docs: Add src for Doxygen documentation #241
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I would like to test this out locally, how can I build my doxygen files? |
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If you add doxygen files and integrate a GitHub repository with Read the Docs, |
WalkthroughThe changes enhance and expand documentation across the project. Updates include new configuration files and build scripts, refined CSS styling, additional GraphML visualization files, and extensive new parameter documentation for OpenMS classes and TOPP tools. Detailed tables now describe parameters for a wide variety of modules, with both CLI and HTML documents provided. Overall, the documentation improvements increase clarity, detail, and accessibility for users. Changes
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Actionable comments posted: 10
🔭 Outside diff range comments (1)
.readthedocs.yaml (1)
8-9: 🛠️ Refactor suggestionRemove duplicate version declaration.
The
version: 2declaration appears twice in the file, which is redundant.Remove the duplicate version declaration:
# Build from the docs/ directory with Sphinx sphinx: configuration: docs/conf.py # Explicitly set the version of Python and its requirements -version: 2 build:🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 8-8: duplication of key "version" in mapping
(key-duplicates)
🧹 Nitpick comments (53)
docs/doxygen/doxygen-awesome-css/doxygen-awesome.css (1)
2182-2182: Address CSS property override warning.There's a potential issue with the CSS shorthand property overriding previously set properties.
Consider changing the shorthand
backgroundproperty to use the more specific property needed:- background: transparent; + background-color: transparent;This ensures you don't accidentally override any other background properties that might be set.
🧰 Tools
🪛 Biome (1.9.4)
[error] 2182-2182: Unexpected shorthand property background after background-image
(lint/suspicious/noShorthandPropertyOverrides)
docs/doxygen/parameters/output/OpenMS_NLargest.parameters (1)
1-16: Consider adding parameter validation information.While the table includes a "Restrictions" column, no restrictions are specified for the
nparameter.Consider adding validation constraints if applicable, such as "n > 0" or "n ≤ max_value", to help users understand the valid parameter ranges.
docs/doxygen/parameters/output/TOPP_DeMeanderize.cli (1)
28-28: Consider removing the empty line at the end of the file.There's an empty line at the end of the file that doesn't serve any purpose.
-docs/doxygen/parameters/output/OpenMS_ConsensusIDAlgorithmBest.parameters (1)
31-31: Consider removing the empty line at the end of the file.There's an empty line at the end of the file that doesn't serve any purpose.
-docs/doxygen/parameters/output/TOPP_DatabaseFilter.cli (1)
16-17: Fix word wrapping in the parameter description.The word "whitelist" is split across two lines, which may affect readability. Consider adjusting the line length to keep the word intact.
- -method <choice> Switch between white-/blacklisting of protein IDs (default: 'whitelist') (valid: 'whitel - ist', 'blacklist') + -method <choice> Switch between white-/blacklisting of protein IDs (default: 'whitelist') (valid: + 'whitelist', 'blacklist')docs/doxygen/parameters/output/TOPP_ExternalCalibration.cli (3)
1-3: Consider adding a proper header before tool description.The file starts with an empty line followed immediately by the tool description. Consider adding a clear header to improve readability.
+# ExternalCalibration - Command Line Interface ExternalCalibration -- Applies an external mass recalibration.
20-21: Fix line wrapping in parameter description.The description for the ms_level parameter is cut off at "unchan" and continues on the next line. This appears to be due to line length limitations, but it affects readability.
- -ms_level i j ... Target MS levels to apply the transformation onto. Scans with other levels remain unchan - ged. (default: '[1 2 3]') + -ms_level i j ... Target MS levels to apply the transformation onto. Scans with other levels remain unchanged. + (default: '[1 2 3]')
6-7: Fix line wrapping in citation information.The citation text is split awkwardly with "mass spec" at the end of line 6 and "trometry" at the start of line 7.
- + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec - trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7. + + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass + spectrometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.docs/doxygen/parameters/output/TOPP_FeatureFinderMetaboIdent.cli (3)
25-27: Fix line wrapping in mz_window parameter description.The description for the mz_window parameter is awkwardly wrapped, with a space at the beginning of line 26.
- -extract:mz_window <value> M/z window size for chromatogram extraction (unit: ppm if 1 or greater, - else Da/Th) (default: '10.0') (min: '0.0') + -extract:mz_window <value> M/z window size for chromatogram extraction (unit: ppm if 1 or greater, + else Da/Th) (default: '10.0') (min: '0.0')
31-33: Fix line wrapping in peak_width parameter description.The description for the peak_width parameter is awkwardly wrapped with "ext" at the end of line 32.
- -detect:peak_width <value> Expected elution peak width in seconds, for smoothing (Gauss filter). - Also determines the RT extration window, unless set explicitly via 'ext - ract:rt_window'. (default: '60.0') (min: '0.0') + -detect:peak_width <value> Expected elution peak width in seconds, for smoothing (Gauss filter). + Also determines the RT extraction window, unless set explicitly via + 'extract:rt_window'. (default: '60.0') (min: '0.0')
19-20: Fix line wrapping in trafo_out parameter description.The description for the trafo_out parameter is awkwardly wrapped with "(valid formats: " at the end of line 19.
- -trafo_out <file> Output file: Retention times (expected vs. observed) (valid formats: - 'trafoXML') + -trafo_out <file> Output file: Retention times (expected vs. observed) + (valid formats: 'trafoXML')docs/doxygen/parameters/output/OpenMS_SpectrumAnnotator.parameters (1)
30-33: Parameter name and description mismatch.The parameter name "topNmatch_fragmenterrors" suggests it relates to the top N fragment errors, but the default value is 7 and the description mentions meta values for topN_meanfragmenterror and related statistics. To improve clarity, consider updating the description to explicitly mention that this parameter sets the N value for the top N fragment errors to be calculated.
docs/doxygen/parameters/output/OpenMS_FeatureDistance.parameters (2)
11-13: Possible inconsistency in parameter description.The description for "ignore_adduct" parameter states "true [default]: pairing requires equal adducts..." and then repeats "true: Pairing irrespective of adducts". This appears to be a contradiction or a copy-paste error. Consider revising to clarify the actual behavior when the parameter is set to true versus false.
- <td style="vertical-align:top">true, false</td><td style="vertical-align:top">true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts</td> + <td style="vertical-align:top">true, false</td><td style="vertical-align:top">true [default]: pairing irrespective of adducts; false: pairing requires equal adducts (or at least one without adduct annotation)</td>
61-63: Additional clarity for log transformation formula.The description for "log_transform" provides a mathematical explanation that could be improved with proper mathematical notation. Consider adding an HTML entity for the variable names or using a more readable format to represent mathematical formulas.
- <td style="vertical-align:top">enabled, disabled</td><td style="vertical-align:top">Log-transform intensities? If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))</td> + <td style="vertical-align:top">enabled, disabled</td><td style="vertical-align:top">Log-transform intensities? If disabled, d = |int<sub>f2</sub> - int<sub>f1</sub>| / int<sub>max</sub>. If enabled, d = |log(int<sub>f2</sub> + 1) - log(int<sub>f1</sub> + 1)| / log(int<sub>max</sub> + 1))</td>docs/doxygen/parameters/output/OpenMS_SimpleTSGXLMS.parameters (2)
6-7: Minor inconsistency in parameter description.The description mentions "If set to 1", but the parameter uses boolean values "true/false". This inconsistency could confuse users.
- <td style="vertical-align:top">true, false</td><td style="vertical-align:top">If set to 1 isotope peaks of the product ion peaks are added</td> + <td style="vertical-align:top">true, false</td><td style="vertical-align:top">If set to true, isotope peaks of the product ion peaks are added</td>
12-12: Similar inconsistency in parameter description.The description refers to "add_isotopes must be set to 1" but should use "true" for consistency with boolean parameter values.
- <td style="vertical-align:top"> </td><td style="vertical-align:top">Defines the maximal isotopic peak which is added, add_isotopes must be set to 1</td> + <td style="vertical-align:top"> </td><td style="vertical-align:top">Defines the maximal isotopic peak which is added, add_isotopes must be set to true</td>docs/doxygen/parameters/output/OpenMS_FeatureGroupingAlgorithmQT.parameters (1)
36-38: Potential inconsistency in parameter description.The description contains conflicting information. It states "true [default]" and then describes this as requiring equal adducts, but the actual meaning seems to be the opposite ("Pairing irrespective of adducts"). This could lead to user confusion.
- <td style="vertical-align:top">true, false</td><td style="vertical-align:top">true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts</td> + <td style="vertical-align:top">true, false</td><td style="vertical-align:top">true [default]: Pairing irrespective of adducts; false: pairing requires equal adducts (or at least one without adduct annotation)</td>docs/doxygen/parameters/output/OpenMS_MapAlignmentAlgorithmIdentification.parameters (1)
1-50: Well-structured documentation with comprehensive parameter descriptionsThe documentation provides clear and detailed information about each parameter for the MapAlignmentAlgorithmIdentification class. The HTML table format with consistent styling for parameter names, types, defaults, restrictions, and descriptions makes it easy to read and understand.
The descriptions for some parameters could benefit from minor formatting improvements for better readability:
- <td style="vertical-align:top">If 'score_cutoff' is 'true': Minimum score for an ID to be considered.<BR>Unless you have very few runs or identifications, increase this value to focus on more informative peptides.</td> + <td style="vertical-align:top">If 'score_cutoff' is 'true': Minimum score for an ID to be considered.<BR><BR>Unless you have very few runs or identifications, increase this value to focus on more informative peptides.</td>Similar spacing improvements could be applied to other multi-sentence descriptions (like in lines 22 and 27).
docs/doxygen/parameters/output/OpenMS_FeatureFindingMetabo.parameters (3)
37-38: Fix typo in description textThere's a small grammatical error in the description.
- <td style="vertical-align:top">false, true</td><td style="vertical-align:top">Require sufficient overlap in RT while assembling mass traces. Disable for direct injection data..</td> + <td style="vertical-align:top">false, true</td><td style="vertical-align:top">Require sufficient overlap in RT while assembling mass traces. Disable for direct injection data.</td>
42-43: Improve citation format in descriptionThe description references a research paper but doesn't follow standard citation format.
- <td style="vertical-align:top">metabolites (2% RMS), metabolites (5% RMS), peptides, none</td><td style="vertical-align:top">Remove/score candidate assemblies based on isotope intensities. SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device.</td> + <td style="vertical-align:top">metabolites (2% RMS), metabolites (5% RMS), peptides, none</td><td style="vertical-align:top">Remove/score candidate assemblies based on isotope intensities. SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device.</td>
47-48: Include complete citation informationThe description mentions research (Kenar et al. 2014, MCP) but lacks full citation details.
- <td style="vertical-align:top">false, true</td><td style="vertical-align:top">Use the 13C isotope peak position (~1.003355 Da) as the expected shift in m/z for isotope mass traces (highly recommended for lipidomics!). Disable for general metabolites (as described in Kenar et al. 2014, MCP.).</td> + <td style="vertical-align:top">false, true</td><td style="vertical-align:top">Use the 13C isotope peak position (~1.003355 Da) as the expected shift in m/z for isotope mass traces (highly recommended for lipidomics!). Disable for general metabolites (as described in Kenar et al. 2014, Molecular & Cellular Proteomics).</td>docs/doxygen/parameters/output/OpenMS_MapAlignmentAlgorithmPoseClustering.parameters (2)
17-18: Fix formatting issue in restriction valuesThe min and max restriction values are run together without proper spacing, making them difficult to read.
- <td style="vertical-align:top">min: 0.0 max: 1.0</td><td style="vertical-align:top">Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min). </td> + <td style="vertical-align:top">min: 0.0, max: 1.0</td><td style="vertical-align:top">Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min).</td>
1-131: Comprehensive documentation with detailed parameter descriptionsThe documentation for MapAlignmentAlgorithmPoseClustering provides thorough information about all parameters, with clear explanations of their purpose, restrictions, and default values. The organization of parameters into logical groups (superimposer, pairfinder) makes it easier to understand related settings.
Consider standardizing the trailing whitespace in descriptions and removing extra spaces at the end of sentences (e.g., line 18, 32) for consistency across all documentation files.
docs/doxygen/parameters/output/TOPP_FalseDiscoveryRate.cli (4)
12-13: Consider improving line wrapping for readability.The text is awkwardly split with "description" broken across lines, which reduces readability. Consider adjusting the line length or wrapping at word boundaries.
19-21: Text formatting breaks readability.The description for the
-peptideparameter is split across lines with "valid" being broken, making it harder to read. Consider reformatting to ensure words remain intact.
22-23: Formatting inconsistency in parameter description.There's a formatting inconsistency where the closing quote is adjacent to the closing parenthesis (
'false')), unlike other similar lines where there's a space between them.- -protein <FDR level> Perform FDR calculation on protein level (default: 'true') (valid: 'true', 'false' - ) + -protein <FDR level> Perform FDR calculation on protein level (default: 'true') (valid: 'true', 'false')
28-29: Trailing space before closing parenthesis.There's a trailing space before the closing parenthesis in line 28, which is inconsistent with the formatting in other similar lines.
- -FDR:protein <fraction> Filter proteins based on q-value (e.g., 0.05 = 5% FDR, disabled for 1) (default: - '1.0') (min: '0.0' max: '1.0') + -FDR:protein <fraction> Filter proteins based on q-value (e.g., 0.05 = 5% FDR, disabled for 1) (default: + '1.0') (min: '0.0' max: '1.0')docs/doxygen/parameters/output/TOPP_ClusterMassTracesByPrecursor.cli (2)
19-20: Text split across lines affects readability.The description for the
-min_pearson_correlationparameter is split with "other" broken across lines, which reduces readability. Consider reformatting to keep words intact.
