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CHANGELOG.md

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Changelog

All notable changes to this project between releases will be documented in this file.

v0.18 (February 14 2023) -- Handbook love

A handbook release matching (delayed) the release of DataLad v0.18.0. This release contains notable changes resulting from a Handbook hackathon in December 2022. It also increases the required version of DataLad to 0.17

Refactoring or deletions

All over the handbook, version notes or information relating to datalad versions lower than 0.17 were removed (#905)

Additions

  • A new standalone chapter about datalad extensions was added, and sections on datalad-catalog (#917), datalad-metalad (#930), and datalad-gooey were included.
  • A new standalone chapter about datalad extensions was added, and sections on datalad-catalog (#917), datalad-metalad (#930), and datalad-gooey were included.

Introduction

Basics

  • The Cheatsheet was updated with modern commands (#912)

  • Advanced

Usecases

  • A new use case about encrypted workflows is now part of the handbook (#895)

Miscellaneous additions

  • The Makefile in the source repository received a more intuitive and fine-grained structure (#901)
  • The handbook has gained an Appveyor configuration that allows building the entire Basis and Beyond Basics parts from scratch, and allows an export of generated code snippets. This makes builds on local machines obsolete for contributors that don't want to go through this trouble (#908)
  • the handbook now has a tool to report readthedocs metrics for authenticated and authorized users (#902)

v0.17 (December 20 2022) -- Better late than never

Handbook release matching the release of DataLad v0.17.0, which was for the most part only an internal change to a different testing framework (pytest instead of nose)

It includes contributions the new contributors @Arshitha, @ajveltri22, @complexbrains, @jkosciessa, @candleindark, and @asmacdo, as well as contributions from established contributors @mslw, @sappelhoff, @kimsin98, @adswa, @yarikoptic.

Refactoring or deletions

Additions

  • A new walkthrough for the neurohackademy was added (#852)

    Introduction

  • The installation instructions were updated for Windows (#872)(#868), conda (#869), and Mac (#875)(#859)(#846)

Basics

  • The midterm project scripts was improved and made functional again (#854), (#853)

  • The GitLFS section now mentions a publication dependency for automation (#842)

    Advanced

  • The alias parameter of create-sibling-ria is now mentioned ([#855][])

Usecases

Miscellaneous additions

  • The JS-based redirection of the handbook now works around an unintentional prefix-redirection glitch of readthedocs (#880)
  • The GitHub repository gained a codespell workflow (#892)

v0.16 (April 13 2022) -- Spring cleaning

Handbook release matching the release of DataLad v0.16.0. This release contains a number of updates for respective changes in DataLad 0.16's API, including the overhaul of existing commands, reimplementations of commands, and additional commands.

It includes contributions the new contributors @eort, @mslw, @tguiot, @jhpb7 and @eltociear, as well as contributions from established contributors @jsheunis, @mih, @adswa, @yarikoptic, and @Remi-Gau.

Refactoring or deletions

Additions

Introduction

  • Installation instructions on Windows now recommend git-annex'es filter-process configuration for performance improvements ([#791][])

Basics

  • The chapter on publishing datasets was overhauled and now includes a general overview of publishing routines and hosting service differences. ([#762][])
  • Content on datalad run now mentions its superglob abilities ([#692][]) and how to glob across directories hierarchies with earlier datalad versions ([#785][])
  • A few fixes and improvements to the section on publishing datasets to Gin ([#793][])

Advanced

  • The enki walkthrough links the FAIRly big paper and tutorial as an improved alternative ([#783][])
  • A new chapter contains a section on contributing to DataLad and DataLad's design docs ([#782][])
  • A new section guides through the process of creating your own extensions ([#812][])
  • The section on configuring additional data providers now includes content on DataLad 0.16's credential integration with Git ([#814][])

Usecases

  • A new general section on how to create interoperable file names was added ([#796][])

Miscellaneous additions

  • The GitHub project of the handbook now uses templates for easier issue generation. ([#768][])
  • A number of CSS improvements fix the rendering of bullet points ([#770][])
  • The ML use case was minified to speed up builds ([#790][])
  • A new code list for the DGPA workshop was added ([#820][])

v0.15 (November 25 2021) -- LaTeX improvements

Handbook release matching the release of DataLad v0.15.0. This release contains major improvements of the handbook's LaTeX backbone.

