Changelog

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)

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)

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)

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)

0.3.0 (2024-08-16)

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)

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)

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)

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)

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

Bug Fixes

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

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)

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)

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)

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)

0.2.0 (2024-07-12)

Features

• actions: add composite action for build_nix_image (1f621ce)

• add merge queue configuration (#470) (14c9328)

• analysis: create module to generate transcriptome properties database (4fe27ae)

• api: typecheck train_model and allow path inputs (fbd34bf)

• argo: add build-images workflow (6697f55)

• argo: add nix image build Workflow resource (8c2179b)

• bazel: add aspect lib (512e127)

• bazel: add helper macro to run test modules (0768837)

• bazel: add remote build cache (0afae63)

• bazel: add tests build (27efc09)

• bazel: add xdoctest macro (b39b26e)

• bazel: generate pip-compile requirements (e38acf6)

• bazel: init module (46195c2)

• bazel: use all_requirements for package library (165b84a)

• ci: check and fast-forward merge PRs (251e11f)

• cid: add job to publish nix flake (5a52753)

• cid: add python 3.11 to test-python matrix (1896c0d)

• cid: add test-bazel job (0fcac1e)

• cid: build workflow execution container (8e9999e)

• cid: enable code-server image build (a8d02a9)

• cid: enable jupyter image build (263c319)

• cid: init cid workflow (0482ea9)

• cid: skip image build if one with commit sha tag already exists (cba38e4)

• codecov: init repo config (d09736c)

• compose: add compose for jupyter server (b6a4ce8)

• conftest: provide global fixture to file for sample data (409d96d)

• containers: add dyngen container (de3abae)

• containers: add pkg and gpu Dockerfiles (690fa7b)

• containers: add script to generate simulated data (05b49c2)

• data: add load_anndata_from_path (7d43e29)

• data: support subsetting during data download (fa066cd)

• data: validate urls and file size before download attempt (b9b6f0b)

• dev: add cluster dev resource manifests (812a327)

• dev: add cue module (9d1e729)

• dev: add example cue values (001a181)

• dev: add hpa config (dadb4d1)

• dev: add job config (da03a27)

• dev: add nixbuild deployment (3678de8)

• devcontainter: update configuration for flake (37475e5)

• dev: enable setting values for accessMode (d92c1a9)

• devshell: add manual activation script (36fe896)

• dev: update example config for job (c956103)

• docker-config: add example.json (346b787)

• docs: add repo CHANGELOG.md to history (86625a8)

• env: add pyrovelocity-specific env vars (6dfa69c)

• execution_utils: support nested dataclasses (a382204)

• flake: add bazelisk (cb34805)

• flake: add CUDA env vars to devcontainerConfig (e004597)

• flake: add devCore lightweight devShell (96fdfe3)

• flake: add GAR images (eaaddfe)

• flake: add htop to devPackages (9dc2760)

• flake: add latex and pandoc (bff7410)

• flake: add openvscode-server to devPackages (af19432)

• flake: add quarto to devPackages (d6e3eca)

• flake: add time to sysPackages (8d1c994)

• flake: add workflow execution container (8215232)

• flake: build code-server container (bfeb171)

• flake: build jupyter container (b424a91)

• flake: init (8a11673)

• flake: update torch >2 (6b838d3)

• flake: use refactored poetryOverrides (7f37d36)

• flyte: add config templates (511f6cb)

• gha: add build-images workflow (abb7266)

• github: add reusable workflow to build nix images (33ab84f)

• help: add help module (d30f670)

• interfaces: add AcceleratorType Enum for future replacement of use_gpu type annotations (0122307)

• interfaces: collect dataclass interfaces (f2c6ea9)

• io: add async ensembl batch query and cache (2b15bf6)

• io: add async ensembl query and cache (997169f)

• io: add data fetch interface (2afa701)

• io: add fsspec interface (eb3ae02)

• io: add gcs interface (1491a1b)

• io: add googleapiclient interface (a7a36b6)

• io: create archive from filtered directory (814f184)

• just: add recipes for teller (72a3676)

• main_configuration: add dataclasses for outputs (abdd8e0)

• main_workflow: add model training task (4ca67b4)

• main_workflow: setup download_data task (9cfdcce)

• main_workflow: use dataclass interfaces (2324654)

• make: add ci targets (8a7c250)

• make: add cluster config targets (3ce33c9)

• make: add cluster-shell target (23c3d5e)

• make: add container targets (e9b158d)

• make: add nix targets (8037ad1)

• make: add pydeps target to render graph (ff2e8b3)

• make: add target to build dyngen image (1c46950)

• make: add target to build nix default package (692b4f7)

• make: add target to copy file to cluster pod (7d22b0c)

• make: add target to disable zsh time reserved word (be99bd9)

• make: add target to forward port from dev pod (f9cff22)

• make: add target to print tree (4080c08)

• make: add target to render dev manifest (b4c11a2)

• make: add target to replace vars in config file (4e9e1a9)

• make: add target to run tests with bazel (3c0ffcd)

• make: add target to show closure size for a store path (a292cd9)

• make: add target to toggle local virtualenvs (b96691d)

• make: add targets for in-cluster dev (0c6cae3)

• make: add targets to (un)pin gha commit hashes (d43b964)

• make: add targets to build and serve nbs (28e3779)

• make: add targets to configure dev env (10aa781)

• make: add targets to set gh vars and secrets (da50e44)

• make: add targets to setup dev env (b69015d)

• make: add update_version target (4a352d3)

• make: add vscode targets (335ed1f)

• make: add workflow execution targets (ed0f2dc)

• make: generate architecture docs (c12607a)

• make: test packaging of dev module (7080a6e)

• models: add deterministic model simulation functions (1445777)

• models: add dimensionless analytical solution (a3c97aa)

• models: add function to save determinstic inference plots (2096303)

• models: add module for calibrating hyperparameters (6ba593d)

• models: add plot_sample_phase_portraits (e136293)

• models: add plot_sample_trajectories function (56eaed3)

• models: add plot_sample_trajectories_with_percentiles (f661696)

• models: add posterior inference for deterministic model (2b5872b)

• models: implement print_inference_data_structure to describe InferenceData objects (32d2a0f)

• models: initialize deterministic inference (a71f4e0)

• nbs: add inference model description (f5176fc)

• nbs: add inference plots to concepts (38b61ef)

• nbs: add inference plots to rrv (44b915a)

• nbs: add interlinks extension (dc99563)

• nbs: add sn extension (7e4331c)

• nbs: add user example to templates (bbeceaf)

• nbs: copy contributing (c7f84d8)

• nbs: draft trajectories and phase portraits (b93eb69)

• nbs: enable api reference docs (cf4e1a9)

• nbs: export ipynb format (b174e95)

• nbs: include plot of analytical solution (3c545a7)

• nbs: init installation (258fdc1)

• nbs: initialize concepts page on inference in dynamical systems (3a7513b)

• nbs: update dimensional analysis (0873628)

• nbs: update inference model without times (756dd55)

• nbs: update references (1c93eb6)

• nix-config: refactor poetryOverrides (13714f1)

• nix: add btop to coreDevPackages (95f060f)

• nix: add code-server container (d8e81ca)

• nix: add jupyter container (36c8e32)

• plots: draft simulation trajectory and phase portrait (582b5b7)

• postprocess: add postprocess module (d565e27)

• preprocess: allow subsets of obs and vars (93a0465)

• preprocess: refactor for compatibility with dataclass interface (19c7b68)

• pypi_template: add workflow execution example (c69767d)

• pypi_template: generate and display figure outputs (a0111e2)

• pypi_template: include training and summary for two distinct model classes (217a3fd)

• pypi: add cpu-only requirements (cbb95d6)

• pyproject: add jupyter server to docs group (68eabde)

• pyproject: add requests-mock for testing (42db104)

• pyproject: add workflow execution dep group (9e8fbcc)

• pyproject: upgrade stable dependencies (7698cf7)

• pyrovelocity: add workflow execution package (ffd2808)

• pyrovelocitydev: add cue module (1aa633a)

• scripts: add colab (3ff98b9)

• scripts: add literate template (2cfbd4d)

• scripts: add manuscript template (ce65847)

• scripts: add nbs build script (59f708f)

• scripts: add script to activate nix flake (2283f11)

• scripts: copy gcs archives to drive (a4eb5f5)

• scripts: draft extraction of gene length and polyA motif counts (b35c55d)

• scripts: extract imported packages from library (8957327)

• scripts: init pypi template (5ed5f10)

• scripts: pull _freeze from dvc cache during nbs build (45d191b)

• scripts: update flake to accept cmd arg (01c2e94)

• skaffold: add config (b4e02bd)

• styles: initialize mpl style file (56395ab)

• summarize: add summarize task module (4c1adbf)

• teller: add kubeconfig (13b0635)

• test_data: add tests for data module methods (dcd8276)

• tests: add tests for deterministic simulation functions (8c2ec75)

• tests: add tests for transcriptome properties module (2a3e19c)

• tests: add utils package (d38a219)

• train: add training script for workflow usage (5fcf4c3)

• utils: add class to suppress function output (76af2cc)

• utils: add function to generate public api candidates (402259e)

• utils: add function to save anndata counts to dataframe file (f9d6a91)

• utils: add print_config_tree (e3546df)

• vscode: add debug test launcher for library code (abef67f)

• vscode: add fileutils (e5dfb0a)

• vscode: config debug launch for cli (610fb8a)

• workflow: add preprocess data tasks (d4f5f89)

• workflows: add main workflow (153e12c)

• workflows: add medium resources category to configuration (aad47f4)

• workflows: add model summary task (1446119)

• workflows: add pbmc68k, pons, and larry data sets (41c18e2)

• workflows: add postprocessing task (5654b6c)

• workflows: add upload summary task (8693728)

• workflows: draft notebooks execution workflow (34b8f47)

• workflows: expose overwrite_cache via ExecutionContext (9c1a633)

• workflows: expose testing and upload flags as environment variables (9ed24f8)

• workflows: map over multiple data sets (4c8cc01)

• workflows: separate summarize cache version (55ada29)

• workflows: use upload_results fields from each WorkflowConfiguration (fbf4ea3)

Bug Fixes

• _velocity: update doctest imports for preprocess (44db75b)

• actions: accept releaseVersion in build-nix-image (fc7f6ed)

• actions: add build_nix_image artifact registry password (fc94cc2)

• actions: enable parallel cache uploads (c3cff98)

