From 8147c6df5d8afae4df50c6c9907eff585fc46ee0 Mon Sep 17 00:00:00 2001 From: Cameron Smith Date: Fri, 7 Jul 2023 17:17:40 -0400 Subject: [PATCH] train model 2 with sample-based enumeration (#370) * use Trace_ELBO * pipeline script: optionally `-f` force retraining * add `force_retraining` to toggle `pipeline.sh -f` * add annoy to plotting dependencies * gitignore posterior phase portraits for pancreas * pipeline: track posterior phase portraits * summarize pancreas models 1/2 lock * add flags to force postprocessing and summarize * increase postprocess and summarize 4 -> 6 threads * update workflow to support forcing stage groups * update config to expect compressed figureS2 output * compress three gene data set * pipeline: track gene subset data file * update pipeline lock * update constraints for tests and release workflows * update dvc lock for dvc >3.0 * use dvc3 cml container * update version constraints --- .github/pipeline.sh | 40 +- .github/workflows/cml.yml | 40 +- .github/workflows/constraints.txt | 4 +- dockerfiles/Dockerfile | 2 +- poetry.lock | 527 +----- pyproject.toml | 20 +- pyrovelocity/_trainer.py | 4 +- pyrovelocity/config.py | 2 +- reproducibility/figures/config.yaml | 2 +- reproducibility/figures/dvc.lock | 1591 +++++++++-------- reproducibility/figures/dvc.yaml | 12 +- .../figures/figS2/figure_extras.py | 10 +- .../models/bonemarrow_model2/metrics.json | 6 +- .../models/bonemarrow_model2/run_info.json | 14 +- .../figures/models/larry_model2/metrics.json | 6 +- .../figures/models/larry_model2/run_info.json | 12 +- .../models/larry_mono_model2/metrics.json | 6 +- .../models/larry_mono_model2/run_info.json | 12 +- .../larry_multilineage_model2/metrics.json | 6 +- .../larry_multilineage_model2/run_info.json | 12 +- .../models/larry_neu_model2/metrics.json | 6 +- .../models/larry_neu_model2/run_info.json | 12 +- .../models/larry_tips_model2/metrics.json | 6 +- .../models/larry_tips_model2/run_info.json | 12 +- .../models/pancreas_model1/metrics.json | 6 +- .../models/pancreas_model2/metrics.json | 6 +- .../models/pancreas_model2/run_info.json | 14 +- .../models/pbmc10k_model2/metrics.json | 6 +- .../models/pbmc10k_model2/run_info.json | 14 +- .../figures/models/pbmc5k_model2/metrics.json | 6 +- .../models/pbmc5k_model2/run_info.json | 14 +- .../models/pbmc68k_model2/metrics.json | 6 +- .../models/pbmc68k_model2/run_info.json | 12 +- .../figures/models/pons_model2/metrics.json | 6 +- .../figures/models/pons_model2/run_info.json | 12 +- .../simulate_medium_model2/metrics.json | 2 +- .../reports/pancreas_model1/.gitignore | 1 + .../reports/pancreas_model2/.gitignore | 1 + 38 files changed, 1151 insertions(+), 1319 deletions(-) diff --git a/.github/pipeline.sh b/.github/pipeline.sh index 1b097d068..77566a501 100755 --- a/.github/pipeline.sh +++ b/.github/pipeline.sh @@ -17,6 +17,20 @@ set -x +DVC_COMMAND="dvc repro" +DVC_COMMAND_POSTPROCESS="dvc repro" +DVC_COMMAND_SUMMARIZE="dvc repro" +FORCE_ALL="" + +while getopts ":ftfsfp" opt; do + case $opt in + f) FORCE_ALL="true"; DVC_COMMAND="dvc repro -f -s"; DVC_COMMAND_POSTPROCESS="dvc repro -f -s"; DVC_COMMAND_SUMMARIZE="dvc repro -f -s" ;; + ft) DVC_COMMAND="dvc repro -f -s" ;; + fp) DVC_COMMAND_POSTPROCESS="dvc repro -f -s" ;; + fs) DVC_COMMAND_SUMMARIZE="dvc repro -f -s" ;; + \?) echo "Invalid option -$OPTARG" >&2 ;; + esac +done ### Define parallel execution function ### function run_parallel_pipeline() { @@ -36,29 +50,29 @@ function run_parallel_pipeline() { dvc repro preprocess # manually execute training stages to distribute over four GPUs - dvc repro train@pancreas_model2 & + $DVC_COMMAND train@pancreas_model2 & sleep 7 - dvc repro train@pbmc68k_model2 & + $DVC_COMMAND train@pbmc68k_model2 & sleep 7 - dvc repro train@pons_model2 & + $DVC_COMMAND train@pons_model2 & sleep 7 - dvc repro train@larry_model2 & + $DVC_COMMAND train@larry_model2 & wait - dvc repro train@larry_tips_model2 & + $DVC_COMMAND train@larry_tips_model2 & sleep 7 - dvc repro train@larry_mono_model2 & + $DVC_COMMAND train@larry_mono_model2 & sleep 7 - dvc repro train@larry_neu_model2 & + $DVC_COMMAND train@larry_neu_model2 & sleep 7 - dvc repro train@larry_multilineage_model2 & + $DVC_COMMAND train@larry_multilineage_model2 & wait - dvc repro train@bonemarrow_model2 & + $DVC_COMMAND train@bonemarrow_model2 & sleep 7 - dvc repro train@pbmc10k_model2 & + $DVC_COMMAND train@pbmc10k_model2 & sleep 7 - dvc repro train@pbmc5k_model2 & + $DVC_COMMAND train@pbmc5k_model2 & wait dvc repro train @@ -66,14 +80,14 @@ function run_parallel_pipeline() { dvc stage list --name-only |\ grep -E "postprocess*" |\ /usr/bin/time -v \ - xargs -t -n 1 -P 4 bash -c 'sleep $((RANDOM % 15 + 5)); dvc repro "$@"' -- + xargs -t -n 1 -P 6 bash -c 'sleep $((RANDOM % 15 + 5)); '"$DVC_COMMAND_POSTPROCESS"' "$@"' -- wait dvc repro postprocess dvc stage list --name-only |\ grep -E "summarize*" |\ /usr/bin/time -v \ - xargs -t -n 1 -P 4 bash -c 'sleep $((RANDOM % 15 + 5)); dvc repro "$@"' -- + xargs -t -n 1 -P 6 bash -c 'sleep $((RANDOM % 15 + 5)); '"$DVC_COMMAND_SUMMARIZE"' "$@"' -- wait dvc repro summarize } diff --git a/.github/workflows/cml.yml b/.github/workflows/cml.yml index e1bbe3470..7abd1d13f 100644 --- a/.github/workflows/cml.yml +++ b/.github/workflows/cml.yml @@ -13,6 +13,26 @@ on: required: true type: boolean default: false + force_retraining: + description: "Force retraining in model execution" + required: true + type: boolean + default: false + force_postprocessing: + description: "Force postprocessing in model execution" + required: true + type: boolean + default: false + force_summarize: + description: "Force summarization in model execution" + required: true + type: boolean + default: false + force_all: + description: "Force all steps in model execution" + required: true + type: boolean + default: false push: branches: - "exp*" @@ -120,5 +140,23 @@ jobs: - name: Run experiment and submit report run: | source .venv/bin/activate - ./.github/pipeline.sh + FLAGS="" + + if [ "${{ github.event.inputs.force_retraining }}" = "true" ]; then + FLAGS="${FLAGS} -ft" + fi + + if [ "${{ github.event.inputs.force_postprocessing }}" = "true" ]; then + FLAGS="${FLAGS} -fp" + fi + + if [ "${{ github.event.inputs.force_summarize }}" = "true" ]; then + FLAGS="${FLAGS} -fs" + fi + + if [ "${{ github.event.inputs.force_all }}" = "true" ]; then + FLAGS="${FLAGS} -f" + fi + + ./.github/pipeline.sh ${FLAGS} shell: bash diff --git a/.github/workflows/constraints.txt b/.github/workflows/constraints.txt index 144b453b4..21e202f41 100644 --- a/.github/workflows/constraints.txt +++ b/.github/workflows/constraints.txt @@ -1,5 +1,5 @@ pip==23.1.2 nox==2023.4.22 nox-poetry==1.0.2 -poetry==1.4.2 -virtualenv==20.21.0 +poetry==1.5.1 +virtualenv==20.23.1 diff --git a/dockerfiles/Dockerfile b/dockerfiles/Dockerfile index ece965530..2d32c9ef6 100644 --- a/dockerfiles/Dockerfile +++ b/dockerfiles/Dockerfile @@ -1,5 +1,5 @@ # syntax=docker/dockerfile:1 -FROM ghcr.io/iterative/cml:0-dvc2-base1-gpu +FROM ghcr.io/iterative/cml:0-dvc3-base1-gpu # FROM ghcr.io/iterative/cml@sha256:ad10a563de25311241f10d9d5509cecab6bc754b6b2c90b61e309e34fe80911e WORKDIR ${CML_RUNNER_PATH} diff --git a/poetry.lock b/poetry.lock index 23da27361..1f99e7eaa 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. [[package]] name = "absl-py" version = "1.4.0" description = "Abseil Python Common Libraries, see https://github.com/abseil/abseil-py." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -16,7 +15,6 @@ files = [ name = "adjusttext" version = "0.7.3" description = "Iteratively adjust text position in matplotlib plots to minimize overlaps" -category = "main" optional = false python-versions = "*" files = [ @@ -31,7 +29,6 @@ numpy = "*" name = "aiohttp" version = "3.8.4" description = "Async http client/server framework (asyncio)" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -140,8 +137,7 @@ speedups = ["Brotli", "aiodns", "cchardet"] name = "aiohttp-retry" version = "2.8.3" description = "Simple retry client for aiohttp" -category = "main" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "aiohttp_retry-2.8.3-py3-none-any.whl", hash = "sha256:3aeeead8f6afe48272db93ced9440cf4eda8b6fd7ee2abb25357b7eb28525b45"}, @@ -155,7 +151,6 @@ aiohttp = "*" name = "aiosignal" version = "1.3.1" description = "aiosignal: a list of registered asynchronous callbacks" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -170,7 +165,6 @@ frozenlist = ">=1.1.0" name = "alabaster" version = "0.7.13" description = "A configurable sidebar-enabled Sphinx theme" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -182,7 +176,6 @@ files = [ name = "alembic" version = "1.10.4" description = "A database migration tool for SQLAlchemy." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -202,8 +195,7 @@ tz = ["python-dateutil"] name = "amqp" version = "5.1.1" description = "Low-level AMQP client for Python (fork of amqplib)." -category = "main" -optional = false +optional = true python-versions = ">=3.6" files = [ {file = "amqp-5.1.1-py3-none-any.whl", hash = "sha256:6f0956d2c23d8fa6e7691934d8c3930eadb44972cbbd1a7ae3a520f735d43359"}, @@ -217,7 +209,6 @@ vine = ">=5.0.0" name = "anndata" version = "0.8.0" description = "Annotated data." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -238,11 +229,21 @@ dev = ["black (>=20.8b1)", "docutils", "setuptools_scm"] doc = ["nbsphinx", "scanpydoc (>=0.7.3)", "sphinx (>=4.1,<4.2)", "sphinx-autodoc-typehints (>=1.11.0)", "sphinx-rtd-theme", "sphinx_issues", "typing_extensions", "zarr"] test = ["boltons", "dask[array]", "joblib", "loompy (>=3.0.5)", "matplotlib", "openpyxl", "pytest (>=6.0)", "pytest-cov (>=2.10)", "scanpy", "sklearn", "zarr"] +[[package]] +name = "annoy" +version = "1.17.3" +description = "Approximate Nearest Neighbors in C++/Python optimized for memory usage and loading/saving to disk." +optional = true +python-versions = "*" +files = [ + {file = "annoy-1.17.3-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:c33a5d4d344c136c84976bfb2825760142a8bb25335165e24e11c9afbfa8c2e9"}, + {file = "annoy-1.17.3.tar.gz", hash = "sha256:9cbfebefe0a5f843eba29c6be4c84d601f4f41ad4ded0486f1b88c3b07739c15"}, +] + [[package]] name = "antlr4-python3-runtime" version = "4.9.3" description = "ANTLR 4.9.3 runtime for Python 3.7" -category = "main" optional = false python-versions = "*" files = [ @@ -253,8 +254,7 @@ files = [ name = "appdirs" version = "1.4.4" description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -category = "main" -optional = false +optional = true python-versions = "*" files = [ {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"}, @@ -265,7 +265,6 @@ files = [ name = "appnope" version = "0.1.3" description = "Disable App Nap on macOS >= 10.9" -category = "main" optional = true python-versions = "*" files = [ @@ -277,7 +276,6 @@ files = [ name = "astropy" version = "5.2.2" description = "Astronomy and astrophysics core library" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -331,7 +329,6 @@ test-all = ["coverage[toml]", "ipython (>=4.2)", "objgraph", "pytest (>=7.0)", " name = "asttokens" version = "2.2.1" description = "Annotate AST trees with source code positions" -category = "main" optional = true python-versions = "*" files = [ @@ -349,7 +346,6 @@ test = ["astroid", "pytest"] name = "async-timeout" version = "4.0.2" description = "Timeout context manager for asyncio programs" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -361,8 +357,7 @@ files = [ name = "asyncssh" version = "2.13.1" description = "AsyncSSH: Asynchronous SSHv2 client and server library" -category = "main" -optional = false +optional = true python-versions = ">= 3.6" files = [ {file = "asyncssh-2.13.1-py3-none-any.whl", hash = "sha256:c90eb5e2b4f9a7cc6e6af01fd844563d722c0d667f8c5f51fe5b3c2a79fa0575"}, @@ -386,8 +381,7 @@ pywin32 = ["pywin32 (>=227)"] name = "atpublic" version = "3.1.1" description = "Keep all y'all's __all__'s in sync" -category = "main" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "atpublic-3.1.1-py3-none-any.whl", hash = "sha256:37f714748e77b8a7b34d59b7b485fd452a0d5906be52cb1bd28d29a2bd84f295"}, @@ -398,7 +392,6 @@ files = [ name = "attrs" version = "23.1.0" description = "Classes Without Boilerplate" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -417,7 +410,6 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte name = "babel" version = "2.12.1" description = "Internationalization utilities" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -429,7 +421,6 @@ files = [ name = "backcall" version = "0.2.0" description = "Specifications for callback functions passed in to an API" -category = "main" optional = true python-versions = "*" files = [ @@ -441,7 +432,6 @@ files = [ name = "bandit" version = "1.7.5" description = "Security oriented static analyser for python code." -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -465,7 +455,6 @@ yaml = ["PyYAML"] name = "beautifulsoup4" version = "4.12.2" description = "Screen-scraping library" -category = "main" optional = true python-versions = ">=3.6.0" files = [ @@ -484,8 +473,7 @@ lxml = ["lxml"] name = "billiard" version = "3.6.4.0" description = "Python multiprocessing fork with improvements and bugfixes" -category = "main" -optional = false +optional = true python-versions = "*" files = [ {file = "billiard-3.6.4.0-py3-none-any.whl", hash = "sha256:87103ea78fa6ab4d5c751c4909bcff74617d985de7fa8b672cf8618afd5a875b"}, @@ -496,7 +484,6 @@ files = [ name = "black" version = "23.3.0" description = "The uncompromising code formatter." -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -546,7 +533,6 @@ uvloop = ["uvloop (>=0.15.2)"] name = "cached-property" version = "1.5.2" description = "A decorator for caching properties in classes." -category = "main" optional = false python-versions = "*" files = [ @@ -558,8 +544,7 @@ files = [ name = "cachetools" version = "5.3.0" description = "Extensible memoizing collections and decorators" -category = "main" -optional = false +optional = true python-versions = "~=3.7" files = [ {file = "cachetools-5.3.0-py3-none-any.whl", hash = "sha256:429e1a1e845c008ea6c85aa35d4b98b65d6a9763eeef3e37e92728a12d1de9d4"}, @@ -570,8 +555,7 @@ files = [ name = "celery" version = "5.2.7" description = "Distributed Task Queue." -category = "main" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "celery-5.2.7-py3-none-any.whl", hash = "sha256:138420c020cd58d6707e6257b6beda91fd39af7afde5d36c6334d175302c0e14"}, @@ -625,7 +609,6 @@ zstd = ["zstandard"] name = "certifi" version = "2022.12.7" description = "Python package for providing Mozilla's CA Bundle." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -637,7 +620,6 @@ files = [ name = "cffi" version = "1.15.1" description = "Foreign Function Interface for Python calling C code." -category = "main" optional = false python-versions = "*" files = [ @@ -714,7 +696,6 @@ pycparser = "*" name = "cfgv" version = "3.3.1" description = "Validate configuration and produce human readable error messages." -category = "main" optional = true python-versions = ">=3.6.1" files = [ @@ -726,7 +707,6 @@ files = [ name = "charset-normalizer" version = "3.1.0" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." -category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -811,7 +791,6 @@ files = [ name = "chex" version = "0.1.7" description = "Chex: Testing made fun, in JAX!" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -832,7 +811,6 @@ typing-extensions = {version = ">=4.2.0", markers = "python_version < \"3.11\""} name = "click" version = "8.1.3" description = "Composable command line interface toolkit" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -847,8 +825,7 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} name = "click-didyoumean" version = "0.3.0" description = "Enables git-like *did-you-mean* feature in click" -category = "main" -optional = false +optional = true python-versions = ">=3.6.2,<4.0.0" files = [ {file = "click-didyoumean-0.3.0.tar.gz", hash = "sha256:f184f0d851d96b6d29297354ed981b7dd71df7ff500d82fa6d11f0856bee8035"}, @@ -862,8 +839,7 @@ click = ">=7" name = "click-plugins" version = "1.1.1" description = "An extension module for click to enable registering CLI commands via setuptools entry-points." -category = "main" -optional = false +optional = true python-versions = "*" files = [ {file = "click-plugins-1.1.1.tar.gz", hash = "sha256:46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b"}, @@ -880,8 +856,7 @@ dev = ["coveralls", "pytest (>=3.6)", "pytest-cov", "wheel"] name = "click-repl" version = "0.2.0" description = "REPL plugin for Click" -category = "main" -optional = false +optional = true python-versions = "*" files = [ {file = "click-repl-0.2.0.tar.gz", hash = "sha256:cd12f68d745bf6151210790540b4cb064c7b13e571bc64b6957d98d120dacfd8"}, @@ -897,7 +872,6 @@ six = "*" name = "cloudpickle" version = "2.2.1" description = "Extended pickling support for Python objects" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -909,7 +883,6 @@ files = [ name = "colorama" version = "0.4.6" description = "Cross-platform colored terminal text." -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" files = [ @@ -921,7 +894,6 @@ files = [ name = "colorlog" version = "6.7.0" description = "Add colours to the output of Python's logging module." