docrev 0.8.1 → 0.8.5

package/dist/lib/schema.d.ts

@@ -0,0 +1,66 @@
+/**
+ * JSON Schema validation for rev.yaml configuration
+ */
+/**
+ * Validation error
+ */
+interface ValidationError {
+    path: string;
+    message: string;
+    value?: unknown;
+}
+/**
+ * Validation warning
+ */
+interface ValidationWarning {
+    path: string;
+    message: string;
+}
+/**
+ * Validation result
+ */
+interface ValidationResult {
+    valid: boolean;
+    errors: ValidationError[];
+    warnings: ValidationWarning[];
+}
+/**
+ * JSON Schema type
+ */
+interface Schema {
+    $schema?: string;
+    title?: string;
+    description?: string;
+    type?: string;
+    properties?: Record<string, Schema>;
+    required?: string[];
+    items?: Schema;
+    oneOf?: Schema[];
+    enum?: string[];
+    pattern?: string;
+    format?: string;
+    minimum?: number;
+    maximum?: number;
+    minItems?: number;
+    maxItems?: number;
+    additionalProperties?: boolean;
+    default?: unknown;
+}
+/**
+ * JSON Schema for rev.yaml
+ */
+export declare const revYamlSchema: Schema;
+/**
+ * Validate rev.yaml configuration
+ */
+export declare function validateConfig(config: Record<string, unknown>): ValidationResult;
+/**
+ * Format validation results for display
+ */
+export declare function formatValidationResult(result: ValidationResult, chalk: {
+    red: (s: string) => string;
+    yellow: (s: string) => string;
+    green: (s: string) => string;
+}): string;
+export {};
+//# sourceMappingURL=schema.d.ts.map