• actions: enable s3 nix cache (234ddf0)

• actions: nix store gc 5 -> 3G (59f74bf)

• 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 post-build garbage collection (37f1d78)

• actions: reenable remote nix cache (2a90045)

• actions: reenable remote s3 cache (c12cadc)

• actions: restrict nix gc (d8c68e9)

• actions: set VERSION to inputs.releaseVersion (ac41ce1)

• 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)

• actions: use skopeo instead of docker (b5b908e)

• analysis: allow PathLike in transcriptome properties (a6384a9)

• analysis: handle missing data in transcriptome properties db generation (08ba799)

• analysis: isolate pyensembl lazy import (ea55ab8)

• analysis: log warning rather than raising error on lazy imports (fa834d2)

• analysis: optionally write gene data to standalone tables (83b0007)

• analysis: summarize genomic and cdna sequences separately (a97feac)

• analysis: update artifact paths for generation vs testing (79dd945)

• analysis: use forward type hint for lazy import (436e526)

• analyze: add types to compute_volcano_data (34885da)

• analyze: define public interface (0ee8e58)

• analyze: separate computation of neighbors (d16b6dc)

• api: discard returned adata in doctest (78456f8)

• api: update doctest imports for preprocess (8cc6683)

• app: restrict workflow to main (5331fc5)

• app: update action versions (283d6c6)

• argo: set provisioning mode and retry strategy (e4165ef)

• bazel: add aspect lib to root rc (b661bff)

• bazel: add ci configs (9c15b5a)

• bazel: add deterministic inference tests module (cbc3321)

• bazel: enable test_deterministic_simulation (d202722)

• bazel: move py_library to workspace-level for xdoctest (29a3a7f)

• bazel: noexperimental_python_import_all_repositories (500b645), closes /www.github.com/bazelbuild/rules_python/issues/792#issuecomment-1264463207

• bazel: remove platform-specific requirements (bfeab1b)

• bazel: remove unused test modules (a724853)

• bazel: separate small and medium test modules (6186da2)

• bazel: set target platforms “all” (3ab6152)

• bazel: update test module list (f9a38aa)

• bazel: use cpu requirements (a040872)

• bazel: use py_test from rules_python in py_test_module_list (fffb0d6)

• bazel: use requirements-bazel.txt (d7f3969)

• bazel: use standard pip hub name (d027451)

• build_nix_image: disable post-build gc (9e52cb0)

• build_nix_image: use cachix cache (e93e951)

• build_nix_image: use default dev shell in clean nix store (fe6e851)

• build-images: add -cpu to pkg.Dockerfile image name (bdb6fa4)

• 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: add actions cache for bazel (85a6576)

• cid: add artifact registry password secret env (30e4652)

• cid: add clean nix store to publish release images (a2daf9a)

• cid: add GAR env to publish release images (790045a)

• cid: add maximize-build-space step to nix image build (3baf69b)

• cid: add names to test-nix job steps (ad25df9)

• cid: add nix envs for GAR images (5fda3ee)

• cid: add note on use-gha-cache (6f79f33)

• cid: cache cpu requirements (4e1b37c)

• cid: check cache for requirements or regenerate (3109d5e)

• cid: check disk usage (db2e99e)

• cid: decrease swap (321341b)

• cid: disable use-gha-cache (db6bcda)

• cid: disable building dev image (5a2e678)

• cid: disable containerfile image builds (850afe8)

• cid: disable lock-bazel (1407ea1)

• cid: disable printing of image build logs (a991dd0)

• cid: disable publishing dev image (e1e4e19)

• cid: do not rerun on draft submission (5314c8d)

• cid: enable cachix cache for build-nix-images job (63e545f)

• cid: enable cachix for release images (49075ef)

• cid: enable cachix for test-nix job (f533984)

• cid: enable impure nix build (936d150)

• cid: enable parallel cache uploads (c448bf6)

• cid: enable publication of code and jupyter images (6e84c8d)

• cid: enable reusable workflow to build nix images (dc224bd)

• cid: enable s3 nix cache for image builds (777c0b2)

• cid: enable s3 nix cache for test and release (a853056)

• cid: ignore conda/** (fdf0cb4)

• cid: ignore changes to colab workflow (3c36296)

• cid: ignore explicit lock files (1552086)

• cid: image builds condition on NOT dev mode (947bfa0)

• cid: include checkout_rev in set-variables outputs (e477c5b)

• cid: include python version in test-python concurrency group (9411e8f)

• cid: increase root reserve and swap (8035847)

• cid: increase swap size (3ea04b7), closes /github.com/actions/runner-images/discussions/7188#discussioncomment-6750749

• cid: increase swap space (737bb28)

• cid: lock-bazel before tests (f53b8f8)

• cid: magic -> cachix (bfdfb91)

• 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: paths-ignore array (9e86990)

• cid: publish flake on release (72c0841)

• cid: publish workflow execution image (8380d2b)

• cid: reduce root reserve (94ec314)

• cid: reduce swap (87cb626)

• cid: reenable all image builds (3af29eb)

• cid: reenable bpdi concurrency group (6b657c9)

• cid: reenable cachix for release job (0513507)

• cid: reenable docs build jobs (efe61c2)

• cid: reenable execute-workflow dep on image builds (#502) (c00124e)

• cid: reenable nixcached (80d384a)

• cid: reenable restriction to x86_64-linux (1d0320e)

• cid: remove debug (95a88f3)

• cid: remove deprecated nix image build matrix (1aa74f0)

• cid: remove line break in test-nix job (70368b7)

• cid: remove unused variables (2c81db3)

• cid: restrict build and release images to x86_64 (6162007)

• cid: root-reserve-mb 34816 -> 38912 (a03d745)

• cid: save updated requirements artifact (793b1c7)

• cid: set build and publish image values for release (88b24c2)

• cid: set build volume mount path /nix (d542fa6)

• cid: set default swap in build-nix-images (8c4d47d)

• cid: set git variables in test-nix job (f41170b)

• cid: set NUMBA_CACHE_DIR to runner.temp (6d759a7), closes /github.com/numba/numba/issues/4032#issuecomment-488102702

• cid: set semantic release token variable (a9bacf3)

• cid: test-nix maximize build space (43600cb)

• cid: update codecov-action to v4 (e0dbda3)

• cid: update nix-installer to main (98a0b78)

• cid: update pages actions hashes (c684dd4)

• cid: update permissions (3691884)

• cid: update swap size (da15b99)

• cid: update swap size (129eb72)

• cid: update test-nix nix build comments (e054a60)

• cid: use github.ref_name in all concurrency group keys (cf2641f)

• cid: use base64 encoded SA creds (29af74e)

• cid: use bazel make targets (a46d544)

• cid: use cachix cache (c5f04c6)

• cid: use composite action to build and publish images (c3d5c69)

• cid: use default dev shell in clean nix store (0894674)

• cid: use dev-mode label (2a4f469)

• cid: use hyphen in run target (7341089)

• cid: use local nix cache (ba638f6)

• cid: use local nix cache (f929dbd)

• cid: use release tag to index release commit (b5ee22b)

• cid: use s3-compatibility HMAC keys (b32e7fd)

• cid: use test-python job name (0b3226f)

• cml-images: reenable CML image workflow (#485) (815e616)

• code: reenable layer compression (3af073c)

• colab: add maximize build space (9d014b1)

• colab: increase root reserve (37058af)

• colab: reenable pytorch and nvidia channels (53f60c4)

• colab: set cuda 12.2 (f8c6a73)

• colab: set unique path for constructor script (aeff7c6)

• colab: update action versions (88bd978)

• compose: set SHELL=zsh (db19f08)

• compose: use zsh in jupyter (a2852ad)

• conda: default to python 3.10 (c093849)

• conda: install pytorch from pytorch channel (750a324)

• conda: move python version to top (fec219b)

• conda: remove redundant cuda installation (d61866b)

• conda: sync virtual packages with colab (75261d8)

• 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: disable top-level source layer (5832044)

• containers: enable atuin daemon (046fa6f)

• containers: fix amd64 in compose configuration (0cad067)

• containers: git move from dockerfiles (a56e5ad)

• containers: note build time difference with surface-level source layer composition (79bc2b8)

• containers: nvidia-smi RPATH expects ld-linux-x86-64.so.2 in /lib64 (436d52d)

• containers: reenable layer compression (3535fa4)

• containers: reenable top-level source layer (fc929c8)

• containers: set default locale variables (6800b08)

• containers: set default scrollback (43172b7)

• containers: skip base images (5c7e001)

• containers: update code extensions (257c5d7)

• containers: update SHELL path (50b2a79)

• containers: use requirements-main.txt (25a13dc)

• cspell: add cytotrace (2fb9099)

• cspell: add scanpy (f9002ac)

• cspell: add type checking (e027023)

• cspell: update dictionary (119f436)

• cytotrace: remove a subset of unnecessary print statements (1847cbd)

• data: lint f-strings (6324327)

• data: make var names unique (8fb44f8)

• data: remove call to copy method (979110a)

• data: set default adata None and handle (2a267e0)

• data: update public interface (54932e6)

• data: use string inputs for download_dataset (887768a)

• deps: async and cli (b258ab9)

• determinstic_inference: note InferenceStage Sum type (53836f5)

• dev: add example security context overrides (4ac343d)

• dev: add minimal/testing example config (c7bd905)

• dev: config pvc name (2d1d08b)

• dev: constraint config.persistence.accessMode to corev1.#PersistentVolumeAccessMode (a6fe1d5)

• devcontainer: sync extensions (3c8bada)

• devcontainer: vsliveshare reference (c151ee2)

• dev: default to deployment vs job (5f3a340)

• dev: default to nfs volumes (4ee68ed)

• dev: host active nixbuild cue config (bb923df)

• dev: host active pyrovelocitydev cue config (b8f2d25)

• dev: host example config in dev dir (5038272)

• dev: parameterize PVC access modes (471bd38)

• dev: remove default latest tag from image spec [no ci] (24a1ff4)

• dev: require command and args in deployment (ff74b8c)

• dev: set default pvc name to dev (0a656eb)

• dev: set replicas default (1->0->1) to toggle state (d5ecb52)

• dev: set update strategy to recreate (f79a958)

• dev: update base resources (b8c41d3)

• dev: update config to use job vs deployment (cd7537f)

• dev: use config pvc name in deployment (3027f0f)

• dev: use config pvc name in job (77e0ca5)

• dev: use config pvc name in pvc (57310ca)

