pinellolab/pyrovelocity issues and pull requests

#651 - ModuleNotFoundError: No module named 'sparse'

Issue - State: closed - Opened by AlexanderAivazidis about 1 month ago - 2 comments
Labels: dependencies

#650 - hash externally downloaded data

Issue - State: open - Opened by cameronraysmith about 1 month ago
Labels: enhancement

#649 - feat(models): add k-NN model

Pull Request - State: open - Opened by AlexanderAivazidis about 1 month ago
Labels: enhancement, python

#648 - fix(manuscript): update mathematical model description

Pull Request - State: open - Opened by mattlevine22 about 1 month ago
Labels: documentation, skip-ci

#647 - feat(plots): plot inferred time-clonal fate potency correlation

Pull Request - State: open - Opened by cameronraysmith about 1 month ago
Labels: enhancement, python, refactoring, dev-mode

#646 - docs(manuscript): update bioarxiv v2

Pull Request - State: closed - Opened by cameronraysmith about 2 months ago
Labels: documentation, skip-ci

#645 - feat(workflows): override model training accelerator from WorkflowConfiguration

Pull Request - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement, python, skip-ci

#644 - parameterize GPUAccelerator type in WorkflowConfiguration dataclasses

Issue - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement

#643 - docs(manuscript): seed bioarxiv v2

Pull Request - State: closed - Opened by cameronraysmith about 2 months ago
Labels: documentation

#642 - docs(reproducibility): build manuscript

Pull Request - State: closed - Opened by cameronraysmith about 2 months ago - 1 comment
Labels: documentation, skip-ci

#641 - feat(workflows): enable model selection for larry data

Pull Request - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement, python, data

#640 - enable model selection for larry data

Issue - State: closed - Opened by cameronraysmith about 2 months ago
Labels: data

#639 - enable model selection for 68k pbmc data set

Issue - State: closed - Opened by cameronraysmith about 2 months ago
Labels: data

#638 - feat(workflows): enable experimental data sets

Pull Request - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement, python, data

#637 - fix(cytotrace): add smoke test module

Pull Request - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement, python, testing

#636 - add tests to cytotrace module

Issue - State: closed - Opened by cameronraysmith about 2 months ago - 1 comment
Labels: testing

#635 - feat(workflows): add configuration for human bone marrow data

Pull Request - State: closed - Opened by cameronraysmith about 2 months ago - 1 comment
Labels: enhancement, python, execute-workflow, dev-mode

#634 - feat(workflows): add configuration for pbmc10k data

Pull Request - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement, python, execute-workflow

#633 - feat(workflows): add configuration for pons data

Pull Request - State: closed - Opened by cameronraysmith about 2 months ago - 2 comments
Labels: enhancement, python, execute-workflow

#632 - feat(workflows): add configuration for pbmc5k data

Pull Request - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement, python, execute-workflow

#631 - add configuration for pons data

Issue - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement

#630 - feat(workflows): add configuration for larry data subsets

Pull Request - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement, python

#629 - add configuration for bone marrow data

Issue - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement

#628 - add configuration for 10k pbmc data

Issue - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement

#627 - add configuration for 5k pbmc data

Issue - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement

#626 - add configuration for larry data subsets

Issue - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement

#625 - chore: release `0.3.0`

Pull Request - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement, python

#624 - feat(workflows): track model metrics with results summaries

Pull Request - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement, python

#623 - feat(workflows): add dataclass for preprocessing outputs interface

Pull Request - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement, python

#622 - add plots module for cospar-cytotrace correlation

Issue - State: open - Opened by cameronraysmith about 2 months ago
Labels: refactoring

#621 - add plots module for cell fate metrics comparison

Issue - State: open - Opened by cameronraysmith about 2 months ago
Labels: refactoring

#620 - apply preprocessing and model summarization guides in hosted data set tutorials

Issue - State: open - Opened by cameronraysmith about 2 months ago
Labels: documentation