package/dist/lib/schema.d.ts.map

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package/dist/lib/schema.js

@@ -0,0 +1,339 @@
+/**
+ * JSON Schema validation for rev.yaml configuration
+ */
+/**
+ * JSON Schema for rev.yaml
+ */
+export const revYamlSchema = {
+    $schema: 'http://json-schema.org/draft-07/schema#',
+    title: 'rev.yaml configuration',
+    description: 'Configuration file for docrev document workflow',
+    type: 'object',
+    properties: {
+        title: {
+            type: 'string',
+            description: 'Document title',
+        },
+        version: {
+            type: 'string',
+            description: 'Document version',
+        },
+        authors: {
+            type: 'array',
+            description: 'List of authors',
+            items: {
+                oneOf: [
+                    { type: 'string' },
+                    {
+                        type: 'object',
+                        properties: {
+                            name: { type: 'string' },
+                            affiliation: { type: 'string' },
+                            email: { type: 'string', format: 'email' },
+                            orcid: { type: 'string', pattern: '^\\d{4}-\\d{4}-\\d{4}-\\d{3}[0-9X]$' },
+                        },
+                        required: ['name'],
+                    },
+                ],
+            },
+        },
+        sections: {
+            type: 'array',
+            description: 'Ordered list of section files to include',
+            items: { type: 'string', pattern: '.*\\.md$' },
+        },
+        bibliography: {
+            type: 'string',
+            description: 'Path to bibliography file (.bib)',
+            pattern: '.*\\.bib$',
+        },
+        csl: {
+            type: 'string',
+            description: 'Path to CSL citation style file',
+        },
+        crossref: {
+            type: 'object',
+            description: 'pandoc-crossref settings',
+            properties: {
+                figureTitle: { type: 'string', default: 'Figure' },
+                tableTitle: { type: 'string', default: 'Table' },
+                figPrefix: {
+                    oneOf: [
+                        { type: 'string' },
+                        { type: 'array', items: { type: 'string' }, minItems: 1, maxItems: 2 },
+                    ],
+                },
+                tblPrefix: {
+                    oneOf: [
+                        { type: 'string' },
+                        { type: 'array', items: { type: 'string' }, minItems: 1, maxItems: 2 },
+                    ],
+                },
+                eqnPrefix: {
+                    oneOf: [
+                        { type: 'string' },
+                        { type: 'array', items: { type: 'string' }, minItems: 1, maxItems: 2 },
+                    ],
+                },
+                secPrefix: {
+                    oneOf: [
+                        { type: 'string' },
+                        { type: 'array', items: { type: 'string' }, minItems: 1, maxItems: 2 },
+                    ],
+                },
+                linkReferences: { type: 'boolean', default: true },
+            },
+            additionalProperties: true,
+        },
+        pdf: {
+            type: 'object',
+            description: 'PDF output settings',
+            properties: {
+                template: { type: 'string' },
+                documentclass: {
+                    type: 'string',
+                    enum: ['article', 'report', 'book', 'memoir', 'scrartcl', 'scrreprt', 'scrbook'],
+                    default: 'article',
+                },
+                fontsize: {
+                    type: 'string',
+                    pattern: '^\\d{1,2}pt$',
+                    default: '12pt',
+                },
+                geometry: { type: 'string', default: 'margin=1in' },
+                linestretch: { type: 'number', minimum: 1, maximum: 3, default: 1.5 },
+                numbersections: { type: 'boolean', default: false },
+                toc: { type: 'boolean', default: false },
+                header: { type: 'string' },
+                footer: { type: 'string' },
+            },
+            additionalProperties: true,
+        },
+        docx: {
+            type: 'object',
+            description: 'Word output settings',
+            properties: {
+                reference: { type: 'string', description: 'Reference document for styling' },
+                keepComments: { type: 'boolean', default: true },
+                toc: { type: 'boolean', default: false },
+            },
+            additionalProperties: true,
+        },
+        tex: {
+            type: 'object',
+            description: 'LaTeX output settings',
+            properties: {
+                standalone: { type: 'boolean', default: true },
+            },
+            additionalProperties: true,
+        },
+    },
+    additionalProperties: true,
+};
+/**
+ * Validate a value against a simple schema
+ */
+function validateValue(value, schema, path = '') {
+    const errors = [];
+    // Handle oneOf
+    if (schema.oneOf) {
+        const validForAny = schema.oneOf.some((subSchema) => {
+            const subErrors = validateValue(value, subSchema, path);
+            return subErrors.length === 0;
+        });
+        if (!validForAny) {
+            errors.push({
+                path,
+                message: `Value does not match any allowed type`,
+                value,
+            });
+        }
+        return errors;
+    }
+    // Type check
+    if (schema.type) {
+        const actualType = Array.isArray(value) ? 'array' : typeof value;
+        if (actualType !== schema.type) {
+            errors.push({
+                path,
+                message: `Expected ${schema.type}, got ${actualType}`,
+                value,
+            });
+            return errors; // Stop further validation if type is wrong
+        }
+    }
+    // String validation
+    if (schema.type === 'string' && typeof value === 'string') {
+        if (schema.pattern) {