• direnv: don’t enforce nix-direnv version (3379a73)

• direnv: update containers watch_path (4e622d3)

• direnv: update pkgs watch_path (84b526c)

• direnv: update poetry watch_file path (ae3db70)

• direnv: use flake (2f4a3b7)

• docs: add CID and GH pages to status (ca1dc54)

• docs: add colab badge to template notebook (7df9970)

• docs: change feature branch to beta (e113dcd)

• docs: clone beta branch in colab template [no ci] (006c631)

• docs: clone branch or tag in colab template (623048c)

• docs: link to example dev env in installation (e6118da)

• docs: mark docs/ as documentation (e0d93d9)

• docs: migrate history to CHANGELOG (1204056)

• docs: separate cool and warm logos (b30e041)

• docs: sync description (98fb385)

• docs: update badges (0a84010)

• docs: update sphinx conf exclude pattern from colab to template (4363b90)

• dotenv: add cluster dev namespace (9d671b7)

• dotenv: update container and cluster config (cc31ec3)

• dvc: update remote path (1476bc2)

• envrc: execute set-git-env script (63c8367)

• envrc: move direnv vars to .env (4a1b343)

• env: set variables for dev access (e54484f)

• 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)

• execute: print fallback logger exceptions (2f98d2e)

• execute: remove unused comments (1dbd3f8)

• execute: truncate git branch length in workflow version (441f102)

• execution_utils: construct dataclasses given defaults (fa95db3)

• extensions: duplicate devcontainer as recs (74ad1b1)

• flake: add ${env}/lib to LD_LIBRARY_PATH (f6f1af3)

• flake: add cluster tools to devPackages (7a5d948)

• flake: add devPackages for rust term IDE (3f21d7d)

• flake: add extraEnv vars to makeContainerConfig (1219d86)

• flake: add file findutils procps to sysPackages (f548403)

• flake: add gnupg to devPackages (15d5ab9)

• flake: add less to sysPackages (28fabf8)

• flake: add nixpkgs cudaPackages.cudnn_8_5 to propagatedBuildInputs for nvidia-cudnn-cu11 (3a93f0a)

• flake: add nvitop to sysPackages for gpu mon (b65ebbf)

• flake: add which to sysPackages (70e4dad)

• flake: add workflows group to python packages (a4ad180)

• flake: align oci manifest package names with image names (44ef896)

• flake: define version variable and make ghcr upload conditional on its being non-empty (47ab603)

• flake: disable checkPhase (07123f1)

• flake: disable llvmlite wheel for all systems (c9db64d)

• flake: disable push to ghcr (319a587)

• flake: disable server image push to ghcr (c97fb9b)

• flake: enable ghcr and gar (ab80d40)

• flake: enable python-versioned dev envs (73465e4)

• flake: enable ssl for default build (b832d65)

• flake: exclude tests requiring pyensembl (a322b8e)

• flake: get cudaPackages.cudnn_8_5_0 from nixpkgs 23.05 (bce8928)

• flake: move nvitop to extraPackages (a15a35d)

• flake: note ghcr for server images (764a534)

• flake: numba depends on tbb_2021_8 (d0e326b)

• flake: only tag with git sha (21bfd06)

• flake: parameterize devShells by python version (e26a1d7)

• flake: pass autoPatchelfHook to overrides (51e2274)

• flake: pass cudaPackages to overrides (6f179f8)

• flake: preferWheel for tensorstore (29118fb)

• flake: print value of NUMBA_CACHE_DIR (70c9587)

• flake: provide required tex packages (535d4c4)

• flake: push containers to artifact registry (3400a34)

• flake: reenable additional tags (df21086)

• flake: reenable train_model test on Linux (e748df3)

• flake: reenable upstream flocken (9150817)

• flake: remove dash from sysPackages (12793a8)

• 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: separate base from source-containing layers (cca450e)

• flake: set NUMBA_CACHE_DIR in default checkPhase (d135d41)

• flake: set QUARTO_PYTHON var in devshell (e368179)

• flake: set ref beta (a9c0728)

• flake: sort sysPackages (6bcca32)

• flake: switch poetry2nix patch ref (3988172)

• flake: switch to stable poetry2nix patch branch (820fa94)

• flake: switch to unstable for code-server (70096cd)

• flake: sysPackages bourne shell via dash (a679b9f)

• flake: sysPackages libgcc (f7c4489)

• flake: tensorstore requires setuptools (24522eb)

• flake: update checkPhase noting Darwin failure (980a0fd)

• flake: update poetry2nix cache public key (5908392)

• flake: use ./nix/poetry (736a757)

• flake: use base64 encoded SA creds (1dea556)

• flake: use env vars directly in image build (7570d41)

• flake: use flocken fork to enable crane tag (2f0c60e)

• flake: use refactored package drv (36410ef)

• flake: use unstable channel for k9s (93084c4)

• gcs: return file url from upload_file_* (7d5698e)

• genes: update logging (5a80f86)

• gha: add setup_environment action (a1d4d30)

• gha: disable independent actions (f3ae9fb)

• gha: pin dependencies in app (81455d3)

• gha: pin dependencies in build-images (a463e72)

• gha: pin dependencies in cid (3408631)

• gha: pin dependencies in cml-images (81c2542)

• gha: pin dependencies in colab (2ff5542)

• gha: pin dependencies in labeler (779225d)

• gha: pin dependencies in setup_environment (51d2349)

• gha: rename containers folder (0e4ccd9)

• gha: rename deploy to app (1540985)

• gha: update download-artifact (41d0119)

• gha: upgrade to node 20-based actions (afd7f60)

• gitattributes: linguist ignore Makefiles (508bddd)

• gitattributes: linguist ignore nbs and reproducibility (7c4f28d)

• gitignore: *-sa.json (9bd3132)

• gitignore: *.*.md and _configuration.yaml (ab45036)

• gitignore: add .uml (7ce78f6)

• gitignore: add nix outputs (b2947ab)

• gitignore: add service-account-credentials.json (13b3985)

• gitignore: all *dev.cue (08c0108)

• gitignore: database files (092deee)

• gitignore: dev.cue (9d904b0)

• gitignore: docker-config.json (dd09617)

• gitignore: ignore ensembl cache directory (920cd20)

• gitignore: ignore local kube config files (9304c35)

• gitignore: ignore top-level reports dir (94d42c6)

• gitignore: mlflow and data (fee99ec)

• gitignore: models directory (f6e4208)

• gitignore: move sample dev pod configs (f77416e)

• gitignore: only ignore top-level data folder by default (8e9daf5)

• gitignore: only ignore top-level models directory (8ad7a6d)

• git: rename master to main (c608f9c)

• git: rename master to main (6743eeb)

• init: reenable workflow-independent public interface (fc2aae5)

• interfaces: declare dataclasses when TYPE_CHECKING (7576b4d)

• interfaces: define public interface (28113b6)

• interfaces: implicit import of typing.Optional (c147643)

• interfaces: use train_dataset from train module (76b5563)

• io: add ensembl batch 429 and 404 error handling (942a175)

• io: declare interface (44b6006)

• io: explicitly declare plumbum command with local (f67f1ad)

• io: use PathLike and Path objects for paths (6593afd)

• jupyter: reenable layer compression (28e9edf)

• labeler: add workflow_dispatch (74cf8bf)

• labels: add PR workflow control labels (b5649fd)

• labels: change workflow-mode-dev to dev-mode (c0c7d8f)

• logging: set local log level (8ee8513)

• magic-nix-cache: revert v3 update (d1c85f8)

• main_configuration: enable testing of primary data sets (5912daf)

• main_configuration: remove list[DataClass] fields from WorkflowConfiguration (016d885)

• main_configuration: remove resource tuples (36fe9dd)

• main_workflow: construct training configurations explicitly (3f9f12c)

• main_workflow: reenable testing for primary data sets (5f04a8c)

• main_workflow: set cache parameters from constants (d247c75)

• main_workflow: specify accelerator type constant (d93d863)

• main_workflow: update docstrings (e1f726d)

• main_workflow: update logging (3f162e1)

• main_workflow: use NamedTuple class (618c430)

• make: add bazel targets (0f7b882)

• make: add commands to set fast forward variables (1e43b30)

• make: add debug and nodocs test targets (2f83b83)

• make: add devcontainer build targets (e7fc2b7)

• make: add docs-clean (430940a)

• make: add git ref/rev vars (1f70ea0)

• make: add HMAC key vars (1dc659d)

• make: add package dev targets (0d31924)

• make: add passthrough render-notebook target (465ebaa)

• make: add refresh target to remove cache (93ccd25)

• make: add s3 nix cache vars (102a3b5)

• make: add target for local jupyter server (84e4c68)

• make: add target to call make in subdirs (d09b4db)

• make: add target to get source archive hash (95768f9)

• make: add target to update a single flake input (56ddb26)

• make: add targets to clear local cache (f588cfe)

• make: add targets to deploy and delete dev module (40b7c64)

• make: add targets to export cpu requirements (fe5e09d)

• make: add update-ratchet target (ea11b10)

• make: add workflow-clean target (b9c1780)

• make: cache requirements with lock-bazel (84f155d)

• make: change _ to - in jupyter targets (29e491d)

• make: clear local cache for parameterized dataset name (dc0d9bd)

• make: comment ghsecrets for encoded GAR SA creds (ed954dc)

• make: deprecate nox and target (8f68d1a)

• make: disable setting CODECOV_TOKEN (d366338)

• make: disable token for local jupyter server (fac8f8f)

• make: do not lock bazel by default (276cffb)

• make: exclude additional modules from dep graph (58850a4)

• make: export hashed PyPI requirements (7e0d7f0)

• make: filter io and configuration from pydeps (ddf6d7d)

• make: install pre-commit from poetry (9778395)

• make: lint and apply cue module (4ccc220)

• make: move pod ID extraction inside cluster-shell target (7e31b54)

• make: parametrize cluster dev instance names (228eae8)

• make: print workflow env vars before execution (823d330)

• make: remove reports with workflow-clean-outputs (7f78b46)

• make: remove unused pydeps exclusion (0df6346)

• make: set cachix in gh vars/secrets (f5098eb)

• make: set codespace default machine to 64GB disk (5d7f747)

• make: set gh artifact registry password secret (36f5f66)

• make: split tree over lines (f9f1d1b)

• make: support multiple dev deployments (15fdda3)

• make: universally accept flake config (f8540f3)

• make: update docs targets (dccf668)

• make: update pre-commit targets (98d4c7c)

