v0.2.0-beta.11

0.2.0-beta.11 (2024-03-14)

Features

• actions: add composite action for build_nix_image (1f621ce)
• cid: add job to publish nix flake (5a52753)
• cid: add python 3.11 to test-python matrix (1896c0d)
• flake: add devCore lightweight devShell (96fdfe3)
• flake: add latex and pandoc (bff7410)
• flake: add quarto to devPackages (d6e3eca)
• flake: use refactored poetryOverrides (7f37d36)
• interfaces: add AcceleratorType Enum for future replacement of use_gpu type annotations (0122307)
• io: add fsspec interface (eb3ae02)
• io: add gcs interface (1491a1b)
• io: add googleapiclient interface (a7a36b6)
• io: create archive from filtered directory (814f184)
• main_configuration: add dataclasses for outputs (abdd8e0)
• make: add target to build nix default package (692b4f7)
• nix-config: refactor poetryOverrides (13714f1)
• nix: add btop to coreDevPackages (95f060f)
• scripts: add colab (3ff98b9)
• scripts: add literate template (2cfbd4d)
• scripts: add manuscript template (ce65847)
• scripts: extract imported packages from library (8957327)
• summarize: add summarize task module (4c1adbf)
• tests: add utils package (d38a219)
• utils: add function to save anndata counts to dataframe file (f9d6a91)
• vscode: add debug test launcher for library code (abef67f)
• workflows: add model summary task (1446119)
• workflows: draft notebooks execution workflow (34b8f47)
• workflows: expose overwrite_cache via ExecutionContext (9c1a633)

