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Recent Releases of book

book - 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.

With thanks to many old and new contributors: @mih @christian-monch @asmacdo @mslw @jsheunis @Remi-Gau @yarikoptic, happy Valentines day, and happy International Love Data Week!

- Python
Published by adswa about 3 years ago

book - 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), and thus delayed on the handbook side.

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.

Thank you to everyone contributing :heart:

- Python
Published by adswa about 3 years ago

book - Spring cleaning!

Handbook release matching the release of DataLad v0.16.0. Among the most notable changes, this release contains adjustments to API changes introduced in DataLad 0.16 as well as documentation on newly introduced commands and features. In addition, it adds additional content on contributing, writing DataLad extensions, and publishing to s3 buckets.

The changelog below is autogenerated. Please see this repos CHANGELOG for an executive summary.

What's Changed

  • docs: add mslw as a contributor for review by @allcontributors in https://github.com/datalad-handbook/book/pull/763
  • Refactor the chapter on publishing by @adswa in https://github.com/datalad-handbook/book/pull/762
  • Refactor the chapter on publishing by @adswa in https://github.com/datalad-handbook/book/pull/761
  • BF: Fix link by @adswa in https://github.com/datalad-handbook/book/pull/764
  • [ENH] replace issue template with the new "form" format by @Remi-Gau in https://github.com/datalad-handbook/book/pull/768
  • docs: add Remi-Gau as a contributor for infra by @allcontributors in https://github.com/datalad-handbook/book/pull/769
  • [FIX] update css unordered list in important note when viewing by @Remi-Gau in https://github.com/datalad-handbook/book/pull/770
  • docs: add Remi-Gau as a contributor for code, design by @allcontributors in https://github.com/datalad-handbook/book/pull/772
  • Fix two minor typos by @eort in https://github.com/datalad-handbook/book/pull/775
  • add author to zenodo by @eort in https://github.com/datalad-handbook/book/pull/777
  • docs: add eort as a contributor for bug by @allcontributors in https://github.com/datalad-handbook/book/pull/776
  • CI: Fix readthedocs build by @adswa in https://github.com/datalad-handbook/book/pull/774
  • Fix typo in section Advanced 1.1 by @eort in https://github.com/datalad-handbook/book/pull/778
  • Fix a typo in a command by @mslw in https://github.com/datalad-handbook/book/pull/780
  • docs: add mslw as a contributor for bug by @allcontributors in https://github.com/datalad-handbook/book/pull/781
  • Computing on clusters: Update chapters with a link to the fairly big workflow by @adswa in https://github.com/datalad-handbook/book/pull/783
  • Add a note on how to currently glob for several levels of directories by @adswa in https://github.com/datalad-handbook/book/pull/785
  • docs: add AKSoo as a contributor for review by @allcontributors in https://github.com/datalad-handbook/book/pull/786
  • New chapter on contributing to datalad by @adswa in https://github.com/datalad-handbook/book/pull/782
  • Install: recommend git annex filter-process on windows installations by @adswa in https://github.com/datalad-handbook/book/pull/791
  • Maintenance - Speed up sections with imagenette dataset by @adswa in https://github.com/datalad-handbook/book/pull/790
  • Mention new recursive glob option in chapter on run by @adswa in https://github.com/datalad-handbook/book/pull/792
  • Update Gin as data source workflow by @mslw in https://github.com/datalad-handbook/book/pull/793
  • docs: add mslw as a contributor for content by @allcontributors in https://github.com/datalad-handbook/book/pull/795
  • Add a section on good practices for creating interoperable file names by @adswa in https://github.com/datalad-handbook/book/pull/794
  • Update filenaming.rst - minor typo and url fixes by @mslw in https://github.com/datalad-handbook/book/pull/796
  • docs: add Myrskyta as a contributor for bug by @allcontributors in https://github.com/datalad-handbook/book/pull/798
  • BF: Makefile - replace leading spaces with tabs by @yarikoptic in https://github.com/datalad-handbook/book/pull/799
  • fix typo by @tguiot in https://github.com/datalad-handbook/book/pull/801
  • docs: add tguiot as a contributor for bug by @allcontributors in https://github.com/datalad-handbook/book/pull/802
  • Workflow: Update package index by @adswa in https://github.com/datalad-handbook/book/pull/804
  • Link fixes for failing link check by @adswa in https://github.com/datalad-handbook/book/pull/803
  • Revert "Links: Remove link to old benchmarks on previous website" by @adswa in https://github.com/datalad-handbook/book/pull/807
  • [ENH] Add new 'Create your own extension' section by @jsheunis in https://github.com/datalad-handbook/book/pull/812
  • New content: Mention credential integration with Git by @adswa in https://github.com/datalad-handbook/book/pull/814
  • Fix/clarify passing git init options though create to change the default branch by @adswa in https://github.com/datalad-handbook/book/pull/815
  • DGPA workshop contents by @adswa in https://github.com/datalad-handbook/book/pull/816
  • fix wrong figure name by @jhpb7 in https://github.com/datalad-handbook/book/pull/820
  • docs: add jhpb7 as a contributor for bug by @allcontributors in https://github.com/datalad-handbook/book/pull/823
  • [ENH] Fix various typos by @jsheunis in https://github.com/datalad-handbook/book/pull/809
  • Update dgpa.rst by @eltociear in https://github.com/datalad-handbook/book/pull/825
  • docs: add eltociear as a contributor for bug by @allcontributors in https://github.com/datalad-handbook/book/pull/826
  • Release-fixes for the chapter on RIA stores by @adswa in https://github.com/datalad-handbook/book/pull/810
  • Remove version pinning of Sphinx by @adswa in https://github.com/datalad-handbook/book/pull/827