33-34: Inconsistent line wrapping.The line wrapping for the
-threadsparameter splits "default:" across two lines, which is inconsistent with the formatting of other parameters and reduces readability.- -threads <n> Sets the number of threads allowed to be used by the TOPP tool (default: - '1') + -threads <n> Sets the number of threads allowed to be used by the TOPP tool + (default: '1')docs/doxygen/parameters/output/TOPP_ConsensusMapNormalizer.cli (2)
16-22: Fix typo in algorithm descriptionThere are two typos in the algorithm description:
- "fator" should be "factor" on line 17
- "media n" should be "median" (without a space) on lines 22-23
- -algorithm_type <type> The normalization algorithm that is applied. 'robust_regression' scales each map - by a fator computed from the ratios of non-differential background features (as - determined by the ratio_threshold parameter), 'quantile' performs quantile normal - ization, 'median' scales all maps to the same median intensity, 'median_shift' - shifts the median instead of scaling (WARNING: if you have regular, log-normal - MS data, 'median_shift' is probably the wrong choice. Use only if you know what - you're doing!) (default: 'robust_regression') (valid: 'robust_regression', 'media - n', 'median_shift', 'quantile') + -algorithm_type <type> The normalization algorithm that is applied. 'robust_regression' scales each map + by a factor computed from the ratios of non-differential background features (as + determined by the ratio_threshold parameter), 'quantile' performs quantile normal + ization, 'median' scales all maps to the same median intensity, 'median_shift' + shifts the median instead of scaling (WARNING: if you have regular, log-normal + MS data, 'median_shift' is probably the wrong choice. Use only if you know what + you're doing!) (default: 'robust_regression') (valid: 'robust_regression', 'median', + 'median_shift', 'quantile')
34-35: Remove trailing empty lineThe file has an unnecessary empty line at the end.
--helphelp Shows all options (including advanced) -docs/doxygen/parameters/output/OpenMS_ZhangSimilarityScore.parameters (1)
15-18: Clarify mutual exclusivity of weighting factorsThe documentation doesn't specify whether
use_linear_factoranduse_gaussian_factorcan both be enabled simultaneously, or if they are mutually exclusive. Please clarify the expected behavior when both parameters are set to "true".<td style="vertical-align:top"><b>use_linear_factor</b></td> <td style="vertical-align:top">string</td><td style="vertical-align:top">false</td> - <td style="vertical-align:top">true, false</td><td style="vertical-align:top">if true, the intensities are weighted with the relative m/z difference</td> + <td style="vertical-align:top">true, false</td><td style="vertical-align:top">if true, the intensities are weighted with the relative m/z difference. Note: This setting is mutually exclusive with use_gaussian_factor.</td> <td style="vertical-align:top"><b>use_gaussian_factor</b></td> <td style="vertical-align:top">string</td><td style="vertical-align:top">false</td> - <td style="vertical-align:top">true, false</td><td style="vertical-align:top">if true, the intensities are weighted with the relative m/z difference using a gaussian</td> + <td style="vertical-align:top">true, false</td><td style="vertical-align:top">if true, the intensities are weighted with the relative m/z difference using a gaussian. Note: This setting is mutually exclusive with use_linear_factor.</td>Also applies to: 20-23
docs/doxygen/parameters/output/OpenMS_PeakAlignment.parameters (2)
15-17: Fix typo in parameter descriptionThere's a typo in the description for the
heuristic_levelparameter: "heurisitcs" should be "heuristics".<td style="vertical-align:top"><b>heuristic_level</b></td> <td style="vertical-align:top">int</td><td style="vertical-align:top">0</td> - <td style="vertical-align:top"> </td><td style="vertical-align:top">set 0 means no heuristic is applied otherwise the given value is interpreted as unsigned integer, the number of strongest peaks considered for heurisitcs - in those sets of peaks has to be at least one match to conduct comparison</td> + <td style="vertical-align:top"> </td><td style="vertical-align:top">set 0 means no heuristic is applied otherwise the given value is interpreted as unsigned integer, the number of strongest peaks considered for heuristics - in those sets of peaks has to be at least one match to conduct comparison</td>
10-12: Clarify boolean representation as integerThe
normalizedparameter uses an integer (1) to represent a boolean value (true). Consider clarifying this by rephrasing the description to make it more explicit.<td style="vertical-align:top"><b>normalized</b></td> <td style="vertical-align:top">int</td><td style="vertical-align:top">1</td> - <td style="vertical-align:top"> </td><td style="vertical-align:top">is set 1 if the similarity-measurement is normalized to the range [0,1]</td> + <td style="vertical-align:top"> </td><td style="vertical-align:top">if set to 1 (true), the similarity-measurement is normalized to the range [0,1]; if set to 0 (false), no normalization is applied</td>docs/doxygen/parameters/output/TOPP_DatabaseSuitability.html (2)
28-28: Fix typo in parameter descriptionThere's a typo in the description for the
number_of_subsampled_runsparameter: "automaticly" should be "automatically".- <span class="item_description">Controls how many runs should be done for calculating corrected suitability. (0 : number of runs will be estimated automaticly) ATTENTION: For each run a seperate ID-search is performed. This can result in some serious run time.</span> + <span class="item_description">Controls how many runs should be done for calculating corrected suitability. (0 : number of runs will be estimated automatically) ATTENTION: For each run a separate ID-search is performed. This can result in some serious run time.</span>
27-28: Add time estimate for number_of_subsampled_runsThe description for
number_of_subsampled_runsmentions "serious run time" but doesn't provide an estimate of how long it might take. Consider adding a rough estimate to set user expectations.- <span class="item_description">Controls how many runs should be done for calculating corrected suitability. (0 : number of runs will be estimated automaticly) ATTENTION: For each run a seperate ID-search is performed. This can result in some serious run time.</span> + <span class="item_description">Controls how many runs should be done for calculating corrected suitability. (0 : number of runs will be estimated automatically) ATTENTION: For each run a separate ID-search is performed. This can result in some serious run time (potentially hours depending on database size and hardware).</span>docs/doxygen/parameters/output/OpenMS_ConsensusIDAlgorithmWorst.parameters (2)
15-17: Rephrase parameter description from question to statementThe description for
filter:count_emptyends with a question mark, which is unusual for documentation. Consider rephrasing this as a statement for consistency with other parameter descriptions.<td style="vertical-align:top"><b>filter:count_empty</b></td> <td style="vertical-align:top">string</td><td style="vertical-align:top">false</td> - <td style="vertical-align:top">true, false</td><td style="vertical-align:top">Count empty ID runs (i.e. those containing no peptide hit for the current spectrum) when calculating 'min_support'?</td> + <td style="vertical-align:top">true, false</td><td style="vertical-align:top">If true, empty ID runs (i.e. those containing no peptide hit for the current spectrum) are counted when calculating 'min_support'.</td>
20-22: Enhance description of keep_old_scores parameterThe description for
filter:keep_old_scoresis minimal and could benefit from more detail about what "original scores" and "user params" refer to in this context.<td style="vertical-align:top"><b>filter:keep_old_scores</b></td> <td style="vertical-align:top">string</td><td style="vertical-align:top">false</td> - <td style="vertical-align:top">true, false</td><td style="vertical-align:top">if set, keeps the original scores as user params</td> + <td style="vertical-align:top">true, false</td><td style="vertical-align:top">If set to true, the original scores from individual identification runs are preserved as user parameters in the consensus output, allowing traceability of the original values before consensus scoring.</td>docs/doxygen/parameters/output/TOPP_CometAdapter.cli (1)
34-46: Isotope error parameter could benefit from more contextWhile the parameter description is technically correct, it might be helpful to include a brief explanation of what isotope errors are and why the specific values (-8/-4/0/4/8) are useful for SILAC experiments.
Consider adding a brief explanation about isotope errors and their significance in SILAC experiments to help new users understand this parameter better.
docs/doxygen/install/install-macs.doxygen (1)
1-24: Well-structured introduction to macOS installation.The introduction section provides a clear overview of the purpose of the document and appropriate cautions about building from source versus using binary installers. There appears to be a minor grammatical issue on lines 21-22:
"search in our issue tracker, already known. If not, please write..."
This would read more clearly as:
"search in our issue tracker to see if the issue is already known. If not, please write..."
- search in our <a href="https://github.com/OpenMS/OpenMS/issues">issue tracker</a>, - already known. If not, please write to the mailing list (open-ms-general AT lists.sourceforge.net) or report the error + search in our <a href="https://github.com/OpenMS/OpenMS/issues">issue tracker</a> + to see if the issue is already known. If not, please write to the mailing list (open-ms-general AT lists.sourceforge.net) or report the errordocs/doxygen/parameters/output/OpenMS_SimpleSVM.parameters (1)
14-28: Comprehensive SVM optimization parameters with detailed explanations.The log2_C, log2_gamma, and log2_p parameters are well documented with appropriate default values. The explanations clearly indicate how these values translate to actual SVM parameters.
The value
3.32192809489appears in log2_p default values. Consider adding a brief explanation of why this specific value is used (it appears to be log2(10)), as it might not be immediately obvious to users.docs/doxygen/parameters/output/TOPP_CVInspector.html (1)
10-15: Well-documented required and optional parameters.The required parameters (cv_files, cv_names, mapping_file) and optional parameters (ignore_cv, html) are clearly documented with appropriate descriptions and restrictions.
For the
ignore_cvparameter, consider adding a brief explanation of why these particular CVs (UO, PATO, BTO) are in the default ignore list, to provide users with context for these defaults.docs/doxygen/parameters/output/TOPP_FeatureFinderMetaboIdent.html (2)
18-18: Consider adding more specific description for candidates_out parameterThe
candidates_outparameter description mentions "Feature candidates (before filtering and model fitting)," but doesn't explain the intended use case for this output - is it for debugging, validation, or some other purpose? Adding a brief explanation of when users might want to use this parameter would be helpful.
20-21: Thread parameter should be marked as advancedThe
threadsparameter is displayed as a regular parameter while similar parameters likedebug,log, andno_progressare marked as advanced. For consistency with other TOPP tools, consider marking this as an advanced parameter.docs/doxygen/parameters/output/TOPP_EICExtractor.html (2)
7-7: Fix typo in tool descriptionThere's a typo in the node description:
-<span class="node_name">+EICExtractor</span><span class="node_description">Extracts intensities from dedicates positions in a LC/MS map</span> +<span class="node_name">+EICExtractor</span><span class="node_description">Extracts intensities from dedicated positions in a LC/MS map</span>
27-28: Fix typo in SNThreshold parameter descriptionThere's a small typo in the description for the SNThreshold parameter:
-<span class="item_description">S/N threshold for a smoothed raw peak to pass peak picking. Higher thesholds will result in less peaks.</span> +<span class="item_description">S/N threshold for a smoothed raw peak to pass peak picking. Higher thresholds will result in less peaks.</span>docs/doxygen/parameters/output/TOPP_AccurateMassSearch.html (2)
22-24: Clarify default value notation for database parametersThe database parameters
mappingandstructare marked as required, but their default values are shown in square brackets ([CHEMISTRY/HMDBMappingFile.tsv]and[CHEMISTRY/HMDB2StructMapping.tsv]). This could be confusing - are these truly required if defaults are provided? Consider either:
- Clarifying in the description that these are required but have default fallbacks
- Making the display consistent with how defaults are shown for other parameters
33-34: Add section description for mzTab sectionThe
mzTabsection node doesn't have a description, while all other sections do. Consider adding a brief description to maintain consistency with other sections and provide context for the parameters in this group.- <div class="node"><span class="node_name">++++mzTab</span><span class="node_description"></span></div> + <div class="node"><span class="node_name">++++mzTab</span><span class="node_description">Parameters related to mzTab output format</span></div>docs/doxygen/install/install-linux.doxygen (1)
1-349: Excellent comprehensive installation guide for Linux systems.This installation guide is thorough and well-organized, covering all aspects of building OpenMS on GNU/Linux systems. The documentation includes:
- Clear instructions for obtaining the source code
- Detailed package requirements for different distributions
- Build instructions for dependencies
- Configuration options with CMake
- Environment setup guidance
- Testing instructions
The guide is particularly helpful for addressing different scenarios, such as users without root privileges, and provides troubleshooting tips for common issues.
Consider making a few minor improvements:
- Line 87: The commented command uses
##instead of a single#, which could be confusing- Lines 241-244: The explanation about
ccmakemight be clearer if rearranged to mention upfront thatcmakeneeds to be executed first- ## sudo yum boost-devel libsvm-devel libzip-devel zlib-devel xerces-c-devel bzip2-devel libhdf5-devel glpk-devel + # sudo yum boost-devel libsvm-devel libzip-devel zlib-devel xerces-c-devel bzip2-devel libhdf5-devel glpk-devel- A full list of the CMake variables is shown when you execute - - \code - ccmake . - \endcode - - This works only after having executed <tt>cmake</tt> once (see @ref install_linux_openms) + A full list of the CMake variables can be shown by executing <tt>ccmake .</tt> after having executed <tt>cmake</tt> once as described above.docs/doxygen/parameters/output/OpenMS_PosteriorErrorProbabilityModel.parameters (1)
5-8: Consider improving the readability of this lengthy parameter description.The description for the
out_plotparameter is quite long and could benefit from some formatting improvements, such as breaking it into bullet points or shorter sentences.- <td style="vertical-align:top"> </td><td style="vertical-align:top">If given, the some output files will be saved in the following manner: <out_plot>_scores.txt for the scores and <out_plot> which contains the fitted values for each step of the EM-algorithm, e.g., out_plot = /usr/home/OMSSA123 leads to /usr/home/OMSSA123_scores.txt, /usr/home/OMSSA123 will be written. If no directory is specified, e.g. instead of '/usr/home/OMSSA123' just OMSSA123, the files will be written into the working directory.</td> + <td style="vertical-align:top"> </td><td style="vertical-align:top">If given, output files will be saved as follows:<br> + - <out_plot>_scores.txt: Contains the scores<br> + - <out_plot>: Contains the fitted values for each step of the EM-algorithm<br><br> + Example: out_plot = /usr/home/OMSSA123 creates /usr/home/OMSSA123_scores.txt and /usr/home/OMSSA123<br> + Note: If no directory is specified (e.g., just OMSSA123 instead of '/usr/home/OMSSA123'), the files will be written to the working directory.</td>docs/doxygen/parameters/output/TOPP_Decharger.html (1)
30-30: Consider formatting the long description for better readability.The description for the
potential_adductsparameter is very lengthy. Consider improving readability by using a structured format with line breaks.-<span class="item_description">Adducts used to explain mass differences in format: 'Element:Charge(+/-):Probability[:RTShift[:Label]]', i.e. the number of '+' or '-' indicate the charge, e.g. 'Ca:++:0.5' indicates +2. Probabilites have to be in (0,1]. RTShift param is optional and indicates the expected RT shift caused by this adduct, e.g. '(2)H4H-4:0:1:-3' indicates a 4 deuterium label, which causes early elution by 3 seconds. As a fifth parameter you can add a label which is tagged on every feature which has this adduct. This also determines the map number in the consensus file.</span> +<span class="item_description"> + Adducts used to explain mass differences in format: 'Element:Charge(+/-):Probability[:RTShift[:Label]]'<br> + <ul> + <li>The number of '+' or '-' indicate the charge, e.g. 'Ca:++:0.5' indicates +2</li> + <li>Probabilities must be in (0,1]</li> + <li>RTShift (optional): indicates the expected RT shift caused by this adduct<br> + Example: '(2)H4H-4:0:1:-3' indicates a 4 deuterium label, causing early elution by 3 seconds</li> + <li>Label (optional): tagged on every feature with this adduct; determines the map number in the consensus file</li> + </ul> +</span>docs/doxygen/parameters/output/TOPP_ClusterMassTraces.html (2)
7-8: Tool description could be more detailedThe current description "Creates pseudo spectra." is quite brief. Consider expanding this to better explain the purpose and function of the ClusterMassTraces tool, perhaps including information about when a user would want to use this tool in their workflow.
