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A framework for fully traceable and reproducible scientific computation

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orcapod

Tests

#!/bin/bash
set -e                                    # stop early on non-zero exit
cargo clippy --all-targets -- -D warnings # syntax and style tests
cargo fmt --check                         # formatting test
cargo llvm-cov -- --nocapture             # integration tests w/ coverage summary
cargo llvm-cov --html -- --nocapture      # integration tests w/ coverage report (target/llvm-cov/html/index.html)

Docs

cargo doc --no-deps                       # gen api docs (target/doc/orcapod/index.html)

Project Management

Progress is tracked under GH project orcapod. We track only issues in the project so don't add PRs.

Flow

  1. Contributor indicates to others they are picking up an issue by:
    • Self-assigning the issue
    • Opening a draft PR to dev branch that links the issue(s) it will fix
    • Updating the issue status to In Progress
  2. Contributor indicates to others their contribution is ready for review by:
    • Marking their draft PR as Ready for Review
    • Assigning reviewers
    • Updating the issue status to Ready for Review
  3. Reviewers should do the following after submitting a review:
    • If any updates were requested:
      • Update the issue status to Changes Requested
    • If changes are approved:
      • Merge the PR
      • Either update the issue status to Done or close the issue manually
  4. Contributors working on reviewer requested changes should:
    • Convert their PR to draft
    • Update the issue status to In Progress
    • Repeat steps 2 and 3 as needed

Views

  • Overview: A birdseye view of issues in table form. Convenient for sorting and updating priority, estimate, assignee, and status.
  • Kanban: A board to capture live progress visually. Status can be updated by dragging cards to their appropriate status column.

Automation Note

  • Newly opened issues are automatically added with the status Todo
  • Reopened issues will automatically update status to Todo
  • Issue will automatically close once their status is updated to Done
  • Manually closed issues will automatically update status to Done

Set permissions to system defaults

# based on debian
chmod u=rwx,g=rx,o=rx $(find . -not -path "./.git*" -type d | sort)  # directories
chmod u=rw,g=r,o=r $(find . -not -path "./.git/*" -type f | sort)  # files

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A framework for fully traceable and reproducible scientific computation

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