v1.1.0

Added

• [workflow] Argelaguet gastrulation dataset: download, format conversion, and analysis report (promoter vs enhancer, as in issue #24)
• [workflow] CRC cell embeddings report with featureset-wise PCA/UMAP
• [workflow] Ecker dataset: applied same embedding and sparse representation procedure as other datasets
• [workflow] adjS vs intervals of DNA methylation
• [workflow] Coordinate validator (validate.smk, validate_yamet_coords.sh) to check yamet output coordinates
• [workflow] Simulations restructured into the main snakemake ruleset, reusing Argelaguet's download rules
• [workflow] Shared embedding utilities (embedding_utils.R)
• [test] Test case for shannon norm with no infinite values (division by zero edge case)

Fixed

• [method] Infinite shannon entropy normalisation values caused by division by zero
• [method] cmake cache and install targets
• [workflow] Cell embeddings no longer impute missing values; sparse representations handle NAs natively
• [workflow] HVG/PCA for sparse data where zero and NA carry distinct biological meaning

Changed

• [workflow] Simulations moved from top-level simulations/ into workflow/rules/simulations.smk and workflow/simulations/
• [workflow] Cell embeddings standardized across datasets; marginal methylation handled via scaling rather than imputation
• [automations] Switched to conda-managed envs