v1.4.0

BioFindr v1.4.0

Diff since v1.3.0

Breaking Changes

There are no breaking changes in this release.

New Features

• Add fit_mixdist_hist function in posteriorprobs_hist.jl: a histogram-based LLR-to-posterior-probability conversion ported from the original Findr C implementation. The function supports all five BioFindr tests (:corr, :link, :med, :relev, :pleio) and uses unequal-bin histogram construction with iterative bin-edge refinement to match the null distribution (#29)
• pprob_col now accepts method="hist" as a third mixture-fitting option in addition to the existing "kde" and "moments" options (#29)

Behavior Changes

• The fallback method used when method="moments" raises an AssertionError in pprob_col is changed from KDE to histogram (fit_mixdist_hist) (#29)
• The default method for pprob_col remains kde (a previous intermediate commit set it to hist; this was reverted back to kde before release)

Dependency Changes

• Add Interpolations as a runtime dependency (required by fit_mixdist_hist for spline interpolation during histogram construction) (#29)
• Bump compat for Interpolations to include version 0.16 (#30)

Tests

• Add a fit_mixdist_hist test set in test/postprobs_tests.jl covering all five BioFindr test types, validating that posterior probabilities are in [0, 1] and are non-decreasing with respect to the LLR values (#29)
• Update existing pprob_col test sets to explicitly test the "hist" method and verify fallback-from-"moments" behaviour (#29)

Documentation

• Add a new ## Histogram-based conversion of the mixture distribution section in docs/src/posteriorprobs.md with API docs for fit_mixdist_hist (#29)
• Update docs/src/index.md to mention all three posterior-probability estimation approaches (histogram, moments, KDE) (#29)
• Update the note at the end of docs/src/posteriorprobs.md to reflect that the histogram method is available as an option (#29)

Full Changelog: v1.3.0...v1.4.0

v1.3.0

BioFindr v1.3.0

Diff since v1.2.0

Breaking Changes

There are no breaking changes in this release.

Behavior Changes

• Change the default LLR mixture-distribution fitting method from moments to kde across public inference entry points (findr, findr_matrix, and pprob_col) and update docstrings accordingly (#27)
• Update posterior-probability tests to validate the new default behavior while keeping explicit method="moments"/method="kde" support (#27)

Documentation

• Clarify posterior-probability docs to highlight that kernel density estimation is now the default method and how to switch methods explicitly (#27)
• Minor markdown cleanup in docs/src/posteriorprobs.md (#27)

Logging

• Reduce noise when π₀ = 1 in KDE fitting by changing a warning log to debug level in fit_mixdist_KDE (#27)

Full Changelog: v1.2.0...v1.3.0

v1.2.0

BioFindr v1.2.0

Diff since v1.1.0

Breaking Changes

There are no breaking changes to the public API in this release. However, users who accessed internal (unexported) functions or module-level constants by name should note:

• The internal module-level string constants corr, link, med, relev, and pleio (accessible as e.g. BioFindr.corr) have been removed
• Internal functions have been renamed to follow Julia's snake_case convention: groupmeans → group_means, realLLR_col → real_llr_col, llrstats_col → llr_stats_col
• Source files renamed for consistency: realLLR.jl → real_llr.jl, randomLLR.jl → random_llr.jl (plus corresponding test and documentation files)

New Exports

• LBeta, coerce_scitypes!, and generate_test_data are now exported (they were previously accessible but unexported despite being used prominently in the documentation)

Bug Fixes

• lbeta.jl: logpdf incorrectly returned 0. for x < 0; corrected to -Inf (the log-probability of an impossible event) (#25)
• posteriorprobs.jl: All five try/catch blocks previously caught every exception, silently masking real bugs. They now only catch AssertionError; all other exceptions are rethrown (#25)
• findr.jl: findr(dX, dG) with a categorical genotype column dG silently produced a result matrix of CategoricalValue objects instead of integers. The function now validates the scitype of dG and uses levelcode() for correct integer conversion (#25)
• utils.jl: getpairs previously caused a MethodError when column names in the two input data frames did not match; it now throws an informative ErrorException (#25)
• utils.jl: symprobs docstring incorrectly claimed the default combination method was "prod"; corrected to "none" (#25)
• utils.jl: qvalue now clamps q-values to the interval [0, 1] and replaces noisy @info logging with @debug (#25)

