Documentation, API reference, and pipeline improvements — merge dev into main

[charliekilpatrick]

Description

This PR merges the dev branch into main, bringing in API documentation, contributing guidelines, pipeline and test updates, and conda environment naming consistency.

Summary of changes

• Documentation

  • New Sphinx API reference under docs/source/api/: generated .rst for instruments (BINOSPEC, DEIMOS, F2, FOURSTAR, GMOS, IMACS, LRIS, MMIRS, MOSFIRE, base instrument), primitives (absphot, calibration, image_procs, photometry, solve_wcs, sort_files), scripts (download_anet_index, download_gemini_data, download_keck_data, main_pipeline), and utils (logger, options, utilities).
  • Updates to docs/source/conf.py, index.rst, and installation.rst.
  • README revised for clarity and structure.

• Contributing and project setup

  • New CONTRIBUTING.md with guidelines for reporting issues, contributing code/docs, and support.
  • Conda environment name standardized to potpyri (replacing potpyri_test) in environment.yml and related docs.
  • pyproject.toml updated (metadata and/or dependencies).

• Pipeline and library

  • Instruments: Base class and all instrument modules updated (e.g. instrument.py extended; small tweaks across BINOSPEC, DEIMOS, F2, FOURSTAR, GMOS, IMACS, LRIS, MMIRS, MOSFIRE).
  • Primitives: Substantial updates to absphot, calibration, image_procs, photometry, solve_wcs, and sort_files.
  • Scripts: potpyri/scripts/__init__.py added; main_pipeline and related script behavior/logic updated.
  • Utils: logger, options, and utilities improved.

• Tests

  • New tests/test_image_procs.py.
  • Broader test updates in test_absphot, test_calibration, test_photometry, test_sort, test_wcs, and others.

Commits on dev (not on main)

• Standardize conda environment name to potpyri
• Update conda environment name from potpyri_test to potpyri

Scope

• 73 files changed, ~3,048 insertions, ~537 deletions.
• No breaking changes to the advertised user workflow; main_pipeline INSTRUMENT DATA_PATH and documented options remain the same.

Checklist

• Docs build locally: cd docs && make html
• Tests pass: pytest tests
• README and CONTRIBUTING reflect current setup and contribution process