Recent Releases of pyrovelocity

pyrovelocity - 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)
timefatecorrelation: comment unused estimate_time_lineage_fate_correlation function (0887ff3)
timefatecorrelation: do not remove centroid obs (fd2295a)
timefatecorrelation: map data set names to labels (e8a297e)
timefatecorrelation: synchronize obs subsets (9a93e18)
utils: dispatch to loadanndatafrom_json on json paths (1493107)
workflows: use updated time lineage fate correlation interface (ae76d9d)

- Python
Published by github-actions[bot] 11 months ago

pyrovelocity - 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)

- Python
Published by github-actions[bot] 11 months ago

pyrovelocity - 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)

- Python
Published by github-actions[bot] 11 months ago

pyrovelocity - 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 calculatecrossboundary_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 evaluatetrajectorymetrics task (bb99a9e)

- Python
Published by github-actions[bot] 11 months ago

pyrovelocity - 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)
lineagefatecorrelation: absorb nan cleanup from plotting function to getclonetrajectory (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)
timefatecorrelation: refactor createtimelineagefatecorrelation_plot for workflow usage (695a98c)
trajectory: use input times and error on empty centroids (71174d2)
workflows: use createtimelineagefatecorrelation_plot task function (07b0ee3)

- Python
Published by github-actions[bot] 11 months ago

pyrovelocity - v0.4.0

0.4.0 (2025-03-14)

Full Changelog: https://github.com/pinellolab/pyrovelocity/compare/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 plotgeneranking (d5bcbe1)
plots: support SubplotSpec for plotparameterposteriors (989c19b)
plots: support SubplotSpec for plotvectorfield_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 acceleratortype to override trainmodel accelerator (1978a25)