+            const regex = new RegExp(schema.pattern);
+            if (!regex.test(value)) {
+                errors.push({
+                    path,
+                    message: `Value "${value}" does not match pattern ${schema.pattern}`,
+                    value,
+                });
+            }
+        }
+        if (schema.enum && !schema.enum.includes(value)) {
+            errors.push({
+                path,
+                message: `Value "${value}" must be one of: ${schema.enum.join(', ')}`,
+                value,
+            });
+        }
+    }
+    // Number validation
+    if (schema.type === 'number' && typeof value === 'number') {
+        if (schema.minimum !== undefined && value < schema.minimum) {
+            errors.push({
+                path,
+                message: `Value ${value} is less than minimum ${schema.minimum}`,
+                value,
+            });
+        }
+        if (schema.maximum !== undefined && value > schema.maximum) {
+            errors.push({
+                path,
+                message: `Value ${value} is greater than maximum ${schema.maximum}`,
+                value,
+            });
+        }
+    }
+    // Array validation
+    if (schema.type === 'array' && Array.isArray(value)) {
+        if (schema.minItems !== undefined && value.length < schema.minItems) {
+            errors.push({
+                path,
+                message: `Array must have at least ${schema.minItems} items`,
+                value,
+            });
+        }
+        if (schema.maxItems !== undefined && value.length > schema.maxItems) {
+            errors.push({
+                path,
+                message: `Array must have at most ${schema.maxItems} items`,
+                value,
+            });
+        }
+        if (schema.items) {
+            value.forEach((item, index) => {
+                errors.push(...validateValue(item, schema.items, `${path}[${index}]`));
+            });
+        }
+    }
+    // Object validation
+    if (schema.type === 'object' && typeof value === 'object' && value !== null) {
+        const obj = value;
+        if (schema.properties) {
+            for (const [key, propSchema] of Object.entries(schema.properties)) {
+                if (obj[key] !== undefined) {
+                    errors.push(...validateValue(obj[key], propSchema, path ? `${path}.${key}` : key));
+                }
+            }
+        }
+        if (schema.required) {
+            for (const key of schema.required) {
+                if (obj[key] === undefined) {
+                    errors.push({
+                        path: path ? `${path}.${key}` : key,
+                        message: `Required property "${key}" is missing`,
+                        value: undefined,
+                    });
+                }
+            }
+        }
+    }
+    return errors;
+}
+/**
+ * Validate rev.yaml configuration
+ */
+export function validateConfig(config) {
+    const errors = validateValue(config, revYamlSchema);
+    const warnings = [];
+    // Additional semantic validations
+    if (config.sections && Array.isArray(config.sections) && config.sections.length === 0) {
+        warnings.push({
+            path: 'sections',
+            message: 'No sections specified - build will auto-detect .md files',
+        });
+    }
+    if (config.bibliography && typeof config.bibliography === 'string' && !config.bibliography.endsWith('.bib')) {
+        warnings.push({
+            path: 'bibliography',
+            message: 'Bibliography file should have .bib extension',
+        });
+    }
+    const pdf = config.pdf;
+    if (pdf?.linestretch && (pdf.linestretch < 1 || pdf.linestretch > 3)) {
+        warnings.push({
+            path: 'pdf.linestretch',
+            message: 'Line stretch values outside 1-3 range may produce unexpected results',
+        });
+    }
+    // Check for common typos
+    const knownKeys = Object.keys(revYamlSchema.properties || {});
+    for (const key of Object.keys(config)) {
+        if (key.startsWith('_'))
+            continue; // Internal keys
+        if (!knownKeys.includes(key)) {
+            // Check for similar keys (possible typos)
+            const similar = knownKeys.find((k) => levenshtein(key.toLowerCase(), k.toLowerCase()) <= 2);
+            if (similar) {
+                warnings.push({
+                    path: key,
+                    message: `Unknown property "${key}" - did you mean "${similar}"?`,
+                });
+            }
+        }
+    }
+    return {
+        valid: errors.length === 0,
+        errors,
+        warnings,
+    };
+}
+/**
+ * Format validation results for display
+ */
+export function formatValidationResult(result, chalk) {
+    const lines = [];
+    if (result.errors.length > 0) {
+        lines.push(chalk.red('Configuration errors:'));
+        for (const error of result.errors) {
+            lines.push(chalk.red(`  ✗ ${error.path}: ${error.message}`));
+        }
+    }
+    if (result.warnings.length > 0) {
+        if (lines.length > 0)
+            lines.push('');
+        lines.push(chalk.yellow('Warnings:'));
+        for (const warning of result.warnings) {
+            lines.push(chalk.yellow(`  ! ${warning.path}: ${warning.message}`));
+        }
+    }
+    if (result.valid && result.warnings.length === 0) {
+        lines.push(chalk.green('✓ Configuration is valid'));
+    }
+    return lines.join('\n');
+}
+/**
+ * Levenshtein distance for typo detection
+ */
+function levenshtein(a, b) {
+    const matrix = Array(b.length + 1)
+        .fill(null)
+        .map(() => Array(a.length + 1).fill(null));
+    for (let i = 0; i <= a.length; i++)
+        matrix[0][i] = i;
+    for (let j = 0; j <= b.length; j++)
+        matrix[j][0] = j;
+    for (let j = 1; j <= b.length; j++) {
+        for (let i = 1; i <= a.length; i++) {
+            const cost = a[i - 1] === b[j - 1] ? 0 : 1;
+            matrix[j][i] = Math.min(matrix[j][i - 1] + 1, matrix[j - 1][i] + 1, matrix[j - 1][i - 1] + cost);
+        }
+    }
+    return matrix[b.length][a.length];
+}
+//# sourceMappingURL=schema.js.map

