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Handbook Changes Over Time#

Changelog#

0.7.0 (2025-02-14)#

Features#

  • Add "What is Machine Learning" page to the handbook (#84) (34b3fab)
  • Add Communications section and BHKLab Gmail page (#131) (648743d)
  • add Introduction to git slides to version control docs and fix up quick git tips (#123) (8eb99fa)
  • add lab server page to Remote_Development (#136) (142eaec)
  • Add new lab expertise page (#145) (bd3be40)
  • added note about adding the BHKLab calendar to your BHKLab Gmail with the email (aa72aa8)
  • Adding a new page for STAR alignment (#93) (ed2e6de)
  • Google Cloud Platform page added (#92) (b2fea5c)
  • make all tables sortable (#147) (a89b5ae)
  • migrate information from the Employee Onboarding Policy (#127) (def834d)
  • update BHKLAB calendar setup (#143) (35d1dff)
  • update BHKLab Gmail page (#135) (0f2dddd)
  • update-SOW-instructions (#138) (b4cee1f)
  • updated BHKLab Calendar instructions (#142) (aa72aa8)
  • updates to the journal club page (#139) (de22192)

Bug Fixes#

  • PGx meetings are biweekly (#133) (4777bcd)
  • update BHKLab Google group to be Members instead of Google Accou… (#134) (51a7ec2)
  • update BHKLab Google group to be Members instead of Google Accounts and update hyperlink (51a7ec2)

0.6.0 (2024-11-27)#

Features#

  • add a page for DESeq (#91) (73d51b6)
  • add angular commit description to contributing (#100) (cd6ee02)
  • add concurrency settings to GitHub workflows to prevent workflows pushing to gh-pages at the same time from failing (6735fd5)
  • add documentation on code-reviews, and embed the presented slides (#111) (e03e6ef)
  • add presentation tools and database (#108) (9c81b17)
  • add QIPCM image retrieval guide (#102) (55cebe5)
  • add table of contents to Confluence SOW tutorial page (#99) (d73f29b)
  • added "basics of RNAseq" under Disciplines/Bioinformatics/Data_Types (#88) (c6390aa)
  • added journal club md (#89) (1f9557f)
  • Added Owl page under General/Meetings/ (#90) (3982918)
  • added page on BHKlab meeting under General/Meetings/ (#85) (f534b03)
  • added project tracking (#94) (a1f250e)
  • added radiomics-meeting-page under General/Meetings (#83) (680f1d4)
  • added sow tutorial page under General (#82) (b8ce45c)
  • Added tidyverse page under software_development/languages/R (#87) (1a9c2a1)
  • cgeady add slicer info (#109) (8779235)
  • Creating vpn page (#95) (d5c9d8a)
  • migrate Clinical Trial Curation page from BHKLab Confluence (#105) (fe2386b)
  • update directory structure with all section heading pages for assigned pages for tutorial (#58) (72f314a)
  • updates to RNA-Seq information (#122) (92607f3)

Bug Fixes#

  • add ... to all .pages (b0d375f)
  • fix pixi run serve warnings (#107) (40c23c6)
  • incremented default port to 8001 (#120) (b086865)
  • Rename Hackathon Page Request to hackathon_page_request (#66) (a37262f)
  • Rename hackathon_page_request to hackathon_page_request.md (0f3f821)
  • update information in Contributing section (#121) (c623418)

0.5.0 (2024-11-06)#

Features#

  • add footnotes support and enhance social links in MkDocs configuration (1a4dd35)
  • add guiding principles for contributing to the handbook (#52) (31e196e)
  • add header autohide feature, reorganize markdown extensions (fc994d8)
  • add markdownlint configuration and ignore rules for improved linting (0fe0d8a)
  • enhance contributing documentation with clearer instructions and new examples (6d7cc6b)
  • link hpc4health site under software development (#51) (f7361aa)
  • update onboarding / offboarding section (#53) (3c86b05)

0.4.0 (2024-11-04)#

Features#

  • add Markdown and MkDocs documentation sections for improved clarity and guidance (90d0e7e)
  • add repository name to mkdocs configuration and update icon reference (6bc7cd1)
  • improve clarity in contributing guide by refining section headings and adding notes (f8b37f1)
  • refactor software development documentation structure with new sections on development environment and related tools (05eb33b)

Bug Fixes#

  • formatting (5c25c0e)
  • formatting (5c25c0e)
  • git config --local only if we checkout (f819f89)
  • lint files (2c958fb)
  • revise handbook introduction and contribute guidelines for clarity and better onboarding experience (2c958fb)

0.3.1 (2024-10-29)#

Bug Fixes#

  • use github action for deployment (f48ce66)

0.3.0 (2024-10-29)#

Features#

  • enhance release workflow to publish version of docs using mike after PR release (72345a7)
  • use mike (ec14831)

Bug Fixes#

0.2.0 (2024-10-29)#

Features#

  • Add issue templates (#28) (0a2c861)
  • Add release and deployment documentation; update pixi.lock for dependencies and versions (27bd2fd)
  • Create detailed guide for submitting issues, including templates and tips for effective reporting (ac69542)
  • replace discipline temp files with index.md pages, organize disciplines (ae1bb27)
  • Update issue templates for bug reports, content updates, documentation questions, and enhancements (30ee8d5)

Bug Fixes#

  • broken links in disciplines home tab (9393314)
  • CI to fetch from depth 0 (dbcae75)
  • remove deploy task so users dont mess it up (92fb375)
  • update git push command in adding_content.md to set upstream for new branch; fixes #30 (df76944)

0.1.0 (2024-10-25)#

Features#

  • add Conventional PR name check (#22) (beb1149)
  • add documentation on Contributing (156c47e)
  • add new documentation for code reviews and merging process, improving contributing guidelines for maintainers (#23) (156c47e)
  • major updates (76ce766)
  • Set up project structure with MkDocs, added configuration, documentation files, and specified dependencies in pixi.toml (0c17072)
  • update structure (ceb66dd)

Bug Fixes#

Miscellaneous Chores#