Bug Fixes

analysis: add max genes per bin argument to topmaegenes (b0d0e76)
analysis: add shadow support for jax arrays (46ad2b5)
analysis: parameterize top mae genes gene filter (890244b)
analysis: remove unused comments from computevolcanodata (d62db2f)
analysis: remove unused list wrappers (c2efd4f)
analysis: update compute volcano data interface types (8af8450)
analysis: update maepergene 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: ignore push to reproducibility directory (d2bcf68)
cid: observe nix store disk usage (38bfcfb)
cid: run nix-channel update to disable warnings (ad9c4f5)
cid: separate docs preview and publish (745c0b0)
cid: set hydra outputs artifact name from set-variables outputs (32e400f)
cid: update cachix config for #200 (4568b63)
cid: update docs build commands (139e6e1)
cid: use checkout branch for cloudflare docs (5338e55)
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)
dvc: specify ignored subdirectory (9359211)
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: disable github for image builds (4bd844d)
flake: fix imageFiles for containerImage (e65b63a)
flake: lock nixpod's home-manager input to 24.11 (45374a0)
flake: override ghcr ids (4fb9151)
flake: reenable manifest github data (f92d066)
flake: remove aarch64 cross-compilation comment (5cdfcd9)
flake: remove extra ghcr params (a212fb7)
flake: set 500MiB download-buffer-size (d4b819b)
flake: temp pin nixpkgs to 24.11-beta (7798b25)
flake: update flocken interface (224561f)
gitignore: add luarc.json (c5aa832)
gitignore: add node_modules (efe63cd)
gitignore: add output for rattler-build (09ffa56)
gitignore: ignore node (5c53f51)
interfaces: add default factory for preprocess selected_genes empty list (be70f2c)
io: add debug logging of attempted serialization dictionary to serialize anndata (7910665)
io: change sparsification notice from warning to debug level (b33d7b4)
io: default to sans serif in table tex wrapper (260af1f)
io: expose density threshold parameter in CompressedPickle.save (c8b0cf3)
io: increase default compression level for posterior samples (160f857)
io: log data hash on pickle save/load (5a0c660)
io: restore types when deserializing json (ea08a4a)
io: serialize np.bool_ to bool (86e54f0)
io: use dill to support pickling matplotlib objects (daf7716)
io: write data sets modified on download (560e31f)
just: docs-setup -> docs-build (fa46927)
make: reference cloudflare vars (592cbfe)
make: test-cov-xml defers to pyproject for pytest markers (2f82907)
manuscript: bold custom caption headings (c59c182)
manuscript: comment showframe and layout to print page layout (a5aba5d)
manuscript: reduce spacing above title (3e0e59c)
manuscript: use bold panel references (b602c35)
manuscript: use dvipsnamed email color (41f386e)
manuscript: use dvipsnames (b7c2618)
models: include std of predictive samples in posterior dict (2dc9414)
models: mark apparently unused sample sites (4684551)
models: retain gene ranking data for all genes (0217660)
nix: add explicit "main" group (f3f78e0)
nix: add just to extraDevPackages for devShells (100826f)
nix: disable dontCheckRuntimeDeps (385c68e)
nix: disable pyrovelocity checkphase markers network and slow (d4487cf)
nix: disable quarto overlay (default to nixpkgs) (1379c3a)
nix: dontCheckRuntimeDeps (b4493fd)
nix: nullify quarto python3 (0f02743)
nix: reenable grpcio wheel on Darwin (65576b0)
nix: update ctan packages (028fa53)
plots: accept List[Axes] input type (03889ba)
plots: add legend data to cell type plot (d8d277d)
plots: add parameter to truncate high error genes by percentile (1e2b244)
plots: allow scaled measures as well as vector fields (4f5d517)
plots: allow setting axis-level label for colorbars (1972b79)
plots: automatically increment axis indices in lineage fate correlation (0845fab)
plots: default parameter posteriors to box plot (dfe987f)
plots: default to CV in vector field plot (9529dd7)
plots: disable default box plot (320cb9a)
plots: disable text axes in self-generated figure (8a93aa6)
plots: disable transparency in lineage fate correlation (ff63d31)
plots: enable type-checking of plot lineage fate correlation (4843c4b)
plots: export lineage fate correlation plot from plots package (601e0c8)
plots: filter invalid adjustText warning (5e57d40)
plots: filter invalid adjustText warning if logger is available (508ee80)
plots: force min-max colorbar tick labels for bounded variables (13e3afd)
plots: include median in parameter plots (9bfa149)
plots: include time and angle uncertainty (f45f308)
plots: increase box plot width (0913328)
plots: make mae scale default for gene ranking (c0a0d27)
plots: make posterior time titles and colorbar optional (f3cf7aa)
plots: move reporting function imports to docstring (8f85769)
plots: optionally force recomputation of volcano data (c2ede44)
plots: organize reporting function for use in summarization task (c5a284d)
plots: parameterize inclusion of complete angular scale (f31d116)
plots: parameterize posterior time color map (155a131)
plots: parameterize state color dictionary (5aab2a5)
plots: parameterize transparency of posterior time (0aa0db1)
plots: parametrize rainbow plot default fontsize (03eea70)
plots: pass boxplot flag to parameter posteriors (1d71472)
plots: reduce likelihood of mutation by copying mutated input (321dfca)
plots: remove additional unused comments from posterior predictive extrapolation (8174ff9)
plots: remove redundant data input from lineage fate correlation (978c2d0)
plots: remove unused comment from posterior predictive extrapolation (44cd705)
plots: reorder angle uncertainty of lineage fate correlation (7683f2e)
plots: retain order of selected genes in report (4cd2ac7)
plots: set posterior time default plot type to hexbin (6fcb630)
plots: set rainbow default plot type to hexbin (b5a99ac)
plots: set vector field uncertainty default plot type to hexbin (e875f2e)
plots: show mean and CV histograms in shared time uncertainty (7db1074)
plots: synchronize vector field color map with rainbowplots (76ffc3f)
plots: type-check get clone trajectory function (7f438b3)
plots: unpack width ratios in rainbow plot (40b57d2)
plots: update lineage fate correlation titles and font size (c83153e)
plots: update major log tick labels for parameter posteriors (daabaee)
plots: update report dpi (388cdb5)
plots: update vector field summary interface (e900db0)
plots: update vector field summary plot (8986fc6)
plots: use black box plots (917ee7f)
plots: use gridspec for shared time uncertainty plot (46c28c5)
plots: use pandas regex str replacement in lineage fate correlation (34cfd15)
plots: use pure text title for plot gene ranking (e0c9466)
plots: use QCD instead of CV in shared time histogram (fd6c652)
plots: use quartile coefficient of dispersion to quantify temporal uncertainty (a90e182)
plots: use vector field basis in shared time uncertainty plot (4fb202b)
pre-commit: disable prettier (d7e11e4)
pre-commit: disable prettier (8d2d266)
preprocess: use sc for umap (b615912)
pyproject: define network marker and disable by default (b849c4f)
pyproject: pin poetry-core <2 (d0b8515)
pyproject: set 3.12-compatible pillow lower bound (74b04f8)
rattler: add dill (85e7da4)
rattler: pin deps for 0.4.0b4 (d29fb71)
rattler: pin poetry <2 (f12a6ce)
report: update docstring (02457d7)
setup_environment: ratchet upgrade action (3be1247)
sparsity: decrease default density threshold to 0.3 (9d8eee1)
styles: enable unicode in latex (febd9a8)
styles: remove unused mplstyle key (dc77b0d)
summarize: make absence of independent vector field summary explicit (93a743b)
summarize: use constant cell type colors (74ec198)
tasks: add row labels and external legend (fde8e62)
tasks: add soft support for selected genes to preprocessing (d3227ac)
tasks: import reporting functions in summarize task (bfb4599)
tasks: include column-level colorbars in gridspec (6bfb6fb)
tasks: map time fate correlation over all data set configurations (3e301b7)
tasks: refactor time fate correlation and note redundancy with workflow task (f738c7b)
tasks: reorganize summarize in preparation for integration of reporting module (21543d5)
tasks: set 4 columns for time fate correlation legend (a9b559b)
tasks: set min mae percentile from candidate dataframe length (9f6e601)
tasks: set top mae genes max genes per bin to 5 (1952b43)
tasks: update time lineage fate correlation layout parameters (9b8e3a9)
tasks: update time lineage fate correlation legend spacing (68a82d1)
tasks: update vector field summary parameters (73352bf)
tasks: use parameterized state color dictionary (e5b9719)
tasks: use report instead of plot gene summary (2808a98)
teller: add reference cloudflare vars (29628c0)
test_compressedpickle: make compatible with xdist execution (53ea888)
test_preprocess: add network marker (5b4800a)
test_summarize: mark as slow integration test (84e7ad0)
tests: add processed data fixture (24e8d28)
tests: add serialization test for uns dict with nested numpy array (6d376d9)
tests: add unprocessed data fixture (d520dcc)
tests: exercise hash check in data serialization (9163a92)
tests: load preprocessed deserialized data fixture globally (8752319)
tests: note handling of selected genes in generate fixture data (351bc17)
tests: rename small deserialized data fixture in plots (a096c8c)
tests: update fixture name for preprocessed34 in plot histograms (4198735)
topmaegenes: handle small data sets (bb69eb8)
utils: add array-based type class aliases (81aef5d)
utils: include type in dictionary log (24c3f27)
utils: log data hash on load (cd56435)
utils: remove unused comments (9292cdd)
vscode: autosave on window change (17281d4)
vscode: disable conflicting json formatting (3c7b3fe)
workflow: remove manual definition of L4 GPUAccelerator (7d0da7e)
workflows: add extra large training resource requests and limits (468bc6b)
workflows: add posterior samples and postprocessed data to summarize outputs class (c32f530)
workflows: import cache flag from constants (784f276)
workflows: import contants in configuration (0741330)
workflows: import contants in workflow (121381c)
workflows: include individual metric tables in CombinedMetricsOutputs (c418960)
workflows: include png in time lineage fate correlation plot uploads (bd51032)
workflows: increase timeouts for long-running tasks (cda7d32)
workflows: io.json -> io.metrics (39f28af)
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: remove unused imports (21ac5df)
workflows: remove unused training arguments (5598ef6)
workflows: reset configurations (9ef2a76)
workflows: reset constants to default values (70dc44e)
workflows: reset training configurations list (4f4bb3a)
workflows: set dev mode to use dev image tag (8e2037c)
workflows: upload figure object files (a77f19e)
workflows: use correct WorkflowConfiguration field name (bbafdfd)
workflows: use helper function to generate and save metrics tables (e43baff)
workflows: use overwrite cache variable to set default value (610d7cc)
workflows: use SummarizeConfiguration to access selected genes (46d4df1)

