marin-dna

Set up and launch a marin-launched DNA training experiment on the shared iris cluster. Each experiment is a self-contained directory with its OWN pyproject (marin packages in BASE deps, local lib as a git dep) — the pattern that makes iris/zephyr workers resolve the runtime. Use when creating a new exp<N>, launching training on the marin/iris cluster, packaging an experiment for marin, or debugging launch failures like "No module named 'zephyr'", "marin-iris client is too old", or a TPU job that won't start. NOT for snakemake pipelines (each snakemake/<pipeline>/ has its own README) or one-off analysis scripts (those go in scripts/).

Long-running, iterative investigation tracked in its own GitHub issue — the issue body is the living results doc, comments are the append-only iteration log, and every code reference is a commit-pinned permalink. Use when the user asks to investigate a question over multiple sessions and track the work in a dedicated issue. Common triggers include "let's investigate X and track it in an issue", "open an issue for this and we'll iterate", "dig into Y across sessions", "why is Z slow — track it", "explore this dataset and log findings as we go". Do NOT use for: running a pipeline by itself (even a snakemake/analysis run), single-session debugging or fixes, one-off questions, or regular feature PRs.

Upload a local file (screenshot, plot, data file) to a user-owned GitHub gist and get back a stable raw URL that renders inline in PR/issue comments and markdown documents. Use whenever you need to share an image or artifact in a GitHub comment, an analysis issue, a README, or any markdown doc and the file is NOT already committed to a repo. Common triggers include "attach this plot to the PR", "include the screenshot in the issue", "embed this figure in the analysis", or "I need a link for this image".