Changes

Revision history for Perl distribution Pheno-Ranker

1.09 2025-0X-0X:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Migrated project documentation from MkDocs to Docusaurus

1.08 2025-05-01:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Refactored internals to split configuration, context, compare, ranking, and graph helpers
 - Added Matrix Market output (--matrix-format mtx) and graph edge filtering options
 - Use Perl-versioned Inline cache directories to avoid stale compiled objects on CPAN testers
 - Canonicalize nested arrays by meaningful content to avoid order-only differences in complex JSON
 - Renamed configuration keys to indexed_terms, index_regex, and identity_paths; legacy names remain supported
 - Added default first-level array identities for generic JSON (format: JSON) when identity_paths is absent
 - bff-pxf-plot:
    - Improved plot aesthetics and readability while preserving the dependencies
 - QR-code utils:
    - Updated PDF template

1.07 2025-06-05:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Revived --patient-of-interest (--poi) option
 - Updated Dockerfile to use perl:stable-bookworm
 - Switched cpan-publish.yml from ubuntu-latest to ubuntu-22.04
 - Fixed issue with --prp and BFF
 - bff-pxf-simulator:
   - PXF: Fixed 'procedure.term.id' with 'procedure.code.id'

1.06 2025-05-27:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Replace --max-matrix-items-in-ram by --max-matrix-records-in-ram

1.05 2025-02-17:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Added key 'zlib_base64_*' to *.ref_binary_hash.json
 - Optimized ‘ref_binary_hash’ data loading for faster performance

1.04 2025-02-11:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Set .Inline at user's home dir

1.03 2025-02-04:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Renamed 'Stats.pm' to 'Metrics.pm'
 - Switched metrics to Inline C to enhance speed for large binary string vectors

1.02 2025-02-02:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Renamed 'Align.pm' to 'Compare.pm'
 - Expanded 'rank.txt' with new columns: REFERENCE-VARS, TARGET-VARS, INTERSECT, INTERSECT-RATE(%), COMPLETENESS(%)
 - Renamed '--max-number-var' to '--max-number-vars' to prevent mistakes
 - Moved t/plot.t to xt/ as Python libraries caused issues in GitHub builds
 - Added "interpretations" to PXF in 'bff-pxf-plot'
 - Introduced '--retain-excluded-phenotypicFeatures' to include "excluded": true in comparisons
 - Added '--precomputed-ref-prefix' for pre-computed cohort data
 - Enabled support for .gz JSON/YAML inputs
 - Added 'share/diseases' with disease-based reference cohorts
 - Introduced '--max-matrix-items-in-ram' as option (+ config) to speed up jobs for users with enough RAM

1.01 2025-01-16:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - DockerHub images now support Linux amd64 and arm64 (M-based Macs)

1.00 2024-11-27:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Added DOI to docs
 - Added term 'phenotypicFeatures' to PXF in bff-pxf-plot
 - Changed { id => 'NCIT:NA0000', label => 'NA' } to { id => 'NCIT:C126101', label => 'Not Available' }

0.12 2024-10-18T00:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Added UTF-8 encoding for writing alignment text files
 - Added parser to guess labels for variables without a key.label

0.11 2024-09-29T00:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Added support for BFF pedigrees (excluded by default via regex in config)
 - Discarded '_id|datasetId' keys using regex in config
 - Used sprintf in 'Average Path Length' at <graph_stats.txt> for CPAN test compliance

0.10 2024-08-07T00:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Fixed UTF-8 printing issue for primary_key in STDOUT
 - Added native support for interpretations nested properties up to 2D in PXF

0.09 2024-05-04T00:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Enhanced the csv2pheno-ranker's guessing mechanism for array fields; now evaluates all rows instead of just the first one
 - New module added: lib/Pheno/Ranker/Graph.pm
 - Introduced option --cytoscape-json to generate graphs compatible with Cytoscape
 - Added option --graph-stats to compute basic statistics using the Graph CPAN module
 - Updated cpanfile and Makefile.PL to include the Graph module

0.08 2024-04-24T00:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Added Unicode support to csv2pheno-ranker
 - Introduced --array-separator option in csv2pheno-ranker with default '\|'
 - Fixed option --age to be used with BFF/PXF formats only

0.07 2024-04-22T00:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Excluded keys with {} or [] values (e.g. subject.vitalStatus: {})
 - Precompiled regex patterns where possible
 - Schema validation errors related to weights are now directed to STDERR
 - Added support for keys with non-word characters (e.g., "Survey.Timestamp.1")

0.06 2024-04-06T00:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Renamed --primary-key to --primary-key-name and --set-primary-key to --generate-primary-key
   in csv2pheno_ranker for clarity
 - Changed from perl:5.36-bullseye to perl:stable-bullseye in Dockerfile
 - Excluded 'NA', 'NaN', undef, {}, and [] from coverage_stats counts
 - Froze a few modules in requirements.txt

0.05 2024-03-19T00:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Implemented sprintf in jaccard function for FreeBSD CPAN test compliance
 - Added utils/bff_pxf_plot to create PNG with stats
 - Updated Dockerfile
 - Ensured termination with an error if primary_key is unset for any object

0.04 2023-12-26T00:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Added List::MoreUtils to cpanfile/Makefile.PL
 - Added error when --include-terms does not exist in cohort(s)
 - Added t/die.t for the above condition (+others)
 - Refactored code in .t and .pm to enhance readability and maintainability
 - Spiced up die/warn messages with bold-colored text
 - Added utils/barcode to deal with QR codes (+Dockerfile and t)
 - csv2pheno-ranker now accepts .tsv (sep \t)
 - Fixed stringification of weights (read from YAML) on JSON export
 - Added flag --similarity-metric-cohort
 - Added terms 'procedures,exposures' to bff-pxf-simulator

0.03 2023-11-27T00:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Updated Align.pm for optimized performance with datasets over 5,000 rows
 - Cleaned up matrix.txt by removing trailing tab characters
 - Refined STDERR messages for clearer communication
 - Introduced a TODO in t/sim.t (test 3) for future improvement (fails in ~10% of CPAN)
 - Streamlined setup by removing Carton instructions from README.md

Note: Versions <= 0.02 were primarily for testing deployment on CPAN.