[ ](https://walkerlab.github.io/orcapod/) [](https://codecov.io/github/walkerlab/orcapod) # orcapod  ## Tests \`\`\`bash #!/bin/bash set -e # fail early on non-zero exit cargo clippy --no-default-features --features=test --all-targets -- -D warnings # Rust syntax and style tests cargo fmt --check # Rust formatting test cargo llvm-cov --no-clean --no-default-features --features=test --ignore-filename-regex "bin/.*|lib\.rs" -- --nocapture # Rust integration tests w/ stdout coverage summary cargo llvm-cov --no-clean --no-default-features --features=test --ignore-filename-regex "bin/.*|lib\.rs" --html -- --nocapture # Rust integration tests w/ HTML coverage report (target/llvm-cov/html/index.html) cargo llvm-cov --no-clean --no-default-features --features=test --ignore-filename-regex "bin/.*|lib\.rs" --codecov --output-path target/llvm-cov-target/codecov.json -- --nocapture # Rust integration tests w/ codecov coverage report cargo llvm-cov --no-clean --no-default-features --features=test --ignore-filename-regex "bin/.*|lib\.rs" --cobertura --output-path target/llvm-cov-target/cobertura.xml -- --nocapture # Rust integration tests w/ cobertura coverage report . ~/.local/share/base/bin/activate && maturin develop --uv && export RUST_BACKTRACE=1 && python tests/extra/python/smoke_test.py -- tests/.tmp && python tests/extra/python/agent_test.py -- tests/.tmp # Python integration tests \`\`\` ## Docs \`\`\`bash cargo doc --no-deps # gen api docs (target/doc/orcapod/index.html) cargo modules dependencies --lib --no-uses --no-fns --focus-on "orcapod::uniffi::\{model::\{Pod,PodJob,PodResult\},store::filestore::LocalFileStore,orchestrator::\{PodRun,docker::LocalDockerOrchestrator\}\}" --layout dot > docs/images/orcapod_diagram.dot # orcapod diagram as DOT cargo modules dependencies --lib --no-uses --no-fns --focus-on "orcapod::uniffi::\{model::\{Pod,PodJob,PodResult\},store::filestore::LocalFileStore,orchestrator::\{PodRun,docker::LocalDockerOrchestrator\}\}" --layout dot | dot -T png > docs/images/orcapod_diagram.png # orcapod diagram as PNG cargo modules dependencies --lib --no-uses --no-fns --focus-on "orcapod::uniffi::\{model::\{Pod,PodJob,PodResult\},store::filestore::LocalFileStore,orchestrator::\{PodRun,docker::LocalDockerOrchestrator\}\}" --layout dot | dot -T svg > docs/images/orcapod_diagram.svg # orcapod diagram as SVG \`\`\` ## Git Worktrees Update your git to at least version 2.48 since that is when the \`--relative-paths\` option was added to git worktree. That option makes it compatible with launching using VSCode DevContainers. \`\`\`bash git worktree add /path/to/new/dir-name branch-name --relative-paths # create git worktree remove dir-name # delete \`\`\` ## Project Management Progress is tracked under GH project [orcapod](https://github.com/orgs/walkerlab/projects/2). 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 \`\`\`bash # 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 \`\`\` ## Limit DevContainer Resource Access You can easily enforce resource limits by adding the following to \`devcontainer.json\`. \`\`\`json \{ // .. "runArgs": [ // .. "--cpus=2", "--memory=8gb", // .. ], // .. \} \`\`\`