cid: disable publishing dev image (e1e4e19)
• cid: set build and publish image values for release (88b24c2)
• code: reenable layer compression (3af073c)
• containers: disable top-level source layer (5832044)
• containers: note build time difference with surface-level source layer composition (79bc2b8)
• containers: reenable layer compression (3535fa4)
• containers: reenable top-level source layer (fc929c8)
• devcontainer: sync extensions (3c8bada)
• flake: disable server image push to ghcr (c97fb9b)
• jupyter: reenable layer compression (28e9edf)

v0.2.0-beta.21

0.2.0-beta.21 (2024-07-10)

Features

• argo: add nix image build Workflow resource (8c2179b)
• github: add reusable workflow to build nix images (33ab84f)

Bug Fixes

• build-nix-images: cache argo cli (416acc8)
• build-nix-images: disable cache (d85c34b)
• build-nix-images: pin actions cache to v4 hash (9dfcd8d)
• build-nix-images: preserve JSON list-formatted images argument (c6dec80)
• build-nix-images: skip build in dev mode (12ba002)
• cid: disable containerfile image builds (850afe8)
• cid: enable reusable workflow to build nix images (dc224bd)
• cid: include checkout_rev in set-variables outputs (e477c5b)
• cid: migrate build-images reusable action usage to source (221c073)
• cid: only test workflow image build by default (59daeb5)
• cid: pass mode to build-nix-images workflow (5c9ebf8)
• cid: reenable all image builds (3af29eb)
• cid: reenable cachix for release job (0513507)
• cid: set semantic release token variable (a9bacf3)
• cid: use github.ref_name in all concurrency group keys (cf2641f)
• containers: set default scrollback (43172b7)
• containers: update code extensions (257c5d7)
• containers: update SHELL path (50b2a79)
• flake: reenable upstream flocken (9150817)
• make: add commands to set fast forward variables (1e43b30)
• mergify: remove conditions from queue_rules (fecedff)
• pkgs: add bazel-buildtools to coreDevPackages (b6e5708)
• pr-merge: declare explicit github actor and pat (ad09bc9)
• vscode: disable python-environment-manager (14e6cba)
• vscode: remove unavailable workspace setting (af62669)

v0.2.0-beta.20

0.2.0-beta.20 (2024-07-08)

Bug Fixes

• actions: add build_nix_image artifact registry password (fc94cc2)
• actions: enable parallel cache uploads (c3cff98)
• actions: enable s3 nix cache (234ddf0)
• actions: print swap usage (f129b8b)
• actions: reenable cachix cache (64b7901)
• actions: reenable hosted cache (da269ff)
• actions: reenable local nix cache (a52c831)
• actions: reenable nixcached (15e9e96)
• actions: reenable remote nix cache (2a90045)
• actions: reenable remote s3 cache (c12cadc)
• actions: simplify build command execution logic (375c4d2)
• actions: temporarily disable nix cache upload (990440a)
• actions: temporarily disable nix cache upload options (2de1ee1)
• actions: use s3-compatibility HMAC keys and disable nixcached (5ef2162)
• cid: add artifact registry password secret env (30e4652)
• cid: decrease swap (321341b)
• cid: enable parallel cache uploads (c448bf6)
• cid: enable s3 nix cache for image builds (777c0b2)
• cid: enable s3 nix cache for test and release (a853056)
• cid: increase swap space (737bb28)
• cid: reenable nixcached (80d384a)
• cid: remove unused variables (2c81db3)
• cid: set default swap in build-nix-images (8c4d47d)
• cid: update permissions (3691884)
• cid: update swap size (da15b99)
• cid: update swap size (129eb72)
• cid: use s3-compatibility HMAC keys (b32e7fd)
• containers: add gcc lib to lib path (6d1c24b)
• containers: add just syntax extension (a9f3b7e)
• containers: add libgcc lib to lib path (30067b8)
• containers: add libgcc.lib lib to lib path (d32d8d1)
• containers: disable compression (853e00b)
• containers: disable timestamp of images (7b67175)
• containers: enable atuin daemon (046fa6f)
• containers: skip base images (5c7e001)
• dev: constraint config.persistence.accessMode to corev1.#PersistentVolumeAccessMode (a6fe1d5)
• dev: update base resources (b8c41d3)
• flake: define version variable and make ghcr upload conditional on its being non-empty (47ab603)
• flake: enable ghcr and gar (ab80d40)
• flake: note ghcr for server images (764a534)
• flake: only tag with git sha (21bfd06)
• flake: push containers to artifact registry (3400a34)
• flake: reenable additional tags (df21086)
• flake: separate base from source-containing layers (cca450e)
• flake: use flocken fork to enable crane tag (2f0c60e)
• make: add HMAC key vars (1dc659d)
• make: add s3 nix cache vars (102a3b5)
• make: set gh artifact registry password secret (36f5f66)
• nix: compress layers with zstandard (667a93d)
• nix: disable compression of base images (158150a)
• nix: move env vars to top layer (b11fea5)
• nix: separate maxLayers by three (86c432e)
• pre-commit: ignore flake.lock (9933c79)

v0.2.0-beta.19

0.2.0-beta.19 (2024-06-29)

Bug Fixes

• models: use ellipsis matching in xdoctests (505a255)

v0.2.0-beta.18

0.2.0-beta.18 (2024-06-29)

Bug Fixes

• models: import xarray.DataArray for type-checking (057022a)
• pyproject: update beartype 0.16.4 -> 0.18.5 (ae3f37c)

v0.2.0-beta.17

0.2.0-beta.17 (2024-06-28)

Bug Fixes

• pre-commit: ignore changelog (a65e750)
• tests: importing config from jax.config is deprecated (7a11ab4), closes /jax.readthedocs.io/en/latest/changelog.html#jax-0-4-25-feb-26-2024