• make: update pydeps exclusions (901115b)

• make: update python lock targets (40fbfb5)

• make: update ratchet 0.7.0 (5337a8b)

• make: update section headings (37d1a64)

• make: use correct requirements file with test-bazel (59f0514)

• make: use pre-commit set git meta variables (5063e86)

• make: use pyreverse for uml generation (ba5b674)

• make: use pyrovelocity cache (c1bf2b4)

• make: write requirements-main (a38380a)

• mergify: queue method fast-forward (f13bb43)

• mergify: remove base branch constraint (d9c4810)

• mergify: remove conditions from queue_rules (fecedff)

• mergify: update check-success names (e07cefd)

• mergify: update bot account for merge (17ac41a)

• mergify: update check-success job names (87c51bf)

• mergify: update condition check names (8457594)

• meta: add pyrovelocity-reviewers to codeowners (b5c1a77)

• meta: sync versions with pyproject.toml (97d3c25)

• models: account for parameter space singularity (0c151c5)

• models: add deterministic inference model to public interface (fa27940)

• models: add newline to print inference data (22109eb)

• models: add observation flag to inference model (719db25)

• models: change logger from warning to debug (0221974)

• models: compute all kwargs inside plot_sample_trajectories_with_percentiles (df611a2)

• models: explicitly split rng keys (9144650)

• models: export deterministic simulation solver (4293af6)

• models: guard usage of latex behind path check (a31f769)

• models: import xarray.DataArray for type-checking (057022a)

• models: make sigma guess a parameter (2f16aec)

• models: multiple concrete dims examples (bc5a254)

• models: observation_flag -> data_observation_flag (b17a8f0)

• models: plot single timepoint data as vectorized series (6dd2256)

• models: refactor solve_model_for_all_genes_cells from model (89de821)

• models: refactor generate_predictive_samples (e835e7b)

• models: refactor plot_trajectory_with_percentiles to work with multiple timepoints per cell (b02d816)

• models: remove solve_model_for_all_genes_cells refactor TODO comment (8593da0)

• models: remove redundant Result container for plot_sample_trajectories (b7ca6e0)

• models: remove result wrapping from save_inference_plots (0aae2fe)

• models: return all indices from sort_times_over_all_cells (91c13ab)

• models: sample times from observed delta distribution (7a9bbd8)

• models: separately normalize plot_sample_phase_portraits colorbar for linear and log (d4ab537)

• models: update deterministic inference (495fde2)

• models: update dimensions in analytical solution test (de7e83c)

• models: update hyperparameter calibration test values (91a7934)

• models: update plot_sample_trajectories styling (a8291ae)

• models: use arbitrary initial condition in analytical solution (a676ca9)

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

• models: use log-normal likelihood (580d2ef)

• models: use tmp_path fixture for model data (e17bf9b)

• models: use vectorized deterministic inference model (b67976a)

• nbs: account for parameter space singularity (cf0bb1e)

• nbs: add make target to update _freeze directory (91a7f03)

• nbs: add manual derivation of analytical solution (77dcce2)

• nbs: add plots to api docs (d247958)

• nbs: add sync-nb make target to upload to gdrive (9d4d7d0)

• nbs: link numpy (df49123)

• nbs: migrate toc to header (75bc1ae)

• nbs: move introduction to tutorials (5f02c73)

• nbs: remove gh pages badge (3574679)

• nbs: remove reference folder (77abb60)

• nbs: soft-link to top-level CHANGELOG.md (15f45ff)

• nbs: static preview port (928a6cc)

• nbs: temporarily link index to readme (06216f7)

• nbs: update index (8945de3)

• nbs: update nb path in Makefile (7d0e389)

• nbs: update references (12e4f9b)

• nbs: update section contents (6883231)

• nbs: use gdrive notebook in colab link (fc760e6)

• nix: add all nvidia libraries to patchelf search path (aca7f99)

• nix: add required ctan pkgs to custom texlive (a09420a)

• nix: compress layers with zstandard (667a93d)

• nix: disable compression of base images (158150a)

• nix: disable package check on darwin (0843fa0)

• nix: draft override for attempted system call from sandbox on darwin (72a8e89)

• nix: include tex and lmodern in syspackages (e1357b9)

• nix: move env vars to top layer (b11fea5)

• nix: reenable impure rev from GIT_SHA var (a028a02)

• nix: refactor extraSysPackages (810e406)

• nix: refactor internal package drv (d8b2e03)

• nix: refactor pkgs to support lightweight devCore devShell (712b044)

• nix: separate maxLayers by three (86c432e)

• nix: update code image name (b9eee4b)

• nix: update package src path (c1bb1b6)

• notebooks: remove deprecated system calls (ccd5e65)

• parameters: comment verbose print statements (3e3f79f)

• pkgs: add bazel-buildtools to coreDevPackages (b6e5708)

• pkgs: add curl and wget to extraSysPackages (745884e)

• plot_gene_ranking: establish compatibility with adjusttext 1.1.1 (cf37f8e)

• plots: add padding to plot gene ranking (9b3fa5e)

• plots: add types to plot_gene_ranking (8ed9a75)

• plots: add types to summarize gene selection (deeaba5)

• plots: address use of deprecated draw_all (1631655)

• plots: close figure in plot_gene_selection_summary (099e6fb)

• plots: close figure in plot_shared_time_uncertainty (ea34035)

• plots: default to loading data for predictive sampling to cpu (abcf58b)

• plots: enforce types for plot_parameter_posterior_distributions (8597820)

• plots: enforce types for plot_vector_field_summary (204db57)

• plots: guard usage of latex behind path check (d302e66)

• plots: reenable refactored rainbowplot (4c130ac)

• plots: set 10^-8 min for log-transformed values (f322d21)

• plots: support parameterized labels (216a512)

• plots: transform integer names to strings (40fc653)

• plots: use package style (2497337)

• poetry2nix: update overrides (06f5be4)

• poetry: default to local virtualenvs (8f475ad)

• postprocess: add types for multiple outputs (0523e73)

• postprocess: ensure data_model_path exists (3cff34f)

• postprocess: use logger for printing (18206f7)

• postrpocess: lint imports (b55e373)

• pr-merge: declare explicit github actor and pat (ad09bc9)

• pre-commit: exclude dev dir (a882457)

• pre-commit: ignore changelog (a65e750)

• pre-commit: ignore flake.lock (9933c79)

• pre-commit: lint (5cddc71)

• pre-commit: remove set-git-env (2c51524)

• pre-commit: skip local hooks in ci (bb26f98)

• pre-commit: sync config with pyproject.toml (becd02e)

• pre-commit: update local hooks (42bc4e7)

• predictive: comment verbose print statements (d5160b6)

• predictive: use data_model input for data set model pairings (666e48e)

• preprocess: add pca rep if not present (96afc5b)

• preprocess: close figure (f776c0e)

• preprocess: ensure n_vars > n_pcs (a892487)

• preprocess: host data set parameters in interface (f51a098)

• preprocess: make log-transformation explicit (ce489dd)

• preprocess: remove completed TODOs (970ac7a)

• preprocess: separate computation of neighbors (dd217c9)

• preprocess: specify public api (4114d9d)

• preprocess: update docstring (fc4a8b8)

• preprocess: update logging (32c42d8)

• pypi_template: add blank header cells (46ecc14)

• pypi_template: add exploration section (1da0a53)

• pypi_template: collapse installation instructions in callout note (266a940)

• pypi_template: remove unnecessary output capture (562892e)

• pypi_template: sync with library updates (954d242)

• pypi_template: update frontmatter (f8094b3)

• pypi_template: update gitignore (78c8447)

• pyproject: add block to export cpu requirements (09951dd)

• pyproject: add docformatter settings (23b715b)

• 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: default to exclude tests that require pyensembl (cbd905e)

• pyproject: disable annoy (51ddce4)

• pyproject: disable poe (56ad8ef)

• pyproject: disable pytest warnings (d4d0ad8)

• pyproject: downgrade flax to remove tensorstore (6c86994)

• pyproject: enable pytorch and nvidia channels for conda-lock export (0f9cdec)

• pyproject: move to src (4e222fc)

• pyproject: omit scripts (55e9311)

• pyproject: pin lxml<5.0.0 (134cede)

• pyproject: pin conda-lock output to python 3.10 (8558b3e)

• pyproject: point main script to workflows cli (e35aa87)

• pyproject: pytest ignore reproducibility folder (434efae)

• pyproject: remove jupyter_contrib_nbextensions (16cd201)

• pyproject: remove desert (92bdd92)

• pyproject: remove marshmallow (e650341)

• pyproject: remove pipeline components (3c08f46)

• pyproject: remove unused deps (e6f66a9)

• pyproject: set default pytest logging to INFO (4522430)

• pyproject: update beartype 0.16.4 -> 0.18.5 (ae3f37c)

• pyproject: update conda-lock deps (4fa975a)

• pyproject: update docs dependencies (77fe0e3)

• pyproject: update extras (5d6063a)

• pyproject: update flax (6b664bf)

• pyproject: update tool configs (34621ec)

• pyrovelocity: add dunder main to launch cli as module (ff5b553)

• pyrovelocity: move to src (5f70c46)

• pyrovelocity: update dunder init (421c1f4)

• quarto: do not hard-code QUARTO_PYTHON in drv (2c8be95)

• quarto: vendor drv (e29b133)

• readme: change feature branch to beta (3ce409a)

• requirements-cpu: remove outdated hashed version (3a36c6e)

• requirements: rename to requirements-main (ed50b4d)

• resources: add cue versions (6b03d3d)

• scripts: cd with subshell (90423be)

• scripts: comment examples authors (8b48b48)

• scripts: disable sudo (073eeed)

• scripts: get colab scripts from beta branch (15a219b)

• scripts: update transcript analysis (9594ab9)

• scripts: use manual installation (ba68cd0)

• scripts: use poetry run (74bc828)

• set-git-env: account for absence of newline (8b475a1)

• setup_environment: add pandoc (2901217)

• setup_environment: add workflows group (fdbecc0)

• setup_environment: update setup-pandoc pin (24a8ef4)

• summarize: check phase portrait cache before exiting (6692a8a)

• summarize: include selected genes in summary figure (16fd344)

• summarize: respect typed interface to plot_vector_field_summary (bac7aad)

• summarize: save anndata dataframe in models directory (e2078e3)

• summarize: update interface and add types for multiple outputs (0dddefd)

• summarize: update shared time plot (8477626)

