pinellolab/pyrovelocity issues and pull requests

#244 - update pbmc10k data set download

Pull Request - State: closed - Opened by lijc0804 over 1 year ago - 1 comment
Labels: bug

#243 - add pipeline summarization for pbmc10k

Pull Request - State: closed - Opened by lijc0804 over 1 year ago - 1 comment
Labels: enhancement

#242 - add new pbmc10k data set

Issue - State: closed - Opened by cameronraysmith over 1 year ago
Labels: enhancement

#241 - preprocess and train model on pbmc10k

Pull Request - State: closed - Opened by lijc0804 over 1 year ago - 1 comment
Labels: enhancement

#240 - Bump pypa/gh-action-pypi-publish from 1.8.5 to 1.8.6

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, github_actions

#239 - Bump werkzeug from 2.2.3 to 2.3.3

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#238 - Bump ipython from 8.12.0 to 8.13.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#237 - add angle uncertainty plots

Issue - State: closed - Opened by cameronraysmith over 1 year ago
Labels: documentation

#236 - plot angle uncertainty metrics

Pull Request - State: closed - Opened by qinqian over 1 year ago - 1 comment
Labels: documentation

#235 - Bump alembic from 1.10.3 to 1.10.4

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#234 - Bump sphinx from 6.2.1 to 7.0.0 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies, python

#233 - Bump virtualenv from 20.21.0 to 20.23.0 in /.github/workflows

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies, python

#232 - add figures for shared time uncertainty

Pull Request - State: closed - Opened by qinqian over 1 year ago - 2 comments
Labels: documentation

#231 - Bump dvc from 2.54.0 to 2.55.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#230 - Bump identify from 2.5.22 to 2.5.23

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#229 - process and train larry mono/neu/multilineage data sets

Issue - State: closed - Opened by cameronraysmith over 1 year ago
Labels: enhancement

#228 - automate deployment of review application

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago
Labels: ci

#227 - automate review application deployment

Issue - State: closed - Opened by cameronraysmith over 1 year ago
Labels: ci

#226 - Bump pynndescent from 0.5.8 to 0.5.10

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#225 - train mono / neu / multi subsets of larry

Pull Request - State: closed - Opened by lijc0804 over 1 year ago - 1 comment
Labels: enhancement

#224 - add pipeline stages for mono / neu lineages

Pull Request - State: closed - Opened by lijc0804 over 1 year ago - 1 comment
Labels: enhancement

#223 - build and deploy review application

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago - 1 comment
Labels: enhancement

#222 - support build and deployment of review application

Issue - State: closed - Opened by cameronraysmith over 1 year ago
Labels: enhancement

#221 - add pipeline stages for mono / neu lineages

Pull Request - State: closed - Opened by lijc0804 over 1 year ago

#220 - Bump importlib-metadata from 6.5.0 to 6.6.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#219 - Bump optax from 0.1.4 to 0.1.5

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#218 - Bump sphinx from 6.2.0 to 6.2.1 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#217 - Bump pip from 23.1.1 to 23.1.2 in /.github/workflows

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#216 - add shared time uncertainty plot to summarize stages

Pull Request - State: closed - Opened by qinqian over 1 year ago - 1 comment
Labels: enhancement

#215 - plot shared time uncertainty

Issue - State: closed - Opened by qinqian over 1 year ago
Labels: enhancement

#214 - preprocess and train with LARRY data

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago
Labels: enhancement

#213 - support preprocessing and model training for LARRY data

Issue - State: closed - Opened by cameronraysmith over 1 year ago
Labels: enhancement

#212 - add DataReview class to app

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago - 1 comment
Labels: refactoring

#211 - refactor common components of app datareview to shared class

Issue - State: closed - Opened by cameronraysmith over 1 year ago
Labels: refactoring

#210 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#209 - add function to estimate criticality index

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago - 1 comment
Labels: enhancement

#208 - support computation of criticality indices

Issue - State: closed - Opened by cameronraysmith over 1 year ago
Labels: enhancement

#207 - add raw count data histograms to app

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago
Labels: enhancement

#206 - plot raw count data histograms in app

Issue - State: closed - Opened by cameronraysmith over 1 year ago
Labels: enhancement

#205 - Bump sqlalchemy from 2.0.9 to 2.0.10

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#204 - Bump yarl from 1.8.2 to 1.9.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#203 - write h5 files to compressed dfs for app consumption

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago
Labels: enhancement

#202 - write anndata to compressed dataframe for app consumption

Issue - State: closed - Opened by cameronraysmith over 1 year ago
Labels: enhancement

#201 - support reading and writing zstandard-compressed pickle files

Issue - State: closed - Opened by cameronraysmith over 1 year ago
Labels: enhancement

#200 - Bump sphinx from 6.1.3 to 6.2.0 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies, python

#199 - Bump nox from 2022.11.21 to 2023.4.22 in /.github/workflows

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#198 - Bump pip from 23.1 to 23.1.1 in /.github/workflows