New Contributors

  • @eort made their first contribution in https://github.com/datalad-handbook/book/pull/775
  • @mslw made their first contribution in https://github.com/datalad-handbook/book/pull/780
  • @tguiot made their first contribution in https://github.com/datalad-handbook/book/pull/801
  • @jhpb7 made their first contribution in https://github.com/datalad-handbook/book/pull/820
  • @eltociear made their first contribution in https://github.com/datalad-handbook/book/pull/825

Full Changelog: https://github.com/datalad-handbook/book/compare/v0.15...v0.16

- Python
Published by adswa almost 4 years ago

book - LaTeX improvements

This release comes 2 months delayed, but belongs to the DataLad 0.15.0 release from September 2021. The changelog is autogenerated, and hopefully does not contain too many errors. The majority of work was maintenance, and improvements of the LaTeX backbone of the handbook (huge thanks to @mih for this), rendering the PDF version of the handbook much more beautiful and towards an actually printable book.

What's Changed

  • riastores: Avoid deprecated --no-storage-sibling by @kyleam in https://github.com/datalad-handbook/book/pull/641
  • Minor changes re code-blocks in PDF by @mih in https://github.com/datalad-handbook/book/pull/647
  • Shorten PDF for printed book by @adswa in https://github.com/datalad-handbook/book/pull/648
  • Even more adjustments for a printed book by @adswa in https://github.com/datalad-handbook/book/pull/650
  • docs: add Remi-Gau as a contributor by @allcontributors in https://github.com/datalad-handbook/book/pull/653
  • Python installation instructions by @adswa in https://github.com/datalad-handbook/book/pull/651
  • Help: Note about asyncio errors and workaround for Jupyter by @adswa in https://github.com/datalad-handbook/book/pull/646
  • More fancy boxes in PDF by @mih in https://github.com/datalad-handbook/book/pull/655
  • Further streamlining boxes by @mih in https://github.com/datalad-handbook/book/pull/656
  • Numbered, listable and referencable boxes by @mih in https://github.com/datalad-handbook/book/pull/657
  • Optional float mode for PDF boxes by @mih in https://github.com/datalad-handbook/book/pull/658
  • No vertical lines in a table by @mih in https://github.com/datalad-handbook/book/pull/659
  • Bettertables by @mih in https://github.com/datalad-handbook/book/pull/660
  • Relax positioning of some boxes, where appropriate by @adswa in https://github.com/datalad-handbook/book/pull/661
  • New boxtype importantnote by @mih in https://github.com/datalad-handbook/book/pull/662
  • Let figures and tables float. by @mih in https://github.com/datalad-handbook/book/pull/663
  • Minor change to align title page with print cover by @mih in https://github.com/datalad-handbook/book/pull/665
  • Logo update by @mih in https://github.com/datalad-handbook/book/pull/667
  • Disentangle too long and nested Findoutmore's by @adswa in https://github.com/datalad-handbook/book/pull/666
  • note -> importantnote by @mih in https://github.com/datalad-handbook/book/pull/664
  • Tune footnotes by @mih in https://github.com/datalad-handbook/book/pull/669
  • TOC fixes by @mih in https://github.com/datalad-handbook/book/pull/670
  • Prevent multiple definition of useless labels by @mih in https://github.com/datalad-handbook/book/pull/671
  • New cover art for the Intro part by @mih in https://github.com/datalad-handbook/book/pull/672
  • Install: Rework macOS installation by @adswa in https://github.com/datalad-handbook/book/pull/675
  • docs: add tamaracha as a contributor by @allcontributors in https://github.com/datalad-handbook/book/pull/676
