Docs, tests, and CI: API reference, unit test coverage, and documentation updates#71
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charliekilpatrick merged 8 commits intomainfrom Mar 6, 2026
Merged
Docs, tests, and CI: API reference, unit test coverage, and documentation updates#71charliekilpatrick merged 8 commits intomainfrom
charliekilpatrick merged 8 commits intomainfrom
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- Introduced test_create_error to validate the output of the create_error function. - Enhanced test coverage for image processing functionalities. - Updated README and CONTRIBUTING.md for clarity on testing procedures and documentation deployment.
- Added unit tests for create_error function to ensure expected behavior. - Enhanced test_image_procs.py for better coverage of image processing features. - Revised README and CONTRIBUTING.md to clarify testing guidelines and documentation processes.
- Added additional unit tests for create_error function to improve coverage. - Further refined test_image_procs.py for comprehensive testing of image processing. - Updated README and CONTRIBUTING.md to provide clearer instructions on testing and documentation practices.
…tions - Updated find_catalog to correctly handle K, Ks, and Kspec filters for 2MASS, mapping them to the K-band columns. - Enhanced convert_filter_name to return 'K' for K, Ks, and Kspec filters. - Added unit tests to validate the new behavior for 2MASS K-band filters in test_utilities and test_absphot.
…ame loading - Added a new helper function to read calibration FITS files into CCDData without parsing WCS, addressing issues with ill-conditioned WCS keywords. - Refactored bias, dark, flat, and sky frame loading methods to utilize the new function, improving code clarity and reducing redundancy.
- Introduced a new function, _sanitize_calibration_header, to remove WCS and coordinate keywords from calibration headers, ensuring safe writing of calibration files. - Updated bias, dark, flat, and sky frame writing methods to utilize the new sanitization function, preventing potential InvalidTransformError during WCS parsing. - Improved logging to ensure messages are only displayed when logging is enabled.
- Introduced tests for _sanitize_calibration_header and _read_calibration_ccd functions to ensure proper handling of calibration FITS files and header sanitization. - Added tests for loading bias, dark, flat, and sky frames, verifying that they correctly utilize the new calibration loading methods. - Implemented additional tests for sky subtraction and static mask filename retrieval to enhance overall test coverage.
- Updated the _read_calibration_ccd function to improve efficiency in loading calibration FITS files. - Refactored related loading methods for bias, dark, flat, and sky frames to streamline the process. - Added new unit tests to ensure robust validation of calibration frame loading and processing.
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Description
This PR merges the
devbranch intomain, bringing in Sphinx API documentation, a larger unit test suite with integration markers, CI/workflow updates, and refreshed README/contributing docs.Documentation
docs/source/api/: generated RST for all instruments (BINOSPEC, DEIMOS, F2, FOURSTAR, GMOS, IMACS, LRIS, MMIRS, MOSFIRE, baseinstrument), 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).docs/source/installation.rst,docs/source/index.rst) updated with testing instructions (unit vs integration), links to README/CONTRIBUTING, and deployment note.docs/DEPLOY.mdadded with steps to enable GitHub Pages and deploy docs to https://ciera-transients.github.io/POTPyRI/.dev, offline test command, and PR target branches.Testing
@pytest.mark.integration(e.g.test_absphot,test_cal,test_photometry,test_sort,test_wcs_integration). Runpytest tests -m "not integration"for unit-only (no network).tests/test_instruments.py—instrument_getter(unsupported instrument), Instrument base and GMOS:match_type_keywords,needs_sky_subtraction, getters (pixscale, rdnoise, gain, target, filter, exptime, ampl, binning, out_size, time, number, instrument_name, catalog),format_datasec,raw_format, naming helpers (stk/sci/bkg, mbias/mdark/mflat/msky).tests/test_options.py—init_options,add_paths(raises when path missing, creates dirs).tests/test_utilities.py—find_catalog(PS1, 2MASS, SDSS, UKIRT, SkyMapper, unsupported filter),is_number,parse_coord(degrees, sexagesimal, invalid).tests/test_image_procs.py—test_create_errorforimage_procs.create_error.potpyri.utils.utilities.find_catalogearly returns now consistently return a 6-tuple(catalog, catalog_ID, ra, dec, mag, err)to match the docstring and final return.CI and workflows
.github/workflows/build-test.yml): runspytest -m "not integration"so CI does not depend on external fixture downloads..github/workflows/documentation.yml): deploy step runs only onpushtomain(not on pull_request), so PRs still build docs without updating the live site.Environment and packaging
potpyriinenvironment.ymland related docs (replacingpotpyri_test).pyproject.tomland package metadata/scripts remain aligned with current layout.Scope
potpyri/(instruments, primitives, utils),tests/, anddocs/.main_pipeline INSTRUMENT DATA_PATHand options are unchanged.pytest tests -m "not integration".Checklist
pytest tests -m "not integration"cd docs && make html