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies, python

#197 - demo code in README has not been updated for `v0.1.2`

Issue - State: closed - Opened by cameronraysmith over 1 year ago
Labels: documentation

#196 - update demo code in README

Pull Request - State: closed - Opened by lijc0804 over 1 year ago - 1 comment
Labels: documentation

#195 - Bump hypothesis from 6.72.0 to 6.72.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#194 - Bump dvc-studio-client from 0.6.2 to 0.8.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies, python

#193 - Bump codecov/codecov-action from 3.1.2 to 3.1.3

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, github_actions

#192 - add pipeline stages for plotting simulated data

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago
Labels: testing

#191 - plot simulated data for pipeline testing

Issue - State: closed - Opened by cameronraysmith over 1 year ago
Labels: testing

#190 - add pipeline stages for training simulated data

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago
Labels: testing

#189 - train model on simulated data for pipeline testing

Issue - State: closed - Opened by cameronraysmith over 1 year ago
Labels: testing

#188 - Bump soupsieve from 2.4 to 2.4.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#187 - Bump tornado from 6.2 to 6.3

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#186 - Bump virtualenv from 20.21.0 to 20.22.0 in /.github/workflows

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies, python

#185 - add pipeline stage for preprocessing simulated data

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago
Labels: testing

#184 - preprocess simulated data for pipeline testing

Issue - State: closed - Opened by cameronraysmith over 1 year ago
Labels: testing

#183 - Bump flax from 0.6.8 to 0.6.9

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#182 - add pipeline stage for generating simulated data

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago - 1 comment
Labels: testing

#181 - generate simulated data for pipeline testing

Issue - State: closed - Opened by cameronraysmith over 1 year ago
Labels: testing

#180 - Bump importlib-metadata from 6.3.0 to 6.5.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#179 - Bump diskcache from 5.5.1 to 5.6.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#178 - Bump scmrepo from 1.0.1 to 1.0.2

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#177 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#176 - Bump importlib-metadata from 6.3.0 to 6.4.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies, python

#175 - Bump pytest from 7.3.0 to 7.3.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#174 - Bump psutil from 5.9.4 to 5.9.5

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#173 - Bump cryptography from 40.0.1 to 40.0.2

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#172 - Bump attrs from 22.2.0 to 23.1.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#171 - Bump hypothesis from 6.71.0 to 6.72.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#170 - Bump mizani from 0.8.1 to 0.9.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#169 - Bump pip from 23.0.1 to 23.1 in /.github/workflows

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#168 - add updated pipeline lock; reduce model 1 pkl output

Pull Request - State: closed - Opened by qinqian over 1 year ago - 1 comment
Labels: refactoring

#167 - release `v0.1.2`

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago - 1 comment
Labels: build

#166 - update minor release `v0.1.2`

Issue - State: closed - Opened by cameronraysmith over 1 year ago
Labels: build

#165 - support python 3.9 and 3.10

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago
Labels: dependencies

#164 - support python 3.9

Issue - State: closed - Opened by cameronraysmith over 1 year ago
Labels: dependencies

#163 - automate build for colab environment

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago - 1 comment
Labels: documentation, dependencies, github_actions

#162 - build conda environment to support colab execution

Issue - State: closed - Opened by cameronraysmith over 1 year ago
Labels: build, dependencies, github_actions

#161 - Bump google-auth from 2.17.2 to 2.17.3

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies, python

#160 - complete reduction of posterior samples file caches

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago
Labels: performance, testing

#159 - Bump dvc-data from 0.47.1 to 0.47.2

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies, python

#158 - Bump protobuf from 4.22.1 to 4.22.3

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies, python

#155 - Bump sphinx-copybutton from 0.5.1 to 0.5.2 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#154 - Bump sphinx-autodoc-typehints from 1.22 to 1.23.0 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#153 - Bump dvc from 2.53.0 to 2.54.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#150 - reduce size of large pkl files

Pull Request - State: closed - Opened by qinqian over 1 year ago - 1 comment
Labels: refactoring

#73 - add pipeline stages for pons oligodendrocyte data

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago - 1 comment
Labels: enhancement

#63 - release `v0.1.1`

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago
Labels: build

#61 - add continuous integration for modeling experiments

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago - 2 comments
Labels: enhancement, ci, star

#55 - conda-lock `1.4.1` fails to generate lock file from pyproject.toml with mixed conda-forge/PyPI dependencies

Issue - State: closed - Opened by cameronraysmith over 1 year ago - 3 comments
Labels: external

#54 - add marker comparison across models

Pull Request - State: closed - Opened by qinqian over 1 year ago
Labels: enhancement, question

#52 - write training/run data to json

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago
Labels: enhancement

#50 - refactor/static/velocity model

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago
Labels: refactoring

#48 - add experiment tracking

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago
Labels: enhancement

#46 - add Docker images and workflow

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago
Labels: enhancement, build, ci

GitHub / pinellolab/pyrovelocity issues and pull requests