Fix broken example code #459
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WalkthroughThis pull request updates documentation and examples. It removes the Changes
Sequence Diagram(s)sequenceDiagram
participant U as User/System
participant FC as FilteringConsumer
participant IC as Internal Consumer
U->>FC: Call consumeSpectrum(spectrum)
FC->>FC: Print spectrum size
alt spectrum.size ≥ min_spec_size
FC->>IC: Forward spectrum for further processing
else spectrum.size < min_spec_size
FC-->>FC: Discard spectrum
end
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🧹 Nitpick comments (2)
docs/source/user_guide/quantitative_data.rst (1)
29-31: Refine FeatureFinder Formatting.
The previous:py:class:directive has been removed from the reference to the FeatureFinder algorithm. The simple backticked link now reads as a plain name linked to the next chapter. Confirm that this format aligns with your overall documentation style and that readers can still easily identify the reference.docs/source/user_guide/reading_raw_ms_data.rst (1)
155-183: Introduce and Validate FilteringConsumer Class.
The newFilteringConsumerclass implementation is clear and demonstrates how to filter spectra by their peak count. The class takes an internal consumer and amin_spec_sizeparameter, and theconsumeSpectrummethod prints the spectrum size and conditionally forwards the spectrum.
A couple of minor suggestions:
- Consider using a logging framework (or at least a configurable verbosity flag) instead of plain
- Ensure that the indentation is consistent when users copy this example into their projects.
Overall, the implementation is effective for documentation purposes.
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📒 Files selected for processing (4)
docs/source/user_guide/quantitative_data.rst(1 hunks)docs/source/user_guide/reading_raw_ms_data.rst(2 hunks)docs/source/_static/custom.css(1 hunks)docs/source/user_guide/installation.rst(1 hunks)
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🔇 Additional comments (3)
docs/source/_static/custom.css (1)
71-74: Update CSS color for parameter names.
The color property for the.sig-param > span.n:nth-child(1) > .preselector has been changed from the previous darker shade to#3f87d3, which should enhance readability. Please verify that this new color meets the accessibility and branding guidelines.docs/source/user_guide/installation.rst (1)
31-35: Expand Supported Python Versions.
The documentation now lists Python 3.9, 3.10, 3.11, 3.12, and 3.13 as supported versions. This update improves compatibility with newer Python releases. Please ensure that any dependent instructions or installation commands elsewhere in the docs are also updated accordingly.docs/source/user_guide/reading_raw_ms_data.rst (1)
184-192: Demonstration of FilteringConsumer Usage.
The subsequent code instantiates aFilteringConsumerwith a minimum peak size of 11 and uses it in conjunction withPlainMSDataWritingConsumerto filter and write out the MS data. This example effectively illustrates the filtering mechanism. Please verify that the example’s input and output file names (e.g.,"test.mzML"and"out.mzML") are consistent with your documentation standards.
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I recall that we changed some code to output to make it work again in notebooks and binder. This is now working ? |
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yes it works, otherwise it would not pass CI :) |
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Also in binder? |
2 participants
fixes #397
Summary by CodeRabbit
Documentation
Style