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MRUEDA / Pheno-Ranker-1.05 / Changes 

            

              
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Revision history for Perl distribution Pheno-Ranker
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.