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PyAutoReduce — Agent Instructions

Data reduction of HST, JWST and Keck-AO (and future other) imaging into modeling-ready datasets for PyAutoLens/PyAutoGalaxy. Part of the PyAutoLabs workspace — the workspace-level AGENTS.md (routing, safety rules, workflow) applies here.

What this repo is

  • Package autoreduce: pipeline stages acquire/, align/, calibrate/ + sky/ (ground-based only), drizzle/, noise/, psf/, package/, with instrument specifics isolated in instruments/ adapters.
  • Output contract: the al.Imaging.from_fits product set — data.fits, noise_map.fits, psf.fits, psf_full.fits — plus reduction.json provenance. The reference quality bar is the SLACS ACS/F814W reductions.
  • Design docs are authoritative while the project is young: docs/design/hst_acs_pipeline.md (HST/ACS stages, defaults vs lensing deviations, validation), the per-instrument delta docs (wfc3.md, jwst.md, keck_ao.md) and docs/design/roadmap.md.

Boundaries

  • Never imports autolens / autogalaxy / autoarray / autofit — it emits their input format only, and stays releasable independently.
  • Default pipelines first: stages wrap the instrument's standard tooling (astroquery.mast, drizzlepac, photutils); any deviation from STScI defaults must be justified by a lensing requirement and documented in the design doc.
  • Unit tests in test_autoreduce/ are numpy/astropy-only — no network, no drizzlepac/jwst stack. The one sanctioned extra is the lightweight standalone drizzle resampler (behind pytest.importorskip) for the nirc2_native backend. Anything needing an archive or the heavy STScI stack lives in prototypes/ or (later) integration scripts.
  • FITS files are never committed (.gitignore enforces this); prototypes/ writes to prototypes/output/ and prototypes/cache/.

The workspace

The user-facing tutorial workspace (per-instrument start_here.py / step_by_step.py / psf.py / simulator.py examples, guides, README, llms.txt) lives in its own repository: https://github.com/PyAutoLabs/autoreduce_workspace (typically cloned as a sibling, ../autoreduce_workspace). It was staged under workspace/ in this repo until 2026-08-07 and extracted with history via git filter-repo --subdirectory-filter workspace. Workspace scripts consume only the public autoreduce API — a public-API change here means the workspace examples may need updating; flag it in your PR.

Never rewrite history

Never rewrite pushed history on any repo with a remote — no git init over a tracked repo, no force-push to main, no fresh-start "Initial commit", no filter-repo / filter-branch / rebase -i on pushed branches. To get a clean tree: git fetch origin && git reset --hard origin/main && git clean -fd.