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Add -i/--input dir mode alongside the existing single-file -r mode. Remove run_kreport2mpa.sh wrapper — batch logic now lives in Python.
Merge decombine.sh + decombine_viruses.sh into a single split_mpa.py. Add --viruses-only and --keep-human flags. Move convert2csv and processing_script into counts/ subpackage.
Replace kraken2csv.sh with pipeline.py. Add run_pipeline() as a callable library function. Add -o/--output and --overwrite flags. Skip binary and hidden files automatically (_is_processable check).
…dation - Add aggregate_by_metadata() to base for metadata grouping - Fix streamgraph grid axis (x→y) - Raise ValueError when cmap list is shorter than taxa count - Add missing-sample validation on sample_order
…modules Remove version.py — version now sourced from package metadata. Dispatcher uses python -m package.module to preserve import context. Default to full pipeline when -i is given without a subcommand.
Add fail-fast: false, flake8 lint step, --no-build-isolation, branch-scoped triggers (dev, main), codecov-action@v5.
Triggers on v* tags. Strips GitHub-specific markup from README before build to ensure clean PyPI rendering.
Unit tests: _parse_line, shannon/pielou/chao1 indices, modify_taxa_names. Integration: kreport_to_mpa, convert_to_csv, relabund, alpha/beta div, split_mpa — all with reproducibility (SHA-256) checks.
Add smoke tests for stacked_barplot, streamgraph, clustermap. Switch test_full_pipeline to direct run_pipeline() call so pipeline.py is included in coverage. Add overwrite protection tests.
Add codecov badge. Document new -o/--output and --overwrite flags. Add Before Visualization section highlighting --relabund -O. Move step-by-step modules to collapsible <details> block. Update Example Output Structure with intermediate/ directory.
biom-format uses a legacy setup.py that imports numpy at metadata generation time. Pre-installing numpy ensures it is available before pip resolves scikit-bio's transitive dependencies.
biom-format (transitive dep of scikit-bio) has no cp314 wheel and its legacy setup.py has undeclared build-time deps (numpy, Cython). Pin support to 3.10–3.13 until scikit-bio ecosystem catches up.
scikit-bio pulls in biom-format which has no cp314 wheel and brittle build-time deps. Reimplement subsample_counts in numpy and use scipy.spatial.distance for Bray-Curtis and Jaccard. Restore Python 3.14 support and bump requires-python to <=3.16.
Rarefaction is stochastic — without a fixed seed results differ between runs. Replace np.random.choice with np.random.default_rng and propagate the seed through calc_beta_div and run_pipeline.
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Summary
Complete modernisation of KrakenParser from a loosely-coupled set of
bash + Python scripts into a proper Python package.
Architecture
transform2mpa.py,split_mpa.py,pipeline.pykrakenparser/mpa/,counts/,stats/,kpplot/— each with__init__.pypipeline.py— orchestrates the full pipeline as a callablerun_pipeline()function (importable, not just CLI)scikit-bioin favour ofscipy— eliminatesbiom-formatdependency and unblocks Python 3.10–3.13 supportNew features
KrakenParser -i data/kreports— no--completerequired (default mode)-o / --output— custom output directory for the full pipeline--overwrite— explicit protection against accidental reruns--keep-human— opt-out of human taxa filtering-s / --seed— reproducible β-diversity rarefaction--kreport2mpa— batch (-i DIR) and single-file (-r FILE) modesOutput structure
Intermediate files (
mpa/,COMBINED.txt,txt/) are now groupedunder
intermediate/; final results (counts/,rel_abund/,diversity/) surface at the top level.Quality
logginginstead ofprint()in library functionsraise FileNotFoundErrorinstead ofsys.exit()in library codeimportlib.metadatafor version (noversion.py)python -m krakenparser.*dispatch preserves package import contextCI/CD
python-package.yml— matrix 3.10–3.13, flake8, codecovpublish.yml— Trusted Publishing onv*tags