- Python
Published by github-actions[bot] 12 months ago

pyrovelocity - 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 plotgeneranking (d5bcbe1)
plots: support SubplotSpec for plotparameterposteriors (989c19b)
plots: support SubplotSpec for plotvectorfield_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 topmaegenes (b0d0e76)
analysis: add shadow support for jax arrays (46ad2b5)
analysis: parameterize top mae genes gene filter (890244b)
analysis: remove unused comments from computevolcanodata (d62db2f)
analysis: remove unused list wrappers (c2efd4f)
analysis: update compute volcano data interface types (8af8450)
analysis: update maepergene 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: override ghcr ids (4fb9151)
flake: reenable manifest github data (f92d066)
flake: remove aarch64 cross-compilation comment (5cdfcd9)
flake: remove extra ghcr params (a212fb7)
flake: set 500MiB download-buffer-size (d4b819b)
flake: temp pin nixpkgs to 24.11-beta (7798b25)
flake: update flocken interface (224561f)
gitignore: add luarc.json (c5aa832)
gitignore: add node_modules (efe63cd)
gitignore: add output for rattler-build (09ffa56)
gitignore: ignore node (5c53f51)
interfaces: add default factory for preprocess selected_genes empty list (be70f2c)
io: add debug logging of attempted serialization dictionary to serialize anndata (7910665)
io: change sparsification notice from warning to debug level (b33d7b4)
io: default to sans serif in table tex wrapper (260af1f)
io: log data hash on pickle save/load (5a0c660)
io: restore types when deserializing json (ea08a4a)
io: serialize np.bool_ to bool (86e54f0)
io: use dill to support pickling matplotlib objects (daf7716)
just: docs-setup -> docs-build (fa46927)
make: reference cloudflare vars (592cbfe)
make: test-cov-xml defers to pyproject for pytest markers (2f82907)
manuscript: bold custom caption headings (c59c182)
manuscript: comment showframe and layout to print page layout (a5aba5d)
manuscript: reduce spacing above title (3e0e59c)
manuscript: use bold panel references (b602c35)
manuscript: use dvipsnamed email color (41f386e)
manuscript: use dvipsnames (b7c2618)
models: include std of predictive samples in posterior dict (2dc9414)
models: mark apparently unused sample sites (4684551)
models: retain gene ranking data for all genes (0217660)
nix: add explicit "main" group (f3f78e0)
nix: add just to extraDevPackages for devShells (100826f)
nix: disable dontCheckRuntimeDeps (385c68e)
nix: disable pyrovelocity checkphase markers network and slow (d4487cf)
nix: disable quarto overlay (default to nixpkgs) (1379c3a)
nix: dontCheckRuntimeDeps (b4493fd)
nix: nullify quarto python3 (0f02743)
nix: reenable grpcio wheel on Darwin (65576b0)
plots: accept List[Axes] input type (03889ba)
plots: add legend data to cell type plot (d8d277d)
plots: add parameter to truncate high error genes by percentile (1e2b244)
plots: allow scaled measures as well as vector fields (4f5d517)
plots: allow setting axis-level label for colorbars (1972b79)
plots: automatically increment axis indices in lineage fate correlation (0845fab)
plots: default parameter posteriors to box plot (dfe987f)
plots: default to CV in vector field plot (9529dd7)
plots: disable default box plot (320cb9a)
plots: disable text axes in self-generated figure (8a93aa6)
plots: disable transparency in lineage fate correlation (ff63d31)
plots: enable type-checking of plot lineage fate correlation (4843c4b)
plots: export lineage fate correlation plot from plots package (601e0c8)
plots: filter invalid adjustText warning (5e57d40)
plots: filter invalid adjustText warning if logger is available (508ee80)
plots: force min-max colorbar tick labels for bounded variables (13e3afd)
plots: include median in parameter plots (9bfa149)
plots: include time and angle uncertainty (f45f308)
plots: increase box plot width (0913328)
plots: make mae scale default for gene ranking (c0a0d27)
plots: make posterior time titles and colorbar optional (f3cf7aa)
plots: move reporting function imports to docstring (8f85769)
plots: optionally force recomputation of volcano data (c2ede44)
plots: organize reporting function for use in summarization task (c5a284d)
plots: parameterize inclusion of complete angular scale (f31d116)
plots: parameterize posterior time color map (155a131)
plots: parameterize state color dictionary (5aab2a5)
plots: parameterize transparency of posterior time (0aa0db1)
plots: parametrize rainbow plot default fontsize (03eea70)
plots: pass boxplot flag to parameter posteriors (1d71472)
plots: reduce likelihood of mutation by copying mutated input (321dfca)
plots: remove additional unused comments from posterior predictive extrapolation (8174ff9)
plots: remove redundant data input from lineage fate correlation (978c2d0)
plots: remove unused comment from posterior predictive extrapolation (44cd705)
plots: reorder angle uncertainty of lineage fate correlation (7683f2e)
plots: retain order of selected genes in report (4cd2ac7)
plots: set posterior time default plot type to hexbin (6fcb630)
plots: set rainbow default plot type to hexbin (b5a99ac)
plots: set vector field uncertainty default plot type to hexbin (e875f2e)
plots: show mean and CV histograms in shared time uncertainty (7db1074)
plots: synchronize vector field color map with rainbowplots (76ffc3f)
plots: type-check get clone trajectory function (7f438b3)
plots: unpack width ratios in rainbow plot (40b57d2)
plots: update lineage fate correlation titles and font size (c83153e)
plots: update major log tick labels for parameter posteriors (daabaee)
plots: update report dpi (388cdb5)
plots: update vector field summary interface (e900db0)
plots: update vector field summary plot (8986fc6)
plots: use black box plots (917ee7f)
plots: use gridspec for shared time uncertainty plot (46c28c5)
plots: use pandas regex str replacement in lineage fate correlation (34cfd15)
plots: use pure text title for plot gene ranking (e0c9466)
plots: use QCD instead of CV in shared time histogram (fd6c652)
plots: use quartile coefficient of dispersion to quantify temporal uncertainty (a90e182)
plots: use vector field basis in shared time uncertainty plot (4fb202b)
pre-commit: disable prettier (d7e11e4)
pre-commit: disable prettier (8d2d266)
preprocess: use sc for umap (b615912)
pyproject: define network marker and disable by default (b849c4f)
pyproject: pin poetry-core <2 (d0b8515)
pyproject: set 3.12-compatible pillow lower bound (74b04f8)
rattler: add dill (85e7da4)
rattler: pin deps for 0.4.0b4 (d29fb71)
rattler: pin poetry <2 (f12a6ce)
report: update docstring (02457d7)
setup_environment: ratchet upgrade action (3be1247)
styles: enable unicode in latex (febd9a8)
styles: remove unused mplstyle key (dc77b0d)
summarize: make absence of independent vector field summary explicit (93a743b)
summarize: use constant cell type colors (74ec198)
tasks: add row labels and external legend (fde8e62)
tasks: add soft support for selected genes to preprocessing (d3227ac)
tasks: import reporting functions in summarize task (bfb4599)
tasks: include column-level colorbars in gridspec (6bfb6fb)
tasks: map time fate correlation over all data set configurations (3e301b7)
tasks: refactor time fate correlation and note redundancy with workflow task (f738c7b)
tasks: reorganize summarize in preparation for integration of reporting module (21543d5)
tasks: set 4 columns for time fate correlation legend (a9b559b)
tasks: set min mae percentile from candidate dataframe length (9f6e601)
tasks: set top mae genes max genes per bin to 5 (1952b43)
tasks: update time lineage fate correlation layout parameters (9b8e3a9)
tasks: update time lineage fate correlation legend spacing (68a82d1)
tasks: update vector field summary parameters (73352bf)
tasks: use parameterized state color dictionary (e5b9719)
tasks: use report instead of plot gene summary (2808a98)
teller: add reference cloudflare vars (29628c0)
test_compressedpickle: make compatible with xdist execution (53ea888)
test_preprocess: add network marker (5b4800a)
test_summarize: mark as slow integration test (84e7ad0)
tests: add processed data fixture (24e8d28)
tests: add serialization test for uns dict with nested numpy array (6d376d9)
tests: add unprocessed data fixture (d520dcc)
tests: exercise hash check in data serialization (9163a92)
tests: load preprocessed deserialized data fixture globally (8752319)
tests: note handling of selected genes in generate fixture data (351bc17)
tests: rename small deserialized data fixture in plots (a096c8c)
tests: update fixture name for preprocessed34 in plot histograms (4198735)
topmaegenes: handle small data sets (bb69eb8)
utils: add array-based type class aliases (81aef5d)
utils: include type in dictionary log (24c3f27)
utils: log data hash on load (cd56435)
utils: remove unused comments (9292cdd)
vscode: autosave on window change (17281d4)
vscode: disable conflicting json formatting (3c7b3fe)
workflows: add posterior samples and postprocessed data to summarize outputs class (c32f530)
workflows: include individual metric tables in CombinedMetricsOutputs (c418960)
workflows: include png in time lineage fate correlation plot uploads (bd51032)
workflows: io.json -> io.metrics (39f28af)
workflows: reset configurations (9ef2a76)
workflows: upload figure object files (a77f19e)
workflows: use correct WorkflowConfiguration field name (bbafdfd)
workflows: use helper function to generate and save metrics tables (e43baff)
workflows: use SummarizeConfiguration to access selected genes (46d4df1)

