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).

BUG FIXES

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

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 gloassary 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.