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openproblems.bio unreleased

MAJOR CHANGES

  • Migrated the result scaling from R to JavaScript to allow dynamically updating the results (PR #332).

MINOR CHANGES

  • Improve Equations visualisation (PR #329).

  • Fix task method and metric descriptions (PR #336).

  • Update base images documentation (PR #342).

  • Add foundation models benchmark page (PR #354).

  • Add url to benchmark datasets to dataset page (PR #362).

  • Change "n x m" to "n cells × m genes" on dataset info (PR #362).

BUG FIXES

  • Fix error in summary figure when not all method info ids are present in the results (PR #330).

  • Fix "used in" section in dataset pages (PR #362).

openproblems.bio v2.3.6

NEW CONTENT

  • Add an event page for the Weekly wednesday work meeting (PR #299).

  • Add Advanced_topics pages to documentation (PR #300).

  • Add your first contribution page to documentation (PR #300).

  • Add Datasets pages (PR #303).

  • Add nextflow used resources to benchmark results (PR #309).

  • Add git branch naming convention to documentation (PR #313).

NEW FUNCTIONALITY

  • Add glossary function to pages and a glossary page (PR #300).

MAJOR CHANGES

  • Update fundamentals pages (PR #300).

  • Refactor the reference view (PR #300).

  • Update reference documentation (PR #300).

  • Update Neurips2021 datasets categories (PR #323).

MINOR CHANGES

  • Several infrastructure updates (PR #298):

    • Update R packages
    • Remove Python from list of dependencies
    • Update Quarto
    • Fixes to styling
    • Simplify footer
    • Update openproblems-v2 submodule

  • Updates to the way tasks are rendered (PR #296):

    • Show task motivation, if present.
    • Allow multiple citations for datasets, methods, and metrics.
    • Render dataset name instead of dataset id in figures and tables.
    • Change the way bibliographic references are rendered.

  • Update documentation (PR #300).

  • Update events pages (PR #300).

  • update results pages (PR #300).

  • Update styles (PR #300).

  • Relocate Style files to styles directory (PR #300).

  • Update results dataset_info.json file (PR #306).

  • Add benchmark statistics (PR #308).

  • Update benchmark listing cards (PR #308).

  • Update card styling (PR #308).

  • Update neurips 2021 datasets data with new dataset_id (PR #315).

  • Update to funkyheatmapjs v0.2.5 (PR #316).

  • Add CSS to fix not active tab color in dark mode (PR #319).

  • Improvements to the documentation (PR #317).

    • Refer to task_info.yml in multiple places.
    • Use glossary to help users find information more quickly.

  • Remove custom css in events.css (PR #318).

BUG FIXES

  • Updated the openproblems-v2 submodule (PR #295). This fixes a deprecation error due to an update in ruamel.yaml.

  • Add redirect from /benchmark_dataset to /events/2021-09_neurips/documentation/data/dataset.html (#292, PR #295).

  • Fixed minor issues in qmd files (PR #295).

  • Fix missing metrics in the results table (PR #301).

  • Fix theme styling with quarto v1.4 update (PR #303).

openproblems.bio v2.3.5

MINOR CHANGES

  • Update Neurips 2023 hero.

BUG FIXES

  • Fix CI failure by updating the openproblems-v2 submodule (PR #291).

openproblems.bio v2.3.4

MINOR CHANGES

  • Update Neurips 2023 title and button to kaggle page (PR #289).

BUG FIXES

  • Fix viash cheat sheet URL (PR #289)

openproblems.bio v2.3.3

MINOR CHANGES

  • Update renv to v1.0.2 to improve processing time. (PR #287)

  • Add more information about task_info.yaml to the documentation (PR #285).

  • Minor updates to the NeurIPS 2023 landing page.

openproblems.bio v2.3.2

MINOR CHANGES

  • Minor updates to the NeurIPS 2023 landing page (PR #286).

openproblems.bio v2.3.1

MINOR CHANGES

  • Added updates button to the NeurIPS 2023 landing page (PR #279).

  • Remove old hero image (PR #280).

  • Reference base-images in create-component pages (PR #282)

BUG FIXES

  • Updated the openproblems-v2 submodule (PR #280).

    • Docker base images were renamed.

    • File format specification files were renamed from **/api/anndata_*.yaml to **/api/file_*.yaml.

  • Restored summary figures by updating funkyheatmapjs (PR #283).

openproblems.bio v2.3.0

MAJOR CHANGES

  • All tasks were moved from src/<task_id> to the src/tasks/<task_id> subdirectory (PR #251).

