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)
• 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)