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -939,7 +911,6 @@ development = ["black", "flake8", "mypy", "pytest", "types-colorama"] name = "commonmark" version = "0.9.1" description = "Python parser for the CommonMark Markdown spec" -category = "main" optional = false python-versions = "*" files = [ @@ -954,8 +925,7 @@ test = ["flake8 (==3.7.8)", "hypothesis (==3.55.3)"] name = "configobj" version = "5.0.8" description = "Config file reading, writing and validation." -category = "main" -optional = false +optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ {file = "configobj-5.0.8-py2.py3-none-any.whl", hash = "sha256:a7a8c6ab7daade85c3f329931a807c8aee750a2494363934f8ea84d8a54c87ea"}, @@ -969,7 +939,6 @@ six = "*" name = "contextlib2" version = "21.6.0" description = "Backports and enhancements for the contextlib module" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -981,7 +950,6 @@ files = [ name = "contourpy" version = "1.0.7" description = "Python library for calculating contours of 2D quadrilateral grids" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1056,7 +1024,6 @@ test-no-images = ["pytest"] name = "cospar" version = "0.1.9" description = "CoSpar: integrating state and lineage information for dynamic inference" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1088,7 +1055,6 @@ docs = ["anndata (>=0.7.5)", "ete3 (>=3.1.2)", "fastcluster (>=1.1.26)", "import name = "coverage" version = "7.2.3" description = "Code coverage measurement for Python" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -1155,8 +1121,7 @@ toml = ["tomli"] name = "cryptography" version = "40.0.2" description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers." -category = "main" -optional = false +optional = true python-versions = ">=3.6" files = [ {file = "cryptography-40.0.2-cp36-abi3-macosx_10_12_universal2.whl", hash = "sha256:8f79b5ff5ad9d3218afb1e7e20ea74da5f76943ee5edb7f76e56ec5161ec782b"}, @@ -1197,7 +1162,6 @@ tox = ["tox"] name = "cycler" version = "0.11.0" description = "Composable style cycles" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1209,7 +1173,6 @@ files = [ name = "darglint" version = "1.8.1" description = "A utility for ensuring Google-style docstrings stay up to date with the source code." -category = "main" optional = true python-versions = ">=3.6,<4.0" files = [ @@ -1221,7 +1184,6 @@ files = [ name = "databricks-cli" version = "0.17.6" description = "A command line interface for Databricks" -category = "main" optional = false python-versions = "*" files = [ @@ -1241,8 +1203,7 @@ tabulate = ">=0.7.7" name = "decorator" version = "5.1.1" description = "Decorators for Humans" -category = "main" -optional = false +optional = true python-versions = ">=3.5" files = [ {file = "decorator-5.1.1-py3-none-any.whl", hash = "sha256:b8c3f85900b9dc423225913c5aace94729fe1fa9763b38939a95226f02d37186"}, @@ -1253,7 +1214,6 @@ files = [ name = "deprecated" version = "1.2.13" description = "Python @deprecated decorator to deprecate old python classes, functions or methods." -category = "main" optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1271,7 +1231,6 @@ dev = ["PyTest", "PyTest (<5)", "PyTest-Cov", "PyTest-Cov (<2.6)", "bump2version name = "desert" version = "2022.9.22" description = "Deserialize to objects while staying DRY" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1292,8 +1251,7 @@ test = ["coverage", "cuvner", "importlib-metadata", "marshmallow-enum", "marshma name = "dictdiffer" version = "0.9.0" description = "Dictdiffer is a library that helps you to diff and patch dictionaries." -category = "main" -optional = false +optional = true python-versions = "*" files = [ {file = "dictdiffer-0.9.0-py2.py3-none-any.whl", hash = "sha256:442bfc693cfcadaf46674575d2eba1c53b42f5e404218ca2c2ff549f2df56595"}, @@ -1310,8 +1268,7 @@ tests = ["check-manifest (>=0.42)", "mock (>=1.3.0)", "pytest (==5.4.3)", "pytes name = "diskcache" version = "5.6.1" description = "Disk Cache -- Disk and file backed persistent cache." -category = "main" -optional = false +optional = true python-versions = ">=3" files = [ {file = "diskcache-5.6.1-py3-none-any.whl", hash = "sha256:558c6a2d5d7c721bb00e40711803d6804850c9f76c426ed81ecc627fe9d2ce2d"}, @@ -1322,7 +1279,6 @@ files = [ name = "distlib" version = "0.3.6" description = "Distribution utilities" -category = "main" optional = true python-versions = "*" files = [ @@ -1334,8 +1290,7 @@ files = [ name = "distro" version = "1.8.0" description = "Distro - an OS platform information API" -category = "main" -optional = false +optional = true python-versions = ">=3.6" files = [ {file = "distro-1.8.0-py3-none-any.whl", hash = "sha256:99522ca3e365cac527b44bde033f64c6945d90eb9f769703caaec52b09bbd3ff"}, @@ -1346,7 +1301,6 @@ files = [ name = "dm-tree" version = "0.1.8" description = "Tree is a library for working with nested data structures." -category = "main" optional = false python-versions = "*" files = [ @@ -1395,7 +1349,6 @@ files = [ name = "docker" version = "6.0.1" description = "A Python library for the Docker Engine API." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1417,7 +1370,6 @@ ssh = ["paramiko (>=2.4.3)"] name = "docrep" version = "0.3.2" description = "Python package for docstring repetition" -category = "main" optional = false python-versions = "*" files = [ @@ -1431,7 +1383,6 @@ six = "*" name = "docstring-parser" version = "0.15" description = "Parse Python docstrings in reST, Google and Numpydoc format" -category = "main" optional = true python-versions = ">=3.6,<4.0" files = [ @@ -1443,7 +1394,6 @@ files = [ name = "docutils" version = "0.19" description = "Docutils -- Python Documentation Utilities" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -1455,7 +1405,6 @@ files = [ name = "dparse" version = "0.6.2" description = "A parser for Python dependency files" -category = "main" optional = true python-versions = ">=3.5" files = [ @@ -1475,8 +1424,7 @@ pipenv = ["pipenv"] name = "dpath" version = "2.1.5" description = "Filesystem-like pathing and searching for dictionaries" -category = "main" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "dpath-2.1.5-py3-none-any.whl", hash = "sha256:559edcbfc806ca2f9ad9e63566f22e5d41c000e4215bbce9dbf1ca4c859f5e0b"}, @@ -1487,8 +1435,7 @@ files = [ name = "dulwich" version = "0.21.3" description = "Python Git Library" -category = "main" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "dulwich-0.21.3-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:25376efc6ea2ee9daa868a120d4f9c905dcb7774f68931be921fba41a657f58a"}, @@ -1562,8 +1509,7 @@ pgp = ["gpg"] name = "dvc" version = "2.58.0" description = "Git for data scientists - manage your code and data together" -category = "main" -optional = false +optional = true python-versions = ">=3.8" files = [ {file = "dvc-2.58.0-py3-none-any.whl", hash = "sha256:2410ad077bb0ce74f6fcd1d5980c8ac772fe7c8fe18a0a20c4fbfe9169a5ebce"}, @@ -1629,8 +1575,7 @@ webhdfs-kerberos = ["dvc-webhdfs[kerberos] (==2.19)"] name = "dvc-data" version = "0.51.0" description = "dvc data" -category = "main" -optional = false +optional = true python-versions = ">=3.8" files = [ {file = "dvc-data-0.51.0.tar.gz", hash = "sha256:32544bb7d3ae509f91c2d07a9dc3739dd87980be5b41582781efb4f246b58497"}, @@ -1656,14 +1601,13 @@ tests = ["mypy (==0.971)", "pylint (==2.15.0)", "pytest (==7.2.0)", "pytest-benc [[package]] name = "dvc-gs" -version = "2.22.0" +version = "2.22.1" description = "gs plugin for dvc" -category = "main" optional = true python-versions = ">=3.8" files = [ - {file = "dvc-gs-2.22.0.tar.gz", hash = "sha256:533616da253f1af2c9778aba12b70b411a007a1c851773eb3138dbf0f12d98d1"}, - {file = "dvc_gs-2.22.0-py3-none-any.whl", hash = "sha256:aac9f3390558518d801f43dd1e2be042c573cbb4963fb25a58099e3805dc8e71"}, + {file = "dvc-gs-2.22.1.tar.gz", hash = "sha256:20a0f07527e8959c2ff13bc71e2715578d8f61e50b86c92ff1cb1b9222732db9"}, + {file = "dvc_gs-2.22.1-py3-none-any.whl", hash = "sha256:d09a5d9e6f3d2f3c441e8af2f8a6830f8f16d6b9c1dae005801d55d6e9655598"}, ] [package.dependencies] @@ -1677,8 +1621,7 @@ tests = ["Pygments (==2.10.0)", "collective.checkdocs (==0.2)", "dvc[testing]", name = "dvc-http" version = "2.30.2" description = "http plugin for dvc" -category = "main" -optional = false +optional = true python-versions = ">=3.8" files = [ {file = "dvc-http-2.30.2.tar.gz", hash = "sha256:d7cf66e8f8359cc9f5ca137de24d259beebdec444516fc7d085ad26fa7d3b34b"}, @@ -1696,8 +1639,7 @@ tests = ["dvc[testing]", "flaky (==3.7.0)", "mypy (==0.910)", "pylint (==2.15.9) name = "dvc-objects" version = "0.22.0" description = "dvc objects" -category = "main" -optional = false +optional = true python-versions = ">=3.8" files = [ {file = "dvc-objects-0.22.0.tar.gz", hash = "sha256:911a5fc0de89ea40118af3a2752a23f769ab5c865484637f47bd74f1e8577f83"}, @@ -1720,8 +1662,7 @@ tests = ["mypy (==0.971)", "pylint (==2.15.0)", "pytest (==7.2.0)", "pytest-cov name = "dvc-render" version = "0.3.1" description = "DVC render" -category = "main" -optional = false +optional = true python-versions = ">=3.8" files = [ {file = "dvc-render-0.3.1.tar.gz", hash = "sha256:af718d813017db9b2e688576f33a8ce27398949620340894afae4f1023f0e07a"}, @@ -1739,8 +1680,7 @@ tests = ["funcy (>=1.17)", "matplotlib", "mypy (==0.981)", "pylint (==2.15.0)", name = "dvc-studio-client" version = "0.9.2" description = "Small library to post data from DVC/DVCLive to Iterative Studio" -category = "main" -optional = false +optional = true python-versions = ">=3.8" files = [ {file = "dvc-studio-client-0.9.2.tar.gz", hash = "sha256:abaadc92126aca874efb177c664a1cdf6e0c642435c51c7187a03b433cbc3472"}, @@ -1761,8 +1701,7 @@ tests = ["pytest (==7.2.0)", "pytest-cov (==3.0.0)", "pytest-mock (==3.8.2)", "p name = "dvc-task" version = "0.2.1" description = "Extensible task queue used in DVC." -category = "main" -optional = false +optional = true python-versions = ">=3.8" files = [ {file = "dvc-task-0.2.1.tar.gz", hash = "sha256:c42b9bb6a8e64c80e20728926f0f8147aa25b696c78876e5dfff0a293d14c735"}, @@ -1785,7 +1724,6 @@ tests = ["celery-types (>=0.11.0)", "flaky (==3.7.0)", "mypy (==0.971)", "pylint name = "entrypoints" version = "0.4" description = "Discover and load entry points from installed packages." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1797,7 +1735,6 @@ files = [ name = "et-xmlfile" version = "1.1.0" description = "An implementation of lxml.xmlfile for the standard library" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1809,7 +1746,6 @@ files = [ name = "ete3" version = "3.1.2" description = "A Python Environment for (phylogenetic) Tree Exploration" -category = "main" optional = false python-versions = "*" files = [ @@ -1820,7 +1756,6 @@ files = [ name = "etils" version = "1.3.0" description = "Collection of common python utils" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1849,7 +1784,6 @@ lazy-imports = ["etils[ecolab]"] name = "exceptiongroup" version = "1.1.1" description = "Backport of PEP 654 (exception groups)" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -1864,7 +1798,6 @@ test = ["pytest (>=6)"] name = "executing" version = "1.2.0" description = "Get the currently executing AST node of a frame, and other information" -category = "main" optional = true python-versions = "*" files = [ @@ -1879,7 +1812,6 @@ tests = ["asttokens", "littleutils", "pytest", "rich"] name = "fastcluster" version = "1.2.6" description = "Fast hierarchical clustering routines for R and Python." -category = "main" optional = false python-versions = ">=3" files = [ @@ -1940,8 +1872,7 @@ test = ["scipy (>=1.6.3)"] name = "filelock" version = "3.11.0" description = "A platform independent file lock." -category = "main" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "filelock-3.11.0-py3-none-any.whl", hash = "sha256:f08a52314748335c6460fc8fe40cd5638b85001225db78c2aa01c8c0db83b318"}, @@ -1956,7 +1887,6 @@ testing = ["covdefaults (>=2.3)", "coverage (>=7.2.2)", "diff-cover (>=7.5)", "p name = "fire" version = "0.5.0" description = "A library for automatically generating command line interfaces." -category = "main" optional = true python-versions = "*" files = [ @@ -1971,7 +1901,6 @@ termcolor = "*" name = "flake8" version = "6.0.0" description = "the modular source code checker: pep8 pyflakes and co" -category = "main" optional = true python-versions = ">=3.8.1" files = [ @@ -1988,7 +1917,6 @@ pyflakes = ">=3.0.0,<3.1.0" name = "flake8-bandit" version = "4.1.1" description = "Automated security testing with bandit and flake8." -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -2004,7 +1932,6 @@ flake8 = ">=5.0.0" name = "flake8-bugbear" version = "23.3.23" description = "A plugin for flake8 finding likely bugs and design problems in your program. Contains warnings that don't belong in pyflakes and pycodestyle." -category = "main" optional = true python-versions = ">=3.8.1" files = [ @@ -2023,7 +1950,6 @@ dev = ["coverage", "hypothesis", "hypothesmith (>=0.2)", "pre-commit", "pytest", name = "flake8-docstrings" version = "1.7.0" description = "Extension for flake8 which uses pydocstyle to check docstrings" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -2039,7 +1965,6 @@ pydocstyle = ">=2.1" name = "flake8-rst-docstrings" version = "0.3.0" description = "Python docstring reStructuredText (RST) validator for flake8" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -2059,7 +1984,6 @@ develop = ["build", "twine"] name = "flask" version = "2.2.3" description = "A simple framework for building complex web applications." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2082,8 +2006,7 @@ dotenv = ["python-dotenv"] name = "flatten-dict" version = "0.4.2" description = "A flexible utility for flattening and unflattening dict-like objects in Python." -category = "main" -optional = false +optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ {file = "flatten-dict-0.4.2.tar.gz", hash = "sha256:506a96b6e6f805b81ae46a0f9f31290beb5fa79ded9d80dbe1b7fa236ab43076"}, @@ -2097,7 +2020,6 @@ six = ">=1.12,<2.0" name = "flax" version = "0.6.9" description = "Flax: A neural network library for JAX designed for flexibility" -category = "main" optional = false python-versions = "*" files = [ @@ -2124,8 +2046,7 @@ testing = ["atari-py (==0.2.5)", "clu", "einops", "gym (==0.18.3)", "jaxlib", "j name = "flufl-lock" version = "7.1.1" description = "NFS-safe file locking with timeouts for POSIX and Windows" -category = "main" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "flufl.lock-7.1.1-py3-none-any.whl", hash = "sha256:96d2c0448ba9fd8fc65d5d681ed7217c8e1625149c1c880bba50559bb680a615"}, @@ -2140,7 +2061,6 @@ psutil = ">=5.9.0" name = "fonttools" version = "4.39.3" description = "Tools to manipulate font files" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2166,7 +2086,6 @@ woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"] name = "frozenlist" version = "1.3.3" description = "A list-like structure which implements collections.abc.MutableSequence" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2250,7 +2169,6 @@ files = [ name = "fsspec" version = "2023.5.0" description = "File-system specification" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2290,8 +2208,7 @@ tqdm = ["tqdm"] name = "funcy" version = "2.0" description = "A fancy and practical functional tools" -category = "main" -optional = false +optional = true python-versions = "*" files = [ {file = "funcy-2.0-py2.py3-none-any.whl", hash = "sha256:53df23c8bb1651b12f095df764bfb057935d49537a56de211b098f4c79614bb0"}, @@ -2302,7 +2219,6 @@ files = [ name = "furo" version = "2023.3.27" description = "A clean customisable Sphinx documentation theme." -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -2320,8 +2236,7 @@ sphinx-basic-ng = "*" name = "gcsfs" version = "2023.5.0" description = "Convenient Filesystem interface over GCS" -category = "main" -optional = false +optional = true python-versions = ">=3.8" files = [ {file = "gcsfs-2023.5.0-py2.py3-none-any.whl", hash = "sha256:4f2ebc41814de3f566f85dec208704cf19823b9d04a55fd12b3142aef9046525"}, @@ -2345,7 +2260,6 @@ gcsfuse = ["fusepy"] name = "gitdb" version = "4.0.10" description = "Git Object Database" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2360,7 +2274,6 @@ smmap = ">=3.0.1,<6" name = "gitpython" version = "3.1.31" description = "GitPython is a Python library used to interact with Git repositories" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2375,8 +2288,7 @@ gitdb = ">=4.0.1,<5" name = "google-api-core" version = "2.11.0" description = "Google API client core library" -category = "main" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "google-api-core-2.11.0.tar.gz", hash = "sha256:4b9bb5d5a380a0befa0573b302651b8a9a89262c1730e37bf423cec511804c22"}, @@ -2400,7 +2312,6 @@ grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0dev)"] name = "google-api-python-client" version = "1.12.11" description = "Google API Client Library for Python" -category = "main" optional = true python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" files = [ @@ -2420,8 +2331,7 @@ uritemplate = ">=3.0.0,<4dev" name = "google-auth" version = "2.17.3" description = "Google Authentication Library" -category = "main" -optional = false +optional = true python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*" files = [ {file = "google-auth-2.17.3.tar.gz", hash = "sha256:ce311e2bc58b130fddf316df57c9b3943c2a7b4f6ec31de9663a9333e4064efc"}, @@ -2445,7 +2355,6 @@ requests = ["requests (>=2.20.0,<3.0.0dev)"] name = "google-auth-httplib2" version = "0.1.0" description = "Google Authentication Library: httplib2 transport" -category = "main" optional = true python-versions = "*" files = [ @@ -2462,8 +2371,7 @@ six = "*" name = "google-auth-oauthlib" version = "1.0.0" description = "Google Authentication Library" -category = "main" -optional = false +optional = true python-versions = ">=3.6" files = [ {file = "google-auth-oauthlib-1.0.0.tar.gz", hash = "sha256:e375064964820b47221a7e1b7ee1fd77051b6323c3f9e3e19785f78ab67ecfc5"}, @@ -2481,7 +2389,6 @@ tool = ["click (>=6.0.0)"] name = "google-cloud-aiplatform" version = "1.25.0" description = "Vertex AI API client library" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -2490,7 +2397,7 @@ files = [ ] [package.dependencies] -google-api-core = {version = ">=1.32.0,<2.0.0 || >=2.8.0,<3.0.0dev", extras = ["grpc"]} +google-api-core = {version = ">=1.32.0,<2.0.dev0 || >=2.8.dev0,<3.0.0dev", extras = ["grpc"]} google-cloud-bigquery = ">=1.15.0,<4.0.0dev" google-cloud-resource-manager = ">=1.3.3,<3.0.0dev" google-cloud-storage = ">=1.32.0,<3.0.0dev" @@ -2519,7 +2426,6 @@ xai = ["tensorflow (>=2.3.0,<3.0.0dev)"] name = "google-cloud-bigquery" version = "3.10.0" description = "Google BigQuery API client library" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -2528,7 +2434,7 @@ files = [ ] [package.dependencies] -google-api-core = {version = ">=1.31.5,<2.0.0 || >2.3.0,<3.0.0dev", extras = ["grpc"]} +google-api-core = {version = ">=1.31.5,<2.0.dev0 || >2.3.0,<3.0.0dev", extras = ["grpc"]} google-cloud-core = ">=1.6.0,<3.0.0dev" google-resumable-media = ">=0.6.0,<3.0dev" grpcio = ">=1.47.0,<2.0dev" @@ -2552,8 +2458,7 @@ tqdm = ["tqdm (>=4.7.4,<5.0.0dev)"] name = "google-cloud-core" version = "2.3.2" description = "Google Cloud API client core library" -category = "main" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "google-cloud-core-2.3.2.tar.gz", hash = "sha256:b9529ee7047fd8d4bf4a2182de619154240df17fbe60ead399078c1ae152af9a"}, @@ -2561,7 +2466,7 @@ files = [ ] [package.dependencies] -google-api-core = ">=1.31.6,<2.0.0 || >2.3.0,<3.0.0dev" +google-api-core = ">=1.31.6,<2.0.dev0 || >2.3.0,<3.0.0dev" google-auth = ">=1.25.0,<3.0dev" [package.extras] @@ -2571,7 +2476,6 @@ grpc = ["grpcio (>=1.38.0,<2.0dev)"] name = "google-cloud-notebooks" version = "1.7.0" description = "Google Cloud Notebooks API client library" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -2580,7 +2484,7 @@ files = [ ] [package.dependencies] -google-api-core = {version = ">=1.34.0,<2.0.0 || >=2.11.0,<3.0.0dev", extras = ["grpc"]} +google-api-core = {version = ">=1.34.0,<2.0.dev0 || >=2.11.dev0,<3.0.0dev", extras = ["grpc"]} grpc-google-iam-v1 = ">=0.12.4,<1.0.0dev" proto-plus = ">=1.22.0,<2.0.0dev" protobuf = ">=3.19.5,<3.20.0 || >3.20.0,<3.20.1 || >3.20.1,<4.21.0 || >4.21.0,<4.21.1 || >4.21.1,<4.21.2 || >4.21.2,<4.21.3 || >4.21.3,<4.21.4 || >4.21.4,<4.21.5 || >4.21.5,<5.0.0dev" @@ -2589,7 +2493,6 @@ protobuf = ">=3.19.5,<3.20.0 || >3.20.0,<3.20.1 || >3.20.1,<4.21.0 || >4.21.0,<4 name = "google-cloud-pipeline-components" version = "1.0.43" description = "This SDK enables a set of First Party (Google owned) pipeline components that allow users