Gtdbtk

Bug Fixes:

* (576) When all genomes fail the prodigal step in the `classify_wf`, The
bac120 summary file is still produced with the all failed genomes listed as 'Unclassified'
* (573) When running the 3 classify steps independently, a genome can be filtered out in the `align`
step but still be classified in the `identify` step. To avoid duplication of row, the genome is classified with a warning.
* (540 ) Empty files are skipped during the sketch step of `Mash`,
they are then catched in the `prodigal` step and are returned as 'Unclassified'
* (549) : `--force` has been modified to deal with 540. `Prodigal`
wasn't returning the empty files as failed genomes, it was only skipping them. These genomes are now returned in the summary file and flagged as Unclassified.

Major Changes:

* `FastANI` has been replaced by `skani` as the primary tool for computing Average Nucleotide Identity (ANI).Users may notice slight variations in the results compared to those obtained using `FastANI`.
* In the generated `summary.tsv` files, several columns have been renamed for clarity and consistency. The following columns have been affected:

- "`fastani_reference`" column has been renamed to "`closest_genome_reference`".
- "`fastani_reference_radius`" column has been renamed to "`closest_genome_reference_radius`".
- "`fastani_taxonomy`" column has been renamed to "`closest_genome_taxonomy`".
- "`fastani_ani`" column has been renamed to "`closest_genome_ani`".
- "`fastani_af`" column has been renamed to "`closest_genome_af`".

These changes have been implemented to improve the readability and understanding of the data within the `summary.tsv` files. Users should update their scripts or processes accordingly to reflect these renamed column headers.

Bug Fixes:

- (528) (529) setup.py has been modified to restrict pydantic version to >=1.9.2 and < 2.0a1

Minor Changes:

- (526) change captures the Mash stderr in a separate buffer ( Thanks wasade for your contribution)

-- Disregard this release

Bug Fixes:

* (508) (509) If **ALL** genomes for a specific domain are either filtered out or classified with ANI they are now reported in the summary file.

Minor changes:

* (491) (498) Allow GTDB-Tk to show ``--help`` and ``-v`` without ``GTDBTK_DATA_PATH`` being set.
* WARNING: This is a breaking change if you are importing GTDB-Tk as a library and importing values from ``gtdbtk.config.config``, instead you need to import as ``from gtdbtk.config.common import CONFIG`` then access values via ``CONFIG.<var>``
* (508) Mash distance is changed from 0.1 to 0.15 . This is will increase the number of FastANI comparisons but will cover cases wheere genomes have a larger Mash distance but a small ANI.
* (497) Add a ``convert_to_species`` function is GTDB-Tk to replace GCA/GCF ids with their GTDB species name
* Add ``--db_version`` flag to ``check_install`` to check the version of previous GTDB-Tk packages.

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Bug Fixes:

* (493) Fix issue with --full-tree flag (related to skipping ANI steps)

Minor changes:

* Change URL for documentation to 'https://ecogenomics.github.io/GTDBTk/installing/index.html'
* Improve portability of the ANI_screen step by regenerating the paths of reference genomes in the current filesystem for mash_db.msh

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Bug Fixes:
* `gtdbtk.json` is now reset when the pipeline is re run and the status of `ani_screen` is not 'complete'

Minor changes:
* When using `--genes` , ANI steps are skipped and warnings are raised to the user to
inform them that classification is less accurate.
* (486) Environment variables can be used in GTDBTK_DATA_PATH
* `is_consistent` function in `mash.py` compares only the filenames, not the full paths
* Add cutoff arguments to PfamScan ( Thanks AroneyS for the contribution)