- Python
Published by github-actions[bot] 12 months ago

pyrovelocity - v0.4.0-beta.4

0.4.0-beta.4 (2024-08-21)

Features

workflows: add accelerator_type to WorkflowConfiguration (d306c48)
workflows: use WorkflowConfiguration acceleratortype to override trainmodel 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)

- Python
Published by pyrovelocity-bot over 1 year ago

pyrovelocity - 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)

- Python
Published by pyrovelocity-bot over 1 year ago

pyrovelocity - 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)

- Python
Published by pyrovelocity-bot over 1 year ago

pyrovelocity - v0.4.0-beta.1

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)

- Python
Published by pyrovelocity-bot over 1 year ago

pyrovelocity - v0.3.0

0.3.0 (2024-08-16)

What's Changed

chore(deps): update actions/checkout digest to 692973e by @renovate in https://github.com/pinellolab/pyrovelocity/pull/568
chore(deps): update actions/download-artifact digest to fa0a91b by @renovate in https://github.com/pinellolab/pyrovelocity/pull/569
chore(deps): update actions/cache digest to 0c45773 by @renovate in https://github.com/pinellolab/pyrovelocity/pull/567
chore(deps): update condaforge/mambaforge docker tag to v23.3.1 by @renovate in https://github.com/pinellolab/pyrovelocity/pull/434
chore(deps): update docker/setup-qemu-action digest to 5927c83 by @renovate in https://github.com/pinellolab/pyrovelocity/pull/578
chore(deps): update docker/metadata-action digest to 8e5442c by @renovate in https://github.com/pinellolab/pyrovelocity/pull/577
chore(deps): update docker/build-push-action digest to ca052bb by @renovate in https://github.com/pinellolab/pyrovelocity/pull/575
chore(deps): update codecov/codecov-action digest to e28ff12 by @renovate in https://github.com/pinellolab/pyrovelocity/pull/573
chore(deps): update actions/upload-artifact digest to 0b2256b by @renovate in https://github.com/pinellolab/pyrovelocity/pull/571
chore(deps): update actions/setup-python digest to 39cd149 by @renovate in https://github.com/pinellolab/pyrovelocity/pull/570
chore(deps): update mikefarah/yq digest to ef6fb92 by @renovate in https://github.com/pinellolab/pyrovelocity/pull/580
chore(deps): update google-github-actions/auth digest to 71fee32 by @renovate in https://github.com/pinellolab/pyrovelocity/pull/579
chore(deps): update docker/login-action digest to 0d4c9c5 by @renovate in https://github.com/pinellolab/pyrovelocity/pull/576
chore(deps): update pypa/gh-action-pypi-publish digest to fb9fc6a by @renovate in https://github.com/pinellolab/pyrovelocity/pull/581
chore(deps): update determinatesystems/flakehub-push digest to d3b4b64 by @renovate in https://github.com/pinellolab/pyrovelocity/pull/574
chore(deps): update rlespinasse/github-slug-action digest to 797d688 by @renovate in https://github.com/pinellolab/pyrovelocity/pull/582
chore(bazel): make 3.11 default python by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/593
docs(guides): provide example interactive results review by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/592
feat(deps): make 3.11 default python by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/594
docs: compare gene selection among model configurations by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/596
feat(io): (de)serialize anndata objects by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/607
feat(tasks): generate plots with preprocessing task by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/605
fix(tests): use importlib resources to refer to fixture data by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/610
feat(models): use sparse arrays for posterior samples by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/612
feat(workflows): add dataclass for preprocessing outputs interface by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/623
feat(workflows): track model metrics with results summaries by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/624
chore: release 0.3.0 by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/625

Full Changelog: https://github.com/pinellolab/pyrovelocity/compare/v0.2.0...v0.3.0

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 getremotetask_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 generateposteriorsamples 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: paretofrontiergenes -> topmaegenes (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)

- Python
Published by pyrovelocity-bot over 1 year ago

pyrovelocity - v0.3.0-beta.7

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)