#619 - add data access guide

Issue - State: open - Opened by cameronraysmith about 2 months ago
Labels: documentation

#618 - add postprocessing guide

Issue - State: open - Opened by cameronraysmith about 2 months ago
Labels: documentation

#617 - add model training guide

Issue - State: open - Opened by cameronraysmith about 2 months ago
Labels: documentation

#616 - add plots modules to render graphical models

Issue - State: open - Opened by cameronraysmith about 2 months ago
Labels: enhancement

#615 - add posterior summary statistics to postprocessed data objects

Issue - State: open - Opened by cameronraysmith about 2 months ago
Labels: enhancement

#614 - include preprocessing plot files in workflow lineage tracking

Issue - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement

#613 - include model metrics with results summaries

Issue - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement

#612 - feat(models): use sparse arrays for posterior samples

Pull Request - State: closed - Opened by cameronraysmith about 2 months ago
Labels: dependencies, python

#611 - automatically persist posterior samples in sparse representation

Issue - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement

#610 - fix(tests): use importlib resources to refer to fixture data

Pull Request - State: closed - Opened by cameronraysmith about 2 months ago
Labels: testing

#609 - pytest fails to find fixture data referenced by local package path

Issue - State: closed - Opened by cameronraysmith about 2 months ago
Labels: bug, testing

#608 - create interactive count data joint histogram plot

Issue - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement

#607 - feat(io): (de)serialize anndata objects

Pull Request - State: closed - Opened by cameronraysmith about 2 months ago - 1 comment
Labels: enhancement, python

#606 - add io functionality to serialize anndata objects to json

Issue - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement

#605 - feat(tasks): generate plots with preprocessing task

Pull Request - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement, python

#604 - render summary plots with preprocessing task

Issue - State: closed - Opened by cameronraysmith about 2 months ago
Labels: enhancement

#603 - chore(deps): update dependency black to v24 [security]

Pull Request - State: open - Opened by renovate[bot] 2 months ago
Labels: dependencies

#602 - chore(deps): update dependency lightning to v2.3.3 [security]

Pull Request - State: open - Opened by renovate[bot] 2 months ago
Labels: dependencies

#601 - chore(deps): update dependency astropy to v5.3.3 [security] - autoclosed

Pull Request - State: closed - Opened by renovate[bot] 2 months ago
Labels: dependencies

#600 - chore(deps): update dependency jupyterlab to v4.0.11 [security]

Pull Request - State: open - Opened by renovate[bot] 2 months ago
Labels: dependencies

#599 - add integration tests for task modules

Issue - State: closed - Opened by cameronraysmith 2 months ago
Labels: testing

#598 - add unit test modules for plotting functions

Issue - State: closed - Opened by cameronraysmith 2 months ago
Labels: testing

#596 - docs: compare gene selection among model configurations

Pull Request - State: closed - Opened by cameronraysmith 2 months ago
Labels: documentation, testing

#595 - document comparison of gene selection among model configurations

Issue - State: closed - Opened by cameronraysmith 2 months ago
Labels: documentation

#594 - feat(deps): make 3.11 default python

Pull Request - State: closed - Opened by cameronraysmith 2 months ago
Labels: dependencies

#593 - chore(bazel): make 3.11 default python

Pull Request - State: closed - Opened by cameronraysmith 2 months ago - 1 comment
Labels: testing

#592 - docs(guides): provide example interactive results review

Pull Request - State: closed - Opened by cameronraysmith 3 months ago
Labels: documentation

#591 - chore(deps): update dependency jaxtyping to v0.2.34

Pull Request - State: open - Opened by renovate[bot] 3 months ago
Labels: dependencies

#590 - chore(deps): update dependency jaxlib to v0.4.31

Pull Request - State: open - Opened by renovate[bot] 3 months ago
Labels: dependencies