With thanks to the new contributors @oesteban, @AKSoo, and @jsheunis, and established contributors @eknahm, @kyleam, @RemiGau, @bpoldrack, @yarikoptic, @effigies @sappelhof, @lilikapa, @arokem

Refactoring or deletions

  • The deprecated --no-storage-sibling parameter was removed from the RIA store chapter (#641)

Additions

Introduction

  • The installation instructions were updated for Python (#651) and Mac (#675), and overall improved (#682)

Basics

  • The help section was extended with a note on asyncio-related errors in Jupyter (#646) and information on line-endings and and autocrfl true configurations for windows users (#723)
  • The section on publishing with Gin was amended with content on using Gin as an autoenabled special remote (#707)
  • The chapter on run now mentions its --assume-ready and `--dry-run parameter ([#699][])`, (#724)
  • There now is a FAQ on how to fix GitHub displaying the git-annex branch as the default (#722)
  • A new chapter on Publishing to S3 walks through publishing to a public S3 bucket (#721)

Miscellaneous additions

  • A wide range of improvements in the LaTeX rendering of the handbook (#647), (#648), (#650), (#655), (#656), (#657), (#658), (#658), (#660), (#661), (#662), (#663), (#665), (#666), (#679), (#684), (#685), (#694), (#759)
  • A number of textual changes to improve the PDF rendering of the handbook ([#48][]), (#669), (#670), (#671), (#678), (#680), (#691), (#704)
  • New artwork (#667), (#672),
  • A new code list for a Repronim Workshop in Yale (#693)
  • Continuous integration was migrated to GitHub actions (#703)
  • The Zenodo record now resolves to the latest version (#717)
  • The code blocks now have copy-buttons (#615)
  • A monthly linkchecker was implemented to better catch unresolving URLs (#743)

v0.14 (January XX 2021) -- slightly less dreadfulness for Windows users

Handbook release matching the release of DataLad v0.14.0. Like the software release, this handbook release improves the situation on/for Windows systems starkly from what we had before. With contributions from Tristan Glatard, Ariel Rokem, Remi Gau, Surya Teja Togaru, Judith Bomba, Konrad Hinsen, Wu Jianxiao, Małgorzata Wierzba, Stefan Appelhoff, and Michael Joseph -- thank you!

Refactoring or deletions

  • Overhaul Windows installation instructions (#588)
  • Adjustments for GitHub's user-password deprecation (#626), (#592)

Additions

Introduction

  • git-annex installations with custom built git-annex with MagicMime support (#603)
  • A quick-start guide for OpenNeuro (#585)

Basics

  • Disambiguation on configurations (#627) with thanks to John Lee for the issue at datalad
  • A new section on how to debug and troubleshoot problems - with thanks to Tristan Glatard for the idea and contributions ([#538][])

Advanced

  • A chapter on large-scale fair processing with parallel datalad-run calls (#591)
  • A new section on configuring subdataset clone candidates and their priority (#548)
  • A new chapter/section that compares the tool DVC to DataLad (#569)

Usecases

  • Addition of a machine-learning application with DataLad (#581)
  • Addition on Human Connectome Project (HCP) AWS credentials (thanks to Michael Joseph) (#622)
  • Addition of a hands-on tutorial for reproducible papers (#608), with thanks to Małgorzata Wierzba for feedback and contributions

Miscellaneous additions

  • A variety of code lists and introductions (#630), (#613)
  • A few new permalinks: git-lfs (#624), MPIB intro (#614)
  • A new expandable section "Windows workaround" for Windows-specific notes and explanations(#532)
  • Large amount of Windows adjustments in the Basics (#588)
  • FAQs on copying locked files out of datasets, and on caveats with the BIDS validator - with thanks to Remi Gau (#570), (#562)
  • The handbook's GitHub repository received a welcome bot (with thanks to The Turing Way project for CC-BY illustrations), and a "Discussions" Forum
  • The handbook's frontpage links to the cheat sheet with a nice illustration (#578)

v0.13 (June 23rd 2020) -- Towards a tetralogy!

