Changes in version 0.99.44                       

  - Remove all requireNamespace("rmda") / rmda code paths from the
    nomogram DCA module (fixes R CMD check WARNING about undeclared
    dependency).
  - Normalize NEWS.md section titles to # GExPipe x.y.z so R can parse
    version history.

                       Changes in version 0.99.43                       

  - Correct co-author names to Naeem Mahmood Ashraf and Prof. Dr.
    Muhammad Farooq Sabar.
  - Remove unavailable Suggests package rmda (Bioconductor CHECK ERROR).
    Nomogram DCA uses dcurves (already preferred in code).

                       Changes in version 0.99.40                       

BiocCheck

  - Rename GSEA map field cat to msig_category so BiocCheck no longer
    flags a false cat() hit.
  - Add maintainer ORCID (0000-0003-2646-8106) in Authors@R.

                       Changes in version 0.99.39                       

Authors

  - Add co-authors Naeem Mahmood Ashraf and Prof. Dr. Muhammad Farooq
    Sabar; Safa Rafique remains maintainer (cre).

                       Changes in version 0.99.38                       

Bioconductor NOTES cleanup

  - Move optional feature packages from Imports to Suggests: Boruta,
    car, cicerone, corrplot, dcurves, kernlab, mixOmics, SHAPforxgboost
    (use requireNamespace guards).
  - Prefer seq_len/seq_along; replace cat()/redundant stop-warn prefixes
    in Shiny servers.
  - Treat Suggests packages as optional during attach/bootstrap (core
    Imports remain required).

                       Changes in version 0.99.37                       

Package hygiene

  - Exclude and untrack GExPipe(original_paper)/ from the Bioconductor
    package tree (.Rbuildignore + .gitignore).

                       Changes in version 0.99.36                       

SPB NOTES cleanup (reviewer request)

  - Expand NAMESPACE importFrom for
    grDevices/graphics/stats/utils/shiny/ggplot2/DT/grid.
  - Expand utils::globalVariables() for NSE column names and Shiny
    symbols.
  - Replace sapply() with vapply(); prefer seq_len() / sample.int().
  - Replace ggplot print(p) with returning p in renderPlot.
  - Remove <<- via env boxes / reactiveValues assignment.
  - Fix gexp_fetch_geo_series_matrix_metadata call in validation server.

                       Changes in version 0.99.35                       

Bioconductor check warnings

  - Replace non-ASCII characters in R/ with ASCII equivalents.
  - Declare Suggests: bslib, crosstalk, devtools, fontawesome,
    htmltools, htmlwidgets, rmda.
  - Replace set.seed() with withr::local_seed() / withr::with_seed()
    (BiocCheck).

                       Changes in version 0.99.34                       

SPB / R CMD check

  - Fix gexp_qc_build_sample_dataset_map man page example matrix
    dimensions.

                       Changes in version 0.99.33                       

Documentation

  - Clarify gexp_align_rnaseq_sample_names() runs after GEO download
    (GSE ID workflow), not manual data entry; fix example matrix
    dimensions in man page.

                       Changes in version 0.99.32                       

SPB / R CMD check

  - Regenerate man/gexp_align_rnaseq_sample_names.Rd example (fixes
    examples ERROR).

                       Changes in version 0.99.31                       

SPB / R CMD check fixes

  - Fix gexp_align_rnaseq_sample_names() example matrix dimensions.
  - Skip source-tree-only bioc-review tests when R/ is not in installed
    layout.
  - Harden server namespace test; avoid false match on
    inst/shinyapp/server.R.
  - Remove install.packages() from GitHub bootstrap (BiocCheck
    compliance).

                       Changes in version 0.99.30                       

Tests

  - Fix test-bioc-review.R shinytest2 readme path for covr /
    installed-package test runs.

