v0.2.0-beta.16

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

Bug Fixes

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

v0.2.0-beta.15

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](ht...

v0.2.0-beta.14

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)

v0.2.0-beta.13

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](fc4a8b817bbf...

v0.2.0-beta.12

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 upload_file_* (7d5698e)
• readme: change feature branch to beta (3ce409a)
• scripts: get colab scripts from beta branch (15a219b)

v0.2.0-beta.11

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

Features

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

Bug Fixes

• actions: nix store gc 5 -> 3G (59f74bf)
• actions: reenable post-build garbage collection (37f1d78)
• actions: restrict nix gc (d8c68e9)
• actions: use skopeo instead of docker (b5b908e)
• app: update action versions (283d6c6)
• cid: add clean nix store to publish release images (a2daf9a)
• cid: add GAR env to publish release images (790045a)
• cid: add names to test-nix job steps (ad25df9)
• cid: do not rerun on draft submission (5314c8d)
• cid: ignore changes to colab workflow (3c36296)
• cid: ignore explicit lock files (1552086)
• cid: image builds condition on NOT dev mode (947bfa0)
• cid: include python version in test-python concurrency group (9411e8f)
• cid: publish flake on release (72c0841)
• cid: reduce root reserve (94ec314)
• cid: reenable restriction to x86_64-linux (1d0320e)
• cid: remove deprecated nix image build matrix (1aa74f0)
• cid: test-nix maximize build space (43600cb)
• cid: update test-nix nix build comments (e054a60)
• cid: use dev-mode label (2a4f469)
• cid: use local nix cache (ba638f6)
• cid: use local nix cache (f929dbd)
• colab: set cuda 12.2 (f8c6a73)
• colab: set unique path for constructor script (aeff7c6)
• colab: update action versions (88bd978)
• conda: default to python 3.10 (c093849)
• conda: move python version to top (fec219b)
• data: lint f-strings (6324327)
• data: remove call to copy method (979110a)
• data: set default adata None and handle (2a267e0)
• direnv: update containers watch_path (4e622d3)
• direnv: update pkgs watch_path (84b526c)
• direnv: update poetry watch_file path (ae3db70)
• examples: add install-tinytex make target (f1f7523)
• examples: force removal of _files dir (518567f)
• examples: ignore .quarto (bc4d21a)
• examples: set html font (3df5652)
• examples: set install-extensions deps (e034add)
• examples: support render without execution (9b6458e)
• execute: add random suffix to remote prod execution version ([4553adf](4...

v0.2.0-beta.10

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)

v0.2.0-beta.9

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)

v0.2.0-beta.8

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)

v0.2.0-beta.7

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)