  • In-text references of find-out-mores by @mih in https://github.com/datalad-handbook/book/pull/678
  • windowsworkarounds -> windows-wit by @mih in https://github.com/datalad-handbook/book/pull/679
  • Adjustments for a printed PDF that work also in html by @adswa in https://github.com/datalad-handbook/book/pull/680
  • Refurbish installation instructions by @mih in https://github.com/datalad-handbook/book/pull/682
  • BF: Fix a mixed up redirection couple by @adswa in https://github.com/datalad-handbook/book/pull/683
  • Beautify the PDF further by @mih in https://github.com/datalad-handbook/book/pull/684
  • Make term references accessible in the printed handbook by @mih in https://github.com/datalad-handbook/book/pull/685
  • Small update of the extension list by @mih in https://github.com/datalad-handbook/book/pull/686
  • Remove quotes from config file displays by @bpoldrack in https://github.com/datalad-handbook/book/pull/689
  • On cloning openneuro/openfmri data from the datalad superdataset by @adswa in https://github.com/datalad-handbook/book/pull/690
  • Print adjustment chapter 3 onwards by @adswa in https://github.com/datalad-handbook/book/pull/691
  • Remove forgotten Windows-workarounds by @adswa in https://github.com/datalad-handbook/book/pull/692
  • Add a rough sketch of a DataLad intro for Repronim workshop in Yale by @adswa in https://github.com/datalad-handbook/book/pull/693
  • Make the index more comprehensive by @mih in https://github.com/datalad-handbook/book/pull/694
  • Add redirector for ?cheatsheet by @yarikoptic in https://github.com/datalad-handbook/book/pull/701
  • Adds a Github-actions based CI setup by @adswa in https://github.com/datalad-handbook/book/pull/703
  • add redirects for chapters mentioned in ukb manuscript by @adswa in https://github.com/datalad-handbook/book/pull/702
  • Another sweep for printing by @adswa in https://github.com/datalad-handbook/book/pull/704
  • Fix typo by @mih in https://github.com/datalad-handbook/book/pull/705
  • Fix ref tag to close #709 by @jsheunis in https://github.com/datalad-handbook/book/pull/710
  • docs: add jsheunis as a contributor by @allcontributors in https://github.com/datalad-handbook/book/pull/711
  • GIN: On using Gin as an autoenabled special remote by @adswa in https://github.com/datalad-handbook/book/pull/707
  • Mention --assume-ready of datalad-run by @adswa in https://github.com/datalad-handbook/book/pull/699
  • ENH: Relative links in sidebar by @effigies in https://github.com/datalad-handbook/book/pull/718
  • ENH: Use Zenodo record that resolves to latest version by @effigies in https://github.com/datalad-handbook/book/pull/717
  • Add FAQ on GitHub displaying git-annex as the default by @adswa in https://github.com/datalad-handbook/book/pull/722
  • docs: add jsheunis as a contributor for content, example by @allcontributors in https://github.com/datalad-handbook/book/pull/726
  • Windows weird behavior with file extensions by @adswa in https://github.com/datalad-handbook/book/pull/725
  • Mention --dry-run by @adswa in https://github.com/datalad-handbook/book/pull/724
  • help: On line endings and autocrfl true configurations for windows users by @adswa in https://github.com/datalad-handbook/book/pull/723
  • Add walkthrough for using S3 as a special remote by @jsheunis in https://github.com/datalad-handbook/book/pull/721
  • docs: add cni-md as a contributor for bug by @allcontributors in https://github.com/datalad-handbook/book/pull/728
  • Fix left-over exit code by @adswa in https://github.com/datalad-handbook/book/pull/727