• summarize: update shared time plot font (cdb1f69)

• summary: support selected genes and marginal histograms (8d38ccd)

• test_data: test failure of mocked download (f18c159)

• test_utils: remove gillespie from random seed diff (df76a7f)

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

• tests: make doctests run on cpu (f4543c5)

• tests: reenable bazel xdoctests (29c2371)

• tests: reenable top-level imports (2ea0032)

• tests: remove unused shape statements (7a0f0df)

• tests: setup_observational_data with explicit return values (7159f59)

• tests: update deterministic inference (c985797)

• tests: update deterministic inference for vectorized model (4f74faf)

• time: remove unused comments (3b7eab8)

• train: use_gpu with lightning AcceleratorRegistry keywords (0d708b6)

• train: close figure (31f508b)

• trainer: cast categorical/integers as floats for log-transformation (62e7fd5)

• 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)

• trainer: use inherited methods from VelocityModule (178abfe)

• train: log anndata contents before and after training (96ec859)

• train: move data set parameters to preprocess (0a0ea5f)

• train: update docstring (e958c45)

• train: update import path in doctest (a8f50d0)

• train: update interface (52e33da)

• train: use tmp_path fixture for loss plot (6af93ea)

• transcription_dynamics: enable type-checking (88e496c)

• uncertainty: comment verbose print statements (f776b80)

• uncertainty: transform integer names to strings (cb65bff)

• utils: comment unused functions (1c05fa2)

• utils: migrate clear_local_cache to workflows (08a6463)

• utils: remove deprecated print output from doctest (9443192)

• utils: remove externalized VelocityModule method (72747fc)

• utils: remove unused function (7bf4ffd)

• utils: specify public api (5e325d9)

• utils: temporarily reenable initialization function (5d4d6dc)

• utils: update AnnData type import (42d21d9)

• utils: update logging (107e2c1)

• utils: use numbers ABCs in output types (9d28080)

• vector_fields: comment verbose print statements (b455e85)

• velocity_model: enable type-checking of get_rna (4ffdfb9)

• velocity_model: handle likelihood not implemented (e5d06d2)

• velocity_model: remove debug logging of plate sizes (4ea3f4c)

• velocity_model: remove optional type defaults for observations (7b3a9bd)

• velocity_model: set create plates log to debug (6259e7a)

• velocity_model: set log name from module (7da7879)

• velocity_model: set u0/s0 types to RNAInputType (d12e0dd)

• velocity_model: update imports (87386a1)

• velocity_module: use_gpu with lightning AcceleratorRegistry keywords (2871370)

• velocity_module: implement required inherited methods (885a841)

• velocity_module: remove deprecated print output from doctest (d283a00)

• velocity_module: update logging (ba81901)

• velocity: use_gpu with lightning AcceleratorRegistry keywords (b53a3c4)

• velocity: cast categorical/integers as floats for log-transformation (6e1ab7f)

• velocity: update logging (21699b3)

• velocity: use configure_logging (3477268)

• velocity: use VelocityModule method instead of utils (8a4afbd)

• vscode: add cspell dictionary (4e5c7ae)

• vscode: add db client (23e0f00)

• vscode: disable search.followSymlinks (7647f76)

• vscode: disable autohide sidebar (e89f240)

• vscode: disable cli debug launch arguments (3b53b51)

• vscode: disable coverage to respect debugging breakpoints (48dd4b8), closes /github.com/microsoft/vscode-python/issues/693#issuecomment-367848085

• vscode: disable python-environment-manager (14e6cba)

• vscode: do not search cue module dependencies (c3868cb)

• vscode: exclude bazel- from search/watch (b2b63b5)

• vscode: exclude search/watch hypothesis cache (60bf2ba)

• vscode: remove unavailable workspace setting (af62669)

• vscode: update extensions (fc89dab)

• vscode: update font sizes (4ea8f6e)

• vscode: update settings (687f2bb)

• vscode: update settings for devcontainer (3113bef)

• vscode: use basic project-manager (d73df90)

• 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: disable spot for preprocess tasks (fdd89f0)

• workflows: enable cache for training tasks (86b9333)

• workflows: increase mem limit for preprocessing tasks (c360594)

• workflows: increase resources for preprocessing and training tasks (b0e81b1)

• workflows: lint docstring (ae7b3f4)

• workflows: make training_workflow dynamic (08d2a45)

• workflows: note migration to CalVer for cache versions (0e0ac49)

• workflows: read cache flag from env var (9488074)

• 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: set preprocess data path (ecde0fa)

• workflows: set task resource limits (7416521)

• workflows: set workflow version to library version (f094130)

• workflows: simplify simulated-only selection (ba3baeb)

• workflows: update configuration for scikit-learn 1.5 (169e052)

• workflows: update training parameters in main configuration (984255b)

• workflows: use new outputs dataclasses (120f70f)

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)

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)

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)

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

Bug Fixes

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

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)

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

0.2.0-beta.16 (2024-06-28)

Bug Fixes

• cid: use release tag to index release commit (b5ee22b)

0.2.0-beta.15 (2024-06-28)

Features

• analysis: create module to generate transcriptome properties database (4fe27ae)

• cid: enable code-server image build (a8d02a9)

• cid: enable jupyter image build (263c319)

• dev: add nixbuild deployment (3678de8)

• dev: enable setting values for accessMode (d92c1a9)

• flake: build code-server container (bfeb171)

• flake: build jupyter container (b424a91)

• io: add async ensembl batch query and cache (2b15bf6)

• io: add async ensembl query and cache (997169f)

• io: add data fetch interface (2afa701)

• just: add recipes for teller (72a3676)

• make: generate architecture docs (c12607a)

• models: add deterministic model simulation functions (1445777)

• models: add dimensionless analytical solution (a3c97aa)

• models: add function to save determinstic inference plots (2096303)

• models: add module for calibrating hyperparameters (6ba593d)

• models: add plot_sample_phase_portraits (e136293)

• models: add plot_sample_trajectories function (56eaed3)

• models: add plot_sample_trajectories_with_percentiles (f661696)

• models: add posterior inference for deterministic model (2b5872b)

• models: implement print_inference_data_structure to describe InferenceData objects (32d2a0f)

• models: initialize deterministic inference (a71f4e0)

• nbs: add inference model description (f5176fc)

• nbs: add inference plots to concepts (38b61ef)

• nbs: add inference plots to rrv (44b915a)

• nbs: draft trajectories and phase portraits (b93eb69)

• nbs: include plot of analytical solution (3c545a7)

• nbs: initialize concepts page on inference in dynamical systems (3a7513b)

• nbs: update dimensional analysis (0873628)

• nbs: update inference model without times (756dd55)

• nbs: update references (1c93eb6)

• nix: add code-server container (d8e81ca)

• nix: add jupyter container (36c8e32)

• plots: draft simulation trajectory and phase portrait (582b5b7)

• scripts: draft extraction of gene length and polyA motif counts (b35c55d)

• styles: initialize mpl style file (56395ab)

• teller: add kubeconfig (13b0635)

• tests: add tests for deterministic simulation functions (8c2ec75)

• tests: add tests for transcriptome properties module (2a3e19c)

Bug Fixes

• actions: accept releaseVersion in build-nix-image (fc7f6ed)

• actions: set VERSION to inputs.releaseVersion (ac41ce1)

• analysis: allow PathLike in transcriptome properties (a6384a9)

• analysis: handle missing data in transcriptome properties db generation (08ba799)

• analysis: isolate pyensembl lazy import (ea55ab8)

• analysis: log warning rather than raising error on lazy imports (fa834d2)

• analysis: optionally write gene data to standalone tables (83b0007)

• analysis: summarize genomic and cdna sequences separately (a97feac)

• analysis: update artifact paths for generation vs testing (79dd945)

• analysis: use forward type hint for lazy import (436e526)

• analyze: separate computation of neighbors (d16b6dc)

• bazel: add deterministic inference tests module (cbc3321)

• bazel: enable test_deterministic_simulation (d202722)

• bazel: noexperimental_python_import_all_repositories (500b645), closes /www.github.com/bazelbuild/rules_python/issues/792#issuecomment-1264463207

• bazel: separate small and medium test modules (6186da2)

• build_nix_image: disable post-build gc (9e52cb0)

• build_nix_image: use cachix cache (e93e951)

• build_nix_image: use default dev shell in clean nix store (fe6e851)

• cid: disable printing of image build logs (a991dd0)

• cid: enable publication of code and jupyter images (6e84c8d)

• cid: magic -> cachix (bfdfb91)

• cid: reenable bpdi concurrency group (6b657c9)

• cid: remove line break in test-nix job (70368b7)

• cid: root-reserve-mb 34816 -> 38912 (a03d745)

• cid: use cachix cache (c5f04c6)

• cid: use composite action to build and publish images (c3d5c69)

• cid: use default dev shell in clean nix store (0894674)

• containers: fix amd64 in compose configuration (0cad067)

• containers: nvidia-smi RPATH expects ld-linux-x86-64.so.2 in /lib64 (436d52d)

• containers: set default locale variables (6800b08)

• deps: async and cli (b258ab9)

• determinstic_inference: note InferenceStage Sum type (53836f5)

• dev: default to deployment vs job (5f3a340)

• dev: default to nfs volumes (4ee68ed)

• dev: host active nixbuild cue config (bb923df)

• dev: host active pyrovelocitydev cue config (b8f2d25)

• dev: host example config in dev dir (5038272)

• dev: parameterize PVC access modes (471bd38)

• direnv: don’t enforce nix-direnv version (3379a73)

• env: set variables for dev access (e54484f)

• flake: add ${env}/lib to LD_LIBRARY_PATH (f6f1af3)

• flake: align oci manifest package names with image names (44ef896)

• flake: disable push to ghcr (319a587)

• flake: enable python-versioned dev envs (73465e4)

• flake: exclude tests requiring pyensembl (a322b8e)

• flake: parameterize devShells by python version (e26a1d7)

• flake: pass autoPatchelfHook to overrides (51e2274)

• flake: pass cudaPackages to overrides (6f179f8)

• flake: update poetry2nix cache public key (5908392)

• flake: use env vars directly in image build (7570d41)

• flake: use refactored package drv (36410ef)

• gitignore: add .uml (7ce78f6)

• gitignore: database files (092deee)

• gitignore: ignore ensembl cache directory (920cd20)

• interfaces: implicit import of typing.Optional (c147643)

• io: add ensembl batch 429 and 404 error handling (942a175)

