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Changelog

[0.0.39] (2025-09-22)

Added

  • Parallel FINEMAP execution: credtools finemap accepts --processes/-np to fan out loci across worker processes, keeping sequential behaviour available with the default of 1.

Changed

  • Per-locus task coordination: Fine-mapping runs now stream through a worker-safe task wrapper, preserving rich progress reporting, capturing tracebacks, and writing locus outputs from whichever worker completes first.
  • CLI artefacts: Run summaries and combined credible set exports remain deterministic under parallel execution, with parameters.json recording the requested worker count.

Tests

  • Added regression coverage for the CLI multiprocessing path by mocking the worker pool to assert identical outputs for 1 vs N processes.

[0.0.38] (2025-09-21)

Added

  • FINEMAP timeout control: credtools finemap now accepts --timeout-minutes (default 30) to cap per-locus runs, with timeout failures reported in run_summary.log.

Changed

  • External tool execution: FINEMAP wrapper and tool manager enforce the timeout and append [timeout] markers to logs when the limit is exceeded, ensuring stalled runs surface immediately.

[0.0.37] (2025-09-20)

Fixed

  • LD matrix ingestion: Replace NaN entries with zeros when loading from lower-triangle text or .npz files, and add regression tests to guard behavior.
  • QC pipeline robustness: Locus-level exceptions no longer abort credtools qc; failures are logged per locus, success/failure counts are summarized to qc_run_summary.log, and CLI feedback reflects mixed outcomes.
  • Error messaging: Intersecting sumstats/LD now reports the offending locus when common variants are missing to simplify debugging.

[0.0.36] (2025-09-18)

Changed

  • CLI preprocessing flows: credtools munge and credtools chunk now accept comma- or newline-separated input paths in addition to TSV config files, with friendlier validation and logging when LD references are omitted.
  • Preprocessing outputs: Munge results retain the sample-size N column in the standard export schema and downstream validators require it.
  • Optional plotting dependency: Centralized the upsetplot import so the plotting module gatekeeps the dependency once and falls back gracefully when the package is absent.

[0.0.35] (2025-09-17)

Added

  • Comprehensive Plotting Module: New visualization capabilities for QC results
  • Added credtools.plot module with publication-quality plotting functions
  • Summary QC Plots (2x2 layout from qc.txt.gz):
    • Lambda-s distribution boxplot by cohort
    • MAF correlation barplot between summary statistics and LD reference
    • Lambda-s outliers count barplot by cohort
    • Dentist-s outliers count barplot by cohort
  • Locus-specific Plots (2x2 layout from individual QC files):
    • Locus p-value plot with credible set annotations (from expected_z.txt.gz)
    • Observed vs expected z-scores QQ plot (from expected_z.txt.gz)
    • LD decay curve plots by cohort (from ld_decay.txt.gz)
    • LD 4th moment boxplots by cohort (from ld_4th_moment.txt.gz)
    • SNP missingness upset plot showing overlap patterns (from snp_missingness.txt.gz)
  • CLI Command:
    • credtools plot: Unified plotting command with auto-detection of plot type
    • Supports all plot types: summary (2x2), locus (2x2), and individual plots
    • Smart auto-detection based on input path (directory for locus, qc.txt.gz for summary)
  • Features:
    • Population-aware color schemes for consistent visualization
    • Support for PNG, PDF, SVG output formats
    • Customizable figure sizes and DPI settings
    • Graceful handling of missing files and optional dependencies
    • Professional styling with seaborn integration

Dependencies

  • Added seaborn>=0.11.0 for enhanced statistical plotting
  • Added upsetplot>=0.6.0 for intersection visualization (optional for SNP missingness plots)

Enhanced

  • QC workflow now generates comprehensive visualizations alongside numerical results
  • All plotting functions integrate seamlessly with existing QC output file formats
  • Error handling with informative messages for missing dependencies or data files

[0.0.34] (2025-09-14)

Fixed

  • CI Test Suite: Fixed failing CI tests and errors
  • Fixed TypeError in test fixtures by adding required locus_start and locus_end parameters to Locus constructor calls
  • Removed unused toml import that was causing ModuleNotFoundError in integration tests
  • Fixed linting issues: converted f-strings without placeholders to regular strings
  • Added missing docstrings for mock classes in QC module
  • All 70 tests now pass successfully

