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)
• 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)