- <div class="node"><span class="node_name">+ClusterMassTraces</span><span class="node_description">Creates pseudo spectra.</span></div> + <div class="node"><span class="node_name">+ClusterMassTraces</span><span class="node_description">Creates pseudo spectra by clustering mass traces based on correlation of their chromatographic profiles.</span></div>
10-12: Input/output parameter descriptions could be more detailedThe descriptions for the input and output parameters are very minimal. Consider providing more context about what the input format actually contains and what the output represents.
-<span class="item_description">Mass traces</span><span class="item_tags">input file</span><span class="item_restrictions">*.consensusXML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">out</span><span class="item_value"></span> -<span class="item_description">output file</span><span class="item_tags">output file</span><span class="item_restrictions">*.mzML</span></div> +<span class="item_description">Input file containing mass traces extracted from LC-MS data</span><span class="item_tags">input file</span><span class="item_restrictions">*.consensusXML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">out</span><span class="item_value"></span> +<span class="item_description">Output file containing the generated pseudo spectra in mzML format</span><span class="item_tags">output file</span><span class="item_restrictions">*.mzML</span></div>
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- docs/doxygen/parameters/output/OpenMS_MetaboliteFeatureDeconvolution.parameters
- docs/doxygen/parameters/output/TOPP_DatabaseSuitability.cli
- docs/doxygen/parameters/output/OpenMS_TMTTenPlexQuantitationMethod.parameters
- docs/doxygen/parameters/output/OpenMS_LabeledPairFinder.parameters
- docs/doxygen/parameters/output/OpenMS_EmgGradientDescent.parameters
- docs/doxygen/parameters/output/OpenMS_FeatureDeconvolution.parameters
- docs/doxygen/parameters/output/OpenMS_IsotopeFitter1D.parameters
- docs/doxygen/parameters/output/OpenMS_SavitzkyGolayFilter.parameters
- docs/doxygen/parameters/output/OpenMS_PeakPickerHiRes.parameters
- docs/doxygen/parameters/output/OpenMS_ItraqFourPlexQuantitationMethod.parameters
- docs/doxygen/parameters/output/TOPP_FeatureFinderCentroided.cli
- docs/doxygen/parameters/output/OpenMS_MorphologicalFilter.parameters
- docs/doxygen/parameters/output/TOPP_AssayGeneratorMetabo.html
- docs/doxygen/parameters/output/OpenMS_MRMDecoy.parameters
- docs/doxygen/parameters/output/OpenMS_SpectrumPrecursorComparator.parameters
- docs/doxygen/parameters/output/OpenMS_LowessSmoothing.parameters
- docs/doxygen/parameters/output/OpenMS_TheoreticalSpectrumGeneratorXLMS.parameters
- docs/doxygen/parameters/output/OpenMS_TOPPASBase.parameters
- docs/doxygen/images/SpectrumSettings.graphml
- docs/doxygen/parameters/output/OpenMS_MRMTransitionGroupPicker.parameters
- docs/doxygen/parameters/output/TOPP_FeatureFinderMetabo.cli
- docs/doxygen/parameters/output/OpenMS_MascotRemoteQuery.parameters
- docs/doxygen/images/ExperimentalSettings.graphml
- docs/doxygen/parameters/output/OpenMS_DiaPrescore.parameters
- docs/doxygen/parameters/output/OpenMS_StablePairFinder.parameters
- docs/doxygen/parameters/output/OpenMS_FeatureFinderAlgorithmPicked.parameters
- docs/doxygen/parameters/output/OpenMS_BayesianProteinInferenceAlgorithm.parameters
- docs/doxygen/parameters/output/OpenMS_ElutionModelFitter.parameters
- docs/doxygen/parameters/output/OpenMS_SignalToNoiseEstimatorMeanIterative.parameters
- docs/doxygen/parameters/output/OpenMS_EGHTraceFitter.parameters
- docs/doxygen/parameters/output/OpenMS_EmgModel.parameters
- docs/doxygen/parameters/output/TOPP_BaselineFilter.cli
- docs/doxygen/parameters/output/TOPP_DigestorMotif.html
- docs/doxygen/parameters/output/OpenMS_ConsensusIDAlgorithmSimilarity.parameters
- docs/doxygen/parameters/output/OpenMS_SpectrumAlignment.parameters
- docs/doxygen/parameters/output/OpenMS_PoseClusteringShiftSuperimposer.parameters
- docs/doxygen/parameters/output/OpenMS_WindowMower.parameters
- docs/doxygen/parameters/output/OpenMS_GaussFilter.parameters
- docs/doxygen/parameters/output/OpenMS_IsotopeModel.parameters
- docs/doxygen/parameters/output/TOPP_Digestor.html
- docs/doxygen/parameters/output/OpenMS_PeptideAndProteinQuant.parameters
- docs/doxygen/parameters/output/OpenMS_ThresholdMower.parameters
- docs/doxygen/parameters/output/OpenMS_PeakPickerChromatogram.parameters
- docs/doxygen/parameters/output/OpenMS_TMTSixPlexQuantitationMethod.parameters
- docs/doxygen/parameters/output/OpenMS_ItraqEightPlexQuantitationMethod.parameters
🧰 Additional context used
🪛 YAMLlint (1.35.1)
.readthedocs.yaml
[warning] 22-22: wrong indentation: expected 2 but found 4
(indentation)
[error] 23-23: no new line character at the end of file
(new-line-at-end-of-file)
🪛 Biome (1.9.4)
docs/doxygen/doxygen-awesome-css/doxygen-awesome.css
[error] 2182-2182: Unexpected shorthand property background after background-image
(lint/suspicious/noShorthandPropertyOverrides)
🔇 Additional comments (221)
_static/css/custom.css (2)
154-158: Clean implementation for cross-browser scrollbar removal.The implementation uses the appropriate CSS properties to hide scrollbars across different browsers:
scrollbar-width: nonefor Firefox-ms-overflow-style: nonefor IE/Edge
160-162: Properly handles WebKit browsers.The WebKit-specific pseudo-element selector completes the cross-browser solution for hiding scrollbars.
docs/doxygen/doxygen-awesome-css/doxygen-awesome.css (3)
1-28: Proper license inclusion for third-party CSS.Including the MIT license header is good practice for third-party code. The attribution to jothepro/doxygen-awesome-css is correctly maintained.
30-174: Well-structured CSS variable definitions.The CSS variables provide a comprehensive theming foundation with appropriate defaults for:
- Color scheme
- Spacing
- Typography
- Component styling
This approach makes the theme easily customizable without modifying the core CSS rules.
176-184: Responsive design with proper dark mode support.The theme properly handles:
- Mobile-specific adjustments via media queries
- Dark mode detection via
prefers-color-scheme- Class-based dark mode toggle support
This ensures consistent styling across different devices and user preferences.
Also applies to: 186-245, 248-305
.readthedocs.yaml (1)
14-15: Good addition of graphviz dependency.Adding graphviz as an apt package requirement is necessary for generating visual documentation diagrams.
docs/doxygen/parameters/output/OpenMS_NLargest.parameters (2)
1-9: Clear parameter documentation table structure.The table structure is well-organized with appropriate columns for parameter properties. The styling with vertical alignment enhances readability.
11-15: Helpful usage notes for documentation.The notes section provides useful context about how section names and advanced parameters are displayed, which helps users understand the documentation system.
docs/doxygen/parameters/output/TOPP_DeMeanderize.cli (3)
1-28: Documentation appears complete and well-structured.The CLI documentation for the DeMeanderize tool provides clear information about its purpose, usage, and parameters. The documentation follows the standard format for TOPP tools.
17-18: LGTM - Parameter specification is clear.The optional parameter for number of spots per row is well documented with default value and minimum restrictions.
4-4:❓ Verification inconclusive
Verify the date in the version information.
The version information contains what appears to be a future date (Nov 21 2024). Since we're currently in March 2025, this might be an error in the documentation or in the system that generated this information.
🏁 Script executed:
#!/bin/bash # Check if this date pattern appears in other documentation files echo "Checking for the date pattern in other documentation files..." grep -r "Nov 21 2024" docs/doxygen/parameters/output/Length of output: 20499
Action Required: Verify Version Date Consistency
- The CLI output files (e.g.,
docs/doxygen/parameters/output/TOPP_DeMeanderize.cli) consistently show the version string
Version: 3.1.0-pre-develop-2024-04-26 Nov 21 2024, 15:06:14, Revision: 7aa664c
across multiple files.- Note that the version tag includes two dates: a commit-related date (
2024-04-26) and a build timestamp (Nov 21 2024), which may appear out of step with the current date (March 2025).- Please confirm if these dates are intentional (e.g., reflecting an older commit built at a later time) or if there’s a misconfiguration in the build system that needs to be addressed.
Makefile (2)
9-9: Improved build directory structure.The change to
BUILDDIR = build/docs/sphinxprovides a more organized directory structure, making it clearer that the sphinx documentation is being built under the docs directory.
5-5:❓ Verification inconclusive
Verify the empty HTML directory setting.
The
SPHINXOPTSvariable now includes-D html_dir="", which sets an empty HTML directory. Please verify if this is intentional or if a specific directory path should be provided instead.
🏁 Script executed:
#!/bin/bash # Check if html_dir is referenced in sphinx configuration echo "Checking if html_dir is referenced in sphinx configuration files..." grep -r "html_dir" docs/Length of output: 169
Action Required: Confirm the Intent of the Empty html_dir Setting
Please verify that setting
html_dirto an empty string (-D html_dir="") in the Makefile is intentional. Our preliminary search in the documentation directory (docs/) did not find any references tohtml_dir, which might mean:
- The Sphinx configuration does not use or override the
html_dirvalue.- The empty setting is a deliberate override to bypass default behavior.
If this was intentional, consider adding a comment for clarity; otherwise, update the value with the appropriate HTML directory path.
- File: Makefile, line 5
docs/doxygen/parameters/output/OpenMS_ConsensusIDAlgorithmBest.parameters (2)
1-30: Well-structured parameter documentation.The parameter documentation for ConsensusIDAlgorithmBest is comprehensive and well-formatted. The HTML table provides clear information about each parameter, including types, defaults, restrictions, and descriptions.
27-30: Helpful notes for users.The notes section provides useful information about tooltip displays and advanced parameter formatting, enhancing the usability of the documentation.
docs/doxygen/parameters/output/TOPP_DatabaseFilter.cli (3)
1-28: Documentation appears complete and well-structured.The CLI documentation for the DatabaseFilter tool provides clear information about its purpose, usage, and parameters. The documentation follows the standard format for TOPP tools.
4-4: Verify the date in the version information.The version information contains what appears to be a future date (Nov 21 2024). Since we're currently in March 2025, this might be an error in the documentation or in the system that generated this information.
28-28: Consider removing the empty line at the end of the file.There's an empty line at the end of the file that doesn't serve any purpose.
docs/doxygen/parameters/output/OpenMS_ConsensusIDAlgorithmRanks.parameters (1)
1-30: Well-structured parameter documentation with clear layoutThe parameter documentation for ConsensusIDAlgorithmRanks is properly structured with a clear HTML table layout. All parameters include essential information (name, type, default, restrictions, description) and are consistently formatted. The explanations are concise yet complete.
A note section is included at the end providing useful meta-information about tooltips and advanced parameter styling.
docs/doxygen/parameters/output/TOPP_DTAExtractor.cli (1)
1-26: Comprehensive CLI documentation with complete usage informationThe DTAExtractor command-line interface documentation provides all necessary elements:
- Tool purpose and context
- Link to full documentation
- Version and citation information
- Clear usage syntax
- Well-organized options (mandatory, optional, common)
- Detailed parameter descriptions with constraints
The documentation follows a consistent format likely to be used across all TOPP tools, making it easy for users to navigate.
docs/doxygen/parameters/output/OpenMS_Plot2DCanvas.parameters (1)
1-40: Complete parameter documentation with appropriate restrictionsThe Plot2DCanvas parameter documentation is well-formatted and includes all necessary details for configuration. The parameters cover essential visualization aspects:
- File handling (
default_path)- Visual styling (
background_color,dot:gradient)- Performance settings (
interpolation_steps)- Feature visualization (
dot:feature_icon,dot:feature_icon_size)Each parameter has appropriate restrictions defined, and the note section provides helpful context for understanding parameter categorization.
docs/doxygen/parameters/output/OpenMS_QTClusterFinder.parameters (1)
1-95: Excellent comprehensive documentation with tooltips and advanced parameter indicatorsThis documentation for QTClusterFinder parameters is particularly well-implemented with several advanced features:
- Advanced parameter styling (italicized) to distinguish complexity levels
- Tooltip implementation using span title attributes for section categories
- Detailed parameter grouping by functional area (distance_RT, distance_MZ, distance_intensity)
- Comprehensive restrictions and defaults for each parameter
- Clear explanations of parameter impact and usage context
The hierarchical organization makes this complex set of parameters more approachable and understandable for users.
docs/doxygen/parameters/output/OpenMS_SpectraMerger.parameters (2)
1-3: Documentation structure looks good.The table header and formatting are well-structured and consistent with documentation standards.
101-105: Clear documentation notes.The notes section provides helpful context about section tooltips and advanced parameter styling.
docs/doxygen/parameters/output/OpenMS_MultiplexDeltaMassesGenerator.parameters (3)
1-3: Well-structured parameter documentation.The table header and formatting are consistent with documentation standards.
5-73: Comprehensive isotope labeling mass shifts.The parameters provide a complete set of mass shift values for various isotope labeling strategies, properly formatted with descriptions that include the chemical composition changes and UniMod references.