  • Fix inconsistent description of push behavior by @AKSoo in https://github.com/datalad-handbook/book/pull/734
  • docs: add AKSoo as a contributor for bug, content by @allcontributors in https://github.com/datalad-handbook/book/pull/735
  • Fix typos using codespell by @sappelhoff in https://github.com/datalad-handbook/book/pull/732
  • docs: add sappelhoff as a contributor for bug by @allcontributors in https://github.com/datalad-handbook/book/pull/737
  • [ENH] add sphinx-copybutton extension by @sappelhoff in https://github.com/datalad-handbook/book/pull/615
  • add Stephan as contributor to zenodo file by @jsheunis in https://github.com/datalad-handbook/book/pull/739
  • Fix errors in 9.3 back and forth in time by @AKSoo in https://github.com/datalad-handbook/book/pull/740
  • MNT: Update outputs to 0.14.4 by @adswa in https://github.com/datalad-handbook/book/pull/742
  • Add a monthly cron job to check links in the handbook by @adswa in https://github.com/datalad-handbook/book/pull/743
  • Fix broken or permanently redirected links, as discovered by Sphinx's make linkcheck by @adswa in https://github.com/datalad-handbook/book/pull/744
  • Update 101-115-symlinks.rst by @lilikapa in https://github.com/datalad-handbook/book/pull/747
  • "ultimatively" => "ultimately" by @arokem in https://github.com/datalad-handbook/book/pull/749
  • Fixes typo by @arokem in https://github.com/datalad-handbook/book/pull/750
  • This is the name of the file that was created earlier on. by @arokem in https://github.com/datalad-handbook/book/pull/751
  • "temper" => "tamper" by @arokem in https://github.com/datalad-handbook/book/pull/752
  • FIX: GIN siblings - fix typo in code and note that --url should not end with .git by @oesteban in https://github.com/datalad-handbook/book/pull/753
  • MAINT: Add @oesteban to zenodo record by @oesteban in https://github.com/datalad-handbook/book/pull/755
  • docs: add oesteban as a contributor for data, data, data, bug by @allcontributors in https://github.com/datalad-handbook/book/pull/754
  • MNT: Fix link to git-annex docs on GitLab, mention deprecation by @adswa in https://github.com/datalad-handbook/book/pull/756
  • Fixlinks by @adswa in https://github.com/datalad-handbook/book/pull/757
  • Numbered boxes and references by @mih in https://github.com/datalad-handbook/book/pull/759

New Contributors

  • @jsheunis made their first contribution in https://github.com/datalad-handbook/book/pull/710
  • @AKSoo made their first contribution in https://github.com/datalad-handbook/book/pull/734
  • @oesteban made their first contribution in https://github.com/datalad-handbook/book/pull/753

Full Changelog: https://github.com/datalad-handbook/book/compare/v.14.0...v0.15

- Python
Published by adswa over 4 years ago

book - We're getting usable on Windows!

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

- Python
Published by adswa about 5 years ago

book - DataLad Handbook v0.13

For zenodo archival

- Python
Published by adswa over 5 years ago

book - 0.13 Release for DataLad 0.13

This handbook release matches today's DataLad 0.13 release.

With contributions from Dorian Pustina, Sarah Oliveira, Tristan Glatard, Hamzah Hamid Baagil, Giulia Ippoliti, Yaroslav Halchenko, Alex Waite, Dorien Huijser, 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

- Python
Published by adswa over 5 years ago

book - Zenodo archival of v0.12.0

This marks the ZENODO archival of The DataLad Handbook v0.12.0

- Python
Published by adswa about 6 years ago

book - v0.12 (Jan. 11 2019) -- 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)

- Python
Published by adswa about 6 years ago