Top 8 reproducible-science Open-Source Projects

Sacred

6 4,157 3.5 Python

Sacred is a tool to help you configure, organize, log and reproduce experiments developed at IDSIA.

Project mention: Sacred VS cascade - a user suggested alternative | libhunt.com/r/sacred | 2023-12-05

nextflow

9 2,538 9.7 Groovy

A DSL for data-driven computational pipelines

Project mention: Nextflow: Data-Driven Computational Pipelines | news.ycombinator.com | 2023-08-10

> It's been a while since you can rerun/resume Nextflow pipelines
Yes, you can resume, but you need your whole upstream DAG to be present. Snakemake can rerun a job when only the dependencies of that job are present, which allows to neatly manage the disk usage, or archive an intermediate state of a project and rerun things from there.
> and yes, you can have dry runs in Nextflow
You have stubs, which really isn't the same thing.
> I have no idea what you're referring to with the 'arbitrary limit of 1000 parallel jobs' though
I was referring to this issue: https://github.com/nextflow-io/nextflow/issues/1871. Except, the discussion doesn't give the issue a full justice. Nextflow spans each job in a separate thread, and when it tries to span 1000+ condor jobs it die with a cryptic error message. The option of -Dnxf.pool.type=sync and -Dnxf.pool.maxThreads=N prevents the ability to resume and attempts to rerun the pipeline.
> As for deleting temporary files, there are features that allow you to do a few things related to that, and other features being implemented.
There are some hacks for this - but nothing I would feel safe to integrate into a production tool. They are implementing something - you're right - and it's been the case for several years now, so we'll see.
Snakemake has all that out of the box.

InfluxDB

www.influxdata.com sponsored

Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.
singularity

6 2,495 0.0 Go

Singularity has been renamed to Apptainer as part of us moving the project to the Linux Foundation. This repo has been persisted as a snapshot right before the changes.
wdl

1 725 6.4

Workflow Description Language - Specification and Implementations (by openwdl)

Project mention: Announcing WDL 1.1.1 | dev.to | 2023-12-06

The OpenWDL community is pleased to announce the release of Workflow Description Language (WDL) 1.1.1! This post highlights the most important changes in this release.

hydra-zen

1 281 9.4 Python

Create powerful Hydra applications without the yaml files and boilerplate code.
itk-wasm

5 179 9.8 Python

High performance spatial analysis in a web browser, Node.js, and across programming languages and hardware architectures
shournal

5 159 7.1 C++

Log shell-commands and used files. Snapshot executed scripts. Fully automatic.
WorkOS

workos.com sponsored

The modern identity platform for B2B SaaS. The APIs are flexible and easy-to-use, supporting authentication, user identity, and complex enterprise features like SSO and SCIM provisioning.
memorization

1 5 10.0 Python

Code for "On Memorization in Probabilistic Deep Generative Models"

NOTE: The open source projects on this list are ordered by number of github stars. The number of mentions indicates repo mentiontions in the last 12 Months or since we started tracking (Dec 2020).