                       Changes in version 0.99.29                       

Bioconductor second-review response

  - Vignette: 30 end-user screenshots in vignettes/images/;
    maintainer-only notes removed.
  - Step 4: title column fallback for poorly annotated GEO series;
    optional group rename at Group Summary.
  - DE/ML contrasts respect custom reference/comparison labels.

                       Changes in version 0.99.28                       

Shinytest2 readiness signal

  - Inject shinytest2::use_shinytest2() in test mode so
    window.shinytest2.ready is set for AppDriver.

                       Changes in version 0.99.27                       

Shinytest2 GEO download scenario

  - Added tests: empty GSE validation and GSE ID + Start Processing
    (GSE62646 by default).
  - Helpers: .gexpipe_shinytest2_poll_output(),
    .gexpipe_shinytest2_start_geo_download().
  - Added inst/scripts/record-shinytest2-geo.R for interactive
    recording.

                       Changes in version 0.99.26                       

Shiny testing (Bioconductor review)

  - Added shinytest2 workflow tests
    (tests/testthat/test-shiny-integration.R) and helper-shinytest2.R
    for welcome → dashboard → QC navigation.
  - Skip full Bioconductor attach in shiny.testmode so shinytest2
    sessions start quickly.
  - Documented usage in inst/scripts/README-shinytest2.md.

                       Changes in version 0.99.25                       

Bioconductor review (second round)

  - Moved Shiny bootstrap from inst/shinyapp/global.R into
    R/gexpipe_shinyapp_bootstrap.R.
  - Replaced all suppressWarnings() / suppressMessages() in R/ with
    targeted quiet I/O helpers.
  - Added tests/testthat/test-shiny-coverage.R and expanded bioc-review
    / app-builder tests for UI tabs, utils_shiny_app, and dummy_imports.
  - Fixed .gexpipe_best_version() for R 4.6+ (package_version
    comparison).

                       Changes in version 0.99.24                       

Vignette (Bioconductor review)

  - Removed maintainer-only text from vignettes/GExPipe.Rmd (screenshot
    paths, internal vignette notes).
  - Moved walkthrough screenshots to vignettes/images/ with direct
    knitr::include_graphics() calls.
  - Added five PNG figures referenced by the vignette; maintainer
    regeneration documented in
    inst/scripts/README-vignette-screenshots.md.

                       Changes in version 0.99.23                       

Bioconductor review (code organization and testing)

  - inst/shinyapp/server.R and ui.R now delegate to gexp_app_server() /
    gexp_app_ui() instead of duplicating modular logic or calling
    source() on tab modules.
  - Added gexpipe_spearman_cor() and removed suppressWarnings(cor(...))
    from ML plots.
  - Added tests/testthat/test-coverage-helpers.R for normalization, ID
    detection, WGCNA prep, download overlap helpers, and UI/ML
    utilities.

                       Changes in version 0.99.22                       

Bioconductor review (testing and code organization)

  - Added tests/testthat/test-pipeline-helpers.R for
    download/QC/classify helpers and namespace-based server wiring.
  - Replaced scattered suppressMessages(capture.output(getGEO...)) with
    .gexpipe_geo_quiet() and centralized count-file reads in
    .gexpipe_fread_counts().
  - Documented remaining suppression (STRINGdb ID mapping, optional
    biomaRt chatter).

Shiny functional review

  - Fix generic V2 sample names from headerless GEO count files; per-GSE
    labels in QC outlier plots before normalization.

                       Changes in version 0.99.21                       

Bioconductor second review

  - BugReports now points to GitHub Issues (safarafique/GExPipe).
  - Shiny server and UI tab modules moved from inst/shinyapp/ to R/ (no
    runtime source() / custom caching for tab modules).
  - Added inst/scripts/make-vignette-extdata.R documenting synthetic
    vignette data.
  - Removed redundant inst/pkg_versions.txt (versions are in
    DESCRIPTION).
  - Reduced suppressWarnings() around namespace unloads; added tests for
    UI/server builders, helpers, and pipeline wiring.

                       Changes in version 0.99.20