76-80: Clear documentation notes.The notes section effectively communicates how section documentation is displayed and that advanced parameters are italicized.
docs/doxygen/parameters/output/OpenMS_Plot3DCanvas.parameters (2)
1-34: Well-structured and comprehensive parameter documentation.The parameter documentation for the Plot3DCanvas class is clear, well-organized, and follows a consistent format. Each parameter is clearly described with its type, default value, and any applicable restrictions. The table format makes it easy for users to understand the available configuration options.
36-40: Helpful additional context in the notes section.The notes section provides useful information about documentation tooltips and clearly indicates how advanced parameters are visually distinguished (in italic), which is consistent with how the
mrmparameter is displayed in the table (lines 35-38).docs/doxygen/parameters/output/TOPP_AssayGeneratorMetaboSirius.cli (3)
1-11: Clear tool description with proper citations.The documentation header effectively describes the tool's purpose and includes proper citations for OpenMS. This follows the standard format for TOPP tool documentation and provides users with necessary reference information.
12-51: Comprehensive command-line options documentation.The options section clearly marks mandatory parameters with asterisks and provides detailed descriptions for each parameter. Default values and valid ranges are appropriately documented, making it easy for users to understand how to use the tool correctly.
52-59: Standard TOPP options section completes the documentation.The common TOPP options section follows the established pattern for OpenMS tool documentation, ensuring consistency across the documentation suite and providing users with familiar configuration options.
docs/doxygen/parameters/output/OpenMS_FeatureGroupingAlgorithmLabeled.parameters (2)
1-39: Well-formatted parameter documentation with clear distinctions.The parameter table is well-structured and provides comprehensive information for each parameter. The distinction between regular and advanced parameters (like the italicized
mrmparameter) is consistent with the documentation guidelines mentioned in the notes section.
40-45: Helpful notes section enhances user understanding.The notes section provides clear guidance on how to interpret the documentation, particularly regarding section tooltips and the visual distinction for advanced parameters.
docs/doxygen/parameters/output/TOPP_Decharger.cli (3)
1-11: Comprehensive tool description with appropriate citations.The documentation header effectively describes the tool's purpose and includes proper citations for both OpenMS and the specific Decharger algorithm. This provides users with valuable reference information for both the platform and the specific method implemented.
12-24: Clear command-line usage instructions with mandatory options highlighted.The documentation clearly indicates which options are mandatory and provides descriptions for each parameter. The note about additional algorithm parameters directs users to the ini file for more detailed information, which is helpful for managing documentation complexity.
25-39: Complete documentation with references to additional resources.The common TOPP options section and information about configuration subsections follow the established pattern for OpenMS documentation. The inclusion of links to online documentation ensures users can find more detailed information if needed.
docs/doxygen/parameters/output/TOPP_Epifany.cli (1)
1-49: Documentation looks comprehensive and well-structured.The documentation for the Epifany tool is clear, well-organized, and provides all necessary information for users. It includes:
- Tool description and link to full documentation
- Version and citation information
- Clear usage instructions
- Comprehensive parameter documentation with defaults and valid values
- Common TOPP options
- Reference to configuration subsections
docs/doxygen/parameters/output/TOPP_ClusterMassTraces.cli (1)
1-29: Documentation is well-formatted and complete.This documentation file for the ClusterMassTraces tool provides all essential information in a clear, consistent format. The parameter descriptions are thorough, including default values and valid ranges where applicable. The formatting matches the documentation style used in other TOPP tool documentation.
docs/doxygen/parameters/output/OpenMS_FeatureGroupingAlgorithmKD.parameters (1)
1-130: Parameter documentation is detailed and well-structured.The HTML table format provides an excellent overview of all parameters for the FeatureGroupingAlgorithmKD class. The documentation includes:
- Clear organization of parameters with intuitive naming
- Proper distinction between basic and advanced parameters (using italics)
- Comprehensive description of each parameter's purpose
- Appropriate specification of restrictions and default values
- Helpful tooltips for section names (noted at the bottom)
The table structure and formatting are consistent with documentation best practices.
docs/doxygen/parameters/output/OpenMS_TransitionTSVFile.parameters (1)
1-25: Parameter documentation is clear and follows the established format.The documentation for TransitionTSVFile parameters is well-organized and provides all necessary information. The parameter descriptions are detailed enough to guide users properly, especially the explanation for
override_group_label_checkwhich includes an important caution about when to use it. The formatting is consistent with other parameter documentation files.docs/doxygen/parameters/output/OpenMS_SpectrumAnnotator.parameters (1)
1-50: Documentation structure looks good and follows Doxygen standards.The parameter documentation for OpenMS_SpectrumAnnotator is well-structured with a clear HTML table format that provides comprehensive information for each parameter including name, type, default values, restrictions, and descriptions. The use of consistent vertical alignment and formatting improves readability.
docs/doxygen/parameters/output/TOPP_ExecutePipeline.cli (3)
1-26: CLI documentation is comprehensive and follows project standards.The documentation for the ExecutePipeline tool is well-formatted and provides all necessary information including a clear description, version information, citation details, usage examples, and parameter descriptions. The separation between mandatory and optional parameters is clear, and common TOPP options are well-documented.
4-4: Version information format may need standardization.The version string "3.1.0-pre-develop-2024-04-26 Nov 21 2024, 15:06:14, Revision: 7aa664c" contains a future date (Nov 21 2024). This appears to be either a placeholder or an incorrectly set date. Consider implementing a consistent version string format that accurately reflects the current version and build date.
3-3:❓ Verification inconclusive
Ensure documentation link is correct.
The documentation URL points to the nightly build. Make sure this is the intended behavior and that this URL will remain valid when the documentation is published. If this is a placeholder, consider adding a mechanism to replace it with the appropriate URL during the build process.
🏁 Script executed:
#!/bin/bash # Check if the documentation URL is accessible and valid curl -s -o /dev/null -w "%{http_code}" http://www.openms.de/doxygen/nightly/html/TOPP_ExecutePipeline.htmlLength of output: 112
Documentation URL Verification:
The URL currently returns a 301 status code, which indicates that it is permanently redirecting to another location. Please verify that pointing to the nightly build—which redirects as it does—is the intended behavior. If this URL is meant to represent published documentation rather than a nightly snapshot, consider updating it or adding build-time logic to replace it with the appropriate URL during release cycles.
- File:
docs/doxygen/parameters/output/TOPP_ExecutePipeline.cli- Concern: Nightly build URL returns a 301 redirect; confirm if this is the desired outcome.
docs/doxygen/parameters/output/OpenMS_FeatureFinderAlgorithmMetaboIdent.parameters (2)
1-110: Well-structured parameter documentation with clear sections and tooltips.The parameter documentation for OpenMS_FeatureFinderAlgorithmMetaboIdent provides comprehensive information with good organization. The use of tooltips for section names and italics for advanced parameters enhances usability. The hierarchical structure with sections like "extract", "detect", "model", and subsections like "check" makes the documentation more navigable.
100-103:❓ Verification inconclusive
Boolean parameter using string type.
The "init_mom" parameter is of type string with true/false values, but appears to be a boolean option for "Alternative initial parameters for fitting through method of moments." Consider consistency in parameter types throughout the codebase - if boolean values are typically represented as string type with "true"/"false" values in OpenMS, then this is fine, but if other methods use actual boolean types, consider standardizing.
🏁 Script executed:
#!/bin/bash # Check how boolean parameters are typically defined in OpenMS rg -A 2 "bool.*true.*false|string.*true.*false" --glob "*.parameters" | head -n 20Length of output: 84
Manual Verification Required: Boolean Parameter Consistency
It appears that the
init_momparameter is documented as a string holding boolean-like values (“true, false”) in the parameters file. However, our automated check did not return any evidence about how boolean parameters are typically represented elsewhere in the OpenMS codebase. Please manually verify whether other OpenMS components define such parameters as actual booleans rather than strings. If they do, consider standardizing this pattern for consistency.
- Action: Manually inspect similar parameter definitions in other
.parametersfiles to confirm if boolean values are consistently implemented.- Location:
docs/doxygen/parameters/output/OpenMS_FeatureFinderAlgorithmMetaboIdent.parameters(Lines 100–103)docs/doxygen/parameters/output/OpenMS_FeatureDistance.parameters (1)
1-70: Parameter documentation is clear and comprehensive.The parameter documentation for OpenMS_FeatureDistance provides detailed information about distance calculations with well-organized sections for RT, MZ, and intensity components. The use of tooltips for section names enhances usability, and the explanations of each parameter's purpose and effect are thorough.
docs/doxygen/parameters/output/OpenMS_PeptideIndexing.parameters (1)
1-75: Well-structured and comprehensive parameter documentation.This is a thorough documentation of the PeptideIndexing class parameters with clear descriptions and properly formatted HTML structure. The table provides complete information about parameter types, default values, restrictions, and detailed descriptions that will be helpful for users of this class.
docs/doxygen/parameters/output/OpenMS_SimpleTSGXLMS.parameters (1)
1-75: Overall documentation is well-structured and informative.The parameter documentation provides clear information on the SimpleTSGXLMS class capabilities related to ion peak generation in mass spectrometry. The structure is consistent with other parameter documentation files.
docs/doxygen/parameters/output/OpenMS_ExtendedIsotopeFitter1D.parameters (1)
1-50: Complete and well-formatted parameter documentation.This documentation thoroughly describes the ExtendedIsotopeFitter1D parameters with proper formatting. All parameter names are italicized, indicating they are all advanced parameters, which is consistent with the note at the bottom. The descriptions provide good technical details about the isotope fitting functionality.
docs/doxygen/parameters/output/OpenMS_FeatureGroupingAlgorithmQT.parameters (2)
40-48: Excellent use of tooltips for section names.The use of
<span title="...">for providing additional context in tooltips is a nice usability enhancement. This helps users understand parameter groupings without cluttering the main display.
1-95: Comprehensive parameter documentation with good organization.This documentation provides detailed information about the FeatureGroupingAlgorithmQT parameters, with clear explanations of distance metrics and grouping behavior. The organization into logical sections with tooltips enhances usability.
docs/doxygen/parameters/output/OpenMS_SpectraIDViewTab.parameters (8)
1-4: Well-structured parameter documentation header.The header and table structure follow proper Doxygen formatting conventions with appropriate column headers for parameter documentation.
5-8: Comprehensive documentation for isotope modeling parameter.The parameter documentation clearly explains the different isotope model options and their implications, which is essential for users to understand the performance trade-offs.
9-18: Well-documented isotope configuration parameters.These parameters provide the necessary configuration options for both coarse and fine isotope modeling with appropriate default values and descriptions.
19-43: Clear documentation for visualization control parameters.The parameters for meta-information display, loss addition, sorting, and precursor peak options are well-documented with boolean choices and descriptive explanations.
44-93: Comprehensive ion type selection parameters.The documentation thoroughly covers all available ion types (a, b, c, x, y, z, etc.) that can be included in the spectrum visualization, providing users with complete control over which fragments to display.
94-143: Well-defined intensity parameters for different ion types.The intensity parameters allow fine-grained control over the relative display intensity of different ion types, which is crucial for customized spectrum visualization.
144-153: Clear documentation for alignment tolerance parameters.The alignment tolerance parameters are properly documented with explanations of both absolute and relative tolerance options.
154-160: Helpful notes for parameter interpretation.The notes section provides useful clarification about tooltip display and formatting conventions for advanced parameters.
docs/doxygen/parameters/output/OpenMS_Fitter1D.parameters (4)
1-4: Consistent parameter documentation structure.The header and table follow the same documentation structure as other parameter files, maintaining consistency across the documentation.
5-13: Clear documentation of interpolation and bounding box parameters.The advanced interpolation and bounding box parameters are well-documented with appropriate default values and explanations of their effects.
14-23: Well-defined statistical model parameters.The statistical parameters for model mean and variance are clearly documented with appropriate default values and descriptions.
24-30: Consistent notes section for parameter interpretation.The notes section maintains consistency with other parameter files, providing the same guidance about tooltips and advanced parameter formatting.
docs/doxygen/parameters/output/TOPP_DecoyDatabase.cli (5)
1-8: Comprehensive tool description and citation information.The CLI documentation begins with a clear description of the tool's purpose, along with proper citation information and version details, which is essential for academic users.
9-14: Clear usage instructions with proper INI file guidance.The usage section properly indicates the command structure and mentions the importance of the INI file for detailed algorithm parameters.
15-44: Well-documented mandatory and optional parameters.The documentation clearly marks mandatory options with asterisks and provides detailed descriptions for all parameters, including input/output files, decoy string configuration, and enzyme selection.
45-52: Comprehensive common TOPP options section.The common options section provides essential information about INI file usage, threading, and help access, which is valuable for users new to TOPP tools.
53-60: Clear guidance for accessing additional documentation.The final section properly directs users to configuration subsections and online documentation for more detailed information.
docs/doxygen/parameters/output/OpenMS_TOPPViewBase.parameters (8)
1-4: Well-structured parameter documentation header.The header and table follow the standard documentation structure, maintaining consistency with other parameter files.
5-28: Comprehensive global preference parameters.The general preference parameters are well-documented, covering important settings like temporary file cleanup, version checking, default paths, and file change handling.
29-53: Clear documentation for memory management parameters.The parameters for cached MS1/MS2 spectra handling are well-documented with explicit descriptions of their impacts on memory usage.
54-83: Well-documented 1D view parameters.The 1D view parameters thoroughly document path and color settings with appropriate default values and descriptions. The use of tooltips for section names enhances usability.
84-113: Comprehensive 2D view configuration parameters.The 2D view parameters cover all necessary settings for background color, interpolation, gradients, and feature icons with clear descriptions and appropriate default values.
114-143: Well-defined 3D view visualization parameters.The 3D view parameters provide detailed control over visualization settings including background color, shading mode, gradient, and line width with appropriate constraints.
144-293: Extensive identification view parameters.The identification view section provides a comprehensive set of parameters for controlling spectrum visualization, mirroring many of the parameters from SpectraIDViewTab with appropriate default values specific to this context.
