docs: describe every module, and fix four broken README examples - #66
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snesmaeili wants to merge 2 commits into
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docs: describe every module, and fix four broken README examples#66snesmaeili wants to merge 2 commits into
snesmaeili wants to merge 2 commits into
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The code has moved ahead of the public-facing story. The source tree ships
asr, dss, icanclean, sns, spectrum_interpolation and zapline, but the README
never mentioned ASR once, and the package description still read "Denoising
Source Separation (DSS) and ZapLine algorithms for MNE-Python".
Reframe the README around choosing a method by contamination structure, with
a table mapping problem -> method -> the information that method uses, and
cover all six modules.
Four Quick Start examples were broken. Each now executes; all seven snippets
in the file were run against synthetic data before committing.
- ZapLine-plus printed `zapline_plus.detected_freq_`, which does not
exist -> AttributeError. The detected frequency lives in
`adaptive_results_["line_freq"]`.
- `dss.transform(epochs, return_type="epochs")` -> TypeError. `transform`
takes only (self, X); `return_type` is a constructor argument.
- `BandpassBias(sfreq=..., freq=10, bandwidth=4)` -> TypeError. The
signature is `BandpassBias(freq_band=(lo, hi), sfreq=...)`.
- The adaptive ZapLine example did not say that adaptive mode calibrates
and cleans together, so it requires fit_transform().
Also add asr, artifact-removal, icanclean and line-noise to the packaging
keywords, and replace the "specializes in DSS" opening of the docs landing
page with the same capability table.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01W6GFfnt85ZSjuRaDrETwpU
ruff 0.16 formats Python code blocks inside Markdown; 0.15 did not. CI installs ruff unpinned, so it picked up the new behaviour and rejected the aligned trailing comments and wrapped call in the DSS example. Cosmetic only -- the example code itself is unchanged. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01W6GFfnt85ZSjuRaDrETwpU
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
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Coverage 95.77% 95.77%
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Files 68 68
Lines 8565 8565
Branches 1512 1512
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Hits 8203 8203
Misses 175 175
Partials 187 187
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Why
The code has moved ahead of the public-facing story.
mne_denoise/ships asr, dss, icanclean, sns, spectrum_interpolation and zapline, but:pyproject.tomlstill described the project as "Denoising Source Separation (DSS) and ZapLine algorithms for MNE-Python"docs/index.rstopened with "specializes in Denoising Source Separation (DSS)"Counting mentions before this PR: DSS 20, ZapLine 17, ASR 0, iCanClean 0, spectrum_interpolation 0, SNS 0.
What changed
Reframed the README around choosing a method by contamination structure — a table mapping problem → method → the information that method uses — and covered all six modules. Same table now opens the docs landing page.
Four Quick Start examples were broken
These are exactly the lines a new user copy-pastes. Each is now fixed, and all seven snippets in the README were executed against synthetic data before committing (7 passed, 0 failed).
zapline_plus.detected_freq_AttributeError— attribute does not existadaptive_results_["line_freq"]dss.transform(epochs, return_type="epochs")TypeError—transformtakes only(self, X)return_typeset on the constructorBandpassBias(sfreq=..., freq=10, bandwidth=4)TypeErrorBandpassBias(freq_band=(8.0, 12.0), sfreq=...)fit/transformworkfit_transformAlso added
asr,artifact-removal,icanclean,line-noiseto the packaging keywords so the project is findable by what it does.Notes