- Python
Published by pyrovelocity-bot over 1 year ago

pyrovelocity - v0.3.0-beta.6

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)

- Python
Published by pyrovelocity-bot over 1 year ago

pyrovelocity - v0.3.0-beta.5

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)

- Python
Published by pyrovelocity-bot over 1 year ago

pyrovelocity - v0.3.0-beta.4

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

Bug Fixes

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

- Python
Published by pyrovelocity-bot over 1 year ago

pyrovelocity - v0.3.0-beta.3

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)

- Python
Published by pyrovelocity-bot over 1 year ago

pyrovelocity - v0.3.0-beta.2

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 getremotetask_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 generateposteriorsamples 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: paretofrontiergenes -> topmaegenes (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)

- Python
Published by pyrovelocity-bot over 1 year ago

pyrovelocity - v0.3.0-beta.1

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)

- Python
Published by pyrovelocity-bot over 1 year ago

pyrovelocity - v0.2.1-beta.1

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)

- Python
Published by pyrovelocity-bot over 1 year ago

pyrovelocity - v0.2.0

What's Changed

chore(deps): update dependency dparse to v0.6.3 by @renovate in https://github.com/pinellolab/pyrovelocity/pull/424
chore(deps): update pypa/gh-action-pypi-publish action to v1.8.10 by @renovate in https://github.com/pinellolab/pyrovelocity/pull/433
chore(deps): update crazy-max/ghaction-github-labeler action to v4.2.0 by @renovate in https://github.com/pinellolab/pyrovelocity/pull/440
chore(deps): update dependency typeguard to v4 by @renovate in https://github.com/pinellolab/pyrovelocity/pull/426
chore(deps): update dependency nbsphinx to v0.9.3 by @renovate in https://github.com/pinellolab/pyrovelocity/pull/430
feat: add merge queue configuration by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/470
chore(deps): update docker/build-push-action action to v5 by @renovate in https://github.com/pinellolab/pyrovelocity/pull/472
chore(deps): update docker/metadata-action action to v5 by @renovate in https://github.com/pinellolab/pyrovelocity/pull/474
chore(deps): update docker/login-action action to v3 by @renovate in https://github.com/pinellolab/pyrovelocity/pull/473
chore(deps): update crazy-max/ghaction-github-labeler action to v5 by @renovate in https://github.com/pinellolab/pyrovelocity/pull/471
refactor: update dev container and pod by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/477
feat: add nix devshell and update ci by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/485
feat: setup workflow execution by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/492
feat(bazel): add test caching by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/499
feat(ci): add shared test cache by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/501
feat(workflows): setup data download tasks by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/502
feat(workflows): map core workflow over multiple data sets by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/510
feat(workflows): enable preprocessing tasks by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/512
feat(workflows): create model training tasks by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/513
feat(workflows): create postprocessing tasks by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/518
feat(workflows): create model summary tasks by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/521
feat(workflows): upload shareable summary archive by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/531
docs: use local workflow execution in template notebooks by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/532
refactor(tasks): migrate tasks modules to package by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/535
feat(data): generate transcriptome db and simulate deterministic data by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/537
fix(flake): push images to artifact registry by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/541
feat(argo): enable ARC build for oci images by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/543
fix(images): use layer compression and composition to speed up builds by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/544
chore: release 0.2.0 by @cameronraysmith in https://github.com/pinellolab/pyrovelocity/pull/545

Full Changelog: https://github.com/pinellolab/pyrovelocity/compare/v0.1.3...v0.2.0

- Python
Published by cameronraysmith over 1 year ago

pyrovelocity - v0.2.0-beta.22

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)

- Python
Published by pyrovelocity-bot over 1 year ago

pyrovelocity - v0.2.0-beta.21

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)

- Python
Published by pyrovelocity-bot over 1 year ago

pyrovelocity - v0.2.0-beta.20

0.2.0-beta.20 (2024-07-08)

Bug Fixes

actions: add buildniximage 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)

- Python
Published by github-actions[bot] over 1 year ago

pyrovelocity - v0.2.0-beta.19

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

Bug Fixes

models: use ellipsis matching in xdoctests (505a255)

- Python
Published by github-actions[bot] over 1 year ago

pyrovelocity - v0.2.0-beta.18

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)

- Python
Published by github-actions[bot] over 1 year ago

pyrovelocity - v0.2.0-beta.17

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

- Python
Published by github-actions[bot] over 1 year ago

pyrovelocity - v0.2.0-beta.16

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

Bug Fixes

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

- Python
Published by github-actions[bot] over 1 year ago

pyrovelocity - 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 plotsamplephase_portraits (e136293)
models: add plotsampletrajectories function (56eaed3)
models: add plotsampletrajectorieswithpercentiles (f661696)
models: add posterior inference for deterministic model (2b5872b)
models: implement printinferencedata_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 testdeterministicsimulation (d202722)
bazel: noexperimentalpythonimportallrepositories (500b645), closes /www.github.com/bazelbuild/rules_python/issues/792#issuecomment-1264463207
bazel: separate small and medium test modules (6186da2)
buildniximage: disable post-build gc (9e52cb0)
buildniximage: use cachix cache (e93e951)
buildniximage: 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 LDLIBRARYPATH (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 plotsampletrajectorieswithpercentiles (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: observationflag -> dataobservation_flag (b17a8f0)
models: plot single timepoint data as vectorized series (6dd2256)
models: refactor solve_model_for_all_genes_cells from model (89de821)
models: refactor generatepredictivesamples (e835e7b)
models: refactor plottrajectorywith_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 plotsampletrajectories (b7ca6e0)
models: remove result wrapping from saveinferenceplots (0aae2fe)
models: return all indices from sorttimesoverallcells (91c13ab)
models: sample times from observed delta distribution (7a9bbd8)
models: separately normalize plotsamplephase_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 plotsampletrajectories 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: setupobservationaldata 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)

- Python
Published by github-actions[bot] over 1 year ago

pyrovelocity - 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)

- Python
Published by github-actions[bot] almost 2 years ago

pyrovelocity - 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 printconfigtree (e3546df)
workflows: add medium resources category to configuration (aad47f4)
workflows: separate summarize cache version (55ada29)

