Reproducibility news

This repository contains recent news about reproducibility that were shown on reproduciblescience.org. The raw RSS feed is here.

Please, do not hesitate to provide news about your own work by opening a Pull Request here or by contacting us. A contributing guide is available to guide you through the process.

RSS Format

The feed is generated from a YAML file, news.yaml, that you can edit here. The format is as follow:

---
title: |
  Some meaningful title here (will be tweeted out)
link: link to the original article or publication
date: 2017-02-21 00:00:00
tags: [reproducibility talk]
description: |
  Multi-line description here. Will show up in RSS readers.
  Like the title field, be careful not to forget the indentation.

---
title: |
  Other entry
link: other link
date: 2016-01-12 00:00:00
tags: [data science, news article]
description: |
  Another entry.

RSS Tags

Tag	Content
case studies	reproducibility case studies
data science	everything related to data science
news article	articles published by scientific bodies
noWorkflow	everything related to noWorkflow
open access	everything related to open access publishing of data and papers
popular news	articles published by popular reporting organizations (NY times, etc.)
replication study	studies that seek to replicate scientific findings
reproducibility bibliography	bibliographies having to do with reproducibility
reproducibility conference	conferences that want reproducible papers/posters accepted AND conferences that discuss reproducibility
reproducibility guidelines	guidelines for reproducibility
reproducibility infrastructure	reports/articles/papers on building reproducibility infrastructure
reproducibility report	reports by governing bodies on reproducibility of a field's work
reproducibility study	studies that seek to reproduce research
reproducibility talk	talks and presentations about reproducibility
reproducible journal	journals that work towards reproducibility efforts (requiring submissions to be reproducible, etc.
reproducible paper	papers that are considered reproducible
ReproZip	everything related to ReproZip
research guide	library guides for reproducibility
retraction	report of a paper being retracted
VisTrails	everything related to VisTrails

List of language-specific reproducibility tools

I'm trying to compile a list of tools that allow reproducibility, or good practices for specific ecosystems for reproducible builds/environments.

Python
- virtualenv/pip are the preferred way to install packages; PyPI is the repository (all of this maintained by PyPA)
  - pip has a concept of "lockfiles": pip freeze writes down exact versions, pip install -r allows installing those (usually in a virtualenv)
- pex is a tool that build single-file Python environments, that can optionally be portable. A pex file is a ZIP file with the requested packages and a runtime that setup the environment to use those when you run the file (and can contain binary extensions, possibly for multiple platforms).
R
- packrat
Ruby
- Ruby packages are called gems, and are managed with the gem command-line tool
  - Seems to have a way of locking
- RVM allows one to have multiple Ruby environments and Ruby versions on her machine, and associate them to specific projects
Rust
- rustup allows one to install whichever version(s) of the tools they want, and associate them to specific projects
- Cargo and crates.io are the preferred build system and package repository for Rust
  - Cargo always uses a lockfile. Versions following semver recommendations are enforced. Git versioning is integrated, and crates.io is built on GitHub.
C/C++
- Lots of build systems (Makefiles, autotools and CMake are the most common)
- Vendoring (& submodules) allow for reproducibility
  - TODO: describe Daniele's setup
Other tools
- Conda is a generic package manager. Usually used for Python, but is good for other things (notably R); distributed binary packages
  - Also see the conda-forge effort

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