to take their experience from Vertex AI SDK and other Google Cloud services and create a corresponding pipeline using KFP or Managed Pipelines." -category = "main" optional = true python-versions = "*" files = [ @@ -2597,7 +2500,7 @@ files = [ ] [package.dependencies] -google-api-core = ">=1.31.5,<2.0.0 || >=2.8.0,<3.0.0dev" +google-api-core = ">=1.31.5,<2.0.dev0 || >=2.8.dev0,<3.0.0dev" google-cloud-aiplatform = ">=1.14.0,<2" google-cloud-notebooks = ">=0.4.0" google-cloud-storage = ">=2.2.1,<3" @@ -2607,13 +2510,12 @@ kfp = ">=1.8.9,<2.0.0" protobuf = ">=3.19.0,<4.0.0dev" [package.extras] -tests = ["flake8 (>=3.0.0)", "google-api-core (>=1.31.5,<2.0.0 || >=2.8.0,<3.0.0dev)", "google-cloud-aiplatform (>=1.14.0,<2)", "google-cloud-notebooks (>=0.4.0)", "google-cloud-storage (>=2.2.1,<3)", "googleapis-common-protos (>=1.56.2,<2.0dev)", "grpcio-status (<=1.47.0)", "kfp (>=1.8.9,<2.0.0)", "mock (>=4.0.0)", "protobuf (>=3.19.0,<4.0.0dev)", "pytest (>=6.0.0)"] +tests = ["flake8 (>=3.0.0)", "google-api-core (>=1.31.5,<2.0.dev0 || >=2.8.dev0,<3.0.0dev)", "google-cloud-aiplatform (>=1.14.0,<2)", "google-cloud-notebooks (>=0.4.0)", "google-cloud-storage (>=2.2.1,<3)", "googleapis-common-protos (>=1.56.2,<2.0dev)", "grpcio-status (<=1.47.0)", "kfp (>=1.8.9,<2.0.0)", "mock (>=4.0.0)", "protobuf (>=3.19.0,<4.0.0dev)", "pytest (>=6.0.0)"] [[package]] name = "google-cloud-resource-manager" version = "1.10.0" description = "Google Cloud Resource Manager API client library" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -2622,7 +2524,7 @@ files = [ ] [package.dependencies] -google-api-core = {version = ">=1.34.0,<2.0.0 || >=2.11.0,<3.0.0dev", extras = ["grpc"]} +google-api-core = {version = ">=1.34.0,<2.0.dev0 || >=2.11.dev0,<3.0.0dev", extras = ["grpc"]} grpc-google-iam-v1 = ">=0.12.4,<1.0.0dev" proto-plus = ">=1.22.0,<2.0.0dev" protobuf = ">=3.19.5,<3.20.0 || >3.20.0,<3.20.1 || >3.20.1,<4.21.0 || >4.21.0,<4.21.1 || >4.21.1,<4.21.2 || >4.21.2,<4.21.3 || >4.21.3,<4.21.4 || >4.21.4,<4.21.5 || >4.21.5,<5.0.0dev" @@ -2631,8 +2533,7 @@ protobuf = ">=3.19.5,<3.20.0 || >3.20.0,<3.20.1 || >3.20.1,<4.21.0 || >4.21.0,<4 name = "google-cloud-storage" version = "2.8.0" description = "Google Cloud Storage API client library" -category = "main" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "google-cloud-storage-2.8.0.tar.gz", hash = "sha256:4388da1ff5bda6d729f26dbcaf1bfa020a2a52a7b91f0a8123edbda51660802c"}, @@ -2640,7 +2541,7 @@ files = [ ] [package.dependencies] -google-api-core = ">=1.31.5,<2.0.0 || >2.3.0,<3.0.0dev" +google-api-core = ">=1.31.5,<2.0.dev0 || >2.3.0,<3.0.0dev" google-auth = ">=1.25.0,<3.0dev" google-cloud-core = ">=2.3.0,<3.0dev" google-resumable-media = ">=2.3.2" @@ -2653,8 +2554,7 @@ protobuf = ["protobuf (<5.0.0dev)"] name = "google-crc32c" version = "1.5.0" description = "A python wrapper of the C library 'Google CRC32C'" -category = "main" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "google-crc32c-1.5.0.tar.gz", hash = "sha256:89284716bc6a5a415d4eaa11b1726d2d60a0cd12aadf5439828353662ede9dd7"}, @@ -2734,8 +2634,7 @@ testing = ["pytest"] name = "google-resumable-media" version = "2.4.1" description = "Utilities for Google Media Downloads and Resumable Uploads" -category = "main" -optional = false +optional = true python-versions = ">= 3.7" files = [ {file = "google-resumable-media-2.4.1.tar.gz", hash = "sha256:15b8a2e75df42dc6502d1306db0bce2647ba6013f9cd03b6e17368c0886ee90a"}, @@ -2753,8 +2652,7 @@ requests = ["requests (>=2.18.0,<3.0.0dev)"] name = "googleapis-common-protos" version = "1.59.0" description = "Common protobufs used in Google APIs" -category = "main" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "googleapis-common-protos-1.59.0.tar.gz", hash = "sha256:4168fcb568a826a52f23510412da405abd93f4d23ba544bb68d943b14ba3cb44"}, @@ -2772,8 +2670,7 @@ grpc = ["grpcio (>=1.44.0,<2.0.0dev)"] name = "grandalf" version = "0.8" description = "Graph and drawing algorithms framework" -category = "main" -optional = false +optional = true python-versions = "*" files = [ {file = "grandalf-0.8-py3-none-any.whl", hash = "sha256:793ca254442f4a79252ea9ff1ab998e852c1e071b863593e5383afee906b4185"}, @@ -2790,7 +2687,6 @@ full = ["numpy", "ply"] name = "greenlet" version = "2.0.2" description = "Lightweight in-process concurrent programming" -category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" files = [ @@ -2864,7 +2760,6 @@ test = ["objgraph", "psutil"] name = "grpc-google-iam-v1" version = "0.12.6" description = "IAM API client library" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -2881,7 +2776,6 @@ protobuf = ">=3.19.5,<3.20.0 || >3.20.0,<3.20.1 || >3.20.1,<4.21.1 || >4.21.1,<4 name = "grpcio" version = "1.54.2" description = "HTTP/2-based RPC framework" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -2939,7 +2833,6 @@ protobuf = ["grpcio-tools (>=1.54.2)"] name = "grpcio-status" version = "1.47.0" description = "Status proto mapping for gRPC" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -2956,7 +2849,6 @@ protobuf = ">=3.12.0" name = "gunicorn" version = "20.1.0" description = "WSGI HTTP Server for UNIX" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -2977,7 +2869,6 @@ tornado = ["tornado (>=0.2)"] name = "h5py" version = "3.8.0" description = "Read and write HDF5 files from Python" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3015,7 +2906,6 @@ numpy = ">=1.14.5" name = "httplib2" version = "0.22.0" description = "A comprehensive HTTP client library." -category = "main" optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -3030,7 +2920,6 @@ pyparsing = {version = ">=2.4.2,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.0.2 || >3.0 name = "hydra-core" version = "1.3.2" description = "A framework for elegantly configuring complex applications" -category = "main" optional = false python-versions = "*" files = [ @@ -3039,7 +2928,7 @@ files = [ ] [package.dependencies] -antlr4-python3-runtime = ">=4.9.0,<4.10.0" +antlr4-python3-runtime = "==4.9.*" omegaconf = ">=2.2,<2.4" packaging = "*" @@ -3047,7 +2936,6 @@ packaging = "*" name = "hydra-zen" version = "0.10.0" description = "Configurable, reproducible, and scalable workflows in Python, via Hydra" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3068,7 +2956,6 @@ test = ["hypothesis (>=6.28.0)", "pytest (>=3.8)"] name = "hypothesis" version = "6.72.1" description = "A library for property-based testing" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -3101,7 +2988,6 @@ zoneinfo = ["backports.zoneinfo (>=0.2.1)", "tzdata (>=2023.3)"] name = "identify" version = "2.5.23" description = "File identification library for Python" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -3116,7 +3002,6 @@ license = ["ukkonen"] name = "idna" version = "3.4" description = "Internationalized Domain Names in Applications (IDNA)" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -3128,7 +3013,6 @@ files = [ name = "igraph" version = "0.10.4" description = "High performance graph data structures and algorithms" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3195,7 +3079,6 @@ test-musl = ["networkx (>=2.5)", "pytest (>=7.0.1)", "pytest-timeout (>=2.1.0)"] name = "imagesize" version = "1.4.1" description = "Getting image size from png/jpeg/jpeg2000/gif file" -category = "main" optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -3207,7 +3090,6 @@ files = [ name = "importlib-metadata" version = "6.6.0" description = "Read metadata from Python packages" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3227,7 +3109,6 @@ testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packag name = "importlib-resources" version = "5.12.0" description = "Read resources from Python packages" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3246,7 +3127,6 @@ testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-chec name = "iniconfig" version = "2.0.0" description = "brain-dead simple config-ini parsing" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -3258,7 +3138,6 @@ files = [ name = "ipython" version = "8.13.1" description = "IPython: Productive Interactive Computing" -category = "main" optional = true python-versions = ">=3.9" files = [ @@ -3298,7 +3177,6 @@ test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.21)", "pa name = "isort" version = "5.12.0" description = "A Python utility / library to sort Python imports." -category = "main" optional = true python-versions = ">=3.8.0" files = [ @@ -3316,8 +3194,7 @@ requirements-deprecated-finder = ["pip-api", "pipreqs"] name = "iterative-telemetry" version = "0.0.8" description = "Common library for sending telemetry" -category = "main" -optional = false +optional = true python-versions = ">=3.8" files = [ {file = "iterative-telemetry-0.0.8.tar.gz", hash = "sha256:5bed9d19109c892cff2a4712a2fb18ad727079a7ab260a28b1e2f6934eec652d"}, @@ -3338,7 +3215,6 @@ tests = ["mypy (==0.971)", "pylint (==2.15.0)", "pytest (==7.2.0)", "pytest-cov name = "itsdangerous" version = "2.1.2" description = "Safely pass data to untrusted environments and back." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3350,7 +3226,6 @@ files = [ name = "jax" version = "0.4.8" description = "Differentiate, compile, and transform Numpy code." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3381,7 +3256,6 @@ tpu = ["jaxlib (==0.4.7)", "libtpu-nightly (==0.1.dev20230327)", "requests"] name = "jaxlib" version = "0.4.7" description = "XLA library for JAX" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3408,7 +3282,6 @@ scipy = ">=1.7" name = "jedi" version = "0.18.2" description = "An autocompletion tool for Python that can be used for text editors." -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -3428,7 +3301,6 @@ testing = ["Django (<3.1)", "attrs", "colorama", "docopt", "pytest (<7.0.0)"] name = "jinja2" version = "3.1.2" description = "A very fast and expressive template engine." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3446,7 +3318,6 @@ i18n = ["Babel (>=2.7)"] name = "joblib" version = "1.2.0" description = "Lightweight pipelining with Python functions" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3458,7 +3329,6 @@ files = [ name = "jsonpickle" version = "3.0.1" description = "Python library for serializing any arbitrary object graph into JSON" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -3475,7 +3345,6 @@ testing-libs = ["simplejson", "ujson"] name = "jsonschema" version = "4.17.3" description = "An implementation of JSON Schema validation for Python" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -3495,7 +3364,6 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- name = "jupyter-core" version = "5.3.0" description = "Jupyter core package. A base package on which Jupyter projects rely." -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -3516,7 +3384,6 @@ test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"] name = "kfp" version = "1.8.21" description = "KubeFlow Pipelines SDK" -category = "main" optional = true python-versions = ">=3.6.1" files = [ @@ -3530,7 +3397,7 @@ cloudpickle = ">=2.0.0,<3" Deprecated = ">=1.2.7,<2" docstring-parser = ">=0.7.3,<1" fire = ">=0.3.1,<1" -google-api-core = ">=1.31.5,<2.0.0 || >2.3.0,<3.0.0dev" +google-api-core = ">=1.31.5,<2.0.dev0 || >2.3.0,<3.0.0dev" google-api-python-client = ">=1.7.8,<2" google-auth = ">=1.6.1,<3" google-cloud-storage = ">=1.20.0,<3" @@ -3555,7 +3422,6 @@ all = ["docker"] name = "kfp-pipeline-spec" version = "0.1.16" description = "Kubeflow Pipelines pipeline spec" -category = "main" optional = true python-versions = ">=3.7.0" files = [ @@ -3569,7 +3435,6 @@ protobuf = ">=3.13.0,<4" name = "kfp-server-api" version = "1.8.5" description = "Kubeflow Pipelines API" -category = "main" optional = true python-versions = "*" files = [ @@ -3586,7 +3451,6 @@ urllib3 = ">=1.15" name = "kiwisolver" version = "1.4.4" description = "A fast implementation of the Cassowary constraint solver" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3664,8 +3528,7 @@ files = [ name = "kombu" version = "5.2.4" description = "Messaging library for Python." -category = "main" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "kombu-5.2.4-py3-none-any.whl", hash = "sha256:8b213b24293d3417bcf0d2f5537b7f756079e3ea232a8386dcc89a59fd2361a4"}, @@ -3696,7 +3559,6 @@ zookeeper = ["kazoo (>=1.3.1)"] name = "kubernetes" version = "25.3.0" description = "Kubernetes python client" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -3714,7 +3576,7 @@ requests-oauthlib = "*" setuptools = ">=21.0.0" six = ">=1.9.0" urllib3 = ">=1.24.2" -websocket-client = ">=0.32.0,<0.40.0 || >0.40.0,<0.41.0 || >=0.43.0" +websocket-client = ">=0.32.0,<0.40.0 || >0.40.0,<0.41.dev0 || >=0.43.dev0" [package.extras] adal = ["adal (>=1.0.2)"] @@ -3723,7 +3585,6 @@ adal = ["adal (>=1.0.2)"] name = "leidenalg" version = "0.9.1" description = "Leiden is a general algorithm for methods of community detection in large networks." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3788,7 +3649,6 @@ igraph = ">=0.10.0,<0.11" name = "lightning-utilities" version = "0.8.0" description = "PyTorch Lightning Sample project." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3810,7 +3670,6 @@ typing = ["mypy (>=1.0.0)"] name = "livereload" version = "2.6.3" description = "Python LiveReload is an awesome tool for web developers" -category = "main" optional = true python-versions = "*" files = [ @@ -3826,7 +3685,6 @@ tornado = {version = "*", markers = "python_version > \"2.7\""} name = "llvmlite" version = "0.39.1" description = "lightweight wrapper around basic LLVM functionality" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3864,7 +3722,6 @@ files = [ name = "loompy" version = "3.0.7" description = "Work with Loom files for single-cell RNA-seq data" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3884,7 +3741,6 @@ setuptools = "*" name = "mako" version = "1.2.4" description = "A super-fast templating language that borrows the best ideas from the existing templating languages." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3904,7 +3760,6 @@ testing = ["pytest"] name = "markdown" version = "3.4.3" description = "Python implementation of John Gruber's Markdown." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3922,7 +3777,6 @@ testing = ["coverage", "pyyaml"] name = "markdown-it-py" version = "2.2.0" description = "Python port of markdown-it. Markdown parsing, done right!" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -3947,7 +3801,6 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"] name = "markupsafe" version = "2.1.2" description = "Safely add untrusted strings to HTML/XML markup." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4007,7 +3860,6 @@ files = [ name = "marshmallow" version = "3.19.0" description = "A lightweight library for converting complex datatypes to and from native Python datatypes." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4028,7 +3880,6 @@ tests = ["pytest", "pytz", "simplejson"] name = "matplotlib" version = "3.7.1" description = "Python plotting package" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4091,7 +3942,6 @@ python-dateutil = ">=2.7" name = "matplotlib-inline" version = "0.1.6" description = "Inline Matplotlib backend for Jupyter" -category = "main" optional = true python-versions = ">=3.5" files = [ @@ -4106,7 +3956,6 @@ traitlets = "*" name = "matplotlib-venn" version = "0.11.9" description = "Functions for plotting area-proportional two- and three-way Venn diagrams in matplotlib." -category = "main" optional = true python-versions = "*" files = [ @@ -4122,7 +3971,6 @@ scipy = "*" name = "mccabe" version = "0.7.0" description = "McCabe checker, plugin for flake8" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -4134,7 +3982,6 @@ files = [ name = "mdit-py-plugins" version = "0.3.5" description = "Collection of plugins for markdown-it-py" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -4154,7 +4001,6 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"] name = "mdurl" version = "0.1.2" description = "Markdown URL utilities" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -4166,7 +4012,6 @@ files = [ name = "mizani" version = "0.9.0" description = "Scales for Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4193,7 +4038,6 @@ test = ["pytest-cov"] name = "ml-collections" version = "0.1.1" description = "ML Collections is a library of Python collections designed for ML usecases." -category = "main" optional = false python-versions = ">=2.6" files = [ @@ -4210,7 +4054,6 @@ six = "*" name = "ml-dtypes" version = "0.1.0" description = "" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4246,7 +4089,6 @@ dev = ["absl-py", "pyink", "pylint (>=2.6.0)", "pytest", "pytest-xdist"] name = "mlflow" version = "2.2.2" description = "MLflow: A Platform for ML Development and Productionization" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4296,7 +4138,6 @@ sqlserver = ["mlflow-dbstore"] name = "msgpack" version = "1.0.5" description = "MessagePack serializer" -category = "main" optional = false python-versions = "*" files = [ @@ -4369,7 +4210,6 @@ files = [ name = "mudata" version = "0.2.2" description = "Multimodal omics analysis framework" -category = "main" optional = false python-versions = ">= 3.8" files = [ @@ -4391,7 +4231,6 @@ test = ["zarr"] name = "multidict" version = "6.0.4" description = "multidict implementation" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4475,7 +4314,6 @@ files = [ name = "multipledispatch" version = "0.6.0" description = "Multiple dispatch" -category = "main" optional = false python-versions = "*" files = [ @@ -4491,7 +4329,6 @@ six = "*" name = "mypy" version = "1.2.0" description = "Optional static typing for Python" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -4538,7 +4375,6 @@ reports = ["lxml"] name = "mypy-extensions" version = "1.0.0" description = "Type system extensions for programs checked with the mypy type checker." -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -4550,7 +4386,6 @@ 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hash = "sha256:3775b01c1a04d07fd9201eac68e83d55542282c6fcb6bbe88b90450254373950"}, {file = "orjson-3.8.10-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:4355c9aedfefe60904e8bd7901315ebbc8bb828f665e4c9bc94b1432e67cb6f7"}, {file = "orjson-3.8.10-cp39-cp39-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:b7b0ba074375e25c1594e770e2215941e2017c3cd121889150737fa1123e8bfe"}, {file = "orjson-3.8.10-cp39-cp39-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:34b6901c110c06ab9e8d7d0496db4bc9a0c162ca8d77f67539d22cb39e0a1ef4"}, @@ -5026,7 +4838,6 @@ files = [ name = "packaging" version = "23.1" description = "Core utilities for Python packages" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -5038,7 +4849,6 @@ files = [ name = "pandas" version = "1.5.3" description = "Powerful data structures for data analysis, time series, and statistics" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -5086,7 +4896,6 @@ test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"] name = "parso" version = "0.8.3" description = "A Python Parser" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -5102,7 +4911,6 @@ testing = ["docopt", "pytest (<6.0.0)"] name = "pastel" version = "0.2.1" description = "Bring colors to your terminal." -category = "main" optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -5114,8 +4922,7 @@ files = [ name = "pathspec" version = "0.11.1" description = "Utility library for gitignore style pattern matching of file paths." -category = "main" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "pathspec-0.11.1-py3-none-any.whl", hash = "sha256:d8af70af76652554bd134c22b3e8a1cc46ed7d91edcdd721ef1a0c51a84a5293"}, @@ -5126,7 +4933,6 @@ files = [ name = "patsy" version = "0.5.3" description = "A Python package for describing statistical models and for building design matrices." -category = "main" optional = false python-versions = "*" files = [ @@ -5145,7 +4951,6 @@ test = ["pytest", "pytest-cov", "scipy"] name = "pbr" version = "5.11.1" description = "Python Build Reasonableness" -category = "main" optional = true python-versions = ">=2.6" files = [ @@ -5157,7 +4962,6 @@ files = [ name = "pep8-naming" version = "0.13.3" description = "Check PEP-8 naming conventions, plugin for flake8" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -5172,7 +4976,6 @@ flake8 = ">=5.0.0" name = "pexpect" version = "4.8.0" description = "Pexpect allows easy control of interactive console applications." -category = "main" optional = true python-versions = "*" files = [ @@ -5187,7 +4990,6 @@ ptyprocess = ">=0.5" name = "pickleshare" version = "0.7.5" description = "Tiny 'shelve'-like database with concurrency support" -category = "main" optional = true python-versions = "*" files = [ @@ -5199,7 +5001,6 @@ files = [ name = "pillow" version = "9.5.0" description = "Python Imaging Library (Fork)" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -5279,8 +5080,7 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa name = "platformdirs" version = "3.2.0" description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -category = "main" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "platformdirs-3.2.0-py3-none-any.whl", hash = "sha256:ebe11c0d7a805086e99506aa331612429a72ca7cd52a1f0d277dc4adc20cb10e"}, @@ -5295,7 +5095,6 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.2.2)", "pytest- name = "plotnine" version = "0.10.1" description = "A grammar of graphics for python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -5323,7 +5122,6 @@ test = ["flake8", "pytest-cov"] name = "pluggy" version = "1.0.0" description = "plugin and hook calling mechanisms for python" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -5339,7 +5137,6 @@ testing = ["pytest", "pytest-benchmark"] name = "poethepoet" version = "0.19.0" description = "A task runner that works well with poetry." -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -5358,7 +5155,6 @@ poetry-plugin = ["poetry (>=1.0,<2.0)"] name = "pre-commit" version = "3.2.2" description = "A framework for managing and maintaining multi-language pre-commit hooks." -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -5377,7 +5173,6 @@ virtualenv = ">=20.10.0" name = "pre-commit-hooks" version = "4.4.0" description = "Some out-of-the-box hooks for pre-commit." -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -5393,8 +5188,7 @@ tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""} name = "prompt-toolkit" version = "3.0.38" description = "Library for building powerful interactive command lines in Python" -category = "main" -optional = false +optional = true python-versions = ">=3.7.0" files = [ {file = "prompt_toolkit-3.0.38-py3-none-any.whl", hash = "sha256:45ea77a2f7c60418850331366c81cf6b5b9cf4c7fd34616f733c5427e6abbb1f"}, @@ -5408,7 +5202,6 @@ wcwidth = "*" name = "proto-plus" version = "1.22.2" description = "Beautiful, Pythonic protocol buffers." -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -5426,7 +5219,6 @@ testing = ["google-api-core[grpc] (>=1.31.5)"] name = "protobuf" version = "3.20.3" description = "Protocol Buffers" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -5458,8 +5250,7 @@ files = [ name = "psutil" version = "5.9.5" description = "Cross-platform lib for process and system monitoring in Python." -category = "main" -optional = false +optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ {file = 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"pyasn1-0.4.8-py2.py3-none-any.whl", hash = "sha256:39c7e2ec30515947ff4e87fb6f456dfc6e84857d34be479c9d4a4ba4bf46aa5d"}, @@ -5562,8 +5349,7 @@ files = [ name = "pyasn1-modules" version = "0.2.8" description = "A collection of ASN.1-based protocols modules." -category = "main" -optional = false +optional = true python-versions = "*" files = [ {file = "pyasn1-modules-0.2.8.tar.gz", hash = "sha256:905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e"}, @@ -5577,7 +5363,6 @@ pyasn1 = ">=0.4.6,<0.5.0" name = "pycodestyle" version = "2.10.0" description = "Python style guide checker" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -5589,7 +5374,6 @@ files = [ name = "pycparser" version = "2.21" description = "C parser in Python" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -5601,7 +5385,6 @@ files = [ name = "pydantic" version = "1.10.7" description = "Data validation and settings management using python type hints" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -5654,7 +5437,6 @@ email = ["email-validator (>=1.0.3)"] name = "pydocstyle" version = "6.3.0" description = "Python docstring style checker" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -5672,8 +5454,7 @@ toml = ["tomli (>=1.2.3)"] name = "pydot" version = "1.4.2" description = "Python interface to Graphviz's Dot" -category = "main" -optional = false +optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ {file = "pydot-1.4.2-py2.py3-none-any.whl", hash = "sha256:66c98190c65b8d2e2382a441b4c0edfdb4f4c025ef9cb9874de478fb0793a451"}, @@ -5687,7 +5468,6 @@ pyparsing = ">=2.1.4" name = "pyerfa" version = "2.0.0.3" description = "Python bindings for ERFA" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -5744,7 +5524,6 @@ test = ["pytest", "pytest-doctestplus (>=0.7)"] name = "pyflakes" version = "3.0.1" description = "passive checker of Python programs" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -5756,8 +5535,7 @@ files = [ name = "pygit2" version = "1.12.0" description = "Python bindings for libgit2." -category = "main" -optional = false +optional = true python-versions = ">=3.8" files = [ {file = "pygit2-1.12.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:b44a3b38e62dbf8cb559a40d2b39506a638d13542502ddb927f1c05565048f27"}, @@ -5800,7 +5578,6 @@ cffi = ">=1.9.1" name = "pygments" version = "2.15.0" description = "Pygments is a syntax highlighting package written in Python." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -5815,8 +5592,7 @@ plugins = ["importlib-metadata"] name = "pygtrie" version = "2.5.0" description = "A pure Python trie data structure implementation." -category = "main" -optional = false +optional = true python-versions = "*" files = [ {file = "pygtrie-2.5.0-py3-none-any.whl", hash = "sha256:8795cda8105493d5ae159a5bef313ff13156c5d4d72feddefacaad59f8c8ce16"}, @@ -5827,7 +5603,6 @@ files = [ name = "pyjwt" version = "2.6.0" description = "JSON Web Token implementation in Python" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -5845,7 +5620,6 @@ tests = ["coverage[toml] (==5.0.4)", "pytest (>=6.0.0,<7.0.0)"] name = "pynndescent" version = "0.5.10" description = "Nearest Neighbor Descent" -category = "main" optional = false python-versions = "*" files = [ @@ -5863,7 +5637,6 @@ scipy = ">=1.0" name = "pyparsing" version = "3.0.9" description = "pyparsing module - Classes and methods to define and execute parsing grammars" -category = "main" optional = false python-versions = ">=3.6.8" files = [ @@ -5878,7 +5651,6 @@ diagrams = ["jinja2", "railroad-diagrams"] name = "pyro-api" version = "0.1.2" description = "Generic API for dispatch to Pyro backends." -category = "main" optional = false python-versions = "*" files = [ @@ -5894,7 +5666,6 @@ test = ["flake8", "pytest (>=5.0)"] name = "pyro-ppl" version = "1.8.3" description = "A Python library for probabilistic modeling and inference" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -5921,7 +5692,6 @@ test = ["black (>=21.4b0)", "flake8", "graphviz (>=0.8)", "jupyter (>=1.0.0)", " name = "pyrsistent" version = "0.19.3" description = "Persistent/Functional/Immutable data structures" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -5958,7 +5728,6 @@ files = [ name = "pytest" version = "7.3.1" description = "pytest: simple powerful testing with Python" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -5981,7 +5750,6 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no name = "pytest-cov" version = "4.0.0" description = "Pytest plugin for measuring coverage." -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -6000,7 +5768,6 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtuale name = "pytest-mock" version = "3.10.0" description = "Thin-wrapper around the mock package for easier use with pytest" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -6018,7 +5785,6 @@ dev = ["pre-commit", "pytest-asyncio", "tox"] name = "python-dateutil" version = "2.8.2" description = "Extensions to the standard Python datetime module" -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" files = [ @@ -6033,7 +5799,6 @@ six = ">=1.5" name = "python-dotenv" version = "1.0.0" description = "Read key-value pairs from a .env file and set them as environment variables" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -6048,7 +5813,6 @@ cli = ["click (>=5.0)"] name = "pytorch-lightning" version = "1.9.4" description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers. Scale your models. Write less boilerplate." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -6084,7 +5848,6 @@ test = ["cloudpickle (>=1.3)", "codecov (==2.1.12)", "coverage (==6.5.0)", "fast name = "pytz" version = "2022.7.1" description = "World timezone definitions, modern and historical" -category = "main" optional = false python-versions = "*" files = [ @@ -6096,7 +5859,6 @@ files = [ name = "pyupgrade" version = "3.3.1" description = "A tool to automatically upgrade syntax for newer versions." -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -6111,7 +5873,6 @@ tokenize-rt = ">=3.2.0" name = "pyvis" version = "0.3.2" description = "A Python network graph visualization library" -category = "main" optional = true python-versions = ">3.6" files = [ @@ -6128,7 +5889,6 @@ networkx = ">=1.11" name = "pywin32" version = "306" description = "Python for Window Extensions" -category = "main" optional = false python-versions = "*" files = [ @@ -6152,7 +5912,6 @@ files = [ name = "pyyaml" version = "5.4.1" description = "YAML parser and emitter for Python" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ @@ -6191,7 +5950,6 @@ files = [ name = "querystring-parser" version = "1.2.4" description = "QueryString parser for Python/Django that correctly handles nested dictionaries" -category = "main" optional = false python-versions = "*" files = [ @@ -6206,7 +5964,6 @@ six = "*" name = "requests" version = "2.28.2" description = "Python HTTP for Humans." -category = "main" optional = false python-versions = ">=3.7, <4" files = [ @@ -6228,8 +5985,7 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] name = "requests-oauthlib" version = "1.3.1" description = "OAuthlib authentication support for Requests." -category = "main" -optional = false +optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ {file = "requests-oauthlib-1.3.1.tar.gz", hash = "sha256:75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a"}, @@ -6247,7 +6003,6 @@ rsa = ["oauthlib[signedtoken] (>=3.0.0)"] name = "requests-toolbelt" version = "0.10.1" description = "A utility belt for advanced users of python-requests" -category = "main" optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -6262,7 +6017,6 @@ requests = ">=2.0.1,<3.0.0" name = "restructuredtext-lint" version = "1.4.0" description = "reStructuredText linter" -category = "main" optional = true python-versions = "*" files = [ @@ -6276,7 +6030,6 @@ docutils = ">=0.11,<1.0" name = "rich" version = "12.6.0" description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal" -category = "main" optional = false python-versions = ">=3.6.3,<4.0.0" files = [ @@ -6295,8 +6048,7 @@ jupyter = ["ipywidgets (>=7.5.1,<8.0.0)"] name = "rsa" version = "4.9" description = "Pure-Python RSA implementation" -category = "main" -optional = false +optional = true python-versions = ">=3.6,<4" files = [ {file = "rsa-4.9-py3-none-any.whl", hash = "sha256:90260d9058e514786967344d0ef75fa8727eed8a7d2e43ce9f4bcf1b536174f7"}, @@ -6310,8 +6062,7 @@ pyasn1 = ">=0.1.3" name = "ruamel-yaml" version = "0.17.21" description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order" -category = "main" -optional = false +optional = true python-versions = ">=3" files = [ {file = "ruamel.yaml-0.17.21-py3-none-any.whl", hash = "sha256:742b35d3d665023981bd6d16b3d24248ce5df75fdb4e2924e93a05c1f8b61ca7"}, @@ -6329,8 +6080,7 @@ jinja2 = ["ruamel.yaml.jinja2 (>=0.2)"] name = "ruamel-yaml-clib" version = "0.2.7" description = "C version of reader, parser and emitter for ruamel.yaml derived from libyaml" -category = "main" -optional = false +optional = true python-versions = ">=3.5" files = [ {file = "ruamel.yaml.clib-0.2.7-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:d5859983f26d8cd7bb5c287ef452e8aacc86501487634573d260968f753e1d71"}, @@ -6375,7 +6125,6 @@ files = [ name = "safety" version = "2.3.4" description = "Checks installed dependencies for known vulnerabilities and licenses." -category = "main" optional = true python-versions = "*" files = [ @@ -6399,7 +6148,6 @@ gitlab = ["python-gitlab (>=1.3.0)"] name = "scanpy" version = "1.9.3" description = "Single-Cell Analysis in Python." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -6449,7 +6197,6 @@ test-min = ["profimp", "pytest (>=4.4)", "pytest-nunit"] name = "scikit-learn" version = "1.2.2" description = "A set of python modules for machine learning and data mining" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -6492,7 +6239,6 @@ tests = ["black (>=22.3.0)", "flake8 (>=3.8.2)", "matplotlib (>=3.1.3)", "mypy ( name = "scikit-misc" version = "0.1.4" description = "Miscellaneous tools for scientific computing." -category = "main" optional = false python-versions = "*" files = [ @@ -6530,7 +6276,6 @@ numpy = "*" name = "scipy" version = "1.10.1" description = "Fundamental algorithms for scientific computing in Python" -category = "main" optional = false python-versions = "<3.12,>=3.8" files = [ @@ -6569,8 +6314,7 @@ test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeo name = "scmrepo" version = "1.0.2" description = "SCM wrapper and fsspec filesystem for Git for use in DVC" -category = "main" -optional = false +optional = true python-versions = ">=3.8" files = [ {file = "scmrepo-1.0.2-py3-none-any.whl", hash = "sha256:d5cf8b088556036d54cb9ba93712e3e890cf45ee169a2ae86b1a84b6d39ec74c"}, @@ -6596,7 +6340,6 @@ tests = ["mock (==5.0.1)", "mypy (==0.971)", "paramiko (==3.1.0)", "pylint (==2. name = "scvelo" version = "0.2.5" description = "RNA velocity generalized through dynamical modeling" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -6627,7 +6370,6 @@ louvain = ["louvain", "python-igraph"] name = "scvi-tools" version = "0.20.3" description = "Deep probabilistic analysis of single-cell omics data." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -6671,7 +6413,6 @@ tutorials = ["genomepy", "huggingface-hub", "leidenalg", "loompy", "pymde", "pyn name = "seaborn" version = "0.11.2" description = "seaborn: statistical data visualization" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -6689,7 +6430,6 @@ scipy = ">=1.0" name = "session-info" version = "1.0.0" description = "session_info outputs version information for modules loaded in the current session, Python, and the OS." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -6703,7 +6443,6 @@ stdlib_list = "*" name = "setuptools" version = "67.7.2" description = "Easily download, build, install, upgrade, and uninstall Python packages" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -6720,7 +6459,6 @@ testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs ( name = "shap" version = "0.41.0" description = "A unified approach to explain the output of any machine learning model." -category = "main" optional = false python-versions = "*" files = [ @@ -6774,7 +6512,6 @@ test = ["catboost", "lightgbm", "opencv-python", "pyod", "pyspark", "pytest", "p name = "shapely" version = "1.8.5.post1" description = "Geometric objects, predicates, and operations" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -6831,8 +6568,7 @@ vectorized = ["numpy"] name = "shortuuid" version = "1.0.11" description = "A generator library for concise, unambiguous and URL-safe UUIDs." -category = "main" -optional = false +optional = true python-versions = ">=3.5" files = [ {file = "shortuuid-1.0.11-py3-none-any.whl", hash = "sha256:27ea8f28b1bd0bf8f15057a3ece57275d2059d2b0bb02854f02189962c13b6aa"}, @@ -6843,8 +6579,7 @@ files = [ name = "shtab" version = "1.6.1" description = "Automagic shell tab completion for Python CLI applications" -category = "main" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "shtab-1.6.1-py3-none-any.whl", hash = "sha256:db2c41d81a61c7ecefd1dad8212bdc4b667e7449b8172aa6445f557f901810c4"}, @@ -6855,7 +6590,6 @@ files = [ name = "six" version = "1.16.0" description = "Python 2 and 3 compatibility utilities" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -6867,7 +6601,6 @@ files = [ name = "slicer" version = "0.0.7" description = "A small package for big slicing." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -6879,7 +6612,6 @@ files = [ name = "smmap" version = "5.0.0" description = "A pure Python implementation of a sliding window memory map manager" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -6891,7 +6623,6 @@ files = [ name = "snowballstemmer" version = "2.2.0" description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms." -category = "main" optional = true python-versions = "*" files = [ @@ -6903,7 +6634,6 @@ files = [ name = "sortedcontainers" version = "2.4.0" description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set" -category = "main" optional = true python-versions = "*" files = [ @@ -6915,7 +6645,6 @@ files = [ name = "soupsieve" version = "2.4.1" description = "A modern CSS selector implementation for Beautiful Soup." -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -6927,7 +6656,6 @@ files = [ name = "sphinx" version = "6.1.3" description = "Python documentation generator" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -6963,7 +6691,6 @@ test = ["cython", "html5lib", "pytest (>=4.6)"] name = "sphinx-autobuild" version = "2021.3.14" description = "Rebuild Sphinx documentation on changes, with live-reload in the browser." -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -6983,7 +6710,6 @@ test = ["pytest", "pytest-cov"] name = "sphinx-basic-ng" version = "1.0.0b1" description = "A modern skeleton for Sphinx themes." -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -7001,7 +6727,6 @@ docs = ["furo", "ipython", "myst-parser", "sphinx-copybutton", "sphinx-inline-ta name = "sphinx-click" version = "4.4.0" description = "Sphinx extension that automatically documents click applications" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -7018,7 +6743,6 @@ sphinx = ">=2.0" name = "sphinxcontrib-applehelp" version = "1.0.4" description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -7034,7 +6758,6 @@ test = ["pytest"] name = "sphinxcontrib-devhelp" version = "1.0.2" description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document." -category = "main" optional = true python-versions = ">=3.5" files = [ @@ -7050,7 +6773,6 @@ test = ["pytest"] name = "sphinxcontrib-htmlhelp" version = "2.0.1" description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -7066,7 +6788,6 @@ test = ["html5lib", "pytest"] name = "sphinxcontrib-jsmath" version = "1.0.1" description = "A sphinx extension which renders display math in HTML via JavaScript" -category = "main" optional = true python-versions = ">=3.5" files = [ @@ -7081,7 +6802,6 @@ test = ["flake8", "mypy", "pytest"] name = "sphinxcontrib-qthelp" version = "1.0.3" description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document." -category = "main" optional = true python-versions = ">=3.5" files = [ @@ -7097,7 +6817,6 @@ test = ["pytest"] name = "sphinxcontrib-serializinghtml" version = "1.1.5" description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)." -category = "main" optional = true python-versions = ">=3.5" files = [ @@ -7113,7 +6832,6 @@ test = ["pytest"] name = "sqlalchemy" version = "2.0.10" description = "Database Abstraction Library" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -7161,7 +6879,7 @@ files = [ ] [package.dependencies] -greenlet = {version = "!=0.4.17", markers = "platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\""} +greenlet = {version = "!=0.4.17", markers = "platform_machine == \"win32\" or platform_machine == \"WIN32\" or platform_machine == \"AMD64\" or platform_machine == \"amd64\" or platform_machine == \"x86_64\" or platform_machine == \"ppc64le\" or platform_machine == \"aarch64\""} typing-extensions = ">=4.2.0" [package.extras] @@ -7191,7 +6909,6 @@ sqlcipher = ["sqlcipher3-binary"] name = "sqlparse" version = "0.4.3" description = "A non-validating SQL parser." -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -7203,8 +6920,7 @@ files = [ name = "sqltrie" version = "0.3.1" description = "SQL-based prefix tree inspired by pygtrie and python-diskcache" -category = "main" -optional = false +optional = true python-versions = ">=3.8" files = [ {file = "sqltrie-0.3.1-py3-none-any.whl", hash = "sha256:8cbb616049ab50cf543c605d0c4c72bc2eadfa94e90823227f7e01acf2ca7b69"}, @@ -7224,7 +6940,6 @@ tests = ["mypy (==0.971)", "pyinstaller", "pylint (==2.15.0)", "pytest (==7.2.0) name = "stack-data" version = "0.6.2" description = "Extract data from python stack frames and tracebacks for informative displays" -category = "main" optional = true python-versions = "*" files = [ @@ -7244,7 +6959,6 @@ tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"] name = "statannotations" version = "0.5.0" description = "add statistical significance or custom annotations on seaborn plots. Based on statannot 0.2.3" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -7263,7 +6977,6 @@ seaborn = ">=0.9.0,<0.12" name = "statsmodels" version = "0.13.2" description = "Statistical computations and models for Python" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -7308,7 +7021,6 @@ docs = ["ipykernel", "jupyter-client", "matplotlib", "nbconvert", "nbformat", "n name = "statsmodels" version = "0.13.3" description = "Statistical computations and models for Python" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -7355,7 +7067,6 @@ docs = ["ipykernel", "jupyter-client", "matplotlib", "nbconvert", "nbformat", "n name = "statsmodels" version = "0.13.5" description = "Statistical computations and models for Python" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -7405,7 +7116,6 @@ docs = ["ipykernel", "jupyter-client", "matplotlib", "nbconvert", "nbformat", "n name = "stdlib-list" version = "0.8.0" description = "A list of Python Standard Libraries (2.6-7, 3.2-9)." -category = "main" optional = false python-versions = "*" files = [ @@ -7420,7 +7130,6 @@ develop = ["sphinx"] name = "stevedore" version = "5.0.0" description = "Manage dynamic plugins for Python applications" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -7435,7 +7144,6 @@ pbr = ">=2.0.0,<2.1.0 || >2.1.0" name = "strip-hints" version = "0.1.10" description = "Function and command-line program to strip Python type hints." -category = "main" optional = true python-versions = "*" files = [ @@ -7449,7 +7157,6 @@ wheel = "*" name = "tabulate" version = "0.9.0" description = "Pretty-print tabular data" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -7464,7 +7171,6 @@ widechars = ["wcwidth"] name = "tensorstore" version = "0.1.35" description = "Read and write large, multi-dimensional arrays" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -7494,7 +7200,6 @@ numpy = ">=1.16.0" name = "termcolor" version = "2.2.0" description = "ANSI color formatting for output in terminal" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -7509,7 +7214,6 @@ tests = ["pytest", "pytest-cov"] name = "texttable" version = "1.6.7" description = "module to create simple ASCII tables" -category = "main" optional = false python-versions = "*" files = [ @@ -7521,7 +7225,6 @@ files = [ name = "threadpoolctl" version = "3.1.0" description = "threadpoolctl" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -7533,7 +7236,6 @@ files = [ name = "tokenize-rt" version = "5.0.0" description = "A wrapper around the stdlib `tokenize` which roundtrips." -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -7545,7 +7247,6 @@ files = [ name = "toml" version = "0.10.2" description = "Python Library for Tom's Obvious, Minimal Language" -category = "main" optional = true python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -7557,7 +7258,6 @@ files = [ name = "tomli" version = "2.0.1" description = "A lil' TOML parser" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -7569,8 +7269,7 @@ files = [ name = "tomlkit" version = "0.11.7" description = "Style preserving TOML library" -category = "main" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "tomlkit-0.11.7-py3-none-any.whl", hash = "sha256:5325463a7da2ef0c6bbfefb62a3dc883aebe679984709aee32a317907d0a8d3c"}, @@ -7581,7 +7280,6 @@ files = [ name = "toolz" version = "0.12.0" description = "List processing tools and functional utilities" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -7593,7 +7291,6 @@ files = [ name = "torch" version = "1.13.1" description = "Tensors and Dynamic neural networks in Python with strong GPU acceleration" -category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -7634,7 +7331,6 @@ opt-einsum = ["opt-einsum (>=3.3)"] name = "torchmetrics" version = "0.11.4" description = "PyTorch native Metrics" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -7660,7 +7356,6 @@ text = ["nltk (>=3.6)", "regex (>=2021.9.24)", "tqdm (>=4.41.0)"] name = "tornado" version = "6.3" description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed." -category = "main" optional = true python-versions = ">= 3.8" files = [ @@ -7681,7 +7376,6 @@ files = [ name = "tqdm" version = "4.65.0" description = "Fast, Extensible Progress Meter" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -7702,7 +7396,6 @@ telegram = ["requests"] name = "traitlets" version = "5.9.0" description = "Traitlets Python configuration system" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -7718,7 +7411,6 @@ test = ["argcomplete (>=2.0)", "pre-commit", "pytest", "pytest-mock"] name = "typeguard" version = "3.0.2" description = "Run-time type checker for Python" -category = "main" optional = true python-versions = ">=3.7.4" files = [ @@ -7738,7 +7430,6 @@ test = ["mypy (>=0.991)", "pytest (>=7)"] name = "typer" version = "0.9.0" description = "Typer, build great CLIs. Easy to code. Based on Python type hints." -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -7760,7 +7451,6 @@ test = ["black (>=22.3.0,<23.0.0)", "coverage (>=6.2,<7.0)", "isort (>=5.0.6,<6. name = "typing-extensions" version = "4.5.0" description = "Backported and Experimental Type Hints for Python 3.7+" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -7772,7 +7462,6 @@ files = [ name = "typing-inspect" version = "0.8.0" description = "Runtime inspection utilities for typing module." -category = "main" optional = false python-versions = "*" files = [ @@ -7788,7 +7477,6 @@ typing-extensions = ">=3.7.4" name = "tzdata" version = "2023.3" description = "Provider of IANA time zone data" -category = "main" optional = false python-versions = ">=2" files = [ @@ -7800,7 +7488,6 @@ files = [ name = "umap-learn" version = "0.5.3" description = "Uniform Manifold Approximation and Projection" -category = "main" optional = false python-versions = "*" files = [ @@ -7823,7 +7510,6 @@ plot = ["bokeh", "colorcet", "datashader", "holoviews", "matplotlib", "pandas", name = "uritemplate" version = "3.0.1" description = "URI templates" -category = "main" optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -7835,7 +7521,6 @@ files = [ name = "urllib3" version = "1.26.15" description = "HTTP library with thread-safe connection pooling, file post, and more." -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ @@ -7852,8 +7537,7 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] name = "vine" version = "5.0.0" description = "Promises, promises, promises." -category = "main" -optional = false +optional = true python-versions = ">=3.6" files = [ {file = "vine-5.0.0-py2.py3-none-any.whl", hash = "sha256:4c9dceab6f76ed92105027c49c823800dd33cacce13bdedc5b914e3514b7fb30"}, @@ -7864,7 +7548,6 @@ files = [ name = "virtualenv" version = "20.21.0" description = "Virtual Python Environment builder" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -7885,8 +7568,7 @@ test = ["covdefaults (>=2.2.2)", "coverage (>=7.1)", "coverage-enable-subprocess name = "voluptuous" version = "0.13.1" description = "" -category = "main" -optional = false +optional = true python-versions = "*" files = [ {file = "voluptuous-0.13.1-py3-none-any.whl", hash = "sha256:4b838b185f5951f2d6e8752b68fcf18bd7a9c26ded8f143f92d6d28f3921a3e6"}, @@ -7897,7 +7579,6 @@ files = [ name = "waitress" version = "2.1.2" description = "Waitress WSGI server" -category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -7913,8 +7594,7 @@ testing = ["coverage (>=5.0)", "pytest", "pytest-cover"] name = "wcwidth" version = "0.2.6" description = "Measures the displayed width of unicode strings in a terminal" -category = "main" -optional = false +optional = true python-versions = "*" files = [ {file = "wcwidth-0.2.6-py2.py3-none-any.whl", hash = "sha256:795b138f6875577cd91bba52baf9e445cd5118fd32723b460e30a0af30ea230e"}, @@ -7925,7 +7605,6 @@ files = [ name = "websocket-client" version = "1.5.1" description = "WebSocket client for Python with low level API options" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -7942,7 +7621,6 @@ test = ["websockets"] name = "werkzeug" version = "2.3.3" description = "The comprehensive WSGI web application library." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -7960,7 +7638,6 @@ watchdog = ["watchdog (>=2.3)"] name = "wheel" version = "0.40.0" description = "A built-package format for Python" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -7975,7 +7652,6 @@ test = ["pytest (>=6.0.0)"] name = "wrapt" version = "1.15.0" description = "Module for decorators, wrappers and monkey patching." -category = "main" optional = true python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" files = [ @@ -8060,7 +7736,6 @@ files = [ name = "xdoctest" version = "1.1.1" description = "A rewrite of the builtin doctest module" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -8090,7 +7765,6 @@ tests-strict = ["codecov (==2.0.15)", "pytest (==4.6.0)", "pytest (==4.6.0)", "p name = "yarl" version = "1.9.1" description = "Yet another URL library" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -8178,8 +7852,7 @@ multidict = ">=4.0" name = "zc-lockfile" version = "3.0.post1" description = "Basic inter-process locks" -category = "main" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "zc.lockfile-3.0.post1-py3-none-any.whl", hash = "sha256:ddb2d71088c061dc8a5edbaa346b637d742ca1e1564be75cb98e7dcae715de19"}, @@ -8196,7 +7869,6 @@ test = ["zope.testing"] name = "zipp" version = "3.15.0" description = "Backport of pathlib-compatible object wrapper for zip files" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -8212,7 +7884,6 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more name = "zstandard" version = "0.21.0" description = "Zstandard bindings for Python" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -8268,12 +7939,12 @@ cffi = {version = ">=1.11", markers = "platform_python_implementation == \"PyPy\ cffi = ["cffi (>=1.11)"] [extras] -dev = ["black", "coverage", "darglint", "dparse", "dvc-gs", "flake8-bandit", "flake8-bugbear", "flake8-docstrings", "flake8-rst-docstrings", "flake8", "hypothesis", "ipython", "isort", "jupyter-core", "mypy", "pep8-naming", "poethepoet", "pre-commit-hooks", "pre-commit", "Pygments", "pytest-cov", "pytest-mock", "pytest", "pyupgrade", "pyvis", "safety", "typeguard", "xdoctest"] -docs = ["furo", "myst-parser", "sphinx-autobuild", "sphinx-click", "sphinx"] +dev = ["Pygments", "black", "coverage", "darglint", "dparse", "dvc-gs", "flake8", "flake8-bandit", "flake8-bugbear", "flake8-docstrings", "flake8-rst-docstrings", "hypothesis", "ipython", "isort", "jupyter-core", "mypy", "pep8-naming", "poethepoet", "pre-commit", "pre-commit-hooks", "pytest", "pytest-cov", "pytest-mock", "pyupgrade", "pyvis", "safety", "typeguard", "xdoctest"] +docs = ["furo", "myst-parser", "sphinx", "sphinx-autobuild", "sphinx-click"] pipeline = ["google-cloud-aiplatform", "google-cloud-pipeline-components", "kfp", "python-dotenv"] -plotting = ["matplotlib-venn", "statannotations"] +plotting = ["annoy", "matplotlib-venn", "statannotations"] [metadata] lock-version = "2.0" python-versions = ">=3.9, <3.11" -content-hash = "7720a968e1c9b20edc57d30d1993dd161f2260230976d9f6e66861bfa1de2d85" +content-hash = "cbe9729f83764f85f9fb53b442c559514b2dd7b1ac67479d5fd5315b71f3a9f1" diff --git a/pyproject.toml b/pyproject.toml index 75ffe3482..257301154 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -38,19 +38,19 @@ marshmallow = ">=3.18.0" mlflow = "2.2.2" omegaconf = "2.3.0" pandas = "1.5.3" -pyro-ppl = "1.8.3" +pyro-ppl = ">=1.8.3" python = ">=3.9, <3.11" -pytorch-lightning = "1.9.4" +pytorch-lightning = ">=1.9.4" rich = "^12.6.0" scikit-misc = "0.1.4" -scipy = "1.10.1" +scipy = ">=1.10.1" scvelo = "0.2.5" scvi-tools = "0.20.3" seaborn = { version = "0.11.2", source = "pypi" } -termcolor = "^2.2.0" -torch = "1.13.1" -torchmetrics = "0.11.4" -zstandard = "0.21.0" +termcolor = ">=2.2.0" +torch = ">=1.13.1" +torchmetrics = ">=0.11.4" +zstandard = ">=0.21.0" # extras Pygments = { version = ">=2.15.0", optional = true } @@ -82,7 +82,7 @@ dparse = { version = ">=0.5.2", optional = true } pytest-cov = { version = ">=4.0.0", optional = true } pytest-mock = { version = ">=3.10.0", optional = true } poethepoet = { version = ">=0.16.0", optional = true, source = "pypi" } -dvc-gs = { version = ">=2.20.0", optional = true } +dvc-gs = { version = ">=2.22.1", optional = true } jupyter-core = { version = ">=5.1.3", optional = true, source = "pypi" } pyvis = { version = ">=0.3.2", optional = true } hypothesis = {version = ">=6.71.0", optional = true } @@ -92,6 +92,7 @@ google-cloud-pipeline-components = { version = ">=1.0.43", optional = true } python-dotenv = { version = ">=1.0.0", optional = true } matplotlib-venn = { version = ">=0.11.9", optional = true } statannotations = { version = ">=0.5.0", optional = true } +annoy = {version = "^1.17.3", optional = true } [tool.conda-lock.dependencies] seaborn = { version = "0.11.2", source = "conda-forge" } @@ -149,6 +150,7 @@ dev = [ ] plotting = [ + "annoy", "matplotlib-venn", "statannotations", ] @@ -204,5 +206,5 @@ show_error_context = true ignore_missing_imports = true [build-system] -requires = ["poetry-core>=1.1.0"] +requires = ["poetry-core>=1.6.0"] build-backend = "poetry.core.masonry.api" diff --git a/pyrovelocity/_trainer.py b/pyrovelocity/_trainer.py index 92073d7d2..f4679f043 100644 --- a/pyrovelocity/_trainer.py +++ b/pyrovelocity/_trainer.py @@ -376,14 +376,14 @@ def train_faster_with_batch( self.module._model, self.module._guide, optim, - TraceEnum_ELBO(strict_enumeration_warning=True), + Trace_ELBO(strict_enumeration_warning=True), ) else: svi = pyro.infer.SVI( self.module._model, new_valid_guide, optim, - TraceEnum_ELBO(strict_enumeration_warning=True), + Trace_ELBO(strict_enumeration_warning=True), ) losses = [] diff --git a/pyrovelocity/config.py b/pyrovelocity/config.py index 67cfa378d..610353638 100644 --- a/pyrovelocity/config.py +++ b/pyrovelocity/config.py @@ -983,7 +983,7 @@ def create_reports_config(model_name: str, model_number: int): tag="figS2", path="${paths.reports}/${.tag}", subset_genes_plot="${.path}/${.tag}_subset3g_pbmc68k.pdf", - subset_pkl="${.path}/${.tag}_subset3g_pbmc68k.pkl", + subset_pkl="${.path}/${.tag}_subset3g_pbmc68k.pkl.zst", ), figureS4=dict( tag="figS4", diff --git a/reproducibility/figures/config.yaml b/reproducibility/figures/config.yaml index 16548adac..03558f64f 100644 --- a/reproducibility/figures/config.yaml +++ b/reproducibility/figures/config.yaml @@ -976,7 +976,7 @@ reports: tag: figS2 path: reports/figS2 subset_genes_plot: reports/figS2/figS2_subset3g_pbmc68k.pdf - subset_pkl: reports/figS2/figS2_subset3g_pbmc68k.pkl + subset_pkl: reports/figS2/figS2_subset3g_pbmc68k.pkl.zst figureS4: tag: figS4 path: reports/figS4 diff --git a/reproducibility/figures/dvc.lock b/reproducibility/figures/dvc.lock index 491132963..7cb720df1 100644 --- a/reproducibility/figures/dvc.lock +++ b/reproducibility/figures/dvc.lock @@ -249,6 +249,7 @@ stages: thresh_histogram_path: data/processed/pbmc10k_thresh_histogram.pdf outs: - path: data/external/pbmc10k.h5ad + hash: md5 md5: d3e04305389fbe783950acfd9c3a7384 size: 808692621 preprocess@simulate_medium: @@ -311,6 +312,7 @@ stages: thresh_histogram_path: data/processed/pons_thresh_histogram.pdf outs: - path: data/processed/pons_processed.h5ad + hash: md5 md5: 7be4dd4a9a7a9a10eab45e5f22086489 