package/dist/lib/schema.js.map

@@ -0,0 +1 @@
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package/dist/lib/scientific-words.d.ts

@@ -0,0 +1,6 @@
+/**
+ * Common scientific and academic words not in standard dictionaries
+ * These words are accepted by Word's spellchecker
+ */
+export declare const scientificWords: Set<string>;
+//# sourceMappingURL=scientific-words.d.ts.map

package/dist/lib/scientific-words.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"scientific-words.d.ts","sourceRoot":"","sources":["../../lib/scientific-words.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,eAAO,MAAM,eAAe,aAmE1B,CAAC"}

package/dist/lib/scientific-words.js

@@ -0,0 +1,66 @@
+/**
+ * Common scientific and academic words not in standard dictionaries
+ * These words are accepted by Word's spellchecker
+ */
+export const scientificWords = new Set([
+    // Biology/Ecology
+    'abiotic', 'biotic', 'biogeographic', 'biogeography', 'phenotypic', 'phenotype',
+    'anthropogenic', 'propagule', 'propagules', 'herbivory', 'herbivore', 'herbivores',
+    'ruderal', 'ruderals', 'refugia', 'refugium', 'hotspot', 'hotspots',
+    'biodiversity', 'ecosystem', 'ecosystems', 'ecotype', 'ecotypes',
+    'taxonomic', 'phylogenetic', 'phylogeny', 'morphological', 'morphology',
+    'allometric', 'allometry', 'biomass', 'biome', 'biomes',
+    'invasibility', 'invasive', 'invasives', 'neophyte', 'neophytes',
+    'archaeophyte', 'archaeophytes', 'naturalisation', 'naturalization',
+    'colonisation', 'colonization', 'dispersal', 'fecundity',
+    'phenology', 'phenological', 'ontogeny', 'ontogenetic',
+    'mesic', 'xeric', 'hydric', 'riparian', 'riverine',
+    'subalpine', 'alpine', 'boreal', 'temperate', 'tropical',
+    'heathland', 'heathlands', 'scrubland', 'scrublands', 'grassland', 'grasslands',
+    'broadleaf', 'broadleaved', 'coniferous', 'deciduous', 'evergreen',
+    'autochory', 'autochorous', 'zoochory', 'zoochorous',
+    'anemochory', 'anemochorous', 'hydrochory', 'hydrochorous',
+    'anthropochory', 'anthropochorous', 'hemerochor', 'hemerochorist',
+    'helophyte', 'helophytes', 'hydrophyte', 'hydrophytes',
+    'therophyte', 'therophytes', 'geophyte', 'geophytes',
+    'chamaephyte', 'chamaephytes', 'phanerophyte', 'phanerophytes',
+    // Statistics
+    'logit', 'logistic', 'probit', 'frequentist', 'bayesian',
+    'overdispersion', 'underdispersion', 'heteroscedasticity', 'homoscedasticity',
+    'multicollinearity', 'autocorrelation', 'covariate', 'covariates',
+    'parameterization', 'parameterisation', 'reparameterization',
+    'bootstrapping', 'resampling', 'imputation', 'interpolation',
+    'standardized', 'standardised', 'normalized', 'normalised',
+    'discretized', 'discretised', 'categorized', 'categorised',
+    // Compound words
+    'overrepresentation', 'underrepresentation', 'overrepresented', 'underrepresented',
+    'outcompete', 'outcompetes', 'outcompeted', 'outcompeting',
+    'subdataset', 'subgroup', 'subgroups', 'subtype', 'subtypes',
+    'dataset', 'datasets', 'datapoint', 'datapoints',
+    'spatiotemporal', 'spatio', 'geospatial',
+    'timestep', 'timesteps', 'timeframe', 'timeframes',
+    'warmup', 'backend', 'frontend', 'workflow', 'workflows',
+    'fallback', 'fallbacks', 'tradeoff', 'tradeoffs',
+    // Academic writing
+    'interpretability', 'reproducibility', 'replicability',
+    'hypothesise', 'hypothesised', 'hypothesize', 'hypothesized',
+    'analyse', 'analysed', 'analyze', 'analyzed',
+    'prioritise', 'prioritised', 'prioritize', 'prioritized',
+    'characterise', 'characterised', 'characterize', 'characterized',
+    'generalise', 'generalised', 'generalize', 'generalized',
+    'parameterise', 'parameterised', 'parameterize', 'parameterized',
+    'visualise', 'visualised', 'visualize', 'visualized',
+    'modelling', 'modeling', 'modelled', 'modeled',
+    // Geography
+    'unvegetated', 'landform', 'landforms', 'topographic', 'topography',
+    'elevational', 'latitudinal', 'longitudinal', 'altitudinal',
+    // Technical
+    'doi', 'dois', 'pdf', 'pdfs', 'csv', 'xlsx',
+    'pandoc', 'markdown', 'bibtex', 'crossref',
+    // R packages and tools
+    'brms', 'cmdstanr', 'rstanarm', 'lme', 'glmm', 'glmer', 'lmer',
+    'ggplot', 'dplyr', 'tidyr', 'tidyverse', 'rmarkdown',
+    // Common in papers
+    'foci', 'et', 'al', 'cf', 'eg', 'ie', 'vs',
+]);
+//# sourceMappingURL=scientific-words.js.map

