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@hpparvi hpparvi commented Jun 25, 2025

This PR modernizes the documentation by adopting sphinx_astropy.conf.v2 with the pydata-sphinx-theme. It also updates and reorganizes several existing sections and introduces new documentation covering 1D wavelength calibration.

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codecov bot commented Jun 25, 2025

Codecov Report

❌ Patch coverage is 95.22901% with 25 lines in your changes missing coverage. Please review.
✅ Project coverage is 89.40%. Comparing base (61a5d4a) to head (c6a96b5).
⚠️ Report is 5 commits behind head on main.

Files with missing lines Patch % Lines
specreduce/wavecal1d.py 94.33% 23 Missing ⚠️
specreduce/line_matching.py 60.00% 2 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #275      +/-   ##
==========================================
+ Coverage   87.11%   89.40%   +2.28%     
==========================================
  Files          15       17       +2     
  Lines        1281     1803     +522     
==========================================
+ Hits         1116     1612     +496     
- Misses        165      191      +26     

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not sure if it fits in this PR or a future one, but we have a lot of example docs implemented within docstrings in various parts of the code (i am one of the guilty parties). as part of a fuller refactor, we should decide whether to leave that as-is, migrate it to specific .rst files, or refactor all examples into notebooks or something notebook-based. i think the last option is the most useful going forward, but the most work up-front.

hpparvi and others added 28 commits July 15, 2025 12:57
… a sum of nearest-line distances between a theoretical line list and a transformed observed line list.
Renamed `wavecal.py` to `lswavecal1d.py` and refactored the `WavelengthSolution1D` class for improved clarity and functionality. Added new methods like `refine_fit`, `pix_to_wav`, and `wav_to_pix`, and modified existing ones to enhance flexibility and maintainability.
Introduce `WavelengthSolution2D` class for 2D wavelength calibration, extending functionality from 1D calibration.
… type hints, documentation, and method structure. Added new methods for calculating inverse transformations and derivatives. Enhanced plotting functionality with additional parameters and refined docstrings for clarity.
… `plim` parameter for pixel range control in plotting.
…, and modularity, while resolving associated issues. Enhanced methods for handling pixel-to-wavelength mappings, line-matching processes, and plotting capabilities. Added new functions and properties for better control over data and fit refinement.
…ns with setters to ensure proper masking and validation. Added `plot_lines_pix` and `plot_lines_wav` methods for enhanced modularity in plotting observed and theoretical lines.
…thods, updated property names, and enhanced plotting functionality.
…umentation for plotting and fitting methods.
…e maximum number of iterations for refining the pixel-to-wavelength transformation. This ensures the process adjusts until convergence or the specified iteration limit is reached.
hpparvi and others added 12 commits October 21, 2025 16:41
- Added `sphinx-copybutton` and `sphinx-design` to documentation dependencies in `pyproject.toml`.
- Improved content structure by renaming and reorganizing documentation files.
- Expanded "Contributing" and "Index" sections.
…action examples; updated `conf.py` with formatting adjustments and extended Sphinx documentation settings.
- Corrected typos and clarified text.
- Renamed `common.py` to `quickstart.py`.
- Updated function and variable names for consistency.
- Streamlined background subtraction and wavelength calibration workflows.
@hpparvi hpparvi force-pushed the documentation_facelift branch from 7ee2d16 to c7344e7 Compare October 21, 2025 21:25
@hpparvi hpparvi marked this pull request as ready for review October 28, 2025 20:13
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hpparvi commented Oct 28, 2025

The documentation update is coming together! Please take a look at the rendered docs at
https://specreduce--275.org.readthedocs.build/en/275/index.html and let me know your thoughts.

No need to worry about the large number of commits and changed files. This PR builds on the 1D wavelength calibration PR, which should be merged first.

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