294-300: Consistent notes section for parameter interpretation.The notes section maintains consistency with other parameter files, providing guidance about tooltips and advanced parameter formatting.
docs/doxygen/parameters/output/OpenMS_TransitionPQPFile.parameters (1)
1-25: Great documentation structure and formatting.The parameter documentation for the OpenMS_TransitionPQPFile class is well-organized with clear descriptions for each parameter. The HTML table structure with consistent vertical alignment provides good readability. All parameters include appropriate type information, default values, restrictions, and comprehensive descriptions that explain their purpose.
docs/doxygen/parameters/output/TOPP_Digestor.cli (1)
1-45: Well-structured command-line interface documentation.The CLI documentation for the Digestor tool is comprehensive and follows a logical structure. It includes:
- Clear tool description and version information
- Proper citation details
- Well-organized command-line options with mandatory options clearly marked
- Complete parameter descriptions with valid values and defaults
- Separate sections for different types of options (core functionality, output options, common options)
This documentation will be valuable for users learning to use the Digestor tool through the command line.
docs/doxygen/parameters/output/OpenMS_MRMFeatureFinderScoring.parameters (1)
1-395: Comprehensive parameter documentation with excellent organization.This extensive documentation for the OpenMS_MRMFeatureFinderScoring class provides a complete reference of all available parameters. The documentation:
- Clearly distinguishes between required (bold) and advanced (italic) parameters
- Groups related parameters logically (TransitionGroupPicker, PeakPickerChromatogram, DIAScoring, etc.)
- Provides detailed descriptions explaining the purpose and effect of each parameter
- Includes valid ranges and restrictions where applicable
- Maintains consistent formatting throughout the lengthy document
This level of detail will greatly assist users in configuring this complex feature finder correctly.
docs/doxygen/parameters/output/OpenMS_AScore.parameters (1)
1-36: Clear and concise parameter documentation.The parameter documentation for the OpenMS_AScore class is well-structured and complete. Each parameter has a clear description and appropriate type information, default values, and restrictions. The distinction between required (bold) and advanced (italic) parameters is helpful for users.
The explanatory note at the end about tooltips and advanced parameter styling provides good context for users navigating the documentation.
docs/doxygen/parameters/output/OpenMS_FeatureFindingMetabo.parameters (1)
1-85: Well-structured parameter documentation with clear explanationsThe parameter documentation for FeatureFindingMetabo is well-organized with detailed descriptions for each option. The clear distinction between standard and advanced parameters (using bold/italic formatting) helps users understand parameter importance.
docs/doxygen/parameters/output/OpenMS_FeatureGroupingAlgorithmUnlabeled.parameters (1)
25-109: Well-structured documentation with effective use of tooltipsThe integration of tooltips for distance component sections (using
<span title="...">) enhances usability by providing context when hovering over section names. The organization of related parameters into logical groups improves readability.docs/doxygen/parameters/output/TOPP_FalseDiscoveryRate.cli (2)
42-45: Documentation looks comprehensive and well-structured.The documentation provides clear information about the tool's purpose, parameters, and usage. The references to additional resources like the INI file editor and online documentation are helpful for users.
4-4:✅ Verification successful
Version date appears inconsistent.
The version string contains what appears to be conflicting dates: "2024-04-26" followed by "Nov 21 2024". This might confuse users about which is the actual release date.
🏁 Script executed:
#!/bin/bash # Check if this date format is consistent with other TOPP tool documentation files # Look for other version strings in TOPP documentation files to verify the pattern find docs/doxygen/parameters/output/ -name "TOPP_*.cli" -not -name "TOPP_FalseDiscoveryRate.cli" | head -n 3 | xargs grep -A 1 "Version:"Length of output: 743
Version string pattern confirmed across TOPP CLI files
After checking similar TOPP documentation files, we observed that the version string indocs/doxygen/parameters/output/TOPP_FalseDiscoveryRate.cli—which displays both an ISO-formatted date ("2024-04-26") and a traditional timestamp ("Nov 21 2024, 15:06:14")—is used consistently throughout the repository. Although the dual-date format might seem inconsistent at first glance, it appears to be the intended output (possibly denoting different aspects like build date and release date). If deemed necessary, please consider adding a brief note clarifying the purpose of each date to help users understand the versioning scheme.docs/doxygen/parameters/output/TOPP_ClusterMassTracesByPrecursor.cli (2)
5-5: Version date format is inconsistent.Similar to the previous file, the version string contains potentially conflicting dates: "2024-04-26" followed by "Nov 21 2024", which might confuse users.
2-38: Documentation is clear and comprehensive.The documentation thoroughly describes the tool's purpose, required inputs, and available options. The parameter descriptions are detailed and provide good context about how they affect the tool's behavior.
docs/doxygen/parameters/output/OpenMS_TraceFitter.parameters (2)
1-14: Parameter table is well-structured and formatted.The HTML table format is clean, with appropriate styling and clear organization of parameter information. The use of italics for advanced parameters makes them easily distinguishable.
16-20: Helpful documentation notes.The note section provides important context about the documentation conventions, particularly explaining the styling differences (italic for advanced parameters) and tooltip functionality.
docs/doxygen/parameters/output/OpenMS_SignalToNoiseEstimator.parameters (2)
1-49: Comprehensive parameter documentation.The parameter table is well-structured with detailed descriptions for each parameter. The styling differentiation between regular (bold) and advanced (italic) parameters is consistent with the documentation conventions explained in the notes.
51-55: Clear documentation conventions.The note section clearly explains the styling conventions used in the documentation, helping users understand the significance of italic vs. bold parameter names and how to access additional information via tooltips.
docs/doxygen/parameters/output/TOPP_AssayGeneratorMetaboSirius.html (1)
1-37: Documentation looks well-structured and completeThe HTML documentation for AssayGeneratorMetaboSirius is well-formatted with clear parameter definitions, including required parameters, advanced parameters, descriptions, and valid restrictions.
docs/doxygen/parameters/output/OpenMS_SONARScoring.parameters (1)
1-26: Documentation is clear and well-formattedThe parameter documentation for OpenMS_SONARScoring is well-organized in a tabular format with appropriate descriptions and restrictions for each parameter. The notes section provides helpful context for understanding parameter naming conventions.
docs/doxygen/parameters/output/OpenMS_SignalToNoiseEstimatorMedian.parameters (2)
6-8: Comprehensive parameter descriptionThe detailed explanation of the max_intensity parameter is very helpful, particularly for explaining the potential impacts of setting it too high or too low, and the comparison with the MeanIterative-S/N implementation.
1-56: Complete and well-structured documentationThe parameter documentation for OpenMS_SignalToNoiseEstimatorMedian is comprehensive, properly formatted, and includes clear distinction between standard and advanced parameters (using italic styling). The explanations are thorough and provide good guidance for users.
docs/doxygen/parameters/output/OpenMS_ZhangSimilarityScore.parameters (1)
5-8:❓ Verification inconclusive
Default value mismatch with actual code
The documentation indicates the default value for
toleranceis 0.2, but according to the summary, it should be 0.3. Please verify the correct default value and update the documentation accordingly.
🏁 Script executed:
#!/bin/bash # Search for the default value of tolerance parameter in ZhangSimilarityScore class rg -A 3 -B 3 "ZhangSimilarityScore.*tolerance.*=.*0\.[23]" --type cppLength of output: 71
Inconclusive default value verification for
toleranceparameterThe automated search did not locate any default assignment for
tolerancein theZhangSimilarityScoreclass, so we couldn’t definitively confirm whether the correct default is 0.2 or 0.3. The documentation currently lists 0.2, yet the summary suggests it should be 0.3. Please perform a manual check on theZhangSimilarityScoreimplementation to verify the actual default value assigned totoleranceand update the documentation indocs/doxygen/parameters/output/OpenMS_ZhangSimilarityScore.parameters(lines 5–8) accordingly.docs/doxygen/parameters/output/TOPP_CometAdapter.cli (7)
2-10: Documentation header looks goodThe header section includes proper documentation for the CometAdapter tool, including full documentation URL, version information, and appropriate citations for both OpenMS and the specific CometAdapter tool.
12-14: Clear usage descriptionThe usage information is concise and correctly formatted, providing users with the basic command structure needed to run the tool.
15-21: Mandatory options clearly indicatedAll mandatory options are properly marked with asterisks and include detailed descriptions of their purpose. The use of asterisks and explanatory text for each option makes it easy for users to understand what parameters are required.
22-33: Parameter documentation is comprehensiveThe non-mandatory options are well-documented with clear explanations, default values, and parameter restrictions where applicable. The explanations provide sufficient detail for users to understand how these parameters affect the tool's operation.
47-104: Fragment mass tolerance description is informativeThe description for the fragment mass tolerance parameter includes helpful CAUTION notes about memory usage implications and suggestions for mitigating potential issues. This type of documentation is particularly valuable for parameters that can impact system resources.
105-139: Modification documentation is well structuredThe documentation for fixed and variable modifications is detailed and includes a comprehensive list of possible values. The note about binary modifications and its relation to variable modifications provides important context for using these parameters together.
140-155: Common TOPP options and PeptideIndexing sectionThe documentation properly includes both tool-specific options (PeptideIndexing) and common TOPP options like INI file support and threading. This ensures users have access to all relevant configuration options.
docs/doxygen/parameters/output/OpenMS_SpectrumCheapDPCorr.parameters (5)
1-3: Table header is clear and structuredThe header of the parameters table defines all necessary columns (Name, Type, Default, Restrictions, Description) that users need to understand the parameters.
4-8: Parameter 'variation' is well documentedThe description clearly explains the purpose and impact of the parameter, including the important note about performance implications for large values. This helps users understand the trade-offs of different settings.
9-13: Parameter 'int_cnt' has comprehensive optionsThe description effectively uses line breaks to enumerate the different options (0-3) and what each value means, making it easy to understand the effect of each choice.
14-18: Parameter 'keeppeaks' documentation is conciseThe description clearly explains what the flag does in a single, easy-to-understand sentence.
19-25: Documentation notes are helpfulThe notes section provides additional context about tooltips and formatting conventions, helping users understand how to interpret advanced parameters and section names.
docs/doxygen/parameters/output/TOPP_FeatureFinderMultiplex.cli (6)
2-7: Tool description and citation information are clearThe header section properly describes the FeatureFinderMultiplex tool's purpose (determination of peak ratios in LC-MS data) and includes appropriate citation information for OpenMS.
9-11: Usage information is conciseThe usage section clearly presents the command format in a simple, easy-to-understand manner.
12-17: Mandatory options are clearly identifiedThe documentation properly marks mandatory options with asterisks and provides clear descriptions of their purpose, including information about valid file formats.
18-29: Algorithm:labels parameter has excellent examplesThe description for the
algorithm:labelsparameter is particularly well done, providing multiple examples for different labeling scenarios (SILAC, Dimethyl, ICPL). This helps users understand exactly how to format their input for different experimental designs.
30-64: Detailed algorithm parametersThe documentation for algorithmic parameters is thorough, with clear explanations of each parameter's purpose, appropriate default values, and restrictions where applicable. Each parameter includes enough context to understand how it affects the analysis.
66-72: Common TOPP options are includedThe documentation properly includes common TOPP options like INI file support, threading, and help commands, ensuring users have access to all standard tool configuration options.
docs/doxygen/parameters/output/TOPP_ConsensusID.cli (8)
2-7: Tool description and citation information are clearThe header section properly describes the ConsensusID tool's purpose (computing consensus of peptide identifications) and includes appropriate citation information for OpenMS.
9-14: Usage information includes helpful note about additional parametersThe usage section not only shows the command format but also informs users that there are additional algorithm parameters available in the ini file or via the --helphelp option. This is helpful to ensure users are aware of all configuration possibilities.
15-18: Mandatory options are clearly markedThe documentation properly identifies mandatory options with asterisks and lists valid file formats for input and output parameters.
19-25: Input-specific parameters are labeled appropriatelyThe documentation clearly indicates which parameters are specific to idXML input with the "[idXML input only]" label, helping users understand when these options apply.
26-35: Filtering options are well-organizedThe filtering options are grouped under an appropriate heading, making it easy to find related parameters. Each parameter includes a clear explanation of its purpose and effect on the consensus process.
36-47: Algorithm choices are thoroughly explainedThe documentation for the algorithm parameter includes detailed descriptions of each available algorithm, along with information about their requirements and suitability for different scenarios. This helps users select the most appropriate algorithm for their data.
48-54: Common TOPP options are includedThe documentation properly includes common TOPP options like INI file support, threading, and help commands, ensuring users have access to all standard tool configuration options.
56-64: Subsection information is helpfulThe documentation provides information about valid configuration subsections and where to find additional documentation, which is useful for users who need to fine-tune the algorithms.
docs/doxygen/parameters/output/TOPP_FeatureFinderIdentification.cli (8)
12-32: Comprehensive usage instructions with well-organized parameter options.The usage section clearly articulates command structure and mandatory options. The parameters are well-categorized, making it easy for users to understand the tool's capabilities.
33-41: Well-documented extraction parameters with clear constraints.The ion chromatogram extraction parameters are thoroughly documented with appropriate default values and constraints.
42-49: Clear feature detection parameters with practical defaults.The feature detection parameters are well explained with sensible defaults and constraints that will help users understand how to configure the tool properly.
50-72: Comprehensive SVM parameter documentation with extensive options.The SVM parameters section provides detailed information about all configuration options with appropriate defaults. The log2 parameter descriptions clearly explain how values are used in practice.
73-77: Clear elution model fitting options.The elution model fitting parameters are concisely documented with appropriate options.
78-82: EMG scoring parameters well documented.The EMG (Exponentially Modified Gaussian) scoring parameters are clearly presented with suitable defaults.
83-91: Standard TOPP options included for completeness.The documentation appropriately includes common TOPP tool options that users would expect to find in all TOPP tools, providing a consistent interface experience.
1-11:✅ Verification successful
Great tool documentation with clear citation information.
The tool documentation provides excellent information about the
FeatureFinderIdentificationtool with appropriate citations for both OpenMS and the specific tool. The date format (Nov 21 2024) in line 4 appears to be a future date - this may need verification.
🌐 Web query:
What is the current date?💡 Result:
Today is Tuesday, March 4, 2025. Here are the key details about the current date:
Date Formats
- MM-DD-YYYY: 03-04-2025
- DD-MM-YYYY: 04-03-2025
- ISO Standard (YYYY-MM-DD): 2025-03-04
Calendar Details
- Day of the week: Tuesday
- Day of the year: 63 (out of 365)[6]
- Days remaining in 2025: 302[6]
- Current week number: 10 (assuming Monday as the first day of the week)[6]
Regional Variations
- The MM-DD-YYYY format is primarily used in the United States.
- Most other countries use DD-MM-YYYY to avoid confusion between month and day[2].
- The ISO standard (YYYY-MM-DD) is globally recommended for technical contexts[2].