Handbook release matching the release of DataLad v0.13.0 With contributions from Dorian Pustina, Sarah Oliveira, Tristan Glatard, Hamzah Hamid Baagil, Giulia Ippoliti, Yaroslav Halchenko, Alex Waite, and Michael Hanke -- thank you!

Refactoring or deletions

  • RF: Replace datalad publish with datalad push (#412)
  • RF: The Basics part was split into a Basics and Advanced part (#450). The chapters "Advanced Options" and "Go big or go home" have been moved/added there.
  • Installation instructions for Windows subsystem for linux have been removed (#397)

Additions

Introduction

  • Installation instructions for rpm-based Linux distributions were added (#435)
  • A "user-type" overview now serves as a guide through the handbook (#403)

Basics

  • A stand-alone section on datalad push summarizes all previous publishing-related information (#417)
  • A section for collecting gists (nifty code snippets for various tasks) is added to the chapter on help(#445)
  • datalad drop is introduced in the first chapter (#463)
  • Gin's new feature of anonymous read-only access to datasets is now mentioned in the chapter on using third party infrastructure(#456)
  • The section on getting help started to collect and explain common warnings and error messages (#418)

Advanced

Miscellaneous additions

  • Introduction of a system to improve intersphinx linkage between the handbook and the technical docs & docstrings of DataLad (#377)
  • Various improvements to the PDF version of the handbook (#367)
  • Major toctree restructuring: Chapter-wise toctrees (#367), robustified URLs (#457)
  • Addition of short, README-ready explanations of DataLad datasets for published projects (#370)
  • Redirections are now possible, using a ?<label> element after handbook.datalad.org/r.html (#518)
  • (Almost) complete correspondence between HTML and PDF part, chapter, and section labeling (#500)

v0.12 (Jan. 11 2020) -- A good weekend read

Beta stage release matching the release of datalad v0.12.0.

Refactoring or deletions

  • RF: Replace datalad install with datalad clone (#326)

Additions

Introduction

  • High-level, one page description "What you really need to know" about DataLad (#295)

Basics

  • The DataLad Cheatsheet (#157)

  • Chapter "One step further" with content on advanced dataset nesting (#226) and computational reproducibility with the datalad-containers extension (#242)

  • Chapter "Further options" with content on DataLad's result hooks (#304), an overview on DataLad's extensions (#242), and how to keep clean datasets despite untracked contents (#84)

  • Chapter "Third party infrastructure" on how to use various hosting services to share DataLad datasets, with concrete demonstrations/step-by-step instructions of sharing via Dropbox and GIN (#111)

  • Section "Frequently Asked Questions" (#239)

  • Section "Back and forth in time" on interacting with dataset history with Git tools/commands (#106)

  • Section "YODA-compliant data analysis project" with an example data science project (including Python API) (#226)

  • Include datalad download-url in first chapter to emphasize provenance capture abilities of DataLad (#294)

Usecases

  • Use case "An automatically reproducible analysis of public neuroimaging data" (#205)

  • Use case "Building a scalable data storage for scientific computing" (#223)

Miscellaneous additions

  • Adjust contents to autorunrecord update to record a flexible set of code snippets in "casts" for live demonstrations. Add cast associations for existing contents with speakernotes (#219)

  • Additional book segment "Code lists from chapters" with code lists used for workshops (#273

  • Illustrations from undraw.co (starting in #329)

  • Tagged "showroom" repositories with branches reflecting dataset states at different book sections (#341)

v0.1 (Oct. 10 2019) -- A lazy afternoon read

Alpha stage release with handbook content covering most of the core commands.

Additions

Basics

  • Chapter "DataLad datasets" on local version control (create, save, status, install)

  • Chapter "DataLad, Run!" on reproducible execution with datalad run and datalad rerun

  • Chapter "Under the hood: git-annex" on the dataset annex and the text2git procedure

  • Chapter "Collaboration" on sharing datasets (on the same computational infrastructure), siblings, and updating.

  • Chapter "Tuning datasets to your needs" on various configurations

  • Chapter "Help yourself" on common file system operations and on help.

  • Chapter "Make the most out of datasets" about the YODA principles

Usecases

  • Use case "A typical collaborative data management workflow"

  • Use case "Basic provenance tracking"

  • Use case "Basic provenance tracking"

  • Use case "Student supervision in a research project"