size: 740872463 - path: data/processed/pons_thresh_histogram.pdf @@ -448,6 +450,7 @@ stages: thresh_histogram_path: data/processed/larry_tips_thresh_histogram.pdf outs: - path: data/processed/larry_tips_processed.h5ad + hash: md5 md5: f19069e9a1a38fca101b73ac91977149 size: 2026603098 - path: data/processed/larry_tips_thresh_histogram.pdf @@ -562,6 +565,7 @@ stages: cmd: python preprocess.py process_data=[pbmc10k] deps: - path: data/external/pbmc10k.h5ad + hash: md5 md5: d3e04305389fbe783950acfd9c3a7384 size: 808692621 - path: preprocess.py @@ -584,6 +588,7 @@ stages: thresh_histogram_path: data/processed/pbmc10k_thresh_histogram.pdf outs: - path: data/processed/pbmc10k_processed.h5ad + hash: md5 md5: 90560495ea8e77d1be26f7902e8ee48b size: 1522738521 - path: data/processed/pbmc10k_thresh_histogram.pdf @@ -712,18 +717,18 @@ stages: loss_plot_path: models/pancreas_model2/loss_plot.png outs: - path: models/pancreas_model2/loss_plot.png - md5: 30e886ec85805fec9350fa575322c524 - size: 11645 + md5: 90b2c9531236f2bd28af33ab400402cd + size: 12391 - path: models/pancreas_model2/model - md5: b7ec6cf4fb301f65ad291676b188cc18.dir + md5: 4105c3f421d85f715413e8af3860b72c.dir size: 1783285 nfiles: 2 - path: models/pancreas_model2/posterior_samples.pkl.zst md5: f965638d564020318d8c28a5e50d7be6 size: 1871866452 - path: models/pancreas_model2/run_info.json - md5: 74fe958f435a06e6466cbd31f9784141 - size: 462 + md5: 2e38e14717eb1a2519bde3089b4fb67c + size: 436 train@pbmc68k_model2: cmd: /usr/bin/time -v python train.py train_models=[pbmc68k_model2] deps: @@ -778,22 +783,23 @@ stages: loss_plot_path: models/pbmc68k_model2/loss_plot.png outs: - path: models/pbmc68k_model2/loss_plot.png - md5: 020f5dba782c1ca953fd078be78ea5e3 - size: 16215 + md5: 07e24305a1e594d8e8c729f2cbc6b3de + size: 17880 - path: models/pbmc68k_model2/model - md5: fd77e7d93bd926f3b0f66b5b1b452531.dir + md5: d1dad7af2c46b8619ce8576c7b94b5a7.dir size: 3521589 nfiles: 2 - path: models/pbmc68k_model2/posterior_samples.pkl.zst - md5: 2334200930efa2baeb2a4cc2e065bb48 - size: 6869182180 + md5: 561cacf6d8dc35d806940ce0ffc9204c + size: 7034738772 - path: models/pbmc68k_model2/run_info.json - md5: 01fb82860efe74926e20e12fc4e840ab + md5: b6353dd06dc5bf39f443edbcc6288a95 size: 435 train@pons_model2: cmd: /usr/bin/time -v python train.py train_models=[pons_model2] deps: - path: data/processed/pons_processed.h5ad + hash: md5 md5: 7be4dd4a9a7a9a10eab45e5f22086489 size: 740872463 - path: train.py @@ -844,17 +850,17 @@ stages: loss_plot_path: models/pons_model2/loss_plot.png outs: - path: models/pons_model2/loss_plot.png - md5: 4a0ae00f44c012ab0d90fa82d57a11ec - size: 12093 + md5: ff8f4a5706c6f48938eecc8e61ac4cee + size: 12382 - path: models/pons_model2/model - md5: db12dbde78ac878ffccc9b094283bae1.dir + md5: 5164ae52f32a480dc2ce5ba1f046f3b3.dir size: 1906485 nfiles: 2 - path: models/pons_model2/posterior_samples.pkl.zst - md5: d9679ddd7b0192cd845325d95057fe30 - size: 2495542100 + md5: b907d599e9be9467690785e539f376f5 + size: 3107095737 - path: models/pons_model2/run_info.json - md5: 9de0354a8aa4a12b7d927442c88b1764 + md5: 6b66e038e69eef1f2627cbe44e4d44ae size: 432 train@larry_model2: cmd: /usr/bin/time -v python train.py train_models=[larry_model2] @@ -910,22 +916,23 @@ stages: loss_plot_path: models/larry_model2/loss_plot.png outs: - path: models/larry_model2/loss_plot.png - md5: 079875138c9e1e054494036fa7dd1e9a - size: 11635 + md5: 964040e6999bbda7ed26e6f25180f49a + size: 11892 - path: models/larry_model2/model - md5: 9ad544ab4786199e32c3fef3fd5f71af.dir + md5: 58c31b611b95498516ebe5e91b5d86c6.dir size: 4037685 nfiles: 2 - path: models/larry_model2/posterior_samples.pkl.zst - md5: c70656d75a5c16a3705a81d4d3bed75c - size: 21398884920 + md5: 0714d4762985af6f258d8eba660e1e39 + size: 22631958611 - path: models/larry_model2/run_info.json - md5: 955d232c81115e69654f6287ff359d82 + md5: bd369743a60f759a3de75ca6ee3ca62e size: 433 train@larry_tips_model2: cmd: /usr/bin/time -v python train.py train_models=[larry_tips_model2] deps: - path: data/processed/larry_tips_processed.h5ad + hash: md5 md5: f19069e9a1a38fca101b73ac91977149 size: 2026603098 - path: train.py @@ -976,17 +983,17 @@ stages: loss_plot_path: models/larry_tips_model2/loss_plot.png outs: - path: models/larry_tips_model2/loss_plot.png - md5: d7a3538d7c19ba5813ef615e32f5bc46 - size: 13510 + md5: 746a8cb24d2a0bd52aff8fc9b274f34d + size: 13628 - path: models/larry_tips_model2/model - md5: 87ea4719e969d21eee4227df0589da68.dir + md5: 17ae66e962b4565d2edd372b23612368.dir size: 2530357 nfiles: 2 - path: models/larry_tips_model2/posterior_samples.pkl.zst - md5: 3676847c16a14530b94334aeb42b6ef8 - size: 7954956389 + md5: 9f86a1621efacaf22fc454a5a6c5b3c7 + size: 8448959747 - path: models/larry_tips_model2/run_info.json - md5: 57a8e230dee82d99d1acf258547d40e3 + md5: 09712a7c4e82c73c864000e9179b17bd size: 438 train@larry_mono_model2: cmd: /usr/bin/time -v python train.py train_models=[larry_mono_model2] @@ -1042,17 +1049,17 @@ stages: loss_plot_path: models/larry_mono_model2/loss_plot.png outs: - path: models/larry_mono_model2/loss_plot.png - md5: d5bc9d1f0491dbd3580dd61ef6c96bd8 - size: 11422 + md5: 20ec4383c011cfbf6b829669fec10ac4 + size: 11605 - path: models/larry_mono_model2/model - md5: c33772575c00a18d3277a5797b554923.dir + md5: 963f9756bbdd6675802b1b42962a695b.dir size: 1159925 nfiles: 2 - path: models/larry_mono_model2/posterior_samples.pkl.zst - md5: 71724b1de658963ceb84e8877c0d5be2 - size: 376534463 + md5: c23f2447470f27c194c6438363998b45 + size: 389144329 - path: models/larry_mono_model2/run_info.json - md5: 685b3255f20e68e80d78e7518b2ff0d0 + md5: 6cea2ed9311321528e1ab1f5047da03b size: 438 train@larry_neu_model2: cmd: /usr/bin/time -v python train.py train_models=[larry_neu_model2] @@ -1108,17 +1115,17 @@ stages: loss_plot_path: models/larry_neu_model2/loss_plot.png outs: - path: models/larry_neu_model2/loss_plot.png - md5: 76926c98e54ee2f69ce1234d3b4b962d - size: 11568 + md5: d163d9a0b601b437ef8a1ad6fdcf2026 + size: 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- path: models/larry_multilineage_model2/posterior_samples.pkl.zst - md5: e60693c4e229ded5fc2c13b0e9267130 - size: 1022220718 + md5: 5a77101e705389f93cdd1cd4e85942b4 + size: 1066788446 - path: models/larry_multilineage_model2/run_info.json - md5: 991e315e2cc2c375f0448254a42bbfee + md5: d920acd882d0a7f151ed91a40425e6be size: 446 train@pbmc10k_model2: cmd: /usr/bin/time -v python train.py train_models=[pbmc10k_model2] deps: - path: data/processed/pbmc10k_processed.h5ad + hash: md5 md5: 90560495ea8e77d1be26f7902e8ee48b size: 1522738521 - path: train.py @@ -1240,18 +1248,18 @@ stages: loss_plot_path: models/pbmc10k_model2/loss_plot.png outs: - path: models/pbmc10k_model2/loss_plot.png - md5: 711249964722e4b0434e4c0eeaf5a78e - size: 11490 + md5: e31731afcc0eeb4c69307e463e66c9f6 + size: 12352 - path: models/pbmc10k_model2/model - md5: 0e9b5585415a7b58f1c793b0a76be3aa.dir + md5: 3843408f91ad72d018dd891b8fc97df9.dir size: 2174133 nfiles: 2 - path: models/pbmc10k_model2/posterior_samples.pkl.zst - md5: 4c6871689a69c0c5621018131886b4dc - size: 4288915469 + md5: 8b7c73e7a8c4950b04e0184dc9388c7b + size: 5919443023 - path: models/pbmc10k_model2/run_info.json - md5: d468d3d4b5f2bf00ca2c2de02e72050a - size: 454 + md5: 2288df4c991a02db6e15e39f1886915b + size: 435 postprocess@simulate_model2: cmd: /usr/bin/time -v python postprocess.py train_models=[simulate_model2] deps: @@ -1313,13 +1321,13 @@ stages: loss_plot_path: models/simulate_medium_model2/loss_plot.png outs: - path: models/simulate_medium_model2/metrics.json - md5: 38f847cd99c28c5685c8c93efa3f7307 + md5: f163b8b640cb4cd10b3b3e985d888a76 size: 95 - path: models/simulate_medium_model2/pyrovelocity.pkl.zst md5: 30542b0697de442d8b7fbb3140f9ea38 size: 44193376 - path: models/simulate_medium_model2/trained.h5ad - md5: 3b2237eb975c861b568803b3352ffc78 + md5: 5ffb5d076238d73cde95d0ebf7502858 size: 275831552 postprocess@pancreas_model2: cmd: /usr/bin/time -v python postprocess.py train_models=[pancreas_model2] @@ -1328,7 +1336,7 @@ stages: md5: 4aaf4084689b5e10c60231552502bd98 size: 424784368 - path: models/pancreas_model2/model - md5: b7ec6cf4fb301f65ad291676b188cc18.dir + md5: 4105c3f421d85f715413e8af3860b72c.dir size: 1783285 nfiles: 2 - path: models/pancreas_model2/posterior_samples.pkl.zst @@ -1382,13 +1390,14 @@ stages: loss_plot_path: models/pancreas_model2/loss_plot.png outs: - path: models/pancreas_model2/metrics.json - md5: eeed17479129137e999f017fca6b7544 - size: 98 + md5: f3465a82eeb3b93c808b8f5622a6dc41 + size: 96 - path: models/pancreas_model2/pyrovelocity.pkl.zst - md5: e2a7e45c53b1876d90ac7b79d0f400a5 - size: 170952134 + md5: 05357ba7befa89f83e4b11439c071d69 + size: 170952530 - path: models/pancreas_model2/trained.h5ad - md5: 70aef236486c45aba779194a2d8d81f2 + hash: md5 + md5: af2ba0069fd94bcea0a606a268ba7e41 size: 492127600 postprocess@pbmc68k_model2: cmd: /usr/bin/time -v python postprocess.py train_models=[pbmc68k_model2] @@ -1397,12 +1406,12 @@ stages: md5: 56203ce58f1c85b251ce9af2ab721b95 size: 1677133574 - path: models/pbmc68k_model2/model - md5: fd77e7d93bd926f3b0f66b5b1b452531.dir + md5: d1dad7af2c46b8619ce8576c7b94b5a7.dir size: 3521589 nfiles: 2 - path: models/pbmc68k_model2/posterior_samples.pkl.zst - md5: 2334200930efa2baeb2a4cc2e065bb48 - size: 6869182180 + md5: 561cacf6d8dc35d806940ce0ffc9204c + size: 7034738772 - path: postprocess.py md5: 2d194b66a6964f4ac39022fe6a4fbb8f size: 5679 @@ -1451,27 +1460,29 @@ stages: loss_plot_path: models/pbmc68k_model2/loss_plot.png outs: - path: models/pbmc68k_model2/metrics.json - md5: 45dbfac6cddba432f1d21232c5c48172 - size: 96 + md5: 62c72a8fc9b6ee4104b209bc097c6e28 + size: 95 - path: models/pbmc68k_model2/pyrovelocity.pkl.zst - md5: b3ae8fc391dda9f35cdb36056fac7223 - size: 679013346 + md5: 8d371e47355b41e2baa329b31bbee28c + size: 964175816 - path: models/pbmc68k_model2/trained.h5ad - md5: 73382ce8ef30d9575757f061a74ecb18 + hash: md5 + md5: 298c11d370c21ca74fc7746022f5bac0 size: 2263902602 postprocess@pons_model2: cmd: /usr/bin/time -v python postprocess.py train_models=[pons_model2] deps: - path: data/processed/pons_processed.h5ad + hash: md5 md5: 7be4dd4a9a7a9a10eab45e5f22086489 size: 740872463 - path: models/pons_model2/model - md5: db12dbde78ac878ffccc9b094283bae1.dir + md5: 5164ae52f32a480dc2ce5ba1f046f3b3.dir size: 1906485 nfiles: 2 - path: models/pons_model2/posterior_samples.pkl.zst - md5: d9679ddd7b0192cd845325d95057fe30 - size: 2495542100 + md5: b907d599e9be9467690785e539f376f5 + size: 3107095737 - path: postprocess.py md5: 2d194b66a6964f4ac39022fe6a4fbb8f size: 5679 @@ -1520,13 +1531,14 @@ stages: loss_plot_path: models/pons_model2/loss_plot.png outs: - path: models/pons_model2/metrics.json - md5: 3f802ffd6886be50fc5bab59b7aa698d - size: 95 + md5: eaba372dfef7a52a9a357653eeae9f8c + size: 93 - path: models/pons_model2/pyrovelocity.pkl.zst - md5: 12705b7d63bd89eb56b30532ab883f1d - size: 175509376 + md5: 7eb7d8a9eb458c087598835bb412a9d6 + size: 292727197 - path: models/pons_model2/trained.h5ad - md5: a566defb5aa1968939cbe740184014ca + hash: md5 + md5: dcc3d7c35f8cafb6fb285ebc5b9eceb5 size: 859080859 postprocess@larry_model2: cmd: /usr/bin/time -v python postprocess.py train_models=[larry_model2] @@ -1535,12 +1547,12 @@ stages: md5: a9bd6a0af7159813195c7ef0b36b9c3a size: 5361840878 - path: models/larry_model2/model - md5: 9ad544ab4786199e32c3fef3fd5f71af.dir + md5: 58c31b611b95498516ebe5e91b5d86c6.dir size: 4037685 nfiles: 2 - path: models/larry_model2/posterior_samples.pkl.zst - md5: c70656d75a5c16a3705a81d4d3bed75c - size: 21398884920 + md5: 0714d4762985af6f258d8eba660e1e39 + size: 22631958611 - path: postprocess.py md5: 2d194b66a6964f4ac39022fe6a4fbb8f size: 5679 @@ -1589,27 +1601,29 @@ stages: loss_plot_path: models/larry_model2/loss_plot.png outs: - path: models/larry_model2/metrics.json - md5: 519155a8b2af32c1394f21ba3bff1d4b + md5: 92bb539d73f8cce4ef577b09de922d4a size: 96 - path: models/larry_model2/pyrovelocity.pkl.zst - md5: 07aabc2f0e592483cb3268ca1bf73675 - size: 1368569189 + md5: 59bf4d321f6cde7f17d41c2b17e7da0a + size: 2344041479 - path: models/larry_model2/trained.h5ad - md5: 3077156894a95741f88ebb0c3eedad02 - size: 6320835070 + hash: md5 + md5: ff50581db4a31025553aed6afa80766d + size: 6320872798 postprocess@larry_tips_model2: cmd: /usr/bin/time -v python postprocess.py train_models=[larry_tips_model2] deps: - path: data/processed/larry_tips_processed.h5ad + hash: md5 md5: f19069e9a1a38fca101b73ac91977149 size: 2026603098 - path: models/larry_tips_model2/model - md5: 87ea4719e969d21eee4227df0589da68.dir + md5: 17ae66e962b4565d2edd372b23612368.dir size: 2530357 nfiles: 2 - path: models/larry_tips_model2/posterior_samples.pkl.zst - md5: 3676847c16a14530b94334aeb42b6ef8 - size: 7954956389 + md5: 9f86a1621efacaf22fc454a5a6c5b3c7 + size: 8448959747 - path: postprocess.py md5: 2d194b66a6964f4ac39022fe6a4fbb8f size: 5679 @@ -1658,13 +1672,14 @@ stages: 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c23f2447470f27c194c6438363998b45 + size: 389144329 - path: postprocess.py md5: 2d194b66a6964f4ac39022fe6a4fbb8f size: 5679 @@ -1727,14 +1742,14 @@ stages: loss_plot_path: models/larry_mono_model2/loss_plot.png outs: - path: models/larry_mono_model2/metrics.json - md5: 97040e222dad65fc38950f5672f27a2a + md5: f6158a405c245d34765df347e2cab10a size: 96 - path: models/larry_mono_model2/pyrovelocity.pkl.zst - md5: 34d8665530998c09c777d2fa626fb5b8 - size: 29734744 + md5: 358814fb1b1b5bfaae92c8dde94d53be + size: 45322527 - path: models/larry_mono_model2/trained.h5ad - md5: e4be131edbd5eccd10ec89ca85278374 - size: 128091984 + md5: f6bc6ed2f25996689499d86c293bce4d + size: 128092240 postprocess@larry_neu_model2: cmd: /usr/bin/time -v python postprocess.py train_models=[larry_neu_model2] deps: @@ -1742,12 +1757,12 @@ stages: md5: 7d1455a6712fb81fead61af3b7aa838a size: 92577976 - path: models/larry_neu_model2/model - md5: f6bd07434e3327170d5a450852557dfc.dir + md5: f665f411afa30aeaa47e327dfd3a8cb6.dir size: 1068981 nfiles: 2 - path: models/larry_neu_model2/posterior_samples.pkl.zst - md5: 63e6e9e5841655fa242e51756749b9c4 - size: 308318767 + md5: 09370432d36f3f0a661b6e4eee91e2e5 + size: 321304810 - path: postprocess.py md5: 2d194b66a6964f4ac39022fe6a4fbb8f size: 5679 @@ -1796,13 +1811,13 @@ stages: loss_plot_path: models/larry_neu_model2/loss_plot.png outs: - path: models/larry_neu_model2/metrics.json - md5: 335e7605ef73e5f95330aa0f835c8137 + md5: 2d3e141538492f7a8c2c4978167de5b4 size: 96 - path: models/larry_neu_model2/pyrovelocity.pkl.zst - md5: 1f8707241085692cc00a16bc61bc50c1 - size: 25862424 + md5: a86d4c10f648140f61e663b115248730 + size: 37803136 - path: models/larry_neu_model2/trained.h5ad - md5: 4dd1e6d0046128f15724f5724b16dc59 + md5: 217a9056f75dac32a960b90c4eaa242d size: 105880284 postprocess@larry_multilineage_model2: cmd: /usr/bin/time -v python postprocess.py train_models=[larry_multilineage_model2] @@ -1811,12 +1826,12 @@ stages: 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reports/pancreas_model2/shared_time.pdf - md5: c1b1f6463e9d2327ddfce577f4b0ae2f - size: 236624 + md5: c6a9d25f461e23db75458fc7e27a7f4e + size: 236324 - path: reports/pancreas_model2/vector_field.pdf - md5: b2022c2bf53ea58ff78a4a6213fb6c51 - size: 397606 + md5: 7c6dc4ebb5baa30935d985a45037a791 + size: 397585 - path: reports/pancreas_model2/vector_field.pdf.png - md5: 1b8261f3e712737c803dff204e944e27 - size: 698872 + md5: 7f6b1532b428dcc88d99bdb3756962d3 + size: 697694 - path: reports/pancreas_model2/volcano.pdf - md5: ab8ccec2f6a67996427ba79b4e23eae7 - size: 35885 + md5: 4c09ffb92a04a00b507b9f1be930308d + size: 35963 - path: reports/pancreas_model2/volcano.pdf.png - md5: ce41883e836fbaac1f9dcfce4f908dab - size: 386741 + md5: 2f7a325c2382893024a4956e962b6efb + size: 397068 summarize@pbmc68k_model2: cmd: /usr/bin/time -v python summarize.py train_models=[pbmc68k_model2] deps: - path: models/pbmc68k_model2/pyrovelocity.pkl.zst - md5: b3ae8fc391dda9f35cdb36056fac7223 - size: 679013346 + 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995204937711bf1c6932fde14ba1d59c - size: 1196338 + md5: 2b85070b21a65cf190a11c0419d5eae5 + size: 1196695 - path: reports/pbmc68k_model2/volcano.pdf - md5: fea7070cb4fbec00b725995fcd413464 - size: 36783 + md5: 81caa8248077e558b964b0745c04ea1d + size: 36395 - path: reports/pbmc68k_model2/volcano.pdf.png - md5: 6ca9a2aa15097480421e3cd5311c2aa3 - size: 353603 + md5: 149a2d2c40a8fb2efe0fa79e44416cfa + size: 347037 summarize@pons_model2: cmd: /usr/bin/time -v python summarize.py train_models=[pons_model2] deps: - path: models/pons_model2/pyrovelocity.pkl.zst - md5: 12705b7d63bd89eb56b30532ab883f1d - size: 175509376 + md5: 7eb7d8a9eb458c087598835bb412a9d6 + size: 292727197 - path: models/pons_model2/trained.h5ad - md5: a566defb5aa1968939cbe740184014ca + hash: md5 + md5: dcc3d7c35f8cafb6fb285ebc5b9eceb5 size: 859080859 - path: summarize.py - md5: af3ae5c1ad5dad0a19d971dc518542e3 - size: 42041 + md5: 424b1ddc7fe21fc2c66aac74cf8c8fbb + size: 46288 params: config.yaml: base: @@ -2165,68 +2195,74 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59bf4d321f6cde7f17d41c2b17e7da0a + size: 2344041479 - path: models/larry_mono_model2/pyrovelocity.pkl.zst - md5: 34d8665530998c09c777d2fa626fb5b8 - size: 29734744 + md5: 358814fb1b1b5bfaae92c8dde94d53be + size: 45322527 - path: models/larry_multilineage_model2/pyrovelocity.pkl.zst - md5: 37b5f641e6470f3bb45712c6ffa313d5 - size: 66381699 + md5: 57a0a976c2caa3f17d4d9cc8d9eac84d + size: 106903368 - path: models/larry_neu_model2/pyrovelocity.pkl.zst - md5: 1f8707241085692cc00a16bc61bc50c1 - size: 25862424 + md5: a86d4c10f648140f61e663b115248730 + size: 37803136 - path: models/larry_tips_model2/pyrovelocity.pkl.zst - md5: d9c7b2b6d2039f7d6b6244129cf5e871 - size: 515003260 + md5: 03ac488dd899ccd189648cccc10770e5 + size: 854598973 - path: models/pancreas_model2/pyrovelocity.pkl.zst - md5: 51ea60ea757bf317cad28b39484e088f - size: 105519424 + md5: 05357ba7befa89f83e4b11439c071d69 + size: 170952530 - path: models/pbmc10k_model2/pyrovelocity.pkl.zst - md5: bd9a02a9b0910eac2a423f79cb2b12bb - size: 330037760 + md5: acba97b0a7230e566b6fb552f5e7ede2 + size: 543552723 - path: models/pbmc68k_model2/pyrovelocity.pkl.zst - md5: b3ae8fc391dda9f35cdb36056fac7223 - size: 679013346 + md5: 8d371e47355b41e2baa329b31bbee28c + size: 964175816 - path: models/pons_model2/pyrovelocity.pkl.zst - md5: 12705b7d63bd89eb56b30532ab883f1d - size: 175509376 + md5: 7eb7d8a9eb458c087598835bb412a9d6 + size: 292727197 params: config.yaml: reports.figureS3: @@ -2471,17 +2520,17 @@ stages: svg_path: reports/figS3/figS3_raw_gene_selection_model2.svg outs: - path: reports/figS3/figureS3_extras_larry_lin.pdf - md5: 64d0f8aa1aa2be14bba01dc67ee2cf9d - size: 82167 + md5: 7cef7967e495cea3f72e0a490395021b + size: 81944 - path: reports/figS3/figureS3_extras_larry_log.pdf - md5: 9752d43bb0c755e6e47640528600ddad - size: 83010 + md5: 0f2a63e9f3f23adbaf8d99ba7601b0f5 + size: 83695 - path: reports/figS3/figureS3_extras_pbmc_lin.pdf - md5: dbb72688199ca24f9ce882948d8cb44c - size: 69336 + md5: 7a3bbd70f467c07d37fc1990d1692227 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models/larry_multilineage_model2/trained.h5ad - md5: 324c410d940e5b11d29f02566d51c12a + md5: 3e6e98912dda87b66346f8c74c1b92e7 size: 334119477 - path: models/larry_neu_model2/pyrovelocity.pkl.zst - md5: 1f8707241085692cc00a16bc61bc50c1 - size: 25862424 + md5: a86d4c10f648140f61e663b115248730 + size: 37803136 - path: models/larry_neu_model2/trained.h5ad - md5: 4dd1e6d0046128f15724f5724b16dc59 + md5: 217a9056f75dac32a960b90c4eaa242d size: 105880284 params: config.yaml: @@ -3204,67 +3277,72 @@ stages: figureS4: reports/figS4/figS4.pdf outs: - path: reports/figS4/figS4.pdf - md5: 1c905b9c029a3ae408316ebb0e5eb00e - size: 1932972 + hash: md5 + md5: be8a05ab485fddacf4e90d28827127a0 + size: 1921300 - path: reports/figS4/figS4.pdf.png - md5: 11799f5a3dcd585546fae58da182f864 - size: 526943 + md5: a11622840ec8e0ecd2ea7a2b915e74f4 + size: 533621 figureS2_extras: - cmd: python figS2/figure_extras.py train_models=[pbmc68k_model2] + cmd: /usr/bin/time -v python figS2/figure_extras.py train_models=[pbmc68k_model2] deps: - path: figS2/figure_extras.py - md5: 20283ba388e23581a16093e1d68297e3 - size: 11273 + md5: b4623932f7f04b7aad6ad9d53fdb116a + size: 11450 - path: models/pbmc68k_model2/pyrovelocity.pkl.zst - md5: b3ae8fc391dda9f35cdb36056fac7223 - size: 679013346 + md5: 8d371e47355b41e2baa329b31bbee28c + size: 964175816 params: config.yaml: reports.figureS2_extras: tag: figS2 path: reports/figS2 subset_genes_plot: reports/figS2/figS2_subset3g_pbmc68k.pdf - subset_pkl: reports/figS2/figS2_subset3g_pbmc68k.pkl + subset_pkl: reports/figS2/figS2_subset3g_pbmc68k.pkl.zst outs: - path: reports/figS2/figS2_subset3g_pbmc68k.pdf - md5: c1eadf935916329f02f949facfc7eb4b - size: 5605317 + hash: md5 + md5: 968b6ba02c8566fa72ebddc92f42541d + size: 5540646 - path: reports/figS2/figS2_subset3g_pbmc68k.pdf.png - md5: 0e79aab1beb3819b1f7fa12824c5998b - size: 1480115 + md5: 922ba14295de416f460672fe93458cd7 + size: 1467474 + - path: reports/figS2/figS2_subset3g_pbmc68k.pkl.zst + md5: 1d8922ccd1bd2ab897459b827e6787fa + size: 398177291 figureS2_extra_2: - cmd: python figS2/figure_extra_2.py train_models=[pancreas_model2,pbmc10k_model2,pbmc68k_model2,pons_model2,larry_model2,larry_neu_model2,larry_mono_model2,larry_multilineage_model2,larry_tips_model2] + cmd: /usr/bin/time -v python figS2/figure_extra_2.py train_models=[pancreas_model2,pbmc10k_model2,pbmc68k_model2,pons_model2,larry_model2,larry_neu_model2,larry_mono_model2,larry_multilineage_model2,larry_tips_model2] deps: - path: figS2/figure_extra_2.py md5: ed35636cfcef647467f0be5f58ac1fee size: 5626 - path: models/larry_model2/pyrovelocity.pkl.zst - md5: 07aabc2f0e592483cb3268ca1bf73675 - size: 1368569189 + md5: 59bf4d321f6cde7f17d41c2b17e7da0a + size: 2344041479 - path: models/larry_mono_model2/pyrovelocity.pkl.zst - md5: 34d8665530998c09c777d2fa626fb5b8 - size: 29734744 + md5: 358814fb1b1b5bfaae92c8dde94d53be + size: 45322527 - path: models/larry_multilineage_model2/pyrovelocity.pkl.zst - md5: 37b5f641e6470f3bb45712c6ffa313d5 - size: 66381699 + md5: 57a0a976c2caa3f17d4d9cc8d9eac84d + size: 106903368 - path: models/larry_neu_model2/pyrovelocity.pkl.zst - md5: 1f8707241085692cc00a16bc61bc50c1 - size: 25862424 + md5: a86d4c10f648140f61e663b115248730 + size: 37803136 - path: models/larry_tips_model2/pyrovelocity.pkl.zst - md5: d9c7b2b6d2039f7d6b6244129cf5e871 - size: 515003260 + md5: 03ac488dd899ccd189648cccc10770e5 + size: 854598973 - path: models/pancreas_model2/pyrovelocity.pkl.zst - md5: 51ea60ea757bf317cad28b39484e088f - size: 105519424 + md5: 05357ba7befa89f83e4b11439c071d69 + size: 170952530 - path: models/pbmc10k_model2/pyrovelocity.pkl.zst - md5: bd9a02a9b0910eac2a423f79cb2b12bb - size: 330037760 + md5: acba97b0a7230e566b6fb552f5e7ede2 + size: 543552723 - path: models/pbmc68k_model2/pyrovelocity.pkl.zst - md5: b3ae8fc391dda9f35cdb36056fac7223 - size: 679013346 + md5: 8d371e47355b41e2baa329b31bbee28c + size: 964175816 - path: models/pons_model2/pyrovelocity.pkl.zst - md5: 12705b7d63bd89eb56b30532ab883f1d - size: 175509376 + md5: 7eb7d8a9eb458c087598835bb412a9d6 + size: 292727197 params: config.yaml: reports.figureS2_extra_2: @@ -3273,11 +3351,12 @@ stages: mean_length_vs_uncertain: reports/figS2/figS2_mean_length_vs_uncertain.pdf outs: - path: reports/figS2/figS2_mean_length_vs_uncertain.pdf - md5: 474492712eb473c321a54ba732033bb3 - size: 5895896 + hash: md5 + md5: 6bc81492a506f17dd843994e5ff3752f + size: 5984382 - path: reports/figS2/figS2_mean_length_vs_uncertain.pdf.png - md5: 54390a076d9fee2af48687d08683dde2 - size: 2783281 + md5: e306afdb62c045994f1db1e520c7e644 + size: 2755600 data_download@bonemarrow: cmd: python data_download.py process_data=[bonemarrow] deps: @@ -3329,6 +3408,7 @@ stages: thresh_histogram_path: data/processed/bonemarrow_thresh_histogram.pdf outs: - path: data/processed/bonemarrow_processed.h5ad + hash: md5 md5: e8e881920c5fdc7fdfe7c8eed676774b size: 651900368 - path: data/processed/bonemarrow_thresh_histogram.pdf @@ -3341,6 +3421,7 @@ stages: cmd: /usr/bin/time -v python train.py train_models=[bonemarrow_model2] deps: - path: data/processed/bonemarrow_processed.h5ad + hash: md5 md5: e8e881920c5fdc7fdfe7c8eed676774b size: 651900368 - path: train.py @@ -3391,31 +3472,32 @@ stages: loss_plot_path: models/bonemarrow_model2/loss_plot.png outs: - path: models/bonemarrow_model2/loss_plot.png - md5: abc038d6c66ee944df1ca61d26fccf26 - size: 11213 + md5: d9a4e6d207bbd30202e409f03cf6cfe4 + size: 12408 - path: models/bonemarrow_model2/model - md5: 8520f73c5216a28351d1bf34c3bed3d1.dir + md5: 02b8e9097f9c90635324f9769f5659a1.dir size: 1884213 nfiles: 2 - path: models/bonemarrow_model2/posterior_samples.pkl.zst - md5: 8b5e05a2017afd651d08a000b37b16da - size: 2518920834 + md5: b01122823ac0766b99eb2c9623f2145d + size: 2870719505 - path: models/bonemarrow_model2/run_info.json - md5: db9c1d357e5bbbd9e3f86e431e1e9bc6 - size: 457 + md5: 9cf75e3ace26d77e4971745a844f772b + size: 438 postprocess@bonemarrow_model2: cmd: /usr/bin/time -v python postprocess.py train_models=[bonemarrow_model2] deps: - path: data/processed/bonemarrow_processed.h5ad + hash: md5 md5: e8e881920c5fdc7fdfe7c8eed676774b size: 651900368 - path: models/bonemarrow_model2/model - md5: 8520f73c5216a28351d1bf34c3bed3d1.dir + md5: 02b8e9097f9c90635324f9769f5659a1.dir size: 1884213 nfiles: 2 - path: models/bonemarrow_model2/posterior_samples.pkl.zst - md5: 8b5e05a2017afd651d08a000b37b16da - size: 2518920834 + md5: b01122823ac0766b99eb2c9623f2145d + size: 2870719505 - path: postprocess.py md5: 2d194b66a6964f4ac39022fe6a4fbb8f size: 5679 @@ -3464,26 +3546,28 @@ stages: loss_plot_path: models/bonemarrow_model2/loss_plot.png outs: - path: models/bonemarrow_model2/metrics.json - md5: a6337d9d768bdc6ec9ed5fafd33dd56c - size: 98 + md5: e205aae2985424d2241ace74a81d2c77 + size: 96 - path: models/bonemarrow_model2/pyrovelocity.pkl.zst - md5: cd0a08363b530eb4e66451b65d87662f - size: 162542506 + md5: 2f77818cdab5e659d6540d6ef12bb4f9 + size: 258703585 - path: models/bonemarrow_model2/trained.h5ad - md5: 5c0d598b6ce53d54015e4abaf4954fb1 - size: 760341824 + hash: md5 + md5: 4983c1f39167c34cdb59be7db2e14bcd + size: 760340800 summarize@bonemarrow_model2: cmd: /usr/bin/time -v python summarize.py train_models=[bonemarrow_model2] deps: - path: models/bonemarrow_model2/pyrovelocity.pkl.zst - md5: cd0a08363b530eb4e66451b65d87662f - size: 162542506 + md5: 2f77818cdab5e659d6540d6ef12bb4f9 + size: 258703585 - path: models/bonemarrow_model2/trained.h5ad - md5: 5c0d598b6ce53d54015e4abaf4954fb1 - size: 760341824 + hash: md5 + md5: 4983c1f39167c34cdb59be7db2e14bcd + size: 760340800 - path: summarize.py - md5: af3ae5c1ad5dad0a19d971dc518542e3 - size: 42041 + md5: 424b1ddc7fe21fc2c66aac74cf8c8fbb + size: 46288 params: config.yaml: base: @@ -3513,56 +3597,61 @@ stages: md5: ab00ad34356484260492e66b2ad8f912 size: 17615324 - path: reports/bonemarrow_model2/clusters_violin_lin.pdf - md5: d9045a5bbdce693ed238e47379c6906f - size: 150717 + md5: 4cc35d7dd11ff06f859cdad7576193f4 + size: 148334 - path: reports/bonemarrow_model2/clusters_violin_lin.pdf.png - md5: 6fd43e195a753036b028a38813e32bef - size: 2316012 + md5: 2158a687224342357bd786ff86b27ed0 + size: 1857965 - path: reports/bonemarrow_model2/clusters_violin_log.pdf - md5: c41264ec200a04a0267d37a60c8bcce8 - size: 151467 + md5: b5cbfc8740aef53d8dcd84723aac25bb + size: 150035 - path: reports/bonemarrow_model2/clusters_violin_log.pdf.png - md5: a846cc0d014b0563216e15eab71dafd7 - size: 2485038 + md5: 54030a39c1d58ac97a903e8c6123a3de + size: 2143225 - path: reports/bonemarrow_model2/fig2_part1_plot.pdf - md5: 6055911c8ca265c2bb09c606b1111e25 - size: 486075 + md5: e3c8f37a06ec76c5c962935f83362954 + size: 485081 - path: reports/bonemarrow_model2/fig2_part1_plot.pdf.png - md5: fa9af7dd5356dc410c07c7c8b09820a4 - size: 418493 + md5: 1e8d604aa1260cba30af36b56507d163 + size: 428749 - path: reports/bonemarrow_model2/fig2_part2_plot.pdf - md5: 6d704cedcec1d5ca0e2af879148e136e - size: 1931458 + hash: md5 + md5: 9e5a304b963e995dbafbde0a48ebebe5 + size: 2005710 - path: reports/bonemarrow_model2/fig2_part2_plot.pdf.png - md5: 682373901caf02aba63df837ce79f68a - size: 511903 + md5: b52989dfa63323da3c3301c0642f766a + size: 489679 - path: reports/bonemarrow_model2/param_uncertainties.pdf - md5: 02932f1b7082629cbe458e033f9f1ce3 - size: 138685 + md5: 5c4ca6d2e2d5ca8e7b3c20efb8b192c5 + size: 140585 - path: reports/bonemarrow_model2/param_uncertainties.pdf.png - md5: 361fca5e5f00f0ccaf95c4005266cc56 - size: 809961 + md5: 6bf42a06ba6b60778a349a4e39f3d76c + size: 904660 + - path: reports/bonemarrow_model2/posterior_phase_portraits + md5: 2f6192f915f821ed09b090c62c03f736.dir + size: 32058101 + nfiles: 20 - path: reports/bonemarrow_model2/rainbow.pdf - md5: 7f457c6441cdf9f54e595a7466ef2cba - size: 8157744 + md5: 2c18dd3588a556e665fd5b3189748b3a + size: 8375639 - path: reports/bonemarrow_model2/rainbow.pdf.png - md5: 98ad0cd2b66713d37d26b4258949f171 - size: 1112702 + md5: f94b218fa72f35acb21f115af462f38f + size: 1236691 - path: reports/bonemarrow_model2/shared_time.pdf - md5: 481bd4148f5b7ef1fa700bb4ffde7cbe - size: 168622 + md5: a68a53f3615134e969250c58d4d4ecd3 + size: 163067 - path: reports/bonemarrow_model2/vector_field.pdf - md5: 8deebe6b8870b7d049cd1d34ed1b6b7b - size: 320629 + md5: 3b21428d48ca70f0668d35ace7bb313c + size: 320661 - path: reports/bonemarrow_model2/vector_field.pdf.png - md5: d4511e2cf1ff27bff8d9b48348438aad - size: 463204 + md5: 4975c00b0d14521de62a9559c42706fc + size: 466505 - path: reports/bonemarrow_model2/volcano.pdf - md5: a41385390bc2922bf2c4beaf24e264a4 - size: 40856 + md5: 4c17d11f9df5981d3282796f2f5e49d3 + size: 38053 - path: reports/bonemarrow_model2/volcano.pdf.png - md5: 860edac120b7ab2fb4be67aa1bbb4e38 - size: 342473 + md5: a6e1227e329e89113787ea30f9a90821 + size: 370085 data_download@pbmc5k: cmd: python data_download.py process_data=[pbmc5k] deps: @@ -3676,18 +3765,18 @@ stages: loss_plot_path: models/pbmc5k_model2/loss_plot.png outs: - path: models/pbmc5k_model2/loss_plot.png - md5: bcac0f2bfb2aa389658ef7f20d277316 - size: 11553 + md5: 54eae82443194c7ecbece0e34ee79efb + size: 12483 - path: models/pbmc5k_model2/model - md5: e5e9e7a8258a817af2ff312a1c299d39.dir + md5: 8d86f5995b964e864831c890f45d8f09.dir size: 1799157 nfiles: 2 - path: models/pbmc5k_model2/posterior_samples.pkl.zst - md5: 7157f59f21091eda65af7df3ad996619 - size: 1671446266 + md5: b955046310d0e16e965a7c4c81aca6d2 + size: 2015440247 - path: models/pbmc5k_model2/run_info.json - md5: 13dd1db03db61ac3392e4c1bd8ba70b6 - size: 453 + md5: 39dba1b10a6961e8c298e359c0e5ffe9 + size: 434 postprocess@pbmc5k_model2: cmd: /usr/bin/time -v python postprocess.py train_models=[pbmc5k_model2] deps: @@ -3695,12 +3784,12 @@ stages: md5: a09eeda00f2f46f2e25fdc3cd72fd411 size: 515978957 - path: models/pbmc5k_model2/model - md5: e5e9e7a8258a817af2ff312a1c299d39.dir + md5: 8d86f5995b964e864831c890f45d8f09.dir size: 1799157 nfiles: 2 - path: models/pbmc5k_model2/posterior_samples.pkl.zst - md5: 7157f59f21091eda65af7df3ad996619 - size: 1671446266 + md5: b955046310d0e16e965a7c4c81aca6d2 + size: 2015440247 - path: postprocess.py md5: 2d194b66a6964f4ac39022fe6a4fbb8f size: 5679 @@ -3749,26 +3838,26 @@ stages: loss_plot_path: models/pbmc5k_model2/loss_plot.png outs: - path: models/pbmc5k_model2/metrics.json - md5: e198e6ab2400d70070fee4e184b2495f - size: 99 + md5: cd69cfba6f676a864fd46fe97025c2d8 + size: 96 - path: models/pbmc5k_model2/pyrovelocity.pkl.zst - md5: 01ab7a8c3168db1a2cb86a0498c5c9d3 - size: 113751597 + md5: 709b4a65f5ea55da6e9ff9f55d50165e + size: 188366017 - path: models/pbmc5k_model2/trained.h5ad - md5: 7392ed14357bc9409ec63f1820a02b96 - size: 587927873 + md5: 8c24d7925bf1caaf8d56338852fab94f + size: 587927361 summarize@pbmc5k_model2: cmd: /usr/bin/time -v python summarize.py train_models=[pbmc5k_model2] deps: - path: models/pbmc5k_model2/pyrovelocity.pkl.zst - md5: 01ab7a8c3168db1a2cb86a0498c5c9d3 - size: 113751597 + md5: 709b4a65f5ea55da6e9ff9f55d50165e + size: 188366017 - path: models/pbmc5k_model2/trained.h5ad - md5: 7392ed14357bc9409ec63f1820a02b96 - size: 587927873 + md5: 8c24d7925bf1caaf8d56338852fab94f + size: 587927361 - path: summarize.py - md5: af3ae5c1ad5dad0a19d971dc518542e3 - size: 42041 + md5: 424b1ddc7fe21fc2c66aac74cf8c8fbb + size: 46288 params: config.yaml: base: @@ -3798,56 +3887,61 @@ stages: md5: 14078b803a0d70bfff0b655357081857 size: 13338832 - path: reports/pbmc5k_model2/clusters_violin_lin.pdf - md5: 71bb92ad7be8430c3b1147063f567739 - size: 139290 + md5: 46fb6b34278e8e983d8a78131f3c7e19 + size: 135413 - path: reports/pbmc5k_model2/clusters_violin_lin.pdf.png - md5: c4b43b9ae2f089a949524dd89fba9c7b - size: 2275202 + md5: 9cfbf5e65043b79fea3eec62d588c2ca + size: 1835527 - path: reports/pbmc5k_model2/clusters_violin_log.pdf - md5: 124f009316cce2652f46564f092602c5 - size: 140082 + md5: 43c06b11547664eaace5a2379321cef9 + size: 137975 - path: reports/pbmc5k_model2/clusters_violin_log.pdf.png - md5: ab47848b71f1944ee25c77c4fd9f0905 - size: 2299584 + md5: 09e00a97e35ceec3f7166adf252e92d7 + size: 2220060 - path: reports/pbmc5k_model2/fig2_part1_plot.pdf - md5: 5f488e9dcdd3c5fa78c24481505dc7bc - size: 461666 + md5: ec5a41535f0eb2c63241b4d6352c67c8 + size: 461099 - path: reports/pbmc5k_model2/fig2_part1_plot.pdf.png - md5: 2e050bf87ce6d7e04f43b403d887020b - size: 680867 + md5: 7d2f32974e8d591c422505a4f1c20d11 + size: 699530 - path: reports/pbmc5k_model2/fig2_part2_plot.pdf - md5: 3a780f9b6a5ca033f9406e3f90661b50 - size: 1290446 + md5: eee44e08f3e599a545eefc148f103584 + size: 1294549 - path: reports/pbmc5k_model2/fig2_part2_plot.pdf.png - md5: 4f82d40b12facc97c4d15ec0d527aa37 - size: 699550 + md5: a1b1ccbbf36b6ec641742bb45bc8646f + size: 675699 - path: reports/pbmc5k_model2/param_uncertainties.pdf - md5: 5d94f3fde0a6c17a2459867f0678fc6a - size: 138835 + md5: a2851beec4562f7e369a8fc154f0bffe + size: 140527 - path: reports/pbmc5k_model2/param_uncertainties.pdf.png - md5: 9a29ce4d8bd25ba206e6314cfc3ab99b - size: 891813 + md5: 15116af84c935e2dd22214fe4c2184ad + size: 912610 + - path: reports/pbmc5k_model2/posterior_phase_portraits + md5: ffc239a2bd70c1446915b348169c7d94.dir + size: 33073418 + nfiles: 20 - path: reports/pbmc5k_model2/rainbow.pdf - md5: 4574c95a43c7758854f2e69c4cfa66e6 - size: 5349095 + hash: md5 + md5: ea684c170d068f174e85a3fe2570e952 + size: 5334549 - path: reports/pbmc5k_model2/rainbow.pdf.png - md5: 2edd2ab88641b17344b3b48f92c1fe8d - size: 1353259 + md5: 1610ac6d6c92ff3290890c50244a8059 + size: 1501775 - path: reports/pbmc5k_model2/shared_time.pdf - md5: 87ce9a96ee2f92febc269403c31afaf7 - size: 328510 + md5: 2882b445dd04dbddd3795dcbf8c54e06 + size: 319537 - path: reports/pbmc5k_model2/vector_field.pdf - md5: a7748bd0c7ee926bdb438d333323b8a7 - size: 469148 + md5: b92de853fce0a4b68292e64bb9bf2e5b + size: 469270 - path: reports/pbmc5k_model2/vector_field.pdf.png - md5: e212774fb78d2642f89960d9d0dcf749 - size: 820922 + md5: 36fd6f01f85f7248fce838f288d72e7d + size: 832418 - path: reports/pbmc5k_model2/volcano.pdf - md5: 99ddf69fb8a58b038a6c1ce8c3df7453 - size: 37846 + md5: 5ce0986e739ab4475d6fcf41407b1979 + size: 38706 - path: reports/pbmc5k_model2/volcano.pdf.png - md5: 5e46acacf3e24deeff7b2dd0c896d692 - size: 379633 + md5: 06dbe3a82ad20474870480116d569a56 + size: 381277 train@pancreas_model1: cmd: /usr/bin/time -v python train.py train_models=[pancreas_model1] deps: @@ -3975,22 +4069,24 @@ stages: loss_plot_path: models/pancreas_model1/loss_plot.png outs: - path: models/pancreas_model1/metrics.json - md5: 80a687e3fd3bf35db19202f193f73cd8 - size: 98 + md5: 9e6754eecc1e19bc946a12ec13fcf120 + size: 95 - path: models/pancreas_model1/pyrovelocity.pkl.zst - md5: b2aab7a3577b99cddc5bb1ec03a02eaf - size: 166153664 + md5: 625ad24059192ddb7c9977a6f0fc2aa3 + size: 166153094 - path: models/pancreas_model1/trained.h5ad - md5: 6fcbc8bbe3cf43cbe7383cc8661b95c7 + hash: md5 + md5: beedf99a6777ed5f6d06bcd2b5805c29 size: 492127600 summarize@pancreas_model1: cmd: /usr/bin/time -v python summarize.py train_models=[pancreas_model1] deps: - path: models/pancreas_model1/pyrovelocity.pkl.zst - md5: b2aab7a3577b99cddc5bb1ec03a02eaf - size: 166153664 + md5: 625ad24059192ddb7c9977a6f0fc2aa3 + size: 166153094 - path: models/pancreas_model1/trained.h5ad - md5: 6fcbc8bbe3cf43cbe7383cc8661b95c7 + hash: md5 + md5: beedf99a6777ed5f6d06bcd2b5805c29 size: 492127600 - path: summarize.py md5: 424b1ddc7fe21fc2c66aac74cf8c8fbb @@ -4024,53 +4120,58 @@ stages: md5: bbff19677beed1c7cf3766506f391723 size: 12359084 - path: reports/pancreas_model1/clusters_violin_lin.pdf - md5: e0e4d14ff05b42e6c3684e4a8ca6227c - size: 126790 + md5: 0f5e51beac6ca30c89ad4578f98f195a + size: 126861 - path: reports/pancreas_model1/clusters_violin_lin.pdf.png - md5: d07eb23ccaa8a55e9569504646568efa - size: 2134075 + md5: 198d860d81f6c1d59adc3a525e6e3472 + size: 2149615 - path: 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reports/pancreas_model1/param_uncertainties.pdf - md5: 960c232ea06bee8e5d43a8772c6d4c34 - size: 139072 + md5: bf46a1467c2f59216bd8eac1a128db83 + size: 139140 - path: reports/pancreas_model1/param_uncertainties.pdf.png - md5: 49073d28fc6ec0003cbe40a8771f1834 - size: 884409 + md5: b68fa4c2fb4d66b8b0b2ee1dea50bcd1 + size: 882820 + - path: reports/pancreas_model1/posterior_phase_portraits + md5: 6db57f10133a2a3b87fedc433dfffd20.dir + size: 25581816 + nfiles: 20 - path: reports/pancreas_model1/rainbow.pdf - md5: da3c17af492b9cd86ab19a11dfae3717 + hash: md5 + md5: 57119ef95f97a95ebade2d36659d6d0a size: 5144270 - path: reports/pancreas_model1/rainbow.pdf.png - md5: c68017154e85e0366985865913f1dc08 - size: 1402720 + md5: 5e2719417cc402fe1d33fcddb18f94e2 + size: 1396174 - path: reports/pancreas_model1/shared_time.pdf - md5: 1588f53ac5d4084370a50ce0d6c535a0 - size: 254000 + md5: 47b8339e51690fe20c53625b21ea9461 + size: 254217 - path: reports/pancreas_model1/vector_field.pdf - md5: a74248e8c578ce9c790986dc67b82aeb - size: 397606 + md5: 20bc4a60a3e78f9ca805804bcf04ec8b + size: 397601 - path: reports/pancreas_model1/vector_field.pdf.png - md5: be1a000c0e2d8fd18255d6daab94dd72 - size: 700814 + md5: e5cc1dc0c8b31c723babd0740ba3b219 + size: 699780 - path: reports/pancreas_model1/volcano.pdf - md5: 756d97e3f9de180a4713c3a65efe87b8 - size: 34522 + md5: c357dcfef641a8ea3722c4774b96faef + size: 34445 - path: reports/pancreas_model1/volcano.pdf.png - md5: c78af31bce4e68ac0e726eeb5af36038 - size: 360024 + md5: 5522fefc35836286e6efc7b25f328ef6 + size: 361286 diff --git a/reproducibility/figures/dvc.yaml b/reproducibility/figures/dvc.yaml index d6132ae5c..6d16530d0 100644 --- a/reproducibility/figures/dvc.yaml +++ b/reproducibility/figures/dvc.yaml @@ -101,6 +101,7 @@ stages: - ${item.violin_clusters_log}.png - ${item.uncertainty_param_plot} - ${item.uncertainty_param_plot}.png + - ${item.posterior_phase_portraits} figureS2: cmd: /usr/bin/time -v python figS2/figure.py train_models=[pbmc5k_model2,pbmc10k_model2_coarse,pancreas_model2,pbmc10k_model2,pbmc68k_model2,pons_model2,larry_model2,larry_neu_model2,larry_mono_model2,larry_tips_model2] @@ -130,7 +131,7 @@ stages: persist: true figureS2_extras: - cmd: python figS2/figure_extras.py train_models=[pbmc68k_model2] + cmd: /usr/bin/time -v python figS2/figure_extras.py train_models=[pbmc68k_model2] deps: - figS2/figure_extras.py - ${model_training.pbmc68k_model2.pyrovelocity_data_path} @@ -140,9 +141,10 @@ stages: outs: - ${reports.figureS2_extras.subset_genes_plot} - ${reports.figureS2_extras.subset_genes_plot}.png + - ${reports.figureS2_extras.subset_pkl} figureS2_extra_2: - cmd: python figS2/figure_extra_2.py train_models=[pancreas_model2,pbmc10k_model2,pbmc68k_model2,pons_model2,larry_model2,larry_neu_model2,larry_mono_model2,larry_multilineage_model2,larry_tips_model2] + cmd: /usr/bin/time -v python figS2/figure_extra_2.py train_models=[pancreas_model2,pbmc10k_model2,pbmc68k_model2,pons_model2,larry_model2,larry_neu_model2,larry_mono_model2,larry_multilineage_model2,larry_tips_model2] deps: - figS2/figure_extra_2.py - ${model_training.pancreas_model2.pyrovelocity_data_path} @@ -177,7 +179,7 @@ stages: # - ${reports.figureS3.svg_path} figureS3_extras: - cmd: python figS3/figure_extras.py train_models=[pancreas_model2,pbmc10k_model2,pbmc68k_model2,pons_model2,larry_model2,larry_neu_model2,larry_mono_model2,larry_multilineage_model2,larry_tips_model2] + cmd: /usr/bin/time -v python figS3/figure_extras.py train_models=[pancreas_model2,pbmc10k_model2,pbmc68k_model2,pons_model2,larry_model2,larry_neu_model2,larry_mono_model2,larry_multilineage_model2,larry_tips_model2] deps: - figS3/figure_extras.py - ${model_training.pancreas_model2.pyrovelocity_data_path} @@ -199,7 +201,7 @@ stages: - ${reports.figureS3_extras.violin_plots_larry_log} figure3: - cmd: python fig3/figure.py + cmd: /usr/bin/time -v python fig3/figure.py deps: - fig3/figure.py - ${model_training.larry_model2.trained_data_path} @@ -218,7 +220,7 @@ stages: - ${reports.figure3.figure3}.png figureS4: - cmd: python figS4/figure.py + cmd: /usr/bin/time -v python figS4/figure.py deps: - figS4/figure.py - ${model_training.larry_model2.trained_data_path} diff --git a/reproducibility/figures/figS2/figure_extras.py b/reproducibility/figures/figS2/figure_extras.py index 1645a5b7e..b34b47b5d 100644 --- a/reproducibility/figures/figS2/figure_extras.py +++ b/reproducibility/figures/figS2/figure_extras.py @@ -166,11 +166,13 @@ def plots( del posterior_samples["s"] del posterior_samples["ut"] del posterior_samples["st"] - with open(pyrovelocity_data_path_3genes, "wb") as f: - pickle.dump(posterior_samples, f) + CompressedPickle.save(pyrovelocity_data_path_3genes, posterior_samples) + # with open(pyrovelocity_data_path_3genes, "wb") as f: + # pickle.dump(posterior_samples, f) else: - with open(pyrovelocity_data_path_3genes, "rb") as f: - posterior_samples = pickle.load(f) + posterior_samples = CompressedPickle.load(pyrovelocity_data_path_3genes) + # with open(pyrovelocity_data_path_3genes, "rb") as f: + # posterior_samples = pickle.load(f) print((posterior_samples["fdri"] < 0.001).sum()) adata.obs.loc[:, "vector_field_rayleigh_test"] = posterior_samples["fdri"] diff --git a/reproducibility/figures/models/bonemarrow_model2/metrics.json b/reproducibility/figures/models/bonemarrow_model2/metrics.json index 8bf262334..ab8e3b713 100644 --- a/reproducibility/figures/models/bonemarrow_model2/metrics.json +++ b/reproducibility/figures/models/bonemarrow_model2/metrics.json @@ -1,5 +1,5 @@ { - "MAE": 0.4653474697231833, - "FDR_HMP": 1.538164764075129e-11, - "FDR_sig_frac": 0.968 + "MAE": 0.375789293540946, + "FDR_sig_frac": 0.999, + "FDR_HMP": 3.55045090399453e-12 } \ No newline at end of file diff --git a/reproducibility/figures/models/bonemarrow_model2/run_info.json b/reproducibility/figures/models/bonemarrow_model2/run_info.json index d30b47400..098b42547 100644 --- a/reproducibility/figures/models/bonemarrow_model2/run_info.json +++ b/reproducibility/figures/models/bonemarrow_model2/run_info.json @@ -1,12 +1,12 @@ { - "artifact_uri": "file:///home/jupyter/pyrovelocity/reproducibility/figures/mlruns/0/7d31ef27cdc2463f875982bc4f4e200e/artifacts", - "end_time": 1686367263392, + "artifact_uri": "mlflow-artifacts:/1a741690552b410eb9c7ba642cf21e2d/af009cb904084dfd82fcefbffab34a79/artifacts", + "end_time": 1688679510252, "experiment_id": "0", "lifecycle_stage": "active", - "run_id": "7d31ef27cdc2463f875982bc4f4e200e", - "run_name": "bonemarrow_model2-7d31ef2", - "run_uuid": "7d31ef27cdc2463f875982bc4f4e200e", - "start_time": 1686366404451, + "run_id": "af009cb904084dfd82fcefbffab34a79", + "run_name": "bonemarrow_model2-af009cb", + "run_uuid": "af009cb904084dfd82fcefbffab34a79", + "start_time": 1688679213760, "status": "FINISHED", - "user_id": "jupyter" + "user_id": "root" } \ No newline at end of file diff --git a/reproducibility/figures/models/larry_model2/metrics.json b/reproducibility/figures/models/larry_model2/metrics.json index fa9a96183..f98c3ecbe 100644 --- a/reproducibility/figures/models/larry_model2/metrics.json +++ b/reproducibility/figures/models/larry_model2/metrics.json @@ -1,5 +1,5 @@ { - "MAE": 0.155686632388138, - "FDR_HMP": 7.36701004289444e-12, - "FDR_sig_frac": 0.978 + "MAE": 0.155563493367409, + "FDR_sig_frac": 0.946, + "FDR_HMP": 1.83718855495429e-11 } \ No newline at end of file diff --git a/reproducibility/figures/models/larry_model2/run_info.json b/reproducibility/figures/models/larry_model2/run_info.json index 97cd20bcd..f2a53407a 100644 --- a/reproducibility/figures/models/larry_model2/run_info.json +++ b/reproducibility/figures/models/larry_model2/run_info.json @@ -1,12 +1,12 @@ { - "artifact_uri": "mlflow-artifacts:/1a741690552b410eb9c7ba642cf21e2d/65c0c34b02ef48ad9e75dcd53573bcf7/artifacts", - "end_time": 1685004169927, + "artifact_uri": "mlflow-artifacts:/1a741690552b410eb9c7ba642cf21e2d/014d5c5d51744199b7bfc08d346cdddc/artifacts", + "end_time": 1688678078186, "experiment_id": "0", "lifecycle_stage": "active", - "run_id": "65c0c34b02ef48ad9e75dcd53573bcf7", - "run_name": "larry_model2-65c0c34", - "run_uuid": "65c0c34b02ef48ad9e75dcd53573bcf7", - "start_time": 1685000167867, + "run_id": "014d5c5d51744199b7bfc08d346cdddc", + "run_name": "larry_model2-014d5c5", + "run_uuid": "014d5c5d51744199b7bfc08d346cdddc", + "start_time": 1688676307034, "status": "FINISHED", "user_id": "root" } \ No newline at end of file diff --git a/reproducibility/figures/models/larry_mono_model2/metrics.json b/reproducibility/figures/models/larry_mono_model2/metrics.json index a99f5f962..8efae25b8 100644 --- a/reproducibility/figures/models/larry_mono_model2/metrics.json +++ b/reproducibility/figures/models/larry_mono_model2/metrics.json @@ -1,5 +1,5 @@ { - "MAE": 0.386205785421911, - "FDR_HMP": 2.94863591739726e-12, - "FDR_sig_frac": 0.997 + "FDR_HMP": 2.65862483044198e-12, + "MAE": 0.381873488560919, + "FDR_sig_frac": 0.995 } \ No newline at end of file diff --git a/reproducibility/figures/models/larry_mono_model2/run_info.json b/reproducibility/figures/models/larry_mono_model2/run_info.json index 07238cede..de40369d5 100644 --- a/reproducibility/figures/models/larry_mono_model2/run_info.json +++ b/reproducibility/figures/models/larry_mono_model2/run_info.json @@ -1,12 +1,12 @@ { - "artifact_uri": "mlflow-artifacts:/1a741690552b410eb9c7ba642cf21e2d/b4f54ffc9dc04efa970abc5bc16463b9/artifacts", - "end_time": 1685004664666, + "artifact_uri": "mlflow-artifacts:/1a741690552b410eb9c7ba642cf21e2d/0edb46e009e74d8781bd32889e8052c1/artifacts", + "end_time": 1688678468654, "experiment_id": "0", "lifecycle_stage": "active", - "run_id": "b4f54ffc9dc04efa970abc5bc16463b9", - "run_name": "larry_mono_model2-b4f54ff", - "run_uuid": "b4f54ffc9dc04efa970abc5bc16463b9", - "start_time": 1685004564638, + "run_id": "0edb46e009e74d8781bd32889e8052c1", + "run_name": "larry_mono_model2-0edb46e", + "run_uuid": "0edb46e009e74d8781bd32889e8052c1", + "start_time": 1688678408147, "status": "FINISHED", "user_id": "root" } \ No newline at end of file diff --git a/reproducibility/figures/models/larry_multilineage_model2/metrics.json b/reproducibility/figures/models/larry_multilineage_model2/metrics.json index 2b6900a2d..acd7ca22d 100644 --- a/reproducibility/figures/models/larry_multilineage_model2/metrics.json +++ b/reproducibility/figures/models/larry_multilineage_model2/metrics.json @@ -1,5 +1,5 @@ { - "FDR_HMP": 5.29020882204213e-12, - "FDR_sig_frac": 0.985, - "MAE": 0.311578999280058 + "MAE": 0.308032609791217, + "FDR_sig_frac": 0.99, + "FDR_HMP": 6.17347965930962e-12 } \ No newline at end of file diff --git a/reproducibility/figures/models/larry_multilineage_model2/run_info.json b/reproducibility/figures/models/larry_multilineage_model2/run_info.json index 52800a54a..a63393db7 100644 --- a/reproducibility/figures/models/larry_multilineage_model2/run_info.json +++ b/reproducibility/figures/models/larry_multilineage_model2/run_info.json @@ -1,12 +1,12 @@ { - "artifact_uri": "mlflow-artifacts:/1a741690552b410eb9c7ba642cf21e2d/f165c67778494b9fa0f6e95ddf3ca246/artifacts", - "end_time": 1685004773573, + "artifact_uri": "mlflow-artifacts:/1a741690552b410eb9c7ba642cf21e2d/6a839d2ce4ab452495919ebe2f483911/artifacts", + "end_time": 1688678509274, "experiment_id": "0", "lifecycle_stage": "active", - "run_id": "f165c67778494b9fa0f6e95ddf3ca246", - "run_name": "larry_multilineage_model2-f165c67", - "run_uuid": "f165c67778494b9fa0f6e95ddf3ca246", - "start_time": 1685004575173, + "run_id": "6a839d2ce4ab452495919ebe2f483911", + "run_name": "larry_multilineage_model2-6a839d2", + "run_uuid": "6a839d2ce4ab452495919ebe2f483911", + "start_time": 1688678420043, "status": "FINISHED", "user_id": "root" } \ No newline at end of file diff --git a/reproducibility/figures/models/larry_neu_model2/metrics.json b/reproducibility/figures/models/larry_neu_model2/metrics.json index a5da1708d..3b1058806 100644 --- a/reproducibility/figures/models/larry_neu_model2/metrics.json +++ b/reproducibility/figures/models/larry_neu_model2/metrics.json @@ -1,5 +1,5 @@ { - "MAE": 0.430193013795227, - "FDR_HMP": 4.32225618320848e-12, - "FDR_sig_frac": 0.963 + "FDR_sig_frac": 0.988, + "MAE": 0.422449021265325, + "FDR_HMP": 4.17301928821601e-12 } \ No newline at end of file diff --git a/reproducibility/figures/models/larry_neu_model2/run_info.json b/reproducibility/figures/models/larry_neu_model2/run_info.json index dfddc0fd5..a16405beb 100644 --- a/reproducibility/figures/models/larry_neu_model2/run_info.json +++ b/reproducibility/figures/models/larry_neu_model2/run_info.json @@ -1,12 +1,12 @@ { - "artifact_uri": "mlflow-artifacts:/1a741690552b410eb9c7ba642cf21e2d/4961a3d13fbf4a88891b8cacd8a06a15/artifacts", - "end_time": 1685004658452, + 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1.78805707279348e-11 + "MAE": 0.187225321898073, + "FDR_HMP": 1.24911755134759e-11, + "FDR_sig_frac": 0.978 } \ No newline at end of file diff --git a/reproducibility/figures/models/larry_tips_model2/run_info.json b/reproducibility/figures/models/larry_tips_model2/run_info.json index 3bbe14f1c..3f59ed832 100644 --- a/reproducibility/figures/models/larry_tips_model2/run_info.json +++ b/reproducibility/figures/models/larry_tips_model2/run_info.json @@ -1,12 +1,12 @@ { - "artifact_uri": "mlflow-artifacts:/1a741690552b410eb9c7ba642cf21e2d/a342cb119acf41a59c9963fae8178903/artifacts", - "end_time": 1685006061714, + "artifact_uri": "mlflow-artifacts:/1a741690552b410eb9c7ba642cf21e2d/7a61c818c4bb421abd597829861b7683/artifacts", + "end_time": 1688679075287, "experiment_id": "0", "lifecycle_stage": "active", - "run_id": "a342cb119acf41a59c9963fae8178903", - "run_name": "larry_tips_model2-a342cb1", - "run_uuid": "a342cb119acf41a59c9963fae8178903", - "start_time": 1685004564638, + "run_id": "7a61c818c4bb421abd597829861b7683", + "run_name": "larry_tips_model2-7a61c81", + "run_uuid": "7a61c818c4bb421abd597829861b7683", + "start_time": 1688678408157, "status": "FINISHED", "user_id": "root" } \ No newline at end of file diff --git a/reproducibility/figures/models/pancreas_model1/metrics.json b/reproducibility/figures/models/pancreas_model1/metrics.json index 11dffdd92..22d181791 100644 --- a/reproducibility/figures/models/pancreas_model1/metrics.json +++ b/reproducibility/figures/models/pancreas_model1/metrics.json @@ -1,5 +1,5 @@ { - "MAE": 0.5235231015512266, - "FDR_HMP": 5.346572460713641e-12, - "FDR_sig_frac": 0.995 + "MAE": 0.523523101551227, + "FDR_sig_frac": 0.995, + "FDR_HMP": 5.3465726602852e-12 } \ No newline at end of file diff --git a/reproducibility/figures/models/pancreas_model2/metrics.json b/reproducibility/figures/models/pancreas_model2/metrics.json index ef7578a9f..fc9dd4a75 100644 --- a/reproducibility/figures/models/pancreas_model2/metrics.json +++ b/reproducibility/figures/models/pancreas_model2/metrics.json @@ -1,5 +1,5 @@ { - "MAE": 0.514212858495671, - "FDR_HMP": 3.5427351646428566e-12, - "FDR_sig_frac": 0.993 + "FDR_HMP": 3.54273433808124e-12, + "FDR_sig_frac": 0.993, + "MAE": 0.514212858495671 } \ No newline at end of file diff --git a/reproducibility/figures/models/pancreas_model2/run_info.json b/reproducibility/figures/models/pancreas_model2/run_info.json index 2c903dac3..8f0e92b9c 100644 --- a/reproducibility/figures/models/pancreas_model2/run_info.json +++ b/reproducibility/figures/models/pancreas_model2/run_info.json @@ -1,12 +1,12 @@ { - "artifact_uri": "file:///home/jupyter/pyrovelocity_latest/reproducibility/figures/mlruns/0/29e7ae055847491d9b4ff70ff38c311a/artifacts", - "end_time": 1688492405004, + "artifact_uri": "mlflow-artifacts:/1a741690552b410eb9c7ba642cf21e2d/c8413cad0bc24d559c9770987be398b6/artifacts", + "end_time": 1688676526256, "experiment_id": "0", "lifecycle_stage": "active", - "run_id": 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a/reproducibility/figures/models/pbmc10k_model2/run_info.json b/reproducibility/figures/models/pbmc10k_model2/run_info.json index f1e7b61dc..616553281 100644 --- a/reproducibility/figures/models/pbmc10k_model2/run_info.json +++ b/reproducibility/figures/models/pbmc10k_model2/run_info.json @@ -1,12 +1,12 @@ { - "artifact_uri": "file:///home/jupyter/pyrovelocity/reproducibility/figures/mlruns/0/dea896e704b4425bbe4e70ca6230481f/artifacts", - "end_time": 1685984407273, + "artifact_uri": "mlflow-artifacts:/1a741690552b410eb9c7ba642cf21e2d/4858fd167ee44cd3a0d53811749d4326/artifacts", + "end_time": 1688679736700, "experiment_id": "0", "lifecycle_stage": "active", - "run_id": "dea896e704b4425bbe4e70ca6230481f", - "run_name": "pbmc10k_model2-dea896e", - "run_uuid": "dea896e704b4425bbe4e70ca6230481f", - "start_time": 1685982751921, + "run_id": "4858fd167ee44cd3a0d53811749d4326", + "run_name": "pbmc10k_model2-4858fd1", + "run_uuid": "4858fd167ee44cd3a0d53811749d4326", + "start_time": 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+++ b/reproducibility/figures/models/pbmc68k_model2/metrics.json @@ -1,5 +1,5 @@ { - "MAE": 0.203661303792626, - "FDR_HMP": 1.34094314793785e-11, - "FDR_sig_frac": 0.994 + "FDR_HMP": 2.28329971086234e-11, + "FDR_sig_frac": 0.95, + "MAE": 0.160461369362006 } \ No newline at end of file diff --git a/reproducibility/figures/models/pbmc68k_model2/run_info.json b/reproducibility/figures/models/pbmc68k_model2/run_info.json index 51734c813..c5200978c 100644 --- a/reproducibility/figures/models/pbmc68k_model2/run_info.json +++ b/reproducibility/figures/models/pbmc68k_model2/run_info.json @@ -1,12 +1,12 @@ { - "artifact_uri": "mlflow-artifacts:/1a741690552b410eb9c7ba642cf21e2d/564f766db86745fdabfd90c3d237a03c/artifacts", - "end_time": 1685001870395, + "artifact_uri": "mlflow-artifacts:/1a741690552b410eb9c7ba642cf21e2d/af8b1fe08e994f8986981aba12154c46/artifacts", + "end_time": 1688676980288, "experiment_id": "0", "lifecycle_stage": "active", - "run_id": "564f766db86745fdabfd90c3d237a03c", - 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5b05b21f9..36091c4e4 100644 --- a/reproducibility/figures/models/pons_model2/run_info.json +++ b/reproducibility/figures/models/pons_model2/run_info.json @@ -1,12 +1,12 @@ { - "artifact_uri": "mlflow-artifacts:/1a741690552b410eb9c7ba642cf21e2d/bcc8392d9ff945898adc1d81a5e03a36/artifacts", - "end_time": 1685001048726, + "artifact_uri": "mlflow-artifacts:/1a741690552b410eb9c7ba642cf21e2d/10484db4fb0e4f4aac97db725ccef944/artifacts", + "end_time": 1688676626837, "experiment_id": "0", "lifecycle_stage": "active", - "run_id": "bcc8392d9ff945898adc1d81a5e03a36", - "run_name": "pons_model2-bcc8392", - "run_uuid": "bcc8392d9ff945898adc1d81a5e03a36", - "start_time": 1685000155950, + "run_id": "10484db4fb0e4f4aac97db725ccef944", + "run_name": "pons_model2-10484db", + "run_uuid": "10484db4fb0e4f4aac97db725ccef944", + "start_time": 1688676306994, "status": "FINISHED", "user_id": "root" } \ No newline at end of file diff --git a/reproducibility/figures/models/simulate_medium_model2/metrics.json b/reproducibility/figures/models/simulate_medium_model2/metrics.json index 0f6c8d124..30f34017a 100644 --- a/reproducibility/figures/models/simulate_medium_model2/metrics.json +++ b/reproducibility/figures/models/simulate_medium_model2/metrics.json @@ -1,5 +1,5 @@ { - "MAE": 7.34875561666667, "FDR_sig_frac": 0.144, + "MAE": 7.34875561666667, "FDR_HMP": 3.46468778402507e-09 } \ No newline at end of file diff --git a/reproducibility/figures/reports/pancreas_model1/.gitignore b/reproducibility/figures/reports/pancreas_model1/.gitignore index acf3635c2..92fce126a 100644 --- a/reproducibility/figures/reports/pancreas_model1/.gitignore +++ b/reproducibility/figures/reports/pancreas_model1/.gitignore @@ -2,3 +2,4 @@ /*.tif /*.pdf /*.png +/posterior_phase_portraits diff --git a/reproducibility/figures/reports/pancreas_model2/.gitignore b/reproducibility/figures/reports/pancreas_model2/.gitignore index acf3635c2..92fce126a 100644 --- a/reproducibility/figures/reports/pancreas_model2/.gitignore +++ b/reproducibility/figures/reports/pancreas_model2/.gitignore @@ -2,3 +2,4 @@ /*.tif /*.pdf /*.png +/posterior_phase_portraits