Performance Improvements

• utils.jl (group_means): findall is now computed once per group instead of evaluating a membership mask three times (#25)
• supernormalization.jl (supernormalize): The quantile lookup table is now built once per column length instead of issuing one quantile() call per element (#25)
• posteriorprobs.jl (pi0est): The λ-grid search now uses O(log n) searchsortedlast instead of an O(n) linear scan (#25)

Dependency Changes

• Add CategoricalArrays as an explicit runtime dependency (it was previously loaded as a hidden transitive dependency via DataFrames) (#25)
• Move Printf from [deps] to [extras] (test-only) (#25)
• Remove Documenter and LiveServer from runtime [deps] — these are documentation-only tools (#25)
• Bump compat for MetaGraphsNext to include version 0.8 (#23)
• Remove Manifest.toml and docs/Manifest.toml from the repository; add Manifest.toml to .gitignore (#25)

New Tests

Total test count increased from 145 to 221 (#25):

• test/findr_tests.jl — comprehensive tests for all findr() and findr_matrix() overloads (the primary public API previously had zero tests)
• test/dagfindr_tests.jl — tests for all three dagfindr! methods, including cycle-freeness assertions
• test/utils_tests.jl — expanded with tests for qvalue, globalfdr, globalfdr!, stackprobs, symprobs, combineprobs, and getpairs

Documentation

• Complete previously unfinished ("TBW") docstrings in bayesiannets.jl (#25)
• Restore push!(LOAD_PATH, "../src/") in docs/make.jl to ensure the local source is used during documentation builds rather than the registered package version (#25)

CI

• Upgrade all GitHub Actions to their latest versions (#25)
• Test against Julia 1 (latest stable) instead of a pinned minor version (#25)

Full Changelog: v1.1.0...v1.2.0

This release has been identified as a backport.
Automated changelogs for backports tend to be wildly incorrect.
Therefore, the list of issues and pull requests is hidden.

v1.1.0

BioFindr v1.1.0

Diff since v1.0.5

Breaking Changes

There are no breaking changes in this release.

Changes

• Broaden function type signatures from concrete to abstract array/float types for improved interoperability (e.g., with JuliaCall): Array{T} → AbstractArray{T}, Vector{T} → AbstractVector{T}, Matrix{T} → AbstractMatrix{T} across realLLR.jl, posteriorprobs.jl, utils.jl, findr_matrix.jl, and findr_pvalues.jl (#22)
• Fix inconsistency in findr_matrix overloads where implementations used T<:Real while docstrings declared T<:AbstractFloat; all overloads now consistently use T<:AbstractFloat (#22)
• Update dependency manifests
• Update Julia version in CI workflow

Full Changelog: v1.0.5...v1.1.0

This release has been identified as a backport.
Automated changelogs for backports tend to be wildly incorrect.
Therefore, the list of issues and pull requests is hidden.

v1.0.5

What's Changed

• Catch error in kernel density estimation when $\pi_0=1$ by returning zero posterior probabilities
• CompatHelper: add new compat entry for ScientificTypes at version 3, (keep existing compat) by @github-actions in #20

Full Changelog: v1.0.4...v1.0.5

v1.0.4

BioFindr v1.0.4

Diff since v1.0.3

• add option to perform causal inference for a subset of regulators without having to modify the input data

v1.0.3

BioFindr v1.0.3

Diff since v1.0.2

added dagfindr! to exported functions

v1.0.2

BioFindr v1.0.2

Diff since v1.0.1

Added functions and documentation for DAG reconstruction

v1.0.1

BioFindr v1.0.1

Diff since v1.0.0

Merged pull requests:

• CompatHelper: add new compat entry for Graphs at version 1, (keep existing compat) (#18) (@github-actions[bot])
• CompatHelper: add new compat entry for MetaGraphsNext at version 0.7, (keep existing compat) (#19) (@github-actions[bot])

Closed issues:

• TagBot trigger issue (#17)

Renaming to BioFindr

The package and repository have been renamed from Findr.jl to BioFindr.jl to bring it inline with Julia package naming guidelines. See this issue for details.

Full Changelog: v0.2.0...v1.0.0