Bug Fixes

analyze: add types to computevolcanodata (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)
plotgeneranking: establish compatibility with adjusttext 1.1.1 (cf37f8e)
plots: add padding to plot gene ranking (9b3fa5e)
plots: add types to plotgeneranking (8ed9a75)
plots: add types to summarize gene selection (deeaba5)
plots: close figure in plotgeneselection_summary (099e6fb)
plots: close figure in plotsharedtime_uncertainty (ea34035)
plots: default to loading data for predictive sampling to cpu (abcf58b)
plots: enforce types for plotparameterposterior_distributions (8597820)
plots: enforce types for plotvectorfield_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 plotvectorfield_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 clearlocalcache to workflows (08a6463)
workflows: note migration to CalVer for cache versions (0e0ac49)
workflows: read cache flag from env var (9488074)

- Python
Published by github-actions[bot] almost 2 years ago

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

- Python
Published by github-actions[bot] almost 2 years ago

pyrovelocity - v0.2.0-beta.11

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

Features

actions: add composite action for buildniximage (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)

- Python
Published by github-actions[bot] almost 2 years ago

pyrovelocity - 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
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 nvars > npcs (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)

- Python
Published by github-actions[bot] about 2 years ago

pyrovelocity - 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 loadanndatafrom_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)

- Python
Published by github-actions[bot] about 2 years ago

pyrovelocity - 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)

- Python
Published by github-actions[bot] about 2 years ago

pyrovelocity - 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)

- Python
Published by github-actions[bot] about 2 years ago

pyrovelocity - v0.2.0-beta.6

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 pytest from rulespython in pytestmodule_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)

- Python
Published by github-actions[bot] about 2 years ago

pyrovelocity - v0.2.0-beta.5

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)

- Python
Published by github-actions[bot] about 2 years ago

pyrovelocity - v0.2.0-beta.4

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

- Python
Published by github-actions[bot] about 2 years ago

pyrovelocity - v0.2.0-beta.3

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.cudnn85 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)

- Python
Published by github-actions[bot] about 2 years ago

pyrovelocity - v0.2.0-beta.2

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

Bug Fixes

git: rename master to main (c608f9c)

- Python
Published by github-actions[bot] about 2 years ago

pyrovelocity - v0.2.0-beta.1

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 NUMBACACHEDIR 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 tbb20218 (d0e326b)
flake: print value of NUMBA_CACHE_DIR (70c9587)
flake: set NUMBACACHEDIR 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)

- Python
Published by github-actions[bot] about 2 years ago

pyrovelocity - v0.1.0

This is the first release of the pyrovelocity package.

- Python
Published by qinqian over 2 years ago

pyrovelocity -

Changes

:rocket: Features

fix: run individual summarize stages in parallel (#409) @cameronraysmith
retrain across all data sets with model 1 (#412) @cameronraysmith
pin dvc >3.0 (#372) @cameronraysmith
train model 2 with sample-based enumeration (#370) @cameronraysmith
add shared time markers to phase portraits (#359) @qinqian
add pbmc5k data set (#358) @cameronraysmith
use predictive with one time point and 30 posterior samples from the … (#348) @qinqian
add bone marrow data set (#344) @cameronraysmith
compute shared time-distance correlation (#341) @cameronraysmith
label pbmc10k clusters (#338) @cameronraysmith
add comparison of angle and magnitude uncertainties (#336) @qinqian
data set prediction from inferred time (#333) @qinqian
update gene selection and parameter distribution estimates (#318) @cameronraysmith
integrate gene selection with parameter distribution estimates (#312) @cameronraysmith
add parameterized count threshold (#305) @cameronraysmith
enable rclone in ci (#303) @cameronraysmith
update figure 3 (#301) @cameronraysmith
add cluster-conditional distribution plots (#298) @lijc0804
add script to upload run data to drive (#296) @cameronraysmith
update figure summary (#289) @qinqian
add violin plots for uncertainty measurements (#282) @lijc0804
add pipeline stages for larry auxiliary data (#280) @cameronraysmith
add hypersphere distribution divergence (#278) @cameronraysmith
add parallel execution to single-node pipeline (#270) @cameronraysmith
add draft for distributed pipeline (#264) @cameronraysmith
build gpu-specific docker image (#262) @cameronraysmith
Reproduce on all Larry-related datasets and generate figureS3_extra (#259) @lijc0804
update embedding space comparison (#253) @qinqian
add differentiated larry (#251) @lijc0804
add magnitude and pca space uncertainties evaluation (#249) @qinqian
Add the summarization on PBMC10k (#243) @lijc0804
preprocess and train model on pbmc10k (#241) @lijc0804
add shared time uncertainty plot to summarize stages (#216) @qinqian
train mono / neu / multi subsets of larry (#225) @lijc0804
build and deploy review application (#223) @cameronraysmith
preprocess and train with LARRY data (#214) @cameronraysmith
add function to estimate criticality index (#209) @cameronraysmith
add raw count data histograms to app (#207) @cameronraysmith
write h5 files to compressed dfs for app consumption (#203) @cameronraysmith

:beetle: Fixes

fix: pin versions for model1 computations (#408) @cameronraysmith
use infer_discrete for posterior predictive plots (#375) @qinqian
use Trace_ELBO (disable exact enumeration) (#367) @qinqian
update pbmc10k data set download (#244) @lijc0804

:racehorse: Performance

retrain across all data sets with model 1 (#412) @cameronraysmith
compare PCA and UMAP Rayleigh on minimal gene set projection (#335) @qinqian

:rotating_light: Testing

add single-node pipeline test sandbox (#267) @cameronraysmith
add pipeline stages for plotting simulated data (#192) @cameronraysmith
add pipeline stages for training simulated data (#190) @cameronraysmith
add pipeline stage for preprocessing simulated data (#185) @cameronraysmith
add pipeline stage for generating simulated data (#182) @cameronraysmith

:construction_worker: Continuous Integration

disable dependabot (#420) @cameronraysmith
configure renovate (#417) @renovate
refactor _get_fn_args_from_batch (#397) @cameronraysmith
add config yaml to drive output (#329) @cameronraysmith
update pipeline ci timeout (#327) @cameronraysmith
enable rclone in ci (#303) @cameronraysmith
build gpu-specific docker image (#262) @cameronraysmith
automate deployment of review application (#228) @cameronraysmith
CML PR for master 91df43ab (#410) @cameronraysmith
fix: ignore reports skip ci @cameronraysmith
CML PR for master 629feb24 (#307) @cameronraysmith

:books: Documentation

plot angle uncertainty metrics (#236) @qinqian
add figures for shared time uncertainty (#232) @qinqian
update demo code in README (#196) @lijc0804

:hammer: Refactoring

refactor _get_fn_args_from_batch (#397) @cameronraysmith
add DataReview class to app (#212) @cameronraysmith
add updated pipeline lock; reduce model 1 pkl output (#168) @qinqian