Bug Fixes

• actions: nix store gc 5 -> 3G (59f74bf)
• actions: reenable post-build garbage collection (37f1d78)
• actions: restrict nix gc (d8c68e9)
• actions: use skopeo instead of docker (b5b908e)
• app: update action versions (283d6c6)
• cid: add clean nix store to publish release images (a2daf9a)
• cid: add GAR env to publish release images (790045a)
• cid: add names to test-nix job steps (ad25df9)
• cid: do not rerun on draft submission (5314c8d)
• cid: ignore changes to colab workflow (3c36296)
• cid: ignore explicit lock files (1552086)
• cid: image builds condition on NOT dev mode (947bfa0)
• cid: include python version in test-python concurrency group (9411e8f)
• cid: publish flake on release (72c0841)
• cid: reduce root reserve (94ec314)
• cid: reenable restriction to x86_64-linux (1d0320e)
• cid: remove deprecated nix image build matrix (1aa74f0)
• cid: test-nix maximize build space (43600cb)
• cid: update test-nix nix build comments (e054a60)
• cid: use dev-mode label (2a4f469)
• cid: use local nix cache (ba638f6)
• cid: use local nix cache (f929dbd)
• colab: set cuda 12.2 (f8c6a73)
• colab: set unique path for constructor script (aeff7c6)
• colab: update action versions (88bd978)
• conda: default to python 3.10 (c093849)
• conda: move python version to top (fec219b)
• data: lint f-strings (6324327)
• data: remove call to copy method (979110a)
• data: set default adata None and handle (2a267e0)
• direnv: update containers watch_path (4e622d3)
• direnv: update pkgs watch_path (84b526c)
• direnv: update poetry watch_file path (ae3db70)
• examples: add install-tinytex make target (f1f7523)
• examples: force removal of _files dir (518567f)
• examples: ignore .quarto (bc4d21a)
• examples: set html font (3df5652)
• examples: set install-extensions deps (e034add)
• examples: support render without execution (9b6458e)
• execute: add random suffix to remote prod execution version (4553adf)
• flake: add extraEnv vars to makeContainerConfig (1219d86)
• flake: enable ssl for default build (b832d65)
• flake: preferWheel for tensorstore (29118fb)
• flake: provide required tex packages (535d4c4)
• flake: reenable train_model test on Linux (e748df3)
• flake: remove texliveSmall from devPackages (01f12b4)
• flake: reset appBuildInputs to none (d172d09)
• flake: restrict nvitop to x86_64-linux (d84dc84)
• flake: restrict torch nvidia overrides to x86_64-linux systems (7877359)
• flake: revert unstable code-server unavailable for aarch64-darwin (647cc10)
• flake: set QUARTO_PYTHON var in devshell (e368179)
• flake: switch to unstable for code-server (70096cd)
• flake: tensorstore requires setuptools (24522eb)
• flake: update checkPhase noting Darwin failure (980a0fd)
• flake: use ./nix/poetry (736a757)
• genes: update logging (5a80f86)
• gitignore: ignore top-level reports dir (94d42c6)
• gitignore: move sample dev pod configs (f77416e)
• interfaces: declare dataclasses when TYPE_CHECKING (7576b4d)
• io: declare interface (44b6006)
• io: use PathLike and Path objects for paths (6593afd)
• labels: change workflow-mode-dev to dev-mode (c0c7d8f)
• main_workflow: update logging (3f162e1)
• make: add docs-clean (430940a)
• make: add target to call make in subdirs (d09b4db)
• make: add target to get source archive hash (95768f9)
• make: add targets to clear local cache (f588cfe)
• make: clear local cache for parameterized dataset name (dc0d9bd)
• make: remove reports with workflow-clean-outputs (7f78b46)
• make: update ratchet 0.7.0 (5337a8b)
• make: use pyrovelocity cache (c1bf2b4)
• mergify: update bot account for merge (17ac41a)
• mergify: update condition check names (8457594)
• nix: reenable impure rev from GIT_SHA var (a028a02)
• nix: refactor pkgs to support lightweight devCore devShell (712b044)
• notebooks: remove deprecated system calls (ccd5e65)
• parameters: comment verbose print statements (3e3f79f)
• plots: address use of deprecated draw_all (1631655)
• plots: transform integer names to strings (40fc653)
• postprocess: add types for multiple outputs (0523e73)
• postrpocess: lint imports (b55e373)
• predictive: comment verbose print statements (d5160b6)
• preprocess: make log-transformation explicit (ce489dd)
• preprocess: update logging (32c42d8)
• pyproject: add workflows deps (687e8c2)
• pyproject: allow python 3.11 installs (5f42c26)
• pyproject: annotate lint rules (75f6431)
• pyproject: convert all pins to lower bounds (8a5db53)
• pyproject: downgrade flax to remove tensorstore (6c86994)
• pyproject: pin conda-lock output to python 3.10 (8558b3e)
• pyproject: remove desert (92bdd92)
• pyproject: remove marshmallow (e650341)
• pyproject: remove unused deps (e6f66a9)
• pyproject: update extras (5d6063a)
• pyproject: update flax (6b664bf)
• summarize: save anndata dataframe in models directory (e2078e3)
• summarize: update interface and add types for multiple outputs (0dddefd)
• test_data: test failure of mocked download (f18c159)
• time: remove unused comments (3b7eab8)
• train: use_gpu with lightning AcceleratorRegistry keywords (0d708b6)
• trainer: migrate epoch-end hooks for lightning >2 (3b68fff), closes /www.github.com/Lightning-AI/pytorch-lightning/pull/16800#discussion_r1110256813
• trainer: update logging (66db9d3)
• train: log anndata contents before and after training (96ec859)
• uncertainty: comment verbose print statements (f776b80)
• uncertainty: transform integer names to strings (cb65bff)
• utils: remove deprecated print output from doctest (9443192)
• utils: remove unused function (7bf4ffd)
• utils: temporarily reenable initialization function (5d4d6dc)
• utils: update logging (107e2c1)
• utils: use numbers ABCs in output types (9d28080)
• vector_fields: comment verbose print statements (b455e85)
• velocity_module: use_gpu with lightning AcceleratorRegistry keywords (2871370)
• velocity_module: remove deprecated print output from doctest (d283a00)
• velocity_module: update logging (ba81901)
• velocity: use_gpu with lightning AcceleratorRegistry keywords (b53a3c4)
• velocity: update logging (21699b3)
• workflows: add dunder main to cli (d0aabe6)
• workflows: add flag to test exclusively with simulated data (dc261fd)
• workflows: add summarizing task resources to configuration (45cd18a)
• workflows: append configurations (a68270e)
• workflows: lint docstring (ae7b3f4)
• workflows: reenable CACHE_FLAG on summarize task (f563b24)
• workflows: set git refs logging to debug level (fc13152)
• workflows: set number of posterior samples in testing mode to 4 (25c8bd9)
• workflows: simplify simulated-only selection (ba3baeb)
• workflows: use new outputs dataclasses (120f70f)