#589 - chore(deps): update dependency jax to v0.4.31

Pull Request - State: open - Opened by renovate[bot] 3 months ago
Labels: dependencies

#588 - chore(deps): update dependency ipywidgets to v8.1.5

Pull Request - State: open - Opened by renovate[bot] 3 months ago
Labels: dependencies

#587 - chore(deps): update dependency flax to v0.9.0

Pull Request - State: open - Opened by renovate[bot] 3 months ago
Labels: dependencies

#586 - chore(deps): update dependency duckdb to v0.10.3 - autoclosed

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#585 - chore(deps): update dependency diskcache to v5.6.3

Pull Request - State: open - Opened by renovate[bot] 3 months ago
Labels: dependencies

#584 - chore(deps): update dependency chex to v0.1.86

Pull Request - State: open - Opened by renovate[bot] 3 months ago - 1 comment
Labels: dependencies

#583 - chore(deps): update dependency anndata to v0.10.9

Pull Request - State: open - Opened by renovate[bot] 3 months ago
Labels: dependencies

#582 - chore(deps): update rlespinasse/github-slug-action digest to 797d688

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#581 - chore(deps): update pypa/gh-action-pypi-publish digest to fb9fc6a

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#580 - chore(deps): update mikefarah/yq digest to ef6fb92

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#579 - chore(deps): update google-github-actions/auth digest to 71fee32

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#578 - chore(deps): update docker/setup-qemu-action digest to 5927c83

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#577 - chore(deps): update docker/metadata-action digest to 8e5442c

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#576 - chore(deps): update docker/login-action digest to 0d4c9c5

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#575 - chore(deps): update docker/build-push-action digest to ca052bb

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#574 - chore(deps): update determinatesystems/flakehub-push digest to d3b4b64

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#573 - chore(deps): update codecov/codecov-action digest to e28ff12

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#572 - chore(deps): update cameronraysmith/maximize-build-space digest to fc881a6

Pull Request - State: closed - Opened by renovate[bot] 3 months ago - 1 comment
Labels: dependencies

#571 - chore(deps): update actions/upload-artifact digest to 0b2256b

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#570 - chore(deps): update actions/setup-python digest to 39cd149

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#569 - chore(deps): update actions/download-artifact digest to fa0a91b

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#568 - chore(deps): update actions/checkout digest to 692973e

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#567 - chore(deps): update actions/cache digest to 0c45773

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#566 - chore(deps): update dependency werkzeug to v3 [security] - autoclosed

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#565 - chore(deps): update dependency gunicorn to v22 [security] - autoclosed

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#564 - chore(deps): update dependency zipp to v3.19.1 [security] - autoclosed

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#563 - chore(deps): update dependency tqdm to v4.66.3 [security] - autoclosed

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#562 - chore(deps): update dependency jupyter-server to v2.11.2 [security] - autoclosed

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#561 - chore(deps): update dependency idna to v3.7 [security] - autoclosed

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#560 - chore(deps): update dependency fonttools to v4.43.0 [security] - autoclosed

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#559 - chore(deps): update dependency azure-identity to v1.16.1 [security] - autoclosed

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#558 - chore(deps): update dependency jupyter-lsp to v2.2.2 [security] - autoclosed

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#557 - chore(deps): update dependency jinja2 to v3.1.4 [security] - autoclosed

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#556 - chore(deps): update dependency aiohttp to v3.9.4 [security] - autoclosed

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#555 - chore(deps): update dependency pillow to v10 [security] - autoclosed

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#554 - chore(deps): update dependency cryptography to v42 [security] - autoclosed

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#553 - chore(deps): update dependency certifi to v2024 [security] - autoclosed

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#552 - chore(deps): update dependency requests to v2.32.2 [security] - autoclosed

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

#551 - chore(deps): update dependency urllib3 to v1.26.19 [security] - autoclosed

Pull Request - State: closed - Opened by renovate[bot] 3 months ago
Labels: dependencies

GitHub / pinellolab/pyrovelocity issues and pull requests