package/dist/lib/scientific-words.js.map

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package/dist/lib/sections.d.ts

@@ -0,0 +1,40 @@
+/**
+ * Section handling - map between section .md files and combined documents
+ */
+import type { SectionConfig, SectionsConfig, ExtractedSection } from './types.js';
+/**
+ * Extract header from a markdown file
+ */
+export declare function extractHeader(filePath: string): string | null;
+/**
+ * Generate sections.yaml from existing .md files
+ */
+export declare function generateConfig(directory: string, excludePatterns?: string[]): SectionsConfig;
+/**
+ * Load sections config from yaml file
+ */
+export declare function loadConfig(configPath: string): SectionsConfig;
+/**
+ * Save sections config to yaml file
+ */
+export declare function saveConfig(configPath: string, config: SectionsConfig): void;
+/**
+ * Match a heading to a section file
+ */
+export declare function matchHeading(heading: string, sections: Record<string, SectionConfig>): {
+    file: string;
+    config: SectionConfig;
+} | null;
+/**
+ * Extract sections from Word document text
+ */
+export declare function extractSectionsFromText(text: string, sections: Record<string, SectionConfig>): ExtractedSection[];
+/**
+ * Parse annotated paper.md and split back to section files
+ */
+export declare function splitAnnotatedPaper(paperContent: string, sections: Record<string, SectionConfig>): Map<string, string>;
+/**
+ * Get ordered list of section files from config
+ */
+export declare function getOrderedSections(config: SectionsConfig): string[];
+//# sourceMappingURL=sections.d.ts.map

package/dist/lib/sections.d.ts.map

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