Treesapp

Added
- New flag '--deduplicate' for `treesapp create` to remove redundant sequences within 99.9% similarity before querying Entrez.
- New option for `treesapp assign` called '--hmm_coverage' that allows users to control minimum percentage of a
profile HMM that a query sequence's alignment must cover

Fixed
- Mapping some EggNOG identifiers with seqs2lineage mapping process

Changed
- Reference package training is now optional with `treesapp update`. A fasta file is no longer required.

Added
- Control of relative abundance metric for `treesapp abundance` to use with `treesapp assign`

Fixed
- Using all predicted ORFs when calculating abundance values for proper TPM values
- Fixed TypeError when `treesapp abundance` is used with single-end or interleaved FASTQ files

Changed
- Using miniconda for installing dependencies in GitHub Action 'tests'

Added
- (33) Checkpointing to all major (i.e. time-consuming) subcommands: `abundance`, `assign`, `create`, `purity`, `train`
- Added `stages` argument to `treesapp abundance` to control checkpoint
- Able to control the maximum number of examples used and SVC kernel for training through `treesapp create`
- (66) Documentation for `treesapp evaluate`
- A new _de novo_ clustering mode for `treesapp phylotu` will infer a new tree of just query sequences
- A new `treesapp phylotu` output mapping classified sequences to their cluster
- Able to append results from `treesapp abundance` to classification table for multiple read datasets

Fixed
- (71) Ability to rerun and append results from `treesapp evaluate` has been restored
- File paths with square brackets and parentheses no longer trip up HMMER or RAxML-NG in various modules.
Some single-quotes were needed.
- Properly truncate sequences in `treesapp evaluate` with '--length' argument
- Can add bipartition support to JPlace trees for visualization. Bipartitions were not formatted properly.
- File paths of reference package trees with support values

Changed
- `treesapp evaluate` uses a tqdm progress bar instead of printing updates to stdout when classifying
- Removed the prodigal header tags when ORFs are predicted by TreeSAPP. Could lead to significant RAM reduction.
- Flag to activate relative abundance calculation in `treesapp assign` changed from '--rpkm' to '--rel_abund'

Added
- More unit tests for file parsers and functions for `treesapp assign`
- More rigorous integrative test for `mcc_calculator.py` with higher coverage.

Fixed
- A KeyError in `treesapp update` caused when ORFs on the same sequence classified to the same refpkg.
Their dictionary keys were overwritten in simulate_entrez_records().
- Mapping sequence names to lineages provided in a seqs2lineage file.
ORF names containing parentheses were not being escaped, messing up regular expression matching.
- (64) Able to overwrite reference packages in the same directory
- `mcc_calculator.py` was not calculating TP, TN and FP correctly.

Changed
- Only `max_lwr` mode in `treesapp assign` will use the linear model for taxonomic rank recommendation
- Warning in `treesapp update` if all query sequences are shorter than the minimum sequence length threshold
- Log files don't contain the sequence names removed from FASTA objects at various steps,
potentially significantly reducing the size of these files.
- `mcc_calculator.py` summarizes the number of queries with missing taxonomic lineages in a single warning.
- Log writes to stderr while `treesapp package view` writes reference package data to sys.stdout.

Added
- New option in `treesapp package` called 'rename' to change the name of a reference package
- MMSeqs2 and MAFFT versions included in `treesapp info` output
- GitHub Actions for CI
- Unit tests

Fixed
- (63) An annoying warning that a fasta with classified nucleotide sequences couldn't be created for protein sequence input.
- (62) Corrected FPKM values.
- (58) List available reference packages (link to [RefPkgs](https://github.com/hallamlab/RefPkgs) in README).

Changed
- Updated required version of `samsum` to 0.1.4

This release is for version 0.9.0 and covers many new features. It is strongly recommended that everyone updates to this version.

There is __no__ backwards compatability of between this and older versions.
All reference packages built using older versions will need to be remade from scratch.

Added
- Uses EPA-NG and RAxML-NG for phylogenetic placement and inference, respectively. Using EPA-NG drops the runtime drastically.
- (48) Reference packages are stored as a single, pickled file.
- The subcommand treesapp package has been specifically designed to allow users to still interact with this binary file.
- (49) Reduced RAM usage by not loading query FASTA, rather loading just headers and loading only the query sequences that matched a reference package's profile HMM.
- Using the RefPkgs repository for version control of all non-core reference packages. Available for everyone to contribute to!
- Profile HMMs are dereplicated at the genus rank for more sensitive profiles.
- Users are able to update reference packages with GTDB-tk lineages by using the --seqs2lineage argument.
- The subcommand treesapp train fully supports checkpointing. Checkpointing in other subcommands is still to come (but well on its way).
- We finally have some sort of a test suite.

Fixed
- (51) Error while parsing some alignments from hmmsearch

Changed
- Format of the classification table (final_outputs/marker_contig_map.tsv) has been changed. Only a single column for the recommended taxonomy and the hmmsearch-derived E-value is reported.
- Reference trees are automatically rooted using ETE3's 'set_outgroup' function with the farthest node. Polytomies are also automatically resolved when the tree is built using FastTree.
- In treesapp create (and therefore treesapp update) reference sequence outlier detection and removal using OD-Seq has been made optional and can be requested using the '--outdet_align' flag.