Update file-handling.md #258
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added subsection compression of mzML files
WalkthroughA new documentation section was added to explain the support for writing compressed mzML files using the Changes
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Actionable comments posted: 0
🧹 Nitpick comments (4)
docs/getting-started/types-of-topp-tools/file-handling.md (4)
38-41: Use fenced code blocks for command examplesTo improve readability and consistency with other TOPP tool examples (which use fenced code blocks), wrap the example invocation in a fenced block. This also enables syntax highlighting if needed.
- `PeakPickerHiRes -in input.mzML -out output.mzML.gz -threads 8` + ```bash + PeakPickerHiRes -in input.mzML -out output.mzML.gz -threads 8 + ```
42-42: Wrap tool names and flags in backticks and simplify the sentenceFor clarity and consistency, code elements like
pigz,Boost's gzip,-threads 8, andomp_get_max_threads()should be formatted as inline code. Also, consider breaking the long sentence into two for readability.- Compression uses pigz (parallel gzip) if installed for faster performance, falling back to Boost's gzip otherwise. When using pigz, OpenMS limits threads to the user-specified value (e.g., -threads 8) via omp_get_max_threads(), ensuring compatibility with cluster schedulers. Install pigz for optimal speed. + Compression uses `pigz` (parallel gzip) if installed, falling back to Boost's gzip otherwise. For `pigz` users, OpenMS limits threads to the user-specified value (e.g., `-threads 8`) via `omp_get_max_threads()` to maintain compatibility with cluster schedulers. + + Install `pigz` for optimal speed.
44-47: Convert trade-offs into a bullet list and improve formattingPresenting the trade-offs as a list enhances scannability. Also, wrap file extensions and tool names in backticks and consider using an en dash and multiplication symbol for clarity.
- Trade-offs: - - Efficiency: .mzML.gz files are 2-3x smaller; pigz is significantly faster but CPU-intensive. - Compatibility: Ensure downstream tools support .mzML.gz. + Trade-offs: + - **Efficiency**: `.mzML.gz` files are 2–3× smaller; `pigz` is significantly faster but CPU-intensive. + - **Compatibility**: Ensure downstream tools support `.mzML.gz`.
49-49: Format class and method names as codeWrap
MzMLHandler::writeToin backticks to indicate code references and improve consistency.- This feature, integrated into MzMLHandler::writeTo, supports indexed mzML and enhances data management. + This feature, integrated into `MzMLHandler::writeTo`, supports indexed mzML and enhances data management.
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docs/getting-started/types-of-topp-tools/file-handling.md(2 hunks)
🧰 Additional context used
🪛 markdownlint-cli2 (0.17.2)
docs/getting-started/types-of-topp-tools/file-handling.md
36-36: Heading style
Expected: setext; Actual: atx
(MD003, heading-style)
added a subsection for the compression of mzML files
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Actionable comments posted: 0
🧹 Nitpick comments (4)
docs/getting-started/types-of-topp-tools/file-handling.md (4)
38-40: Use fenced code block for CLI example
For better readability, convert the inline backtick-wrapped command into a fenced code block with a language hint:PeakPickerHiRes -in input.mzML -out output.mzML.gz -threads 8
42-42: Clarify threading behavior description
The phrase “limits threads to the user-specified value viaomp_get_max_threads()” may confuse readers. Consider rephrasing to explain that OpenMS sets pigz’s thread count to the value passed with-threads(e.g., by settingOMP_NUM_THREADS) to avoid over-subscription.
44-49: Convert trade-offs to a bulleted list
For consistency and improved readability, format the trade-offs section as a Markdown list:Trade-offs: - **Efficiency**: `.mzML.gz` files are 2–3× smaller; pigz is significantly faster but CPU-intensive. - **Compatibility**: Ensure downstream tools support `.mzML.gz`.
42-43: Add pigz installation guidance
To help users enable optimal performance, include a link or example install command for pigz, for example:# Debian/Ubuntu sudo apt-get install pigz # macOS (Homebrew) brew install pigz
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📒 Files selected for processing (1)
docs/getting-started/types-of-topp-tools/file-handling.md(2 hunks)
🧰 Additional context used
🪛 markdownlint-cli2 (0.17.2)
docs/getting-started/types-of-topp-tools/file-handling.md
36-36: Heading style
Expected: setext; Actual: atx
(MD003, heading-style)
🔇 Additional comments (1)
docs/getting-started/types-of-topp-tools/file-handling.md (1)
36-37: Heading style consistency OK
The new "Compression of mzML files" section uses the same ATX (##) heading style as other second-level headings in this file. No change needed.🧰 Tools
🪛 markdownlint-cli2 (0.17.2)
36-36: Heading style
Expected: setext; Actual: atx(MD003, heading-style)
added subsection compression of mzML files
Describe the change
PR checklist
CHANGELOG.mdis updated.Summary by CodeRabbit
.mzML.gzextension.