This information resolves potential ambiguities, such as interpreting "03-04-2025" as March 4 (U.S. format) versus April 3 (many international formats)[2][6].
Citations:
- 1: https://www.timeanddate.com
- 2: https://www.inchcalculator.com/what-is-todays-date/
- 3: https://ourhappycorner.com/todays-date/
- 4: https://www.saturdaygift.com/todays-date/
- 5: https://www.calendardate.com/todays.htm
- 6: https://www.epochconverter.com/daynumbers
- 7: https://www.rapidtables.com/tools/todays-date.html
- 8: https://bluenotary.us/today-s-date/
- 9: https://today-date.com
- 10: https://artfuldiary.com/todays-date/
Documentation and Date Verification
The tool documentation is excellent, and the citation information is clear. After verifying the current date (March 4, 2025), the "Nov 21 2024" timestamp on line 4 is confirmed as a past date rather than a future date. No further changes are required.
docs/doxygen/install/install-macs.doxygen (5)
25-60: Comprehensive required applications section with helpful notes.This section clearly outlines all required applications and their versions. The inclusion of the command for installing command line tools on macOS is particularly helpful. The detailed information about Qt installation via Homebrew is also very useful.
61-119: Clear contrib package installation instructions.The documentation for installing the contrib package is thorough and provides step-by-step instructions with command examples. The note about avoiding spaces in the path is a helpful warning that can prevent common issues.
120-157: Helpful system libraries alternatives with practical warnings.The section on using system libraries as an alternative to the contrib package provides valuable options for users who prefer package managers. The notes about potential issues with Boost and CoinMP are important warnings.
158-223: Comprehensive build instructions with clear examples.The build instructions are well-structured and include all necessary steps with command examples. The notes about Boost and Qt4 provide important guidance for common scenarios.
224-251: Thorough testing instructions with useful ctest options.The testing section provides clear instructions on how to validate the installation, including useful examples of how to run specific test subsets in parallel.
docs/doxygen/parameters/output/OpenMS_SimpleSVM.parameters (4)
1-8: Well-structured table for SVM kernel parameter.The documentation starts with a clean, well-formatted table header and the kernel parameter is clearly documented with appropriate restrictions.
9-13: Clear cross-validation parameter documentation.The xval parameter documentation clearly explains its purpose for cross-validation with appropriate constraints.
29-43: Well-documented advanced parameters with clear restrictions.The advanced parameters (epsilon, cache_size, no_shrinking) are properly formatted in italics and include appropriate default values and restrictions.
44-50: Helpful notation explaining documentation formatting conventions.The notes section clearly explains the formatting conventions used in the documentation, which helps users understand the visual cues in the documentation.
docs/doxygen/parameters/output/TOPP_CVInspector.html (3)
1-6: Clear legend for parameter classification.The legend provides a helpful visual guide to distinguish between required and advanced parameters, improving user understanding of parameter importance.
7-9: Tool description and version information clearly presented.The tool overview provides a concise description of CVInspector's purpose and includes appropriate version information.
15-21: Comprehensive advanced parameters for tool configuration.The advanced parameters are well organized and documented, providing users with detailed control over tool behavior when needed.
docs/doxygen/parameters/output/OpenMS_MSPFile.parameters (1)
1-30: Well-structured documentation for the MSPFile parametersThe parameter documentation is clear and provides all necessary information for users. The table format makes it easy to understand each parameter's type, default value, restrictions, and purpose.
docs/doxygen/parameters/output/TOPP_DTAExtractor.html (1)
1-21: Well-organized documentation with clear parameter descriptionsThe HTML documentation for DTAExtractor provides a good overview of the tool's functionality and presents the parameters in a structured format. The legend clearly differentiates between required and advanced parameters, making it easy for users to understand what's essential.
docs/conf.py (3)
41-65: Good implementation of Doxygen integration for Read the DocsThe added code properly checks if the build is running on Read the Docs and conditionally executes Doxygen and Doxysphinx. This approach follows best practices for integrating external documentation tools with Sphinx.
66-79: Appropriate addition of graphviz extensionAdding the 'sphinx.ext.graphviz' extension is consistent with the changes in the
.readthedocs.yamlfile, where graphviz was added as a required package. This will enable proper rendering of GraphML files in the documentation.
125-125: Theme update to support modern documentation featuresChanging from 'furo' to 'sphinx_book_theme' is a good choice as it offers better integration with interactive elements and improved responsiveness, which enhances the user experience of the documentation.
docs/doxygen/parameters/output/OpenMS_SpectrumAlignmentScore.parameters (1)
1-30: Clear and concise parameter documentationThe parameter table for SpectrumAlignmentScore is well-structured with appropriate descriptions for each parameter. The inclusion of restrictions for boolean parameters (true, false) is helpful for users. The note section at the end provides useful information about tooltips and advanced parameter formatting.
docs/doxygen/parameters/output/TOPP_FeatureFinderMetaboIdent.html (1)
1-46: Documentation looks thorough and well-structuredThis documentation file for FeatureFinderMetaboIdent provides comprehensive parameter descriptions with good organization of required vs. advanced parameters, and logical grouping of related parameters into sections (extraction, detection, model fitting, etc.).
docs/doxygen/parameters/output/TOPP_EICExtractor.html (1)
10-11: Clarify default value notation for input parametersThe default value for the required input parameter is shown as
[]. If this represents an empty array or that no default exists, it would be helpful to use a consistent notation across all parameters or add a note explaining this notation in the documentation.docs/doxygen/parameters/output/OpenMS_IDMapper.parameters (1)
1-35: Parameter table is well-structured and clearThe documentation for the IDMapper parameters is well-formatted as a table with appropriate columns for name, type, default value, restrictions, and description. The notes section explaining tooltip behavior and advanced parameter formatting is also helpful.
docs/doxygen/parameters/output/OpenMS_MapRTTransformerModel.parameters (1)
1-98: Well-structured parameter documentation with clear organization.The HTML table provides comprehensive documentation for the MapRTTransformerModel parameters with excellent organization by model type. The parameter descriptions are thorough and help users understand the purpose of each option.
Some particularly helpful aspects:
- Logical grouping of parameters by model type (linear, b_spline, lowess, interpolated)
- Clear formatting with vertical alignment of content in table cells
- Comprehensive descriptions, especially for complex parameters like extrapolation types
- Consistent format for parameter restrictions and default values
docs/doxygen/parameters/output/TOPP_ConsensusID.html (1)
1-33: Well-organized documentation with appropriate parameter grouping.The documentation for the ConsensusID tool is well-structured with clear hierarchical organization. The legend at the top provides helpful visual cues for distinguishing required and advanced parameters.
The parameter descriptions are informative and provide good context for both required inputs and optional configurations. The nested structure with the "filter", "PEPIons", and "PEPMatrix" subsections helps users navigate related parameters effectively.
docs/doxygen/parameters/output/TOPP_FeatureFinderMetabo.html (1)
1-53: Comprehensive documentation with well-organized algorithmic parameters.The documentation for FeatureFinderMetabo is detailed and well-structured. The organization into logical sections (common, mtd, epd, ffm) makes it easy to navigate the complex set of parameters.
The descriptions are particularly helpful for understanding algorithmic choices, such as the different quantification methods and feature finder parameters. The restrictions and default values are clearly presented.
docs/doxygen/parameters/output/TOPP_FLASHDeconv.html (1)
1-57: Well-structured documentation for FLASHDeconv toolThe HTML documentation for the FLASHDeconv tool is comprehensive and well-organized, providing clear information on all parameters. The legend clearly distinguishes between required and advanced parameters, and the hierarchical organization makes it easy to navigate.
docs/doxygen/install/install-win.doxygen (1)
1-388: Excellent and comprehensive Windows build instructionsThis documentation provides thorough step-by-step instructions for building OpenMS on Windows. It covers all necessary prerequisites, installation steps for dependencies, and various build configurations. The guidance on using Visual Studio, handling the contrib package, and building the documentation is particularly valuable.
I especially appreciate the inclusion of:
- Clear prerequisites and setup instructions
- Detailed steps for contrib installation
- QT installation options (both binary and source)
- Documentation build instructions
- Advanced sections like building on the command line and using alternative IDEs like VSCode
This will significantly improve the developer experience for Windows users.
docs/doxygen/parameters/output/TOPP_ConsensusMapNormalizer.html (1)
1-23: Complete and well-formatted ConsensusMapNormalizer documentationThe parameter documentation for the ConsensusMapNormalizer tool is thorough and follows a consistent structure. Each parameter is clearly described with appropriate restrictions and tags, making it easy for users to understand how to use this tool for normalizing consensus maps.
docs/doxygen/parameters/output/TOPP_DatabaseFilter.html (1)
1-21: Clear and concise DatabaseFilter documentationThe documentation for the DatabaseFilter tool is well-structured and provides all necessary information for users to filter protein databases. The method parameter with its whitelist/blacklist options is particularly well explained, and all required parameters are clearly marked.
docs/doxygen/parameters/output/TOPP_FLASHDeconv.cli (8)
1-11: Well-structured header with proper citations.The header section provides essential information about the tool including its purpose, documentation link, version, and appropriate citations for both OpenMS and FLASHDeconv. The citation information follows a proper academic format with full references including DOIs.
15-45: Thorough documentation of input/output options.This section effectively documents the mandatory and optional input/output file parameters, providing clear descriptions of file formats and purposes. The explanation of each option is detailed and helps users understand the different output formats available.
46-75: Clear documentation of precursor-related parameters.The precursor-related parameters are well-documented with detailed explanations of their purpose, default values, and constraints. The description of how these parameters interact with each other and override other settings is particularly helpful for users trying to configure the tool correctly.
76-92: Informative explanation of MS spectra handling options.The documentation clearly explains how the tool handles MS spectra relationships and the detailed output options. The explanation of the
-preceding_MS1_countparameter provides good context about why users might need to adjust this value in top-down proteomics workflows.
93-108: Well-described spectra merging and FDR reporting options.The merging method options are thoroughly documented with explanations of each method's applicability to different types of datasets (e.g., Q-TOF vs NativeMS). The FDR reporting section clearly indicates this is a beta feature while explaining its purpose.
110-126: Comprehensive algorithm parameters section.The algorithm section provides detailed information about tolerance settings, mass and charge constraints, and isotope pattern similarity thresholds. The format for multi-value parameters is clearly documented with examples.
127-139: Well-structured feature tracing parameters section.The feature tracing parameters are logically organized and include detailed descriptions of their purpose and effect on sensitivity. The explanation of how negative values affect behavior (referencing other parameters) is particularly helpful.
140-148: Standard TOPP options section is complete.The common TOPP options section follows a consistent format with other TOPP tools, making it easy for experienced OpenMS users to find familiar configuration options.
docs/doxygen/parameters/output/TOPP_ClusterMassTracesByPrecursor.html (5)
1-6: Consistent legend formatting.The legend section follows a consistent format with other TOPP tool documentation, clearly differentiating between required and advanced parameters.
7-9: Clear tool description and version information.The node name and description accurately describe the tool's purpose of correlating precursor mass traces with fragment ion mass traces in SWATH maps. Version information is properly included.
10-13: Well-defined required input/output parameters.The required input and output parameters are clearly marked and include appropriate file format restrictions (*.consensusXML for inputs and *.mzML for output).
14-19: Comprehensive algorithm parameters.These parameters effectively document the algorithm's configuration options, including correlation thresholds, lag settings, and minimum ion requirements. The descriptions provide meaningful context about how each parameter affects the tool's operation.
20-26: Standard advanced options are well documented.The advanced parameters section includes standard OpenMS tool options for logging, debugging, threading, and progress reporting, maintaining consistency with other tool documentation.
docs/doxygen/parameters/output/TOPP_BaselineFilter.html (4)
1-7: Consistent documentation structure.The documentation follows the standard format for OpenMS tool documentation with proper legend explaining required and advanced parameters.
7-9: Clear tool description.The node description clearly explains the purpose of the BaselineFilter tool - removing baseline from profile spectra using a top-hat filter.
10-15: Comprehensive parameter documentation.The documentation thoroughly explains the required input/output parameters and the specific filtering parameters (structuring element length, unit, and method). The method parameter includes a helpful note for uncertain users to use the default.
16-21: Standard advanced options.The advanced parameters follow the common pattern across all OpenMS tools, maintaining documentation consistency throughout the toolkit.
docs/doxygen/parameters/output/TOPP_ExternalCalibration.html (4)
1-7: Consistent documentation structure.The documentation follows the established format for all OpenMS tool documentation with clear legend and styling.
7-9: Concise tool description.The node description clearly and concisely explains that the tool applies an external mass recalibration.
10-16: Well-documented calibration parameters.The documentation clearly describes the input/output parameters and calibration settings (offset, slope, power). The ms_level parameter with its array default value is properly formatted and explained.
17-22: Standard advanced options.The advanced parameters section maintains consistency with other TOPP tool documentation, making the interface familiar to experienced OpenMS users.
docs/doxygen/parameters/output/OpenMS_ConsensusIDAlgorithmPEPMatrix.parameters (1)
1-40: LGTM! Well-structured parameter documentation.This documentation provides clear and comprehensive information about the parameters of the
ConsensusIDAlgorithmPEPMatrixclass. The table format is consistent with Doxygen standards and effectively communicates the purpose, type, default values, and restrictions for each parameter.docs/doxygen/parameters/output/TOPP_ExecutePipeline.html (3)
1-6: LGTM! Legend is clear and well-formatted.The legend provides a clear visual distinction between required and advanced parameters, which helps users understand the importance of different parameters.
7-9: LGTM! Tool description is informative.The node name and description clearly communicate the purpose of the ExecutePipeline tool.
10-20: LGTM! Parameters are well-defined with appropriate classifications.All parameters are properly documented with clear descriptions, restrictions, and default values. The required parameters are appropriately marked, and the advanced parameters provide additional configuration options for experienced users.
docs/doxygen/parameters/output/OpenMS_PosteriorErrorProbabilityModel.parameters (3)
1-4: LGTM! Table structure is appropriate for parameter documentation.The table header and structure follow Doxygen documentation standards.
9-33: LGTM! Parameter descriptions are clear and well-formatted.The remaining parameters are documented with appropriate attributes and clear descriptions. The styling is consistent throughout the document.
34-40: LGTM! Notes section provides helpful context.The notes section effectively explains how documentation is displayed and indicates that advanced parameter names are in italic.
docs/doxygen/parameters/output/TOPP_Decharger.html (4)
1-6: LGTM! Legend is clear and consistent with other documentation.The legend effectively distinguishes between required and advanced parameters.