• io: explicitly declare plumbum command with local (f67f1ad)

• make: add target to update a single flake input (56ddb26)

• make: disable token for local jupyter server (fac8f8f)

• make: install pre-commit from poetry (9778395)

• make: split tree over lines (f9f1d1b)

• make: support multiple dev deployments (15fdda3)

• make: use pyreverse for uml generation (ba5b674)

• models: account for parameter space singularity (0c151c5)

• models: add deterministic inference model to public interface (fa27940)

• models: add newline to print inference data (22109eb)

• models: add observation flag to inference model (719db25)

• models: change logger from warning to debug (0221974)

• models: compute all kwargs inside plot_sample_trajectories_with_percentiles (df611a2)

• models: explicitly split rng keys (9144650)

• models: export deterministic simulation solver (4293af6)

• models: guard usage of latex behind path check (a31f769)

• models: make sigma guess a parameter (2f16aec)

• models: multiple concrete dims examples (bc5a254)

• models: observation_flag -> data_observation_flag (b17a8f0)

• models: plot single timepoint data as vectorized series (6dd2256)

• models: refactor solve_model_for_all_genes_cells from model (89de821)

• models: refactor generate_predictive_samples (e835e7b)

• models: refactor plot_trajectory_with_percentiles to work with multiple timepoints per cell (b02d816)

• models: remove solve_model_for_all_genes_cells refactor TODO comment (8593da0)

• models: remove redundant Result container for plot_sample_trajectories (b7ca6e0)

• models: remove result wrapping from save_inference_plots (0aae2fe)

• models: return all indices from sort_times_over_all_cells (91c13ab)

• models: sample times from observed delta distribution (7a9bbd8)

• models: separately normalize plot_sample_phase_portraits colorbar for linear and log (d4ab537)

• models: update deterministic inference (495fde2)

• models: update dimensions in analytical solution test (de7e83c)

• models: update hyperparameter calibration test values (91a7934)

• models: update plot_sample_trajectories styling (a8291ae)

• models: use arbitrary initial condition in analytical solution (a676ca9)

• models: use log-normal likelihood (580d2ef)

• models: use vectorized deterministic inference model (b67976a)

• nbs: account for parameter space singularity (cf0bb1e)

• nbs: add manual derivation of analytical solution (77dcce2)

• nbs: update nb path in Makefile (7d0e389)

• nbs: update references (12e4f9b)

• nix: add all nvidia libraries to patchelf search path (aca7f99)

• nix: add required ctan pkgs to custom texlive (a09420a)

• nix: disable package check on darwin (0843fa0)

• nix: draft override for attempted system call from sandbox on darwin (72a8e89)

• nix: include tex and lmodern in syspackages (e1357b9)

• nix: refactor extraSysPackages (810e406)

• nix: refactor internal package drv (d8b2e03)

• nix: update code image name (b9eee4b)

• nix: update package src path (c1bb1b6)

• pkgs: add curl and wget to extraSysPackages (745884e)

• plots: guard usage of latex behind path check (d302e66)

• plots: set 10^-8 min for log-transformed values (f322d21)

• plots: support parameterized labels (216a512)

• plots: use package style (2497337)

• poetry2nix: update overrides (06f5be4)

• poetry: default to local virtualenvs (8f475ad)

• preprocess: separate computation of neighbors (dd217c9)

• pyproject: default to exclude tests that require pyensembl (cbd905e)

• pyproject: disable annoy (51ddce4)

• pyproject: disable poe (56ad8ef)

• pyproject: omit scripts (55e9311)

• quarto: do not hard-code QUARTO_PYTHON in drv (2c8be95)

• quarto: vendor drv (e29b133)

• scripts: update transcript analysis (9594ab9)

• tests: remove unused shape statements (7a0f0df)

• tests: setup_observational_data with explicit return values (7159f59)

• tests: update deterministic inference (c985797)

• tests: update deterministic inference for vectorized model (4f74faf)

• vscode: add db client (23e0f00)

• vscode: use basic project-manager (d73df90)

• workflows: make training_workflow dynamic (08d2a45)

• workflows: update configuration for scikit-learn 1.5 (169e052)

0.2.0-beta.14 (2024-03-29)

Bug Fixes

• bazel: update test module list (f9a38aa)

• docs: update badges (0a84010)

• gitattributes: linguist ignore Makefiles (508bddd)

• gitattributes: linguist ignore nbs and reproducibility (7c4f28d)

0.2.0-beta.13 (2024-03-26)

Features

• ci: check and fast-forward merge PRs (251e11f)

• help: add help module (d30f670)

• make: add targets to build and serve nbs (28e3779)

• nbs: add interlinks extension (dc99563)

• nbs: add sn extension (7e4331c)

• nbs: add user example to templates (bbeceaf)

• nbs: copy contributing (c7f84d8)

• nbs: enable api reference docs (cf4e1a9)

• nbs: export ipynb format (b174e95)

• nbs: init installation (258fdc1)

• pypi_template: add workflow execution example (c69767d)

• pypi_template: generate and display figure outputs (a0111e2)

• pypi_template: include training and summary for two distinct model classes (217a3fd)

• scripts: add nbs build script (59f708f)

• scripts: init pypi template (5ed5f10)

• scripts: pull _freeze from dvc cache during nbs build (45d191b)

• utils: add class to suppress function output (76af2cc)

• utils: add print_config_tree (e3546df)

• workflows: add medium resources category to configuration (aad47f4)

• workflows: separate summarize cache version (55ada29)

Bug Fixes

• analyze: add types to compute_volcano_data (34885da)

• conda: install pytorch from pytorch channel (750a324)

• containers: use requirements-main.txt (25a13dc)

• cytotrace: remove a subset of unnecessary print statements (1847cbd)

• dev: add minimal/testing example config (c7bd905)

• docs: migrate history to CHANGELOG (1204056)

• docs: separate cool and warm logos (b30e041)

• docs: sync description (98fb385)

• docs: update sphinx conf exclude pattern from colab to template (4363b90)

• dvc: update remote path (1476bc2)

• gitignore: *.*.md and _configuration.yaml (ab45036)

• gitignore: only ignore top-level data folder by default (8e9daf5)

• init: reenable workflow-independent public interface (fc2aae5)

• make: add passthrough render-notebook target (465ebaa)

• make: add refresh target to remove cache (93ccd25)

• make: add workflow-clean target (b9c1780)

• make: print workflow env vars before execution (823d330)

• make: write requirements-main (a38380a)

• nbs: add make target to update _freeze directory (91a7f03)

• nbs: add plots to api docs (d247958)

• nbs: add sync-nb make target to upload to gdrive (9d4d7d0)

• nbs: link numpy (df49123)

• nbs: migrate toc to header (75bc1ae)

• nbs: move introduction to tutorials (5f02c73)

• nbs: remove gh pages badge (3574679)

• nbs: remove reference folder (77abb60)

• nbs: soft-link to top-level CHANGELOG.md (15f45ff)

• nbs: static preview port (928a6cc)

• nbs: temporarily link index to readme (06216f7)

• nbs: update index (8945de3)

• nbs: update section contents (6883231)

• nbs: use gdrive notebook in colab link (fc760e6)

• plot_gene_ranking: establish compatibility with adjusttext 1.1.1 (cf37f8e)

• plots: add padding to plot gene ranking (9b3fa5e)

• plots: add types to plot_gene_ranking (8ed9a75)

• plots: add types to summarize gene selection (deeaba5)

• plots: close figure in plot_gene_selection_summary (099e6fb)

• plots: close figure in plot_shared_time_uncertainty (ea34035)

• plots: default to loading data for predictive sampling to cpu (abcf58b)

• plots: enforce types for plot_parameter_posterior_distributions (8597820)

• plots: enforce types for plot_vector_field_summary (204db57)

• plots: reenable refactored rainbowplot (4c130ac)

• postprocess: use logger for printing (18206f7)

• predictive: use data_model input for data set model pairings (666e48e)

• preprocess: close figure (f776c0e)

• preprocess: update docstring (fc4a8b8)

• pypi_template: add blank header cells (46ecc14)

• pypi_template: add exploration section (1da0a53)

• pypi_template: collapse installation instructions in callout note (266a940)

• pypi_template: remove unnecessary output capture (562892e)

• pypi_template: sync with library updates (954d242)

• pypi_template: update frontmatter (f8094b3)

• pypi_template: update gitignore (78c8447)

• pyrovelocity: update dunder init (421c1f4)

• requirements: rename to requirements-main (ed50b4d)

• scripts: cd with subshell (90423be)

• scripts: comment examples authors (8b48b48)

• scripts: disable sudo (073eeed)

• scripts: use manual installation (ba68cd0)

• scripts: use poetry run (74bc828)

• summarize: check phase portrait cache before exiting (6692a8a)

• summarize: include selected genes in summary figure (16fd344)

• summarize: respect typed interface to plot_vector_field_summary (bac7aad)

• summarize: update shared time plot (8477626)

• summarize: update shared time plot font (cdb1f69)

• summary: support selected genes and marginal histograms (8d38ccd)

• train: close figure (31f508b)

• train: update docstring (e958c45)

• utils: migrate clear_local_cache to workflows (08a6463)

• workflows: note migration to CalVer for cache versions (0e0ac49)

• workflows: read cache flag from env var (9488074)

0.2.0-beta.12 (2024-03-16)

Features

• env: add pyrovelocity-specific env vars (6dfa69c)

• scripts: copy gcs archives to drive (a4eb5f5)

• workflows: add upload summary task (8693728)

• workflows: expose testing and upload flags as environment variables (9ed24f8)

• workflows: use upload_results fields from each WorkflowConfiguration (fbf4ea3)

Bug Fixes

• cid: add note on use-gha-cache (6f79f33)

• cid: disable use-gha-cache (db6bcda)

• docs: change feature branch to beta (e113dcd)

• gcs: return file url from uploadfile* (7d5698e)

• readme: change feature branch to beta (3ce409a)

• scripts: get colab scripts from beta branch (15a219b)

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)

0.2.0-beta.10 (2024-02-24)

Features

• cid: skip image build if one with commit sha tag already exists (cba38e4)

• containers: add dyngen container (de3abae)

• containers: add script to generate simulated data (05b49c2)

• dev: add hpa config (dadb4d1)

• dev: add job config (da03a27)

• dev: update example config for job (c956103)

• execution_utils: support nested dataclasses (a382204)

• flake: add GAR images (eaaddfe)

• flake: add time to sysPackages (8d1c994)

