⬆️ version bump to v4.5

- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5"
- Update version.txt from 4.29 → .30
(automated by Makefile)

autodoc/docmd/pkg_obitools_obimatrix.md

@@ -0,0 +1,40 @@
+# `obimatrix` Package: Semantic Overview
+
+The `obimatrix` package enables high-performance construction, manipulation, and export of biological sequence count matrices (e.g., OTU/ASV tables) in the OBITools4 ecosystem. Built around a sparse matrix representation, it supports flexible attribute handling, parallelized input processing, and multiple output formats—ideal for downstream ecological or bioinformatic analysis.
+
+## Core Functionalities
+
+### Matrix Construction & Management
+- **`MakeMatrixData()` / `NewMatrixData(naVal string, fixedCols []string)`**:  
+  Initializes a new `MatrixData` instance with configurable NA placeholder and fixed column headers (e.g., `"id"`, `"count"`).
+- **`Update(seq obiseq.BioSequence, mapKey string)`**:  
+  Populates the matrix using a biological sequence’s annotations. Extracts per-taxon counts or arbitrary map attributes (e.g., sample IDs), inserting them into the sparse matrix under `row = seq.ID`, with dynamic column detection.
+- **`TransposeMatrixData(md *MatrixData)`**:  
+  Flips rows/columns: original columns become new `"id"` attributes; preserves metadata and NA handling.
+
+### Merging & Parallelization
+- **`MergeMatrixData(a, b *MatrixData)`**:  
+  Combines two matrices row-wise; panics on duplicate sequence IDs to prevent silent overwrites.
+- **`IMatrix(iter obiseq.Iterator, mapKey string)`**:  
+  Builds a full matrix in parallel from an iterator of sequences. Auto-detects extra sample columns if enabled (via `--auto-cols`), supporting dynamic batch processing.
+
+### Export & CLI Integration
+- **`CLIWriteCSVToStdout(md *MatrixData)`**:  
+  Outputs a wide-format CSV: rows = sequences, columns = fixed attributes + detected samples. Handles Phred encoding (ASCII 33/64) for quality strings and supports transpose via `--transpose`.
+- **`CLIWriteThreeColumnsToStdout(md *MatrixData)`**:  
+  Outputs a long-format CSV with columns: `sample`, sequence ID, and value—suited for tools expecting tidy data.
+- **CLI Option Aggregation**:  
+  Integrates with `getoptions` to expose flags like:
+    - `-m, --map-attribute`: grouping key (default: `"merged_sample"`)
+    - `--value-name`, `--sample-name`: column headers (defaults: `"count"`, `"sample"`)
+    - `-t, --transpose`: toggle row/column orientation
+    - `--allow-empty`, `--strict-attributes`: control handling of missing annotations
+
+### Robustness & Flexibility
+- **NA Handling**: Replaces absent mapping attributes with a configurable placeholder (default: `"0"`).
+- **Strict Mode**: Panics on type mismatches or uncastable values (e.g., non-numeric counts in numeric context).
+- **Attribute Extensibility**: Supports arbitrary metadata (taxonomic labels, quality strings) via dynamic column inference.
+
+## Design Philosophy
+
+Focused on **speed**, **type safety**, and **reproducibility** for amplicon sequencing workflows. The package avoids implicit defaults beyond core conventions, favoring explicit CLI configuration and clear error signaling for data integrity.