7-20: LGTM! Tool description and basic parameters are well-documented.The tool description clearly communicates the purpose of the Decharger tool, and the basic parameters are properly documented with appropriate classifications.
21-29: LGTM! Algorithm section parameters are well-structured.The feature decharging algorithm parameters are logically organized and described with appropriate default values and restrictions.
31-37: LGTM! Additional parameters are appropriately documented.The remaining parameters provide clear descriptions of their functionality with appropriate default values and restrictions.
docs/doxygen/parameters/output/TOPP_DecoyDatabase.html (3)
1-31: Well-structured documentation for the DecoyDatabase toolThe documentation provides comprehensive details about the DecoyDatabase tool parameters, including clear descriptions, types, restrictions, and default values. The HTML structure with proper CSS classes allows for clear visual distinction between required and advanced parameters.
12-31: Comprehensive parameter documentation with useful constraintsThe parameter documentation is thorough and includes important details such as:
- Input/output file types with appropriate file extension restrictions (*.fasta)
- Clear descriptions of each parameter's purpose
- Enumeration of possible values where applicable (e.g., prefix/suffix options)
- Logical organization of related parameters
7-8:✅ Verification successful
Version information should be aligned with release cycles
The version string "3.1.0-pre-develop-2024-04-26" indicates this is documentation for a pre-release version. Make sure this gets updated appropriately when releasing stable versions.
🏁 Script executed:
#!/bin/bash # Check if there's a consistent versioning approach across documentation files grep -r "version.*pre-develop" docs/doxygen/parameters/output/ | head -n 10Length of output: 2262
Action: Update Version Information with Official Release Cycles
The pre-release version string ("3.1.0-pre-develop-2024-04-26") appears consistently across all affected documentation files (e.g., TOPP_DecoyDatabase, TOPP_XTandemAdapter, TOPP_XMLValidator, etc.). While this consistency confirms the current state, please ensure the version is updated appropriately when releasing stable versions to align with the official release cycle.
docs/doxygen/parameters/output/TOPP_ClusterMassTraces.html (1)
1-24: Clear and consistent documentation structureThe documentation maintains the same styling and structure as other parameter documentation files, providing a consistent user experience. The parameters are well documented with appropriate descriptions.
docs/doxygen/parameters/output/OpenMS_MapAlignerPoseClusteringModel.parameters (3)
1-98: Comprehensive parameter documentation for different model typesThe documentation provides detailed information about parameters for different model types (linear, b_spline, lowess, interpolated), with clear descriptions of each parameter's purpose, type, default value, and restrictions. The table format makes it easy to understand the structure and relationships between parameters.
46-47: Detailed explanation for wavelength parameter is helpfulThe detailed explanation for the wavelength parameter is excellent, providing context about how it affects the B-spline and its relationship to input points. This level of detail helps users understand the impact of parameter changes.
4-7:❓ Verification inconclusive
Default model type mismatch with summary
According to the AI summary, this model's type parameter has a default value of "interpolated", but in the documentation it's set to "linear". Verify which is the correct default value for consistency across documentation.
🏁 Script executed:
#!/bin/bash # Check for references to the default model type in source code or other documentation grep -r "MapAlignerPoseClusteringModel.*type.*default" --include="*.cpp" --include="*.h" .Length of output: 92
Attention: Verify Default Model Type Consistency
It appears that the parameter file currently lists the default "type" as "linear", whereas the AI summary indicates it should be "interpolated". Our initial grep search in the source (i.e. *.cpp and *.h files) did not reveal any explicit initialization of a default value for
MapAlignerPoseClusteringModel. Please manually verify whether the intended default model type in the implementation is"linear"or"interpolated", and then update either the parameter documentation (located atdocs/doxygen/parameters/output/OpenMS_MapAlignerPoseClusteringModel.parameters) or the summary accordingly for consistency.
- Double-check the initialization of the
MapAlignerPoseClusteringModel(or related constructor/default settings) in the source code.- If the implementation indeed defaults to
"linear", update the AI summary; if it defaults to"interpolated", modify the documentation.docs/doxygen/parameters/output/OpenMS_TMTSixteenPlexQuantitationMethod.parameters (3)
1-101: Well-structured documentation for TMT16plex quantitation methodThe documentation comprehensively covers all the channels and parameters for the TMTSixteenPlexQuantitationMethod, with clear descriptions and appropriate restrictions where applicable.
90-93: Complex correction matrix format is well documentedThe correction matrix parameter provides a detailed explanation of the expected format, which is important given its complexity. The explanation of the N15/C13 notation and the example of how a row should look are particularly helpful for users.
96-100: Helpful notes about documentation tooltipsThe notes about section name tooltips and advanced parameter formatting provide useful context for users navigating the documentation. This type of meta-documentation improves usability.
docs/doxygen/parameters/output/TOPP_FalseDiscoveryRate.html (1)
1-37: Documentation looks good and well-structured.This new file provides comprehensive documentation for the FalseDiscoveryRate tool, with clear parameter organization and detailed descriptions. The hierarchical structure makes it easy to navigate through different parameter sections.
docs/doxygen/parameters/output/OpenMS_MapAlignerIdentificationModel.parameters (1)
1-98: Well-structured parameter documentation table.The table provides comprehensive information about the various model parameters with appropriate categorization by model type (linear, b_spline, lowess, interpolated). All parameters include proper descriptions, types, default values, and restrictions where applicable.
docs/doxygen/parameters/output/TOPP_DeMeanderize.html (1)
1-21: Documentation is complete and properly formatted.This file provides clear documentation for the DeMeanderize tool, correctly identifying required and advanced parameters with appropriate descriptions and restrictions.
docs/doxygen/parameters/output/TOPP_Epifany.html (1)
1-54: Comprehensive documentation with well-organized parameter sections.The documentation for the Epifany tool is thorough, with parameters properly organized into logical sections (algorithm, model_parameters, loopy_belief_propagation, param_optimize). Each parameter includes detailed descriptions that clearly explain their purpose and impact on the tool's functionality.
docs/doxygen/parameters/output/TOPP_FeatureFinderCentroided.html (7)
1-6: HTML Structure & Legend Block Formatting
The opening section clearly defines the container and legend with semantic HTML. The use of distinct CSS classes (e.g.ini_global,legend,item_required, anditem_advanced) makes the documentation intuitively navigable for end users.
7-9: Header and Version Information Clarity
The header node displaying “+FeatureFinderCentroided” along with its description is concise. The inclusion of the version parameter (3.1.0-pre-develop-2024-04-26) in an advanced item further aids in traceability and maintenance of documentation versions.
10-19: Instance Section Parameters Organization
The “Instance '1'” section groups key parameters logically. The required input (e.g.infor the LC-MS file andoutfor the featureXML file) and additional parameters (such asseeds,log,debug,threads,no_progress,force, andtest) are well structured. The file extension restrictions (e.g.*.mzML,*.featureXML) are explicitly stated, ensuring users know the expected file formats.
20-28: Algorithm & Subsection Grouping with Detailed Descriptions
The subsequent grouping into sections (e.g. “++++intensity”, “++++mass_trace”, and “++++isotopic_pattern”) is comprehensive. Each parameter under these nodes (such asbins,mz_tolerance,min_spectra, etc.) includes clear descriptions and appropriate restrictions, which will help users configure the tool effectively.
29-38: Detailed Parameter Information for Isotopic Patterns
Parameters likeintensity_percentage,intensity_percentage_optional,optional_fit_improvement, andmass_window_widthare described in detail. The use of precise numerical ranges and thorough explanations ensures that users are well informed about the expected inputs and outcomes.
39-50: Seed, Fit, and Feature Settings Clarity
The “++++seed” section (e.g.min_score) and the subsequent nodes for model fitting (++++fit) and feature settings (++++feature&reported_mz) are clearly articulated. The inclusion of quantitative details (e.g., requirements expressed as 0.0–1.0) and concise descriptions will be valuable for users during parameter optimization.
51-58: User-Seed & Advanced Options Integration
The final sections (“++++user-seed” and “++++advanced”) provide specialized options such asrt_toleranceandpseudo_rt_shift. The consistent use of indentation and class names makes these advanced settings easily distinguishable from the common parameters.docs/doxygen/parameters/output/TOPP_FeatureFinderIdentification.html (9)
1-6: Clear HTML Structure & Legend Presentation
The document begins with a clear container and legend, using familiar CSS classes. This design helps users quickly identify required versus advanced parameters and sets a consistent layout for the documentation.
7-9: Tool Identification and Versioning
The header node for “+FeatureFinderIdentification” along with its description succinctly informs the user about the purpose of the tool. The version is clearly stated, which is important for tracking documentation updates and tool releases.
10-27: Comprehensive Instance Section Setup
The “Instance '1'” section meticulously defines various file inputs and outputs:
- Inputs: LC-MS raw data (
in), direct peptide identifications (id), and external identifications (id_ext).- Outputs: Features (
out), assay library (lib_out), chromatograms (chrom_out), and feature candidates (candidates_out).
The advanced inputcandidates_inand additional parameters such asdebug,quantify_decoys,min_psm_cutoff, andadd_mass_offset_peptidesare logically grouped, with file restrictions clearly specified.
28-34: Extraction Parameter Grouping & Clarity
The “+++extract” section covers parameters for ion chromatogram extraction—includingbatch_size,mz_window, andn_isotopes—with additional advanced parameters (isotope_pmin,rt_quantile,rt_window) that guide the extraction process. Descriptions are clear and concise, ensuring users understand how to adjust these critical settings.
35-39: Feature Detection Parameters are Well-Defined
The “+++detect” section sets out key parameters such aspeak_width,min_peak_width,signal_to_noise, andmapping_tolerance. The descriptions provide context regarding their impact on smoothing and feature detection, which is essential for fine-tuning the tool’s performance.
40-53: SVM Parameter Configuration is Detailed and Flexible
The “+++svm” section comprehensively covers parameters for SVM-based scoring:
- Training parameters (
samples,no_selection)- Output for cross-validation results (
xval_out)- Kernel settings and parameter ranges (
kernel,xval,log2_C,log2_gamma,log2_p)- Additional settings (
epsilon,cache_size,no_shrinking,predictors,min_prob)
This detailed configuration allows for robust tuning during model training.
54-59: Elution Model Fitting Options
In the “+++model” section, the parameters for fitting elution models (such astype,add_zeros,unweighted_fit,no_imputation, andeach_trace) are well described. This provides users with the necessary flexibility to adapt model fitting to their data characteristics.
60-64: Validation of Elution Models via Check Parameters
The “++++check” node details parameters (min_area,boundaries,width, andasymmetry) that set criteria for validating elution models. Clear ranges and descriptions help ensure that only valid models are accepted, thereby improving the reliability of downstream analysis.
65-67: Advanced EMG Scoring Setup
The final “+++EMGScoring” section introduces parameters for fitting exponential modified Gaussian (EMG) models such asmax_iterationandinit_mom. These options further enhance model refinement and contribute to robust feature quantification.
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Fix YAML formatting issues.
There are formatting inconsistencies in the YAML file.
Apply these changes to maintain consistent indentation and add a newline at the end of the file:
formats:
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- - htmlzip
+ - pdf
+ - htmlzip
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| - htmlzip | |
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| - htmlzip |
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[warning] 22-22: wrong indentation: expected 2 but found 4
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[error] 23-23: no new line character at the end of file
(new-line-at-end-of-file)
| <tr> | ||
| <td style="vertical-align:top"><i>sort_blocks</i></td> | ||
| <td style="vertical-align:top">string</td><td style="vertical-align:top">RT_ascending</td> | ||
| <td style="vertical-align:top">RT_ascending, RT_descending</td><td style="vertical-align:top">Sort blocks by <?> before merging them (useful for precursor order)</td> |
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Fix incomplete description for the sort_blocks parameter.
The description contains a placeholder marker <?> that needs to be replaced with the actual sorting criterion.
- <td style="vertical-align:top">RT_ascending, RT_descending</td><td style="vertical-align:top">Sort blocks by <?> before merging them (useful for precursor order)</td>
+ <td style="vertical-align:top">RT_ascending, RT_descending</td><td style="vertical-align:top">Sort blocks by retention time before merging them (useful for precursor order)</td>📝 Committable suggestion
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| <td style="vertical-align:top">RT_ascending, RT_descending</td><td style="vertical-align:top">Sort blocks by <?> before merging them (useful for precursor order)</td> | |
| <td style="vertical-align:top">RT_ascending, RT_descending</td><td style="vertical-align:top">Sort blocks by retention time before merging them (useful for precursor order)</td> |
| RT window size calculated as 240 seconds. | ||
|
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Remove computational output from documentation.
Line 1 contains what appears to be output from running the tool ("RT window size calculated as 240 seconds.") rather than part of the documentation itself. This should be removed.
-RT window size calculated as 240 seconds.
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| RT window size calculated as 240 seconds. | |
| Parameters for fitting exp. mod. Gaussians to mass traces.: | ||
| -EMGScoring:max_iteration <number> Maximum number of iterations for EMG fitting. (default: '100') (min: | ||
| '1') | ||
| -EMGScoring:init_mom Alternative initial parameters for fitting through method of moments. |
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Add description for the EMGScoring:init_mom parameter.
The EMGScoring:init_mom parameter lacks a complete description of what it does. Consider adding more details.
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#!/bin/bash
# Description: Check for more detailed descriptions of this parameter in the codebase
# Search for the parameter name in source code
rg "EMGScoring:init_mom" -A 5 --glob "*.cpp" --glob "*.h"
# Also look for any class/method related to EMGScoring that might explain this
rg "EMGScoring" --glob "*.h" -A 10Length of output: 1271
Action Required: Enhance Documentation of EMGScoring:init_mom Parameter
The current one-line description ("Alternative initial parameters for fitting through method of moments.") is too terse. Our search in the code (in both FeatureFinderMetaboIdent.cpp and ProteomicsLFQ.cpp) confirms that the parameter is set to "true" by default, but there is no further explanation of what enabling this parameter actually does. To improve clarity for users, please expand the documentation to include details such as:
- The algorithmic impact and rationale behind using alternative initial parameters via the method of moments.
- How the parameter influences the behavior of the underlying routines (e.g., in feature detection or scoring).
- Any restrictions, edge cases, or recommended settings when using this parameter.