  • Upgrade to quarto v1.4 (PR #273).

MINOR CHANGES

  • Minor changes to the documentation pages (PR #248).

  • Add documentation link to Neurips 2021 documentation on the Neurips 2021 page (PR #250).

  • Add prefix "PR " to PR references in changelog (PR #250).

  • Replace "baseline" with "control" in v2 documentation pages (PR #252).

  • Add Dark/Light mode theming for Mermaid diagrams (PR #254).

  • Use api to add more information to the datasets reference documentation (PR #255).

  • Extend the documentation on designing the task API (PR #257).

  • Inform users that they might need to specify a different value for --type in tasks with multiple method / metric subtypes (#259, PR #260).

  • Add general information on AnnData and Viash (PR #261).

  • Explicitly mention the __merge__ notation in the docs (PR #267).

  • Add link to task issue example (PR #271).

  • Add page for NeurIPS 2023 competition (PR #273).

  • Add VS Code install to requirements page (PR #275).

  • changed cheat sheet to link hosted on viash.io (PR #276)

openproblems.bio v2.2.1

BUG FIXES

  • Minor fixes to the documentation pages (PR #246).

openproblems.bio v2.2.0

NEW FUNCTIONALITY

  • Documentation was added for OpenProblems v2 at /documentation (multiple PRs).

  • Added an events page at /events (PR #227).

MAJOR CHANGES

  • For some of the pages, only render executable code when the 'evaluate_code' profile is active (PR #214).

  • Moved competition pages from /competitions to /events (PR #227). Added redirects to ensure links on external websites keep working.

MINOR CHANGES

  • Update to Quarto 1.3 (PR #221).

  • Update license to Creative Commons CC-BY (PR #216).

  • Revert temporary navbar transition fix (PR #231).

  • Revert quarto 1.3 weight changes (PR #236 & PR #244).

  • Fix alignment issues in headings (PR #236).

  • Fix mermaid background rendering (PR #243).

  • Make the funkyheatmap interactive settings visible (PR #169).

BUG FIX

  • Rename create_skeleton to create_component in documentation (PR #213).

  • Add target: _blank to external links in navbar (PR #230).

  • Revert intentional typo .thumnail-image to .thumbnail-image (PR #232)

  • Added ../docs.css to neurips 2021 documentation to activate the .thumbnail-image change (PR #232).

  • Fix broken links (on other websites) by adding redirects to previously existing pages (PR #227).

  • Fix redirects with subdirs to events link (PR #245).

openproblems.bio v2.1.2

MINOR CHANGES

  • Updating task images from .png to .svg (PR #205).
  • Set funkyheatmap colors for dark mode via js instead of css (PR #208).

openproblems.bio v2.1.1

BUG FIXES

  • Fixed a typo in batch_integration_embed task description (PR #201)
  • Fix link-external-filter to recognise internal filters on published website (#202)

openproblems.bio v2.1.0

Dark mode has been added to the website, along with minor changes such as an improved hero image for the results and bibliography pages and the removal of a stub task.

NEW FUNCTIONALITY

  • Dark mode was added (PR #153, PR #162, PR #172, PR #173, PR #184, PR #190, PR #191, PR #194).

MINOR CHANGES

  • Ported missing site metadata (PR #160).

  • Changed the results and bibliography heros (PR #178, PR #181).

  • Removed sub-stub regulatory effect prediction task (PR #197).

BUG FIXES

  • Fix internal links being treated as external links in PR eviews (PR #179).
  • FIx link-external-filter te recognise internal filters on published website (#202)

openproblems.bio v2.0.0

Quarto reimplementation of the original openproblems.bio website.

Pages:

  • Main page

  • Benchmark results:

    • Per task:
      • Summary funky heatmap (implemented in funkyheatmap-js)
      • Results table (using DataTables)
      • Additional information on datasets, methods, metrics
      • QC report
      • Data files as jsons
    • Overall QC report

  • Competitions pages:

    • NeurIPS 2021
    • NeurIPS 2021 Documentation
    • NeurIPS 2022

  • Team view

  • Documentation

    • OpenProblems v1 (links to v1 repo CONTRIBUTING.md)
    • OpenProblems v2 (links to v2 repo CONTRIBUTING.md)
    • Bibliography
    • OpenProblems v2 WIP documentation (hidden)

openproblems.bio v1.0.0

Website created with Hugo + Wowchemy.