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).

Full Changelog: v2.3.5...v2.3.6

openproblems.bio v2.3.5

Update the neurips 2023 page again

openproblems.bio v2.3.4

MINOR CHANGES

• Update NeurIPS 2023 competition 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.

• 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

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).

openproblems.bio v2.2.1

BUG FIX

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

openproblems.bio v2.2.0

NEW FUNCTIONALITY

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

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

MAJOR CHANGES

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

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

MINOR CHANGES

• Update to Quarto 1.3 (#221).

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

• Revert temporary navbar transition fix (#231).

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

• Fix alignment issues in headings (#236).

• Fix mermaid background rendering (#243).

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

BUG FIX

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

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

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

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

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

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

openproblems.bio v2.1.1

BUG FIXES

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