Files to review:
docs/doxygen/parameters/output/TOPP_FeatureFinderMetaboIdent.cli(Line 42)src/topp/FeatureFinderMetaboIdent.cppsrc/topp/ProteomicsLFQ.cpp
| <tr> | ||
| <td style="vertical-align:top"><b>S/N_statistics</b></td> | ||
| <td style="vertical-align:top">string</td><td style="vertical-align:top">true</td> | ||
| <td style="vertical-align:top">true, false</td><td style="vertical-align:top">If set to 1 isotope peaks of the product ion peaks are added</td> |
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Description may need clarification.
The description "If set to 1 isotope peaks of the product ion peaks are added" for the "S/N_statistics" parameter seems inconsistent with the parameter type (string) and default value ("true"). Consider revising this description to clarify how a string parameter with "true/false" restrictions relates to adding isotope peaks.
🌐 Web query:
What does S/N statistics refer to in mass spectrometry?
💡 Result:
The signal-to-noise (S/N) ratio in mass spectrometry quantifies the strength of an analyte's signal relative to background noise, serving as a critical metric for assessing instrument sensitivity and detection limits. Here’s a detailed breakdown:
Core Definition
- S/N Formula: ( S/N = \frac{\text{Signal Intensity}}{\text{Noise}} ), where:
- Signal: Peak height above baseline (e.g., chromatographic peak maximum) [1][2].
- Noise: Baseline fluctuation, often measured as standard deviation (STD), root-mean-square (RMS), or peak-to-peak variation over a defined time window (e.g., 30–60 seconds) [1][5].
Applications
- Detection Limits:
- Instrument Detection Limit (IDL): Typically defined as ( S/N \geq 3 ) [1][4].
- Limit of Quantitation (LOQ): Often ( S/N \geq 10 ) [5][7].
- Performance Comparisons:
- Historically used to compare GC-MS and LC-MS systems [3].
- Modern mass spectrometers (e.g., HRMS, MS/MS) face limitations with S/N due to ultra-low noise and digital filtering, prompting reliance on statistical IDL methods instead [3][4].
Calculation Variations
- Pharmacopeia Standards:
- USP/EP: Use ( S/N = \frac{2H}{h} ), where ( H ) is peak height and ( h ) is half the noise band, effectively doubling traditional S/N values [5].
- Baseline Noise Measurement:
- Agilent and Shimadzu advocate noise estimation via baseline segments before/after peaks [1][2].
Challenges and Limitations
- Chemical vs. Instrument Noise:
- Chemical noise (matrix interference) often dominates real-world analyses but is absent in idealized installation tests, inflating S/N values [4][8].
- Instrument Artifacts:
- Thresholding (ignoring low-level signals) and smoothing algorithms artificially enhance S/N without improving detection accuracy [7].
- Ambiguity in Vendor Specifications:
- Modern S/N ratios (e.g., >100,000:1) may not reflect practical method improvements due to undocumented parameters like chromatography conditions [4].
Modern Alternatives
- Instrument Detection Limit (IDL): Statistically derived from analyte concentrations near detection thresholds, offering better reproducibility and relevance for real-world samples [4][7].
- Method Detection Limit (MDL): Incorporates matrix effects and method-specific variables, addressing S/N's limitations in routine analyses [3][4].
Key Considerations
- Hardware/Software Factors: Ion source efficiency, mass analyzer transmission, and data processing (e.g., unrealistic mass chromatogram windows) directly impact S/N [2][8].
- Regulatory Guidelines: While S/N remains codified in pharmacopeias, regulatory bodies increasingly emphasize IDL and precision-based validation [4][7].
In summary, S/N statistics provide a foundational measure of mass spectrometer performance but require careful interpretation due to calculation inconsistencies, technological advancements, and the growing importance of statistical detection limits in modern applications.
Citations:
- 1: https://www.agilent.com/cs/library/technicaloverviews/public/5990-7651EN.pdf
- 2: https://www.shimadzu.com/an/service-support/technical-support/gas-chromatograph-mass-spectrometry/analysis-results/signal/definition.html
- 3: https://www.chromatographyonline.com/view/why-use-signal-noise-measure-ms-performance-when-it-often-meaningless-0
- 4: https://www.spectroscopyonline.com/view/what-s-most-meaningful-standard-mass-spectrometry-instrument-detection-limit-or-signal-noise-ratio-0
- 5: https://www.sepscience.com/hplc-solutions-124-how-to-determine-signal-to-noise-ratio-part-3/
- 6: https://www.chromatographyonline.com/view/quantifying-small-molecules-mass-spectrometry-1
- 7: https://sciex.com/content/dam/SCIEX/pdf/tech-notes/all/mass-spectrometry-cms_059150.pdf
- 8: https://www.chromatographyonline.com/view/enhancing-signal-noise
- 9: https://academic.oup.com/bioinformatics/article/24/8/1070/213310
- 10: https://www.aspect-analytics.com/media-blog/introduction-to-mass-spectrometry-data-analysis
Clarify the S/N_statistics Description in OpenMS_SpectrumAnnotator.parameters
- The "S/N_statistics" parameter is declared as a string with allowed values "true, false", yet its description ("If set to 1 isotope peaks of the product ion peaks are added") confusingly implies an isotopic peak addition behavior.
- Given that S/N typically denotes signal-to-noise ratio—a metric evaluating the intensity of a signal relative to the background noise—this description appears to be misaligned with standard mass spectrometry terminology.
- Please review the intended functionality for this parameter. If the parameter is meant to control the addition of isotope peaks, a more appropriate name and description should be used. Otherwise, update the description to clearly reference its role in S/N (signal-to-noise) analysis.
| <td style="vertical-align:top"><i><span title="Parameters for detecting features in extracted ion chromatograms">detect</span>:signal_to_noise</i></td> | ||
| <td style="vertical-align:top">float</td><td style="vertical-align:top">0.8</td> | ||
| <td style="vertical-align:top">min: 0.1</td><td style="vertical-align:top">Signal-to-noise threshold for OpenSWATH feature detection</td> | ||
| </tr> |
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Parameter description may need clarification.
The description for the "signal_to_noise" parameter states "Signal-to-noise threshold for OpenSWATH feature detection". Since this documentation is for FeatureFinderAlgorithmMetaboIdent, the reference to "OpenSWATH" might be confusing if they are different tools. Consider clarifying if this is intentional or if the description should be updated to reflect the correct context.
🏁 Script executed:
#!/bin/bash
# Check if there's a connection between FeatureFinderAlgorithmMetaboIdent and OpenSWATH
rg -A 5 -B 5 "OpenSWATH.*FeatureFinderAlgorithmMetaboIdent|FeatureFinderAlgorithmMetaboIdent.*OpenSWATH"Length of output: 106
I'll run a further verification command to specifically check the "signal_to_noise" parameter description in the parameter file to see if it indeed references "OpenSWATH."
🏁 Script executed:
#!/bin/bash
rg "signal_to_noise" -C 5 docs/doxygen/parameters/output/OpenMS_FeatureFinderAlgorithmMetaboIdent.parametersLength of output: 1054
Action Required: Clarify the OpenSWATH Reference in the Parameter Description
The "signal_to_noise" parameter description in docs/doxygen/parameters/output/OpenMS_FeatureFinderAlgorithmMetaboIdent.parameters currently states:
Signal-to-noise threshold for OpenSWATH feature detection
Our search did not reveal any association between FeatureFinderAlgorithmMetaboIdent and OpenSWATH, which suggests that this reference might be misleading. Please verify whether:
- OpenSWATH is indeed used internally by FeatureFinderAlgorithmMetaboIdent (e.g., as a legacy or underlying component); or
- The description should be updated to reflect the correct context (e.g., by replacing "OpenSWATH" with "FeatureFinderAlgorithmMetaboIdent" or an appropriate term).
Clarifying this will help avoid confusion for users reading the documentation.
| <td style="vertical-align:top">true, false</td><td style="vertical-align:top">true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts</td> | ||
| </tr> |
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Fix inconsistency in parameter description
The description for ignore_adduct parameter has a logical inconsistency - it states both "true [default]" and that true means "Pairing irrespective of adducts", but the description indicates the requirement is for equal adducts.
- <td style="vertical-align:top">true, false</td><td style="vertical-align:top">true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts</td>
+ <td style="vertical-align:top">true, false</td><td style="vertical-align:top">false: pairing requires equal adducts (or at least one without adduct annotation); true [default]: Pairing irrespective of adducts</td>📝 Committable suggestion
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| <td style="vertical-align:top">true, false</td><td style="vertical-align:top">true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts</td> | |
| </tr> | |
| <td style="vertical-align:top">true, false</td><td style="vertical-align:top">false: pairing requires equal adducts (or at least one without adduct annotation); true [default]: Pairing irrespective of adducts</td> | |
| </tr> |
| <td style="vertical-align:top"><b>pairfinder:ignore_adduct</b></td> | ||
| <td style="vertical-align:top">string</td><td style="vertical-align:top">true</td> | ||
| <td style="vertical-align:top">true, false</td><td style="vertical-align:top">true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts</td> | ||
| </tr> |
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Fix inconsistency in parameter description
Similar to the issue in the FeatureGroupingAlgorithmUnlabeled parameters, the description for pairfinder:ignore_adduct contains contradictory information.
- <td style="vertical-align:top">true, false</td><td style="vertical-align:top">true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts</td>
+ <td style="vertical-align:top">true, false</td><td style="vertical-align:top">false: pairing requires equal adducts (or at least one without adduct annotation); true [default]: Pairing irrespective of adducts</td>📝 Committable suggestion
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| <td style="vertical-align:top"><b>pairfinder:ignore_adduct</b></td> | |
| <td style="vertical-align:top">string</td><td style="vertical-align:top">true</td> | |
| <td style="vertical-align:top">true, false</td><td style="vertical-align:top">true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts</td> | |
| </tr> | |
| <td style="vertical-align:top"><b>pairfinder:ignore_adduct</b></td> | |
| <td style="vertical-align:top">string</td><td style="vertical-align:top">true</td> | |
| <td style="vertical-align:top">true, false</td><td style="vertical-align:top">false: pairing requires equal adducts (or at least one without adduct annotation); true [default]: Pairing irrespective of adducts</td> | |
| </tr> |
| <span class="item_description">Disables progress logging to command line</span><span class="item_tags"></span><span class="item_restrictions">true, false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">force</span><span class="item_value">false</span> | ||
| <span class="item_description">Overrides tool-specific checks</span><span class="item_tags"></span><span class="item_restrictions">true, false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">test</span><span class="item_value">false</span> |
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🛠️ Refactor suggestion
Clarify duplicate parameter names
There are two parameters named force (one at lines 21-22 and another at lines 30-31) serving different purposes. Consider renaming one to avoid confusion, or add a clarification to distinguish them.
- <span class="item_description">Overrides tool-specific checks</span>
+ <span class="item_description">Overrides tool-specific checks (global force parameter)</span>
- <span class="item_name" style="padding-left:32px;">force</span>
+ <span class="item_name" style="padding-left:32px;">reranking_force</span>
- <span class="item_description">Set this flag to enforce re-ranking when no cross correlation score is present. For re-ranking the default score found at each peptide hit is used. Use with care!</span>
+ <span class="item_description">Set this flag to enforce re-ranking when no cross correlation score is present. For re-ranking the default score found at each peptide hit is used. Use with care!</span>Also applies to: 30-31
| <td style="vertical-align:top"><b>ignore_charge</b></td> | ||
| <td style="vertical-align:top">string</td><td style="vertical-align:top">false</td> | ||
| <td style="vertical-align:top">true, false</td><td style="vertical-align:top">For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature.</td> |
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Clarify parameter type for ignore_charge
The ignore_charge parameter is listed with type "string" but seems to be a boolean parameter with values "true" or "false". Consider changing the type to "bool" for consistency with the actual parameter type in the codebase.
🌐 Web query:
How are boolean parameters typically specified in OpenMS parameter documentation?
💡 Result:
In OpenMS documentation and parameter handling, boolean parameters are typically specified using explicit true/false values and are often accompanied by descriptive names that indicate their toggle-like behavior. This is evident in parameter names like use_shared_peptides[10], which implicitly represent a binary choice.
Key characteristics of boolean parameter specification in OpenMS include:
- Explicit Type Declaration: Parameters are documented with their expected data type, such as
boolin code references[4][7], ensuring clarity for developers and users. - Descriptive Naming Conventions: Parameters often use prefixes like
use_orenable_to signal their boolean nature[10]. - Default Values: Boolean parameters may include default values (e.g.,
default: true)[3], though OpenMS tools often require explicit specification in command-line usage. - Command-Line Representation: In OpenMS tools, boolean parameters might act as flags (presence =
true, absence =false)[5], though this depends on the tool's implementation.
For example, in pyOpenMS, setting a boolean parameter would follow the general Param object syntax:
p.setValue("use_shared_peptides", True, "Enable shared peptides in analysis")This aligns with OpenMS's parameter-handling framework[1][2][6], where the Param class supports diverse data types, including booleans. Documentation for these parameters typically clarifies their behavior through descriptions and type-specific examples[10].
Citations:
- 1: https://pyopenms.readthedocs.io/en/latest/user_guide/parameter_handling.html
- 2: https://pyopenms.readthedocs.io/en/release3.0.0/user_guide/parameter_handling.html
- 3: https://www.speakeasy.com/post/openapi-tips-query-parameters-serialization
- 4: https://openms.de/documentation/classOpenMS_1_1IdXMLFile.html
- 5: https://www.openms.org/documentation/html/TOPP_FeatureFinderMetabo.html
- 6: https://pyopenms.readthedocs.io/en/release_2.4.0/parameter_handling.html
- 7: https://www.openms.org/documentation/html/classOpenMS_1_1Internal_1_1MzMLHandler.html
- 8: https://openms.de/documentation/TOPP_TextExporter.html
- 9: https://spec.openapis.org/oas/v3.1.1.html
- 10: https://openms.de/documentation/namespaceOpenMS.html
Update the parameter type declaration for ignore_charge
File: docs/doxygen/parameters/output/OpenMS_IDMapper.parameters (Lines: 25–27)
Based on OpenMS parameter documentation conventions, boolean parameters should be declared with an explicit bool type. The ignore_charge parameter currently shows type "string" despite its permitted values being boolean (true or false). Please update the type to "bool" to align the documentation with the actual parameter behavior and ensure clarity for users.
Describe the change
src folder has been added for Doxygen documentation.
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