:package: Dependencies

chore(release): v0.1.3 (#428) @cameronraysmith
chore(deps): update dependency click to v8.1.7 (#422) @renovate
disable dependabot (#420) @cameronraysmith
configure renovate (#417) @renovate
Bump nox-poetry from 1.0.2 to 1.0.3 in /.github/workflows (#373) @dependabot
Bump actions/checkout from 3 to 4 (#414) @dependabot
fix: pin versions for model1 computations (#408) @cameronraysmith
Bump sphinx-autodoc-typehints from 1.23.0 to 1.23.3 in /docs (#360) @dependabot
Bump pypa/gh-action-pypi-publish from 1.8.6 to 1.8.7 (#361) @dependabot
Bump release-drafter/release-drafter from 5.23.0 to 5.24.0 (#362) @dependabot
updates for compatibility with cml 0.19.1 (#365) @cameronraysmith
Bump codecov/codecov-action from 3.1.3 to 3.1.4 (#258) @dependabot
Bump nbsphinx from 0.9.1 to 0.9.2 in /docs (#310) @dependabot
Bump setuptools from 67.6.1 to 67.7.2 (#257) @dependabot
Bump etils from 1.2.0 to 1.3.0 (#247) @dependabot
Bump sphinx from 6.2.1 to 7.0.1 in /docs (#255) @dependabot
Bump myst-parser from 1.0.0 to 2.0.0 in /docs (#347) @dependabot
Bump gcsfs from 2023.4.0 to 2023.5.0 (#256) @dependabot
Bump dvc from 2.55.0 to 2.58.0 (#286) @dependabot
Bump furo from 2023.3.27 to 2023.5.20 in /docs (#284) @dependabot
Bump pypa/gh-action-pypi-publish from 1.8.5 to 1.8.6 (#240) @dependabot
Bump importlib-metadata from 6.5.0 to 6.6.0 (#220) @dependabot
Bump werkzeug from 2.2.3 to 2.3.3 (#239) @dependabot
Bump ipython from 8.12.0 to 8.13.1 (#238) @dependabot
Bump alembic from 1.10.3 to 1.10.4 (#235) @dependabot
Bump identify from 2.5.22 to 2.5.23 (#230) @dependabot
Bump pynndescent from 0.5.8 to 0.5.10 (#226) @dependabot
Bump optax from 0.1.4 to 0.1.5 (#219) @dependabot
Bump dvc from 2.54.0 to 2.55.0 (#231) @dependabot
Bump sphinx from 6.2.0 to 6.2.1 in /docs (#218) @dependabot
Bump pip from 23.1.1 to 23.1.2 in /.github/workflows (#217) @dependabot
Bump sqlalchemy from 2.0.9 to 2.0.10 (#205) @dependabot
Bump yarl from 1.8.2 to 1.9.1 (#204) @dependabot
Bump sphinx from 6.1.3 to 6.2.0 in /docs (#200) @dependabot
Bump nox from 2022.11.21 to 2023.4.22 in /.github/workflows (#199) @dependabot
Bump pip from 23.1 to 23.1.1 in /.github/workflows (#198) @dependabot
Bump dvc-studio-client from 0.6.2 to 0.8.0 (#194) @dependabot
Bump hypothesis from 6.72.0 to 6.72.1 (#195) @dependabot
Bump soupsieve from 2.4 to 2.4.1 (#188) @dependabot
Bump codecov/codecov-action from 3.1.2 to 3.1.3 (#193) @dependabot
Bump tornado from 6.2 to 6.3 (#187) @dependabot
Bump flax from 0.6.8 to 0.6.9 (#183) @dependabot
Bump diskcache from 5.5.1 to 5.6.1 (#179) @dependabot
Bump scmrepo from 1.0.1 to 1.0.2 (#178) @dependabot
Bump importlib-metadata from 6.3.0 to 6.5.0 (#180) @dependabot
Bump pytest from 7.3.0 to 7.3.1 (#175) @dependabot
Bump psutil from 5.9.4 to 5.9.5 (#174) @dependabot
Bump cryptography from 40.0.1 to 40.0.2 (#173) @dependabot
Bump attrs from 22.2.0 to 23.1.0 (#172) @dependabot
Bump hypothesis from 6.71.0 to 6.72.0 (#171) @dependabot
Bump mizani from 0.8.1 to 0.9.0 (#170) @dependabot
Bump pip from 23.0.1 to 23.1 in /.github/workflows (#169) @dependabot

Full Changelog: https://github.com/pinellolab/pyrovelocity/compare/v0.1.2...v0.1.3

- Python
Published by github-actions[bot] over 2 years ago

pyrovelocity - v0.1.2

Changes

:rocket: Features

add simulated data for app testing (#146) @cameronraysmith
add manual gene or cell selection (#100) @cameronraysmith
add dashboard review application (#96) @cameronraysmith
add pipeline stages for data set summary (#94) @cameronraysmith
set preprocessing to macroscopic gene set by default and retrain (#92) @cameronraysmith
produce summary plots package for all data sets (#91) @cameronraysmith
add model summary configuration in hydra-zen (#90) @cameronraysmith
add magnitude uncertainty figure (#87) @qinqian
add doctests to PyroVelocity class (#85) @cameronraysmith
add utility to pretty print dictionaries (#84) @cameronraysmith
add html callgraph (#83) @cameronraysmith
add uncertainty analysis boxplot for the kinetics parameters (#76) @qinqian
add pipeline stages for pons oligodendrocyte data (#73) @cameronraysmith

:racehorse: Performance

complete reduction of posterior samples file caches (#160) @cameronraysmith
reduce file size of model output cache (#107) @qinqian

:rotating_light: Testing

complete reduction of posterior samples file caches (#160) @cameronraysmith
add simulated data for app testing (#146) @cameronraysmith
add doctests to PyroVelocity class (#85) @cameronraysmith

:books: Documentation

automate build for colab environment (#163) @cameronraysmith
add simulated data for app testing (#146) @cameronraysmith
update docs to reflect environment upgrade (#136) @cameronraysmith
add citation bib (#82) @cameronraysmith

:hammer: Refactoring

add updated pipeline lock (#152) @qinqian
Reduced pkl file (#150) @qinqian
refactor velocity model (#104) @cameronraysmith
support experimentation with updated dependencies (#102) @cameronraysmith