• make: add target to build dyngen image (1c46950)

• make: add target to copy file to cluster pod (7d22b0c)

• make: add target to disable zsh time reserved word (be99bd9)

• make: add target to forward port from dev pod (f9cff22)

• make: add target to toggle local virtualenvs (b96691d)

• postprocess: add postprocess module (d565e27)

• preprocess: allow subsets of obs and vars (93a0465)

• utils: add function to generate public api candidates (402259e)

• workflows: add postprocessing task (5654b6c)

Bug Fixes

• analyze: define public interface (0ee8e58)

• cid: add nix envs for GAR images (5fda3ee)

• cid: set build volume mount path /nix (d542fa6)

• cid: use base64 encoded SA creds (29af74e)

• colab: add maximize build space (9d014b1)

• colab: increase root reserve (37058af)

• conda: remove redundant cuda installation (d61866b)

• data: update public interface (54932e6)

• dev: config pvc name (2d1d08b)

• dev: remove default latest tag from image spec [no ci] (24a1ff4)

• dev: set default pvc name to dev (0a656eb)

• dev: set update strategy to recreate (f79a958)

• dev: update config to use job vs deployment (cd7537f)

• dev: use config pvc name in deployment (3027f0f)

• dev: use config pvc name in job (77e0ca5)

• dev: use config pvc name in pvc (57310ca)

• execute: print fallback logger exceptions (2f98d2e)

• execute: remove unused comments (1dbd3f8)

• flake: use base64 encoded SA creds (1dea556)

• gitignore: *-sa.json (9bd3132)

• gitignore: all *dev.cue (08c0108)

• interfaces: define public interface (28113b6)

• logging: set local log level (8ee8513)

• main_configuration: enable testing of primary data sets (5912daf)

• main_configuration: remove list[DataClass] fields from WorkflowConfiguration (016d885)

• main_configuration: remove resource tuples (36fe9dd)

• main_workflow: construct training configurations explicitly (3f9f12c)

• main_workflow: reenable testing for primary data sets (5f04a8c)

• main_workflow: set cache parameters from constants (d247c75)

• main_workflow: specify accelerator type constant (d93d863)

• make: comment ghsecrets for encoded GAR SA creds (ed954dc)

• models: use tmp_path fixture for model data (e17bf9b)

• postprocess: ensure data_model_path exists (3cff34f)

• preprocess: add pca rep if not present (96afc5b)

• preprocess: ensure n_vars > n_pcs (a892487)

• preprocess: host data set parameters in interface (f51a098)

• preprocess: specify public api (4114d9d)

• pyrovelocity: add dunder main to launch cli as module (ff5b553)

• train: move data set parameters to preprocess (0a0ea5f)

• train: update interface (52e33da)

• train: use tmp_path fixture for loss plot (6af93ea)

• utils: specify public api (5e325d9)

• velocity_model: remove debug logging of plate sizes (4ea3f4c)

• workflows: update training parameters in main configuration (984255b)

0.2.0-beta.9 (2024-02-03)

Features

• api: typecheck train_model and allow path inputs (fbd34bf)

• conftest: provide global fixture to file for sample data (409d96d)

• data: add load_anndata_from_path (7d43e29)

• data: support subsetting during data download (fa066cd)

• flake: update torch >2 (6b838d3)

• interfaces: collect dataclass interfaces (f2c6ea9)

• main_workflow: add model training task (4ca67b4)

• main_workflow: use dataclass interfaces (2324654)

• make: add cluster-shell target (23c3d5e)

• preprocess: refactor for compatibility with dataclass interface (19c7b68)

• pyproject: add requests-mock for testing (42db104)

• pyproject: upgrade stable dependencies (7698cf7)

• test_data: add tests for data module methods (dcd8276)

• train: add training script for workflow usage (5fcf4c3)

• workflows: add pbmc68k, pons, and larry data sets (41c18e2)

Bug Fixes

• api: discard returned adata in doctest (78456f8)

• bazel: remove unused test modules (a724853)

• cid: enable cachix cache for build-nix-images job (63e545f)

• cid: enable cachix for release images (49075ef)

• cid: enable cachix for test-nix job (f533984)

• cid: increase root reserve and swap (8035847)

• cid: increase swap size (3ea04b7), closes /github.com/actions/runner-images/discussions/7188#discussioncomment-6750749

• cid: reduce swap (87cb626)

• cid: remove debug (95a88f3)

• cid: update codecov-action to v4 (e0dbda3)

• cid: update nix-installer to main (98a0b78)

• cspell: update dictionary (119f436)

• data: make var names unique (8fb44f8)

• dev: add example security context overrides (4ac343d)

• execution_utils: construct dataclasses given defaults (fa95db3)

• gitignore: models directory (f6e4208)

• gitignore: only ignore top-level models directory (8ad7a6d)

• interfaces: use train_dataset from train module (76b5563)

• magic-nix-cache: revert v3 update (d1c85f8)

• main_workflow: update docstrings (e1f726d)

• main_workflow: use NamedTuple class (618c430)

• make: exclude additional modules from dep graph (58850a4)

• make: filter io and configuration from pydeps (ddf6d7d)

• make: move pod ID extraction inside cluster-shell target (7e31b54)

• make: remove unused pydeps exclusion (0df6346)

• make: set cachix in gh vars/secrets (f5098eb)

• preprocess: remove completed TODOs (970ac7a)

• pyproject: pytest ignore reproducibility folder (434efae)

• requirements-cpu: remove outdated hashed version (3a36c6e)

• setup_environment: update setup-pandoc pin (24a8ef4)

• trainer: cast categorical/integers as floats for log-transformation (62e7fd5)

• train: update import path in doctest (a8f50d0)

• transcription_dynamics: enable type-checking (88e496c)

• utils: comment unused functions (1c05fa2)

• utils: update AnnData type import (42d21d9)

• velocity_model: handle likelihood not implemented (e5d06d2)

• velocity_model: remove optional type defaults for observations (7b3a9bd)

• velocity_model: set u0/s0 types to RNAInputType (d12e0dd)

• velocity_model: update imports (87386a1)

• velocity: cast categorical/integers as floats for log-transformation (6e1ab7f)

• vscode: disable coverage to respect debugging breakpoints (48dd4b8), closes /github.com/microsoft/vscode-python/issues/693#issuecomment-367848085

• workflows: enable cache for training tasks (86b9333)

• workflows: increase resources for preprocessing and training tasks (b0e81b1)

• workflows: set preprocess data path (ecde0fa)

• workflows: set task resource limits (7416521)

0.2.0-beta.8 (2024-01-26)

Features

• workflow: add preprocess data tasks (d4f5f89)

Bug Fixes

• _velocity: update doctest imports for preprocess (44db75b)

• api: update doctest imports for preprocess (8cc6683)

• cid: update pages actions hashes (c684dd4)

• make: add update-ratchet target (ea11b10)

• workflows: disable spot for preprocess tasks (fdd89f0)

• workflows: increase mem limit for preprocessing tasks (c360594)

0.2.0-beta.7 (2024-01-24)

Features

• workflows: map over multiple data sets (4c8cc01)

Bug Fixes

• execute: truncate git branch length in workflow version (441f102)

• gha: update download-artifact (41d0119)

• gha: upgrade to node 20-based actions (afd7f60)

0.2.0-beta.6 (2024-01-24)

Features

• bazel: add aspect lib (512e127)

• bazel: add xdoctest macro (b39b26e)

• bazel: generate pip-compile requirements (e38acf6)

• bazel: use all_requirements for package library (165b84a)

• data: validate urls and file size before download attempt (b9b6f0b)

• main_workflow: setup download_data task (9cfdcce)

• make: add pydeps target to render graph (ff2e8b3)

• pypi: add cpu-only requirements (cbb95d6)

• vscode: add fileutils (e5dfb0a)

• workflows: add main workflow (153e12c)

Bug Fixes

• bazel: add aspect lib to root rc (b661bff)

• bazel: add ci configs (9c15b5a)

• bazel: move py_library to workspace-level for xdoctest (29a3a7f)

• bazel: remove platform-specific requirements (bfeab1b)

• bazel: set target platforms “all” (3ab6152)

• bazel: use cpu requirements (a040872)

• bazel: use py_test from rules_python in py_test_module_list (fffb0d6)

• bazel: use requirements-bazel.txt (d7f3969)

• bazel: use standard pip hub name (d027451)

• cid: add actions cache for bazel (85a6576)

• cid: cache cpu requirements (4e1b37c)

• cid: check cache for requirements or regenerate (3109d5e)

• cid: check disk usage (db2e99e)

• cid: disable lock-bazel (1407ea1)

• cid: lock-bazel before tests (f53b8f8)

• cid: reenable execute-workflow dep on image builds (#502) (c00124e)

• cid: save updated requirements artifact (793b1c7)

• cid: use bazel make targets (a46d544)

• cid: use test-python job name (0b3226f)

• cspell: add cytotrace (2fb9099)

• cspell: add scanpy (f9002ac)

• cspell: add type checking (e027023)

• data: use string inputs for download_dataset (887768a)

• gitignore: mlflow and data (fee99ec)

• make: add bazel targets (0f7b882)

• make: add debug and nodocs test targets (2f83b83)

• make: add targets to export cpu requirements (fe5e09d)

• make: cache requirements with lock-bazel (84f155d)

• make: do not lock bazel by default (276cffb)

• make: update pydeps exclusions (901115b)

• make: use correct requirements file with test-bazel (59f0514)

• mergify: update check-success job names (87c51bf)

• pyproject: add block to export cpu requirements (09951dd)

• pyproject: add docformatter settings (23b715b)

• pyproject: disable pytest warnings (d4d0ad8)

• pyproject: point main script to workflows cli (e35aa87)

• pyproject: set default pytest logging to INFO (4522430)

• test_utils: remove gillespie from random seed diff (df76a7f)

• tests: make doctests run on cpu (f4543c5)

• tests: reenable bazel xdoctests (29c2371)

• tests: reenable top-level imports (2ea0032)

• trainer: use inherited methods from VelocityModule (178abfe)

• utils: remove externalized VelocityModule method (72747fc)

• velocity_model: enable type-checking of get_rna (4ffdfb9)

• velocity_model: set create plates log to debug (6259e7a)

• velocity_model: set log name from module (7da7879)

• velocity_module: implement required inherited methods (885a841)

• velocity: use configure_logging (3477268)

• velocity: use VelocityModule method instead of utils (8a4afbd)

