raven-toolbox 3.0.0b1

First beta toward 3.0, matching the upcoming MATLAB RAVEN 3.0 beta.

• keep ftinit() as the only extraction pipeline.
• analysis.compare_fluxes replaces follow_changed — a compareFluxes port, following RAVEN
  dropping followChanged/followFluxes/mapCompartments.
• comparison.compare_models gained EC-code / metabolite-name / equation overlap matrices,
  folded from compareRxnsGenesMetsComps.
• New: curation.rename_model_genes, ported from renameModelGenes.
• New: curation.get_gene_data, download_genome_data, process_protein_fasta_file — the
  genome-data cluster.
• New: manipulation.replace_metabolite, ported from replaceMets.
• New: gapfilling.find_leak_metabolite, ported from findLeakMetabolite.
• New: manipulation.remove_bad_reactions, ported from removeBadRxns.
• New: gapfilling.gap_report, ported from gapReport.
• New: analysis.trace_flux_path, ported from traceFluxPath.
• New: analysis.get_flux_z / analyze_sampling, ported from getFluxZ/analyzeSampling.
• New: analysis.fit_parameters, ported from fitParameters.
• New: utils.guess_composition, ported from guessComposition.
• New: analysis.walk_fluxes / FluxWalker, ported from walkFluxes.
• New: analysis.get_min_nr_fluxes, ported from getMinNrFluxes.
• New: utils.generate_new_ids, ported from generateNewIds.
• init.ftinit implements the metabolomics production-bonus (metabolomics=, prod_weight=).
• init.ftinit reproducibility parameters renamed: strict_gap/canonical are now
  prove_abs_gap/resolve_ties, with corrected determinism numbers.
• ftINIT task gap-filling now edits the reference model in place instead of copying it — ~23%
  faster on a genome-scale extraction.
• Fixed three ftINIT/task-essential bugs: a task-essential boundary default, a checkpoint
  file-handle leak, and a non-finite tie-break objective.
• manipulation.close_model boundary-reaction detection is now structural, matching RAVEN.
• manipulation.convert_to_irreversible now splits exchange reactions too, carries a negative
  objective coefficient onto the reverse reaction, and gained an optional rxns restriction.
• conditions.apply_condition raises on unknown charge during charge balancing instead of
  silently miscalculating.
• annotation.load_delta_g_csv now always records CSV values literally, matching deltaGCSV.
• manipulation.remove_dead_end_reactions dead-end detection is now bounds-blind, matching RAVEN.
• analysis.get_min_nr_fluxes no longer crashes with GurobiError reading fluxes from an
  infeasible solve.
• analysis.fseof gained an explicit min_target scan-floor override.
• Fixed six redundant-calculation hot spots: merge_linear, batched add_reactions callers,
  analyse_topology, trace_flux_path, remove_dead_end_reactions, find_task_essential_reactions.
• random_sampling and fill_gaps_fast_lp parallelized with ProcessPool.
• io.write_yaml_model fixed: an infinite/NaN bound wrote as a bare word instead of the YAML
  token; sort_ids=True dropped the !!omap tag on compartments; unknown metaData fields
  are now preserved on write; empty gene_reaction_rule is now dropped. read_yaml_model treats
  a null genes/reactions/metabolites key as empty.
• Parameter defaults measured and unified: BLAST/DIAMOND/HMMER threading, homology
  min_align_len/evalue, get_init_model.allow_excretion.
• Removed io.export_model_to_sif — a mislabeled port of a MATLAB function that never existed.