Improved

  • Enhanced test coverage and reliability of CI pipeline
  • Improved code quality with resolved linting and documentation issues

[0.0.33] (2025-09-12)

Added

  • QC Summary Statistics: Enhanced quality control with comprehensive summary reports
  • Added locus-level QC summary files (qc.txt.gz) in each locus directory
  • Added global QC summary file (qc.txt.gz) in output root directory
  • Summary includes key QC metrics: SNP counts, significance thresholds, MAF correlations, lambda-s values, and outlier counts
  • Configurable thresholds for flip detection, lambda-s outliers, and Dentist-S outliers
  • New locus_qc_summary() function to generate summary statistics from detailed QC results
  • Enhanced QC metrics:
    • n_1e-5, n_5e-8: Count of SNPs below significance thresholds
    • maf_corr: Correlation between summary statistics and LD reference MAF
    • n_flip: Count of potential allele flips (logLR > 2 AND |z| > 2)
    • n_lambda_s_outlier: Count of lambda-s outliers (|z_std_diff| > 3)
    • n_dentist_s_outlier: Count of Dentist-S outliers (-log10p ≥ 4 AND r² ≥ 0.6)

Changed

  • Modified locus_qc() function to accept threshold parameters for outlier detection
  • Updated qc_locus_cli() to return both locus ID and summary statistics
  • Enhanced loci_qc() function to aggregate and save global QC summary across all loci
  • Improved QC workflow output structure with hierarchical summary files

[0.0.32] (2025-09-12)

Changed

  • BREAKING: Removed strategy parameter from fine-mapping interface
  • Fine-mapping strategy is now automatically determined based on tool type and data structure
  • Multi-input tools (susiex, multisusie) automatically process all loci together
  • Single-input tools automatically combine results when multiple loci are provided
  • Added deprecation warning for backward compatibility
  • Enhanced CLI with enum validation for combination methods
  • Added CombineCred enum for credible set combination methods (union, intersection, cluster)
  • Added CombinePIP enum for PIP combination methods (max, min, mean, meta)
  • Improved input validation and auto-completion support

Removed

  • Web visualization feature moved to v2 (will be available in future release)
  • Removed credtools web command documentation
  • Removed web-related installation instructions
  • Removed web tutorial files and examples
  • Updated all workflow examples to reference output files instead

Improved

  • Simplified user interface with automatic strategy selection
  • Better CLI help with enum option display
  • Updated documentation to reflect streamlined workflow

[0.0.31] (2025-09-11)

Fixed

  • CI error

[0.0.30] (2025-09-11)

Added

  • ABF+COJO
  • adaptive causal

[0.0.28] (2025-06-13)

Added

  • add api docs

[0.0.27] (2025-06-12)

Added

  • add set_L_by_cojo to cli:pipeline

[0.0.26] (2025-06-02)

Added

  • add web visualization

[0.0.25] (2025-06-02)

Added

  • add tutorial

[0.0.23] (2025-02-01)

Fixed

  • fix finemap cred bug

[0.0.21] (2025-01-20)

Fixed

  • fix no install error for carma

[0.0.20] (2025-01-20)

Fixed

  • fix zero maf in finemap

[0.0.19] (2025-01-20)

Added

  • qc support for multiprocessing

[0.0.18] (2025-01-19)

Fixed

  • fix the bug of no credible set

[0.0.17] (2025-01-18)

Added

  • support for multiprocessing
  • add progress bar

[0.0.16] (2025-01-18)

Added

  • support for sumstats.gz and ldmap.gz

[0.0.15] (2024-12-17)

Added

  • cli args

[0.0.14] (2024-12-16)

Added

  • cli

[0.0.13] (2024-12-16)

Added

  • pipeline

[0.0.12] (2024-12-15)

Added

  • ensemble fine-mapping

[0.0.11] (2024-12-15)

Added

  • multisusie

[0.0.10] (2024-12-15)

Added

  • susiex
  • Rsparseld
  • CARMA

[0.0.9] (2024-10-21)

Added

  • abf
  • susie
  • finemap

[0.0.8] (2024-10-10)

Added

  • load ld matrix and ld map
  • munge sumstat
  • example data

[0.0.7] (2024-10-09)

Added

  • test for ldmatrix

[0.0.6] (2024-10-09)

Added

  • functions for load LD
  • test for ColName

[0.0.5] (2024-10-08)

  • First release on PyPI.