v0.4.5

0.4.5 (2025-04-10)

Bug Fixes

• make: update run-instructions target (37a4d20)
• pyproject: do not exclude tests with network mark by default (4324962)
• pyproject: update test extra group to include ipdb (a6c7fc1)
• run-workflow: qualify hydra outputs artifact by execution mode (3981426)
• scripts: include unzipped directories in copying gcs files to drive remotes (b63fce2)
• time_fate_correlation: comment unused estimate_time_lineage_fate_correlation function (0887ff3)
• time_fate_correlation: do not remove centroid obs (fd2295a)
• time_fate_correlation: map data set names to labels (e8a297e)
• time_fate_correlation: synchronize obs subsets (9a93e18)
• utils: dispatch to load_anndata_from_json on json paths (1493107)
• workflows: use updated time lineage fate correlation interface (ae76d9d)

v0.4.4

0.4.4 (2025-04-08)

Bug Fixes

• analyze: set seeds in third-party calls (5afe372)
• constants: read or set PYROVELOCITY_SEED from env (22a4954)
• io: add logic to retry dataset downloads (dd4b371)
• models: set seeds in third-party calls (a19ec6a)
• plots: set seeds in third-party calls (fd23ec8)
• postprocess: set seeds in third-party calls (79522bb)
• preprocess: set seeds in third-party calls (7f14f5c)
• random_state: add functions to set rng seeds and states (82bd12e)
• tasks: reset seed in evaluate (72ffcec)
• tasks: reset seed in postprocess (79087b5)
• tasks: reset seed in preprocess (81a7671)
• tasks: reset seed in summarize (ccbae6e)
• tasks: reset seed in train (5fefd01)
• tasks: use download with retry enabled by default (f7ec55b)
• workflows: condition all uploads on upload results var (3da221d)
• workflows: use global seed constant (84f8be2)
• workflows: use seed constant in main configuration (0994b72)

v0.4.3

0.4.3 (2025-04-04)

Bug Fixes

• cid: enable all data sets for workflow execution (f955657)
• make: add targets to selectively execute workflows (fe8b596)
• make: make version updates match exactly (bd10c32)
• workflows: add DatasetRegistry class to support selective execution (309c08f)
• workflows: document data set selection from cli (4c695e2)
• workflows: use DatasetRegistry to select data sets for execution (c4d61ef)

v0.4.2

0.4.2 (2025-04-02)

Bug Fixes

• constants: map model identifiers to velocity layer keys (71032aa)
• constants: presume developmental cluster orderings (ff996fc)
• constants: update model ordering (fde8c65)
• evaluate: accept in-memory objects in addition to file paths (832e359)
• evaluate: decompose calculate_cross_boundary_correctness (08f7044)
• evaluate: perform all dataframe manipulation outside plot helper (f86f056)
• metrics: add external trajectory metrics (325169f)
• metrics: handle sparse and dense neighbor graph data (9edb447)
• tasks: add evaluation task (0f1cc42)
• tasks: export evaluation task (21d3e18)
• tasks: set evaluation data set and model ordering (9487e4d)
• tasks: update time fate correlation output directory (c9d90b4)
• utils: refactor string diff line endings (912b107)
• workflows: add task to evaluate trajectory metrics (f965992)
• workflows: add trajectory evaluation outputs (1c80ccb)
• workflows: increase memory limit for evaluate trajectory metrics (65890b2)
• workflows: set time lineage fate correlation upload path (3c0fc4a)
• workflows: set trajectory metrics upload path (c41bca4)
• workflows: update combine time fate correlation task output directory (a1d3429)
• workflows: use evaluate_trajectory_metrics task (bb99a9e)

v0.4.1

0.4.1 (2025-03-31)

