changelog:
- All files are streamed to input files, rather than just files without associated background files.
- Background filenames (stripped of extensions) are no longer part of the input stream for `rules.score`, preventing odd errors
- Updated associated files to pull all input files as desired.

changelog:
- NOTE THAT WORKFLOW IS CURRENTLY BROKEN DUE TO SNAKEMAKE I/O REASONS AND I AM COMMITTING INTERRIM CHANGES
- fix: redo file glob -- file globbing now proceeds through `glob_wildcards` to more cleanly grab input files
- fix: enable unzip -- unzipping has been overhauled (these are forward changes adapted from snekmer 2.0.0 / the biotite-kmers branch).
- fix: add background -- changes have been made to collate background files and use their kmer distribution to subtract a background from protein family kmer models. These fixes work piece-by-piece locally but have not been fully tested and may not work ideally yet.

- Note: changes did NOT work, hence the "broken" tag.

changelog:
- snakemake now correctly builds DAG for background workflow, including file unzipping
- some files have been renamed for simplicity
- some instances of `skm.io.load_npz` have been replaced with `np.load` due to KeyError (perhaps due to numpy or pickle version?)
- `rules.combine_background` now uses kmer basis set for each family to reshape each background vector. should make files smaller and workflow more compact
- NOTE: WORKFLOW IS BROKEN AT `rules.score_with_background` due to file load / array shape issues that will be fixed in the next commit.
- addresses #37

changelog:
- kmer probability scoring using background subtraction is now the default scoring method
- `snekmer.score.feature_class_probabilities` now performs either background subtraction based scoring, family label based scoring, or a combination thereof depending on user input
- TODO: integration with `snekmer.score.KmerScorer` object

changelog:
- new config parameter config['score']['method'] added for compatibility with additional new(!) scoring methods
- uptick version from v1.1.1 -> v1.4.0
  - upticked +3 minor versions in anticipation of two pending PRs
- remove no longer needed files

changelog:
- kmers can now be scored by probability score subtracting the observed kmers in a supplied background set, family set, or combining both background and family
  - note: some column headers have changed, which may affect downstream analysis (e.g. integration with #115, #116)
- to handle user-supplied background files, new rules have been created to count background kmers and combine background kmer counts into a background matrix. The appropriate files for the new workflow have been created.
- extensive changes have been made to `snekmer.score` to accommodate the new changes, including:
  - `snekmer.score.score` now has 3 distinct formulae to compute probability scores according to the desired scoring method
  - `snekmer.score.feature_class_probabilities` now also integrates the scoring method
- the main scoring rule itself has been significantly altered as follows"
  - all references to the old and not-working "background subtraction" (e.g. separating sequences by "sample" or "background" labels) have been removed
  - extraneous kmer probability scores for every family are no longer calculated; only the family in question's kmer profile is scored
  - scoring method now integrated

changelog:
- fix: `snekmer.utils.get_family` now accepts `regex=None` by default as to not erroneously truncate filenames.
- fix: small change to `snekmer.utils.get_family` to correctly identify directories.
- refactor: overhaul `snekmer.utils.split_file_ext` to split at the point of an .faa, .fa, .fna, or .fasta extension instead of assuming at most 2 potential extensions

changelog:
- file unzipping is now handled by top-level unzip code in each snakefile; thus, `process.smk` is outdated and has been deleted as it is no longer needed.

changelog:
- file wildcard globbing previously proceeded through `glob.glob`, but had been updated in the model workflow to use snakemake's `glob_wildcards` utility. This method has the added benefit of preventing recursion errors with wildcard retrieval from gzipped files. The changes have now been applied to cluster and search workflows.

changelog:
- refactor: move `cluster_cluster.py` -> `cluster.py`
- refactor: move cluster report generation to separate script directive
- fix: change cluster mode file globbing to mirror model mode changes, i.e. uses snakemake `glob_wildcards` instead of python `glob.glob`. This should also fix unzipping issues and recursion errors related to unzipping.

changelog:
- fix: search file globbing updated to use snakemake's `glob_wildcards` rather than python's `glob.glob` in search mode. Should also resolve issues with file detection for files requiring unzipping and avoid recursion errors. Tested locally with a small subset of small families.
- style: applied snakefmt to `cluster.smk` and `search.smk`

changelog:
- feat: Snakemake `--resources` flag has been added to Snekmer CLI for all modes and tested locally.
- refactor: Wrapped all snakemake command line arguments into dictionary which is now passed to all snekmer subcommands. Removes the redundancy in specifying the same command line arguments every time a subcommand is called.

changelog:
- fix: resolve error with array shapes due to matrix dimensions (transpose matrix required)
- refactor: renamed variables to streamline code

changelog:
- basis harmonization now accounts for either 1D or 2D array cases
- 1D arrays are explicitly handled to match expected shape parameters set by the assumption that input arrays are 2D
- `utils.check_n_seqs` now uses boolean input arg to handle gz files rather than inferring from filename

changelog:
- Workflow now accounts for cases where no background files are included when either "combined" or "background" mode are selected. (TODO: raise warning in this case)
- Bypass UnicodeDecodeError for `utils.check_n_seqs`