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 py_test from rules_python in py_test_module_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 ([f09413...

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)

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] (006c631)
• vscode: exclude bazel- from search/watch (b2b63b5)

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.cudnn_8_5 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](29e491d1...

v0.2.0-beta.2

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

Bug Fixes

• git: rename master to main (c608f9c)

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 NUMBA_CACHE_DIR 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 tbb_2021_8 (d0e326b)
• flake: print value of NUMBA_CACHE_DIR (70c9587)
• flake: set NUMBA_CACHE_DIR 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)
  *...

v0.1.3

Changes

🚀 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

🪲 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

🐎 Performance

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

🚨 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

👷 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 91df43a (#410) @cameronraysmith
• fix: ignore reports [skip ci] (#326) @cameronraysmith
• CML PR for master 629feb2 (#307) @cameronraysmith

📚 Documentation

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

🔨 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

📦 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: v0.1.2...v0.1.3

v0.1.2

Changes

🚀 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

🐎 Performance

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

🚨 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

📚 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

🔨 Refactoring

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

📦 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: v0.1.1...v0.1.2

v0.1.1

Changes

🚀 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

🪲 Fixes

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

🐎 Performance

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

🚨 Testing

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

👷 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

📚 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

🔨 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

📦 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: v0.1.0...v0.1.1

v0.1.0

This is the first release of the pyrovelocity package.