Bug Fixes

• analysis: include trajectory functions (16d382e)
• ci: include log files in manuscript artifacts (16253ae)
• ci: include tmp log files in manuscript artifacts (92926e2)
• ci: note artifact path to include latexdiff log (3ed2de2)
• constants: disable demo flag (ef3518b)
• datasets: add clone trajectory data sets (e2b4e5c)
• fixture: add function to generate larry data fixture (9b9491c)
• lineage_fate_correlation: absorb nan cleanup from plotting function to get_clone_trajectory (d194fea)
• main_workflow: reenable all data sets (776ed2c)
• make: support cleaning up workflow artifacts for multiple data sets (9fcd1af)
• manuscript: add local latexmkrc to ensure xelatex (7a2de6d)
• manuscript: make model formulation eqs align (be84321)
• manuscript: note how to retain latexdiff log (267dc1d)
• manuscript: note local tmpdir build (be9070e)
• manuscript: remove paragraph break in align env (481000a)
• manuscript: set explicit figure width percentages (f62edd0)
• manuscript: support unicode thin space in tex (9d7cc90)
• manuscript: update header to include keepaspectratio in includegraphics (8c73ad7), closes #1
• plots: downsample cluster data for larger than 5000 obs (e02e02f)
• plots: prefer hexbin in lineage fate correlation plot (77e2487)
• plots: use trajectory functions from analysis package (38809fc)
• scripts: use trajectory functions from analysis package (5c38692)
• subpopulation: update types (cc3b3d8)
• tasks: compute clone trajectories in time lineage fate correlation task (4f557a9)
• tasks: use trajectory functions from analysis package (6f50788)
• tasks: use vendored data for multilineage clone trajectory (ce26b54)
• time_fate_correlation: refactor create_time_lineage_fate_correlation_plot for workflow usage (695a98c)
• trajectory: use input times and error on empty centroids (71174d2)
• workflows: use create_time_lineage_fate_correlation_plot task function (07b0ee3)

v0.4.0

0.4.0 (2025-03-14)

Full Changelog: v0.3.0...v0.4.0

Features

• cid: add job to publish docs to cloudflare pages (95d731a)
• github: add reusable workflow for docs deployment (0053dd8)
• io: add function to generate and save separate and combined metrics tables (5c8d858)
• io: check and log error for mismatching data download hashes (4b5a75b)
• io: check data download hashes before and after download preprocessing (8653653)
• io: log dataset hash on load (cd00e8a)
• io: optionally check file hashes when (de)serializing json files (0b63cc6)
• just: add docs recipes (2e3bfaa)
• labels: add docs-preview (7910f2c)
• plots: add functions to render graphical model sketches (186ef1e)
• plots: draft lineage fate correlation plot (ee3ae34)
• plots: serialize figure layout and its panels separately (74254ce)
• plots: set base for report (2049cd8)
• plots: support SubplotSpec for plot_gene_ranking (d5bcbe1)
• plots: support SubplotSpec for plot_parameter_posteriors (989c19b)
• plots: support SubplotSpec for plot_vector_field_summary (3685fd8)
• plots: support SubplotSpec for rainbowplot (f205304)
• plots: use mae percentile in gene ranking plot (e6b5343)
• pyproject: install of pytest-xdist and note condition to enable (d7f9823)
• serialization: optionally load as sparse (9a3d50e)
• styles: add function to set matplotlib style globally (e682a63)
• styles: add module for explicit specification of colors (7622639)
• tasks: draft time fate correlation task (d07e961)
• tests: add function to generate fixture data (3986cd4)
• tests: add function to generate postprocessed fixture data (793a72e)
• tests: add preprocessed pancreas 50x13 fixture data (0c71a68)
• tests: test ability to load and log data string diff with serialized (a7ec817)
• utils: add function to compute file hashes (7ede4bc)
• utils: add function to compute the quartile coefficient of dispersion (63115c9)
• utils: include size and category information in data string representation (04b8e7d)
• workflows: add accelerator_type to WorkflowConfiguration (d306c48)
• workflows: add demo flag (7a55e69)
• workflows: add human bone marrow configuration (fdda157)
• workflows: add larry monocyte precursor configuration (168af3e)
• workflows: add larry multilineage configuration (0232207)
• workflows: add larry neutrophil precursor configuration (055d1e0)
• workflows: add pbmc10k configuration (a36ad8e)
• workflows: add pbmc5k configuration (c11cd9c)
• workflows: add selected genes configuration to data sets (8755cde)
• workflows: add task to generate time lineage fate correlation analysis (e5a69c4)
• workflows: enable execution for human bone marrow data (c118a5c)
• 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)
• workflows: enable execution for pbmc10k data (43e0658)
• workflows: enable execution for pbmc5k data (db73f75)
• workflows: enable execution for pons data (3b2ef4b)
• workflows: enable larry data model selection (57d27d3)
• workflows: enable pbmc68k model selection (8a6c997)
• workflows: use WorkflowConfiguration accelerator_type to override train_model accelerator (1978a25)

