0.19.4

What's Changed

• Fix NaN values in adata.obs by @suu-yi in #74
• Gene symbols patch by @suu-yi in #76
• logging improvements and version bump by @parashardhapola in #79

Full Changelog: 0.19.3...0.19.4

0.19.3

What's Changed

• Update version to 0.19.3 and enhance gene symbol handling by @parashardhapola in #72

Full Changelog: 0.19.2...0.19.3

0.19.2

What's Changed

• Update version to 0.19.2 and enhance metadata handling in CyteType by @parashardhapola in #71

Full Changelog: 0.19.1...0.19.2

0.19.1

What's Changed

• Update version to 0.19.1 and improve file upload initiation by @parashardhapola in #70

Full Changelog: 0.19.0...0.19.1

0.19.0

What's Changed

• Update version to 0.19.0 and enhance file upload functionality by @parashardhapola in #69

Full Changelog: 0.18.1...0.19.0

0.18.1

What's Changed

• Update version to 0.18.1 and enhance public API formatting by @parashardhapola in #68

Full Changelog: 0.18.0...0.18.1

0.18.0

✨ What's New

🧬 Raw Counts in vars.h5 Artifact

• The save_features_matrix function now writes an optional raw group to the H5 artifact containing integer raw counts (LZ4-compressed CSR).
• CyteType.__init__ auto-resolves raw counts from adata.layers['counts'], adata.raw.X, or adata.X (if integer-valued), and embeds them alongside normalized counts.

🚀 rank_genes_groups_backed — Memory-Efficient Differential Expression

• New public function — a drop-in replacement for sc.tl.rank_genes_groups that works on backed/on-disk _CSRDataset matrices.
• Streams cell chunks in a single pass, computes Welch's t-test (one-vs-rest) with BH or Bonferroni correction, and writes scanpy-compatible output to adata.uns.
• Exported at cytetype.rank_genes_groups_backed.

✂️ subsample_by_group — Per-Group Cell Subsampling

• New preprocessing utility that caps each cluster to a configurable maximum number of cells (max_cells_per_group), keeping smaller groups intact.
• Works with both in-memory and backed AnnData objects.

🔍 Auto-Detection of Gene Symbols Column

• gene_symbols_column now defaults to None and auto-detects by checking well-known column names (feature_name, gene_symbols, etc.), then adata.var_names, then a heuristic scan of all var columns.
• Detects and skips composite gene values (e.g., TSPAN6_ENSG00000000003).
• Candidates are scored by ID-like percentage, uniqueness ratio, and priority — the best non-ID column wins.

🎨 marker_dotplot — Category-Grouped Dot Plot

• New plotting module (cytetype.plotting) with marker_dotplot that reads stored CyteType results and creates a scanpy dotplot grouped by cluster categories with top supporting marker genes.

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⚡ Improvements

🏗️ Artifact Pipeline Restructuring

• Artifacts (vars.h5, obs.duckdb) are now built during __init__ and uploaded during run(), decoupling build from upload.
• vars_h5_path and obs_duckdb_path moved from run() to __init__() parameters.
• New cleanup() method replaces the removed cleanup_artifacts parameter on run().

💾 CSR-Backed Write Path for Normalized Counts

• New two-pass column-group scatter algorithm (_write_csc_via_row_batches) converts CSR-backed data to CSC in the H5 file without loading the full matrix.
• Configurable memory budget via WRITE_MEM_BUDGET (default 4 GB).

📊 Expression Percentage Calculation

• Refactored to use single-pass row-batched accumulation (reuses _accumulate_group_stats) instead of gene-batched pandas groupby.
• Default pcent_batch_size increased from 2000 to 5000.

☁️ Upload Enhancements

• vars_h5 max upload size increased from 10 GB to 50 GB.
• Upload progress now uses tqdm progress bars when available.
• Default connect timeout increased from 30s to 60s.

📈 Progress Reporting

• tqdm progress bars added throughout: rank_genes_groups, subsampling, raw counts writing, normalized counts writing, and chunk uploads.

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🐛 Bug Fixes / Error Handling

• 🆕 New ClientDisconnectedError exception for HTTP 499 / CLIENT_DISCONNECTED responses.
• 🗑️ Removed stale hasattr(adata.var, gene_symbols_col) check (was always True for DataFrames).
• 🛡️ Raw counts write failures are caught gracefully — the raw group is cleaned up and skipped with a warning.

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⚠️ Breaking Changes

• gene_symbols_column default changed from "gene_symbols" to None (auto-detect).
• vars_h5_path and obs_duckdb_path moved from run() to CyteType.__init__().
• cleanup_artifacts parameter removed from run(); use cleanup() method instead.
• pcent_batch_size default changed from 2000 to 5000.
• batch_size parameter in aggregate_expression_percentages renamed to cell_batch_size.

0.17.0

What's Changed

• Obsm in duckdb by @parashardhapola in #66

Full Changelog: 0.16.1...0.17.0

0.16.1

What's Changed

• Retry chunk uploads and allow partial artifacts by @parashardhapola in #64

Full Changelog: 0.16.0...0.16.1

0.16.0

What's Changed

• Support parallel chunked uploads and bump version by @parashardhapola in #63

Full Changelog: 0.15.0...0.16.0