• vscode: add cspell dictionary (4e5c7ae)

• vscode: disable search.followSymlinks (7647f76)

• vscode: disable autohide sidebar (e89f240)

• vscode: disable cli debug launch arguments (3b53b51)

• vscode: exclude search/watch hypothesis cache (60bf2ba)

• vscode: update extensions (fc89dab)

• vscode: update settings (687f2bb)

• workflows: set workflow version to library version (f094130)

0.2.0-beta.5 (2024-01-15)

Features

• bazel: add remote build cache (0afae63)

• cid: add test-bazel job (0fcac1e)

Bug Fixes

• gitignore: add service-account-credentials.json (13b3985)

0.2.0-beta.4 (2024-01-15)

Features

• bazel: add helper macro to run test modules (0768837)

• bazel: add tests build (27efc09)

• bazel: init module (46195c2)

• flake: add bazelisk (cb34805)

• make: add target to run tests with bazel (3c0ffcd)

Bug Fixes

• docs: clone beta branch in colab template [no ci] (006c631)

• vscode: exclude bazel- from search/watch (b2b63b5)

0.2.0-beta.3 (2024-01-11)

Features

• cid: build workflow execution container (8e9999e)

• dev: add cluster dev resource manifests (812a327)

• dev: add cue module (9d1e729)

• dev: add example cue values (001a181)

• docker-config: add example.json (346b787)

• flake: add htop to devPackages (9dc2760)

• flake: add openvscode-server to devPackages (af19432)

• flake: add workflow execution container (8215232)

• make: add cluster config targets (3ce33c9)

• make: add container targets (e9b158d)

• make: add target to render dev manifest (b4c11a2)

• make: add target to show closure size for a store path (a292cd9)

• make: add targets for in-cluster dev (0c6cae3)

• make: add targets to (un)pin gha commit hashes (d43b964)

• make: add vscode targets (335ed1f)

• make: add workflow execution targets (ed0f2dc)

• make: test packaging of dev module (7080a6e)

• pyproject: add workflow execution dep group (9e8fbcc)

• pyrovelocity: add workflow execution package (ffd2808)

• pyrovelocitydev: add cue module (1aa633a)

• skaffold: add config (b4e02bd)

Bug Fixes

• build-images: add -cpu to pkg.Dockerfile image name (bdb6fa4)

• cid: add maximize-build-space step to nix image build (3baf69b)

• cid: paths-ignore array (9e86990)

• cid: publish workflow execution image (8380d2b)

• cid: set git variables in test-nix job (f41170b)

• cid: use hyphen in run target (7341089)

• compose: set SHELL=zsh (db19f08)

• compose: use zsh in jupyter (a2852ad)

• devcontainer: vsliveshare reference (c151ee2)

• dev: require command and args in deployment (ff74b8c)

• dev: set replicas default (1->0->1) to toggle state (d5ecb52)

• docs: link to example dev env in installation (e6118da)

• docs: mark docs/ as documentation (e0d93d9)

• dotenv: add cluster dev namespace (9d671b7)

• dotenv: update container and cluster config (cc31ec3)

• envrc: execute set-git-env script (63c8367)

• extensions: duplicate devcontainer as recs (74ad1b1)

• flake: add cluster tools to devPackages (7a5d948)

• flake: add file findutils procps to sysPackages (f548403)

• flake: add gnupg to devPackages (15d5ab9)

• flake: add less to sysPackages (28fabf8)

• flake: add nixpkgs cudaPackages.cudnn_8_5 to propagatedBuildInputs for nvidia-cudnn-cu11 (3a93f0a)

• flake: add which to sysPackages (70e4dad)

• flake: add workflows group to python packages (a4ad180)

• flake: get cudaPackages.cudnn_8_5_0 from nixpkgs 23.05 (bce8928)

• flake: move nvitop to extraPackages (a15a35d)

• flake: remove dash from sysPackages (12793a8)

• flake: sort sysPackages (6bcca32)

• flake: sysPackages bourne shell via dash (a679b9f)

• flake: sysPackages libgcc (f7c4489)

• flake: use unstable channel for k9s (93084c4)

• gha: pin dependencies in app (81455d3)

• gha: pin dependencies in build-images (a463e72)

• gha: pin dependencies in cid (3408631)

• gha: pin dependencies in cml-images (81c2542)

• gha: pin dependencies in colab (2ff5542)

• gha: pin dependencies in labeler (779225d)

• gha: pin dependencies in setup_environment (51d2349)

• gitignore: add nix outputs (b2947ab)

• gitignore: dev.cue (9d904b0)

• gitignore: docker-config.json (dd09617)

• gitignore: ignore local kube config files (9304c35)

• make: add devcontainer build targets (e7fc2b7)

• make: add target for local jupyter server (84e4c68)

• make: add targets to deploy and delete dev module (40b7c64)

• make: change _ to - in jupyter targets (29e491d)

• make: deprecate nox and target (8f68d1a)

• make: export hashed PyPI requirements (7e0d7f0)

• make: lint and apply cue module (4ccc220)

• make: parametrize cluster dev instance names (228eae8)

• make: set codespace default machine to 64GB disk (5d7f747)

• make: update pre-commit targets (98d4c7c)

• make: update python lock targets (40fbfb5)

• make: update section headings (37d1a64)

• make: use pre-commit set git meta variables (5063e86)

• mergify: remove base branch constraint (d9c4810)

• meta: sync versions with pyproject.toml (97d3c25)

• pre-commit: exclude dev dir (a882457)

• pre-commit: remove set-git-env (2c51524)

• pre-commit: skip local hooks in ci (bb26f98)

• pre-commit: update local hooks (42bc4e7)

• pyproject: remove jupyter_contrib_nbextensions (16cd201)

• resources: add cue versions (6b03d3d)

• set-git-env: account for absence of newline (8b475a1)

• setup_environment: add workflows group (fdbecc0)

• vscode: do not search cue module dependencies (c3868cb)

0.2.0-beta.2 (2024-01-03)

Bug Fixes

• git: rename master to main (c608f9c)

0.2.0-beta.1 (2024-01-03)

Features

• add merge queue configuration (#470) (14c9328)

• argo: add build-images workflow (6697f55)

• cid: init cid workflow (0482ea9)

• codecov: init repo config (d09736c)

• compose: add compose for jupyter server (b6a4ce8)

• containers: add pkg and gpu Dockerfiles (690fa7b)

• devcontainter: update configuration for flake (37475e5)

• devshell: add manual activation script (36fe896)

• docs: add repo CHANGELOG.md to history (86625a8)

• flake: add CUDA env vars to devcontainerConfig (e004597)

• flake: init (8a11673)

• flyte: add config templates (511f6cb)

• gha: add build-images workflow (abb7266)

• make: add ci targets (8a7c250)

• make: add nix targets (8037ad1)

• make: add target to print tree (4080c08)

• make: add target to replace vars in config file (4e9e1a9)

• make: add targets to configure dev env (10aa781)

• make: add targets to set gh vars and secrets (da50e44)

• make: add targets to setup dev env (b69015d)

• make: add update_version target (4a352d3)

• pyproject: add jupyter server to docs group (68eabde)

• scripts: add script to activate nix flake (2283f11)

• scripts: update flake to accept cmd arg (01c2e94)

• vscode: config debug launch for cli (610fb8a)

Bug Fixes

• app: restrict workflow to main (5331fc5)

• cid: enable impure nix build (936d150)

• cid: ignore conda/** (fdf0cb4)

• cid: reenable docs build jobs (efe61c2)

• cid: restrict build and release images to x86_64 (6162007)

• cid: set NUMBA_CACHE_DIR to runner.temp (6d759a7), closes /github.com/numba/numba/issues/4032#issuecomment-488102702

• cml-images: reenable CML image workflow (#485) (815e616)

• colab: reenable pytorch and nvidia channels (53f60c4)

• conda: sync virtual packages with colab (75261d8)

• containers: git move from dockerfiles (a56e5ad)

• direnv: use flake (2f4a3b7)

• docs: add CID and GH pages to status (ca1dc54)

• docs: add colab badge to template notebook (7df9970)

• docs: clone branch or tag in colab template (623048c)

• envrc: move direnv vars to .env (4a1b343)

• flake: add devPackages for rust term IDE (3f21d7d)

• flake: add nvitop to sysPackages for gpu mon (b65ebbf)

• flake: disable checkPhase (07123f1)

• flake: disable llvmlite wheel for all systems (c9db64d)

• flake: numba depends on tbb_2021_8 (d0e326b)

• flake: print value of NUMBA_CACHE_DIR (70c9587)

• flake: set NUMBA_CACHE_DIR in default checkPhase (d135d41)

• flake: set ref beta (a9c0728)

• flake: switch poetry2nix patch ref (3988172)

• flake: switch to stable poetry2nix patch branch (820fa94)

• gha: add setup_environment action (a1d4d30)

• gha: disable independent actions (f3ae9fb)

• gha: rename containers folder (0e4ccd9)

• gha: rename deploy to app (1540985)

• git: rename master to main (6743eeb)

• labeler: add workflow_dispatch (74cf8bf)

• labels: add PR workflow control labels (b5649fd)

• make: add git ref/rev vars (1f70ea0)

• make: add package dev targets (0d31924)

• make: disable setting CODECOV_TOKEN (d366338)

• make: universally accept flake config (f8540f3)

• make: update docs targets (dccf668)

• mergify: queue method fast-forward (f13bb43)

• mergify: update check-success names (e07cefd)

• meta: add pyrovelocity-reviewers to codeowners (b5c1a77)

• pre-commit: lint (5cddc71)

• pre-commit: sync config with pyproject.toml (becd02e)

• pyproject: enable pytorch and nvidia channels for conda-lock export (0f9cdec)

• pyproject: move to src (4e222fc)

• pyproject: pin lxml<5.0.0 (134cede)

• pyproject: remove pipeline components (3c08f46)

• pyproject: update conda-lock deps (4fa975a)

• pyproject: update docs dependencies (77fe0e3)

• pyproject: update tool configs (34621ec)

• pyrovelocity: move to src (5f70c46)

• setup_environment: add pandoc (2901217)

• vscode: update font sizes (4ea8f6e)

• vscode: update settings for devcontainer (3113bef)

0.1.3 (2023-09-05)

• See 0.1.3

0.1.2 (2023-04-16)

• See 0.1.2

0.1.1 (2023-02-16)

• See 0.1.1

0.1.0 (2022-09-05)

• See 0.1.0