:package: Dependencies

release v0.1.2 (#167) @cameronraysmith
Bump google-auth from 2.17.2 to 2.17.3 (#161) @dependabot
support python 3.9 and 3.10 (#165) @cameronraysmith
Bump dvc-data from 0.47.1 to 0.47.2 (#159) @dependabot
automate build for colab environment (#163) @cameronraysmith
Bump protobuf from 4.22.1 to 4.22.3 (#158) @dependabot
Bump sphinx-copybutton from 0.5.1 to 0.5.2 in /docs (#155) @dependabot
Bump sphinx-autodoc-typehints from 1.22 to 1.23.0 in /docs (#154) @dependabot
Bump dvc from 2.53.0 to 2.54.0 (#153) @dependabot
Bump ml-dtypes from 0.0.4 to 0.1.0 (#147) @dependabot
Bump packaging from 23.0 to 23.1 (#148) @dependabot
Bump dvc-studio-client from 0.6.1 to 0.6.2 (#149) @dependabot
Bump gcsfs from 2023.3.0 to 2023.4.0 (#140) @dependabot
Bump diskcache from 5.4.0 to 5.5.1 (#142) @dependabot
update app to reflect environment upgrade (#139) @cameronraysmith
Bump pygments from 2.14.0 to 2.15.0 (#134) @dependabot
bump importlib-metadata from 6.2.1 to 6.3.0 (#133) @dependabot
Bump nox-poetry from 1.0.1 to 1.0.2 in /.github/workflows (#122) @dependabot
Bump sphinx-autodoc-typehints from 1.19.4 to 1.22 in /docs (#111) @dependabot
Bump pip from 22.2.2 to 23.0.1 in /.github/workflows (#125) @dependabot
Bump sphinx-click from 4.3.0 to 4.4.0 (#130) @dependabot
Bump sphinx-click from 4.3.0 to 4.4.0 in /docs (#118) @dependabot
Bump furo from 2022.9.29 to 2023.3.27 in /docs (#132) @dependabot
Bump docker/build-push-action from 3 to 4 (#123) @dependabot
Bump virtualenv from 20.16.5 to 20.21.0 in /.github/workflows (#121) @dependabot
Bump furo from 2022.9.29 to 2023.3.27 (#131) @dependabot
Bump sphinx from 5.2.3 to 6.1.3 in /docs (#116) @dependabot
Bump sphinx from 5.2.3 to 6.1.3 (#127) @dependabot
Bump orjson from 3.8.9 to 3.8.10 (#129) @dependabot
Bump nbsphinx from 0.8.9 to 0.9.1 in /docs (#119) @dependabot
Bump nox from 2022.8.7 to 2022.11.21 in /.github/workflows (#117) @dependabot
Bump crazy-max/ghaction-github-labeler from 4.0.0 to 4.1.0 (#114) @dependabot
Bump importlib-metadata from 6.2.0 to 6.2.1 (#128) @dependabot
Bump salsify/action-detect-and-tag-new-version from 2.0.2 to 2.0.3 (#113) @dependabot
Bump pypa/gh-action-pypi-publish from 1.5.1 to 1.8.5 (#115) @dependabot
Bump release-drafter/release-drafter from 5.21.0 to 5.23.0 (#120) @dependabot
Bump poetry from 1.2.2 to 1.4.2 in /.github/workflows (#124) @dependabot
Bump myst-parser from 0.18.1 to 1.0.0 (#126) @dependabot
Bump myst-parser from 0.18.1 to 1.0.0 in /docs (#112) @dependabot
Bump sphinx-copybutton from 0.5.0 to 0.5.1 in /docs (#110) @dependabot
automate upgrade notifications (#109) @cameronraysmith
upgrade package dependencies (#106) @cameronraysmith
Upgrade packages with few pinned versions (#105) @qinqian

Full Changelog: https://github.com/pinellolab/pyrovelocity/compare/v0.1.1...v0.1.2

- Python
Published by github-actions[bot] almost 3 years ago

pyrovelocity - v0.1.1

Changes

:rocket: Features

add continuous integration for modeling experiments (#61) @cameronraysmith
add marker comparison across models (#54) @qinqian
write training/run data to json (#52) @cameronraysmith
add experiment tracking (#48) @cameronraysmith
add Docker images and workflow (#46) @cameronraysmith
reproducibility pipeline for figure S3 (#44) @cameronraysmith
add configuration, data version control, and reproducibility pipelines (#41) @cameronraysmith
Reproducibility update (#25) @qinqian
update type annotations based on calls from fig2_pancreas_data.py (#24) @cameronraysmith
cleanup root directory (#20) @cameronraysmith
add IaC development environment (#19) @cameronraysmith
add pre-commit and github action for testing (#15) @cameronraysmith
add poetry dependency management system (#13) @cameronraysmith
conda configuration (#10) @cameronraysmith
connect readthedocs (#2) @cameronraysmith

:beetle: Fixes

Reproducibility update (#25) @qinqian
update reproducibility scripts (#16) @cameronraysmith
convert documentation from rST to MyST (#5) @cameronraysmith

:racehorse: Performance

document reproducibility input/output for v0.1.0 (#28) @cameronraysmith

:rotating_light: Testing

add tests to validate module load (#30) @cameronraysmith

:construction_worker: Continuous Integration

add continuous integration for modeling experiments (#61) @cameronraysmith
add Docker images and workflow (#46) @cameronraysmith
add tests to validate module load (#30) @cameronraysmith

:books: Documentation

update build process (#34) @cameronraysmith
Suppfig5 (#31) @qinqian
document reproducibility input/output for v0.1.0 (#28) @cameronraysmith
Reproducibility update (#25) @qinqian
cleanup root directory (#20) @cameronraysmith
add bioconda package recipe; improve installation in document (#7) @qinqian
convert documentation from rST to MyST (#5) @cameronraysmith
connect readthedocs (#2) @cameronraysmith

:hammer: Refactoring

refactor/static/velocity model (#50) @cameronraysmith
document reproducibility input/output for v0.1.0 (#28) @cameronraysmith
update type annotations based on calls from fig2_pancreas_data.py (#24) @cameronraysmith

:package: Dependencies

release v0.1.1 (#63) @cameronraysmith
add Docker images and workflow (#46) @cameronraysmith
Anaconda and Bioconda with poetry (#36) @qinqian
update build process (#34) @cameronraysmith
add release automation (#21) @cameronraysmith
add bioconda package recipe; improve installation in document (#7) @qinqian

Full Changelog: https://github.com/pinellolab/pyrovelocity/compare/v0.1.0...v0.1.1

- Python
Published by github-actions[bot] about 3 years ago