Bug Fixes

• analysis: add max genes per bin argument to top_mae_genes (b0d0e76)
• analysis: add shadow support for jax arrays (46ad2b5)
• analysis: parameterize top mae genes gene filter (890244b)
• analysis: remove unused comments from compute_volcano_data (d62db2f)
• analysis: remove unused list wrappers (c2efd4f)
• analysis: update compute volcano data interface types (8af8450)
• analysis: update mae_per_gene function and add docstring (0ac2cdf)
• bazel: add mplstyle as data (5f3bcba)
• cid: build only minimal container (8bf5ba2)
• cid: distinguish sphinx docs job (18604fd)
• cid: ignore manuscript workflow ([4821cd7](https://github.com/pinellolab...

v0.4.0-beta.5

0.4.0-beta.5 (2025-03-13)

Features

• cid: add job to publish docs to cloudflare pages (95d731a)
• github: add reusable workflow for docs deployment (0053dd8)
• io: add function to generate and save separate and combined metrics tables (5c8d858)
• io: check and log error for mismatching data download hashes (4b5a75b)
• io: check data download hashes before and after download preprocessing (8653653)
• io: log dataset hash on load (cd00e8a)
• io: optionally check file hashes when (de)serializing json files (0b63cc6)
• just: add docs recipes (2e3bfaa)
• labels: add docs-preview (7910f2c)
• plots: add functions to render graphical model sketches (186ef1e)
• plots: draft lineage fate correlation plot (ee3ae34)
• plots: serialize figure layout and its panels separately (74254ce)
• plots: set base for report (2049cd8)
• plots: support SubplotSpec for plot_gene_ranking (d5bcbe1)
• plots: support SubplotSpec for plot_parameter_posteriors (989c19b)
• plots: support SubplotSpec for plot_vector_field_summary (3685fd8)
• plots: support SubplotSpec for rainbowplot (f205304)
• plots: use mae percentile in gene ranking plot (e6b5343)
• pyproject: install of pytest-xdist and note condition to enable (d7f9823)
• serialization: optionally load as sparse (9a3d50e)
• styles: add function to set matplotlib style globally (e682a63)
• styles: add module for explicit specification of colors (7622639)
• tasks: draft time fate correlation task (d07e961)
• tests: add function to generate fixture data (3986cd4)
• tests: add function to generate postprocessed fixture data (793a72e)
• tests: add preprocessed pancreas 50x13 fixture data (0c71a68)
• tests: test ability to load and log data string diff with serialized (a7ec817)
• utils: add function to compute file hashes (7ede4bc)
• utils: add function to compute the quartile coefficient of dispersion (63115c9)
• utils: include size and category information in data string representation (04b8e7d)
• workflows: add demo flag (7a55e69)
• workflows: add selected genes configuration to data sets (8755cde)
• workflows: add task to generate time lineage fate correlation analysis (e5a69c4)

Bug Fixes

• analysis: add max genes per bin argument to top_mae_genes (b0d0e76)
• analysis: add shadow support for jax arrays (46ad2b5)
• analysis: parameterize top mae genes gene filter (890244b)
• analysis: remove unused comments from compute_volcano_data (d62db2f)
• analysis: remove unused list wrappers (c2efd4f)
• analysis: update compute volcano data interface types (8af8450)
• analysis: update mae_per_gene function and add docstring (0ac2cdf)
• bazel: add mplstyle as data (5f3bcba)
• cid: build only minimal container (8bf5ba2)
• cid: distinguish sphinx docs job (18604fd)
• cid: ignore manuscript workflow (4821cd7)
• cid: observe nix store disk usage (38bfcfb)
• cid: run nix-channel update to disable warnings (ad9c4f5)
• cid: separate docs preview and publish (745c0b0)
• cid: update cachix config for #200 (4568b63)
• cid: update docs build commands (139e6e1)
• cid: use default github token (9cb6825)
• ci: update cachix config for #200 (d3bb57e)
• codecov: temporarily set default threshold to 20% (588a46b)
• containers: add main dep group to package envs (4ddabb3)
• deploy-docs-cloudflare: pin yarn version (d4a9354)
• deps: explicitly lower bound dill (cb2bbbe)
• ensembl_batch: generalize in migration to expression (c3181f0)
• envrc: fix direnv notice spacing (dfd3e90)
• flake: containers only build on stdenv.isLinux (e4ed20d)
• flake: default to disabled ghcr (93bab6a)
• flake: default to disabled github (6125965)
• flake: fix imageFiles for containerImage (e65b63a)
• flake: lock nixpod's home-manager input to 24.11 (45374a0)
• flake: ...

v0.4.0-beta.4

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)

v0.4.0-beta.3

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)

v0.4.0-beta.2

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)