2025-02-03 - main needs bioblend to do Galaxy API stuff
2025-02-03 - merging
2025-02-03 - taxonomy projection into GBIF is not working. I think we can live with that.
2025-02-03 - params that are delegated to blastn are None in all cases tested so far. A default empty dict is therefore needed or bad things happen downstream.
2025-02-03 - domain needs protocol specification (i.e. https:// in our case).
2025-01-31 - adding skip patterns for .env file and AI output
2025-01-30 - Edit README.md
2025-01-30 - Edit pyproject.toml
2025-01-30 - Edit CODE_OF_CONDUCT.md
2025-01-30 - Upload New File
2025-01-30 - Edit README.md
2025-01-30 - Edit environment.yml
2025-01-30 - Edit README.md
2025-01-30 - Add new file
2025-01-30 - The pyproject.toml is now the canonical list of dependencies
2025-01-30 - This file is deleted because nbitk is on bioconda: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/nbitk/meta.yaml
2025-01-30 - we no longer use a hardcoded requirements.txt because it can be generated from the pyproject.toml as follows (should you ever need it): `pip-compile pyproject.toml -o requirements.txt`
2025-01-24 - expanded documentation, used modern typing in method signatures, added optional pass-through of additional blast parameters
2025-01-24 - expanded documentation to explain constructor parameterization and inheritance
2025-01-24 - expanded documentation to explain optional Config object fields
2025-01-16 - corrected package name
2025-01-16 - adding unit tests for the TaxonValidator
2025-01-16 - adding taxonomic validation client, which is a subclass of BLASTN with tailored inputs and outputs for the CSC
2024-12-24 - removed default config parameters
2024-12-24 - reduced default verbosity
2024-12-24 - default implementation returns taxonomic lineage
2024-12-24 - updated pipe-separated parameterization
2024-12-24 - changed defaults
2024-12-24 - moved _download_result() to superclass
2024-12-24 - simplified signature
2024-12-24 - result download succeeds but should be delegated to base class instead
2024-12-23 - initial commit (WIP)
2024-11-26 - Merge branch 'tools' into 'main'
2024-11-25 - fixing unit test subprocess call  errors
2024-11-25 - documentation edits
2024-11-25 - add vsearch dependency
2024-11-25 - fixed unit-test errors arising from long prefix differences
2024-11-25 - added logging and error handling and param validation
2024-11-22 - validate vsearch params before running the tool
2024-11-22 - add a method to capture valid tool params; it just runs tool_name --help then parses help output to find valid commandline args. this is useful to validate the params before running the tool
2024-11-22 - documentations
2024-11-22 - clean up
2024-11-22 - fixed linting
2024-11-22 - fixed linting
2024-11-22 - adding unit test for vsearch
2024-11-22 - refactored how we set params; take params as a dict and unpack this instead of one function for each param
2024-11-21 - adding vsearch clustering params
2024-11-13 - added setting to set or autodetect cores to use
2024-10-15 - code cleanup to fix linting errors
2024-10-09 - adding vsearch merge pairs params
2024-10-08 - adding vsearch merge pairs
2024-10-03 - logger should only create a handler first time
2024-09-26 - install cutadapt from environment.yaml
2024-09-24 - point python path to nbitk local directory to enable  testing  tools or scripts that are not yet published to pip
2024-09-24 - adding the first version of cutadapt and its unit test
2024-09-23 - Merge branch 'tools' into 'main'
2024-09-19 - Merge branch 'main' into 'tools'
2024-09-19 - adding unit tests for megatree-pruner
2024-09-19 - writes output to file via redirect
2024-09-19 - adding unit tests for megatree-loader
2024-09-19 - works on gitlab
2024-09-19 - `perl-bio-phylo-forest-dbtree` appears to install locally, let's test on gitlab
2024-09-19 - adding unit tests for raxml-ng
2024-09-19 - actions are appended after all args, therefore are not args themselves
2024-09-19 - adding unit tests for hmmalign
2024-09-19 - hmmalign [args] <hmmfile> <seqfile>, so hmmfile and seqfile aren't actual arguments
2024-09-19 - Add check to see if key is actually a command line flag, or just an internal placeholder, e.g. for when `tool <infile> <outfile>` without flags
2024-09-19 - adding COI-5P HMM for hmmalign testing
2024-09-19 - adding unit tests for blastn
2024-09-19 - blastn long args have single dash prefix
2024-09-19 - adding unit tests for blastdbcmd
2024-09-19 - info is a flag, so check for empty string. long arguments have single dash prefix.
2024-09-19 - adding unit tests for blastdb_aliastool
2024-09-19 - adding example seqidlist
2024-09-19 - blastdb_aliastool has single dash long arg prefix
2024-09-19 - adding unit tests for makeblastdb
2024-09-19 - makeblastdb has single dash prefix for long command line arguments
2024-09-18 - running minios3 tests requires docker
2024-09-18 - minios3 client doesn't use logger instance anymore
2024-09-18 - config only makes non-nested file paths absolute
2024-09-18 - attempting to persist environment between jobs
2024-09-18 - reformatted with black
2024-09-18 - gitlab chokes on multiline script
2024-09-18 - only create if env doesn't exist yet, otherwise update
2024-09-18 - remove logger instance
2024-09-18 - increasing max-line-length to pycharm default
2024-09-17 - topology test now also verifies interior node annotations (GUIDs)
2024-09-17 - Updated BOLD sheet
2024-09-13 - W391 blank line at end of file
2024-09-13 - E501 line too long + W391 blank line at end of file
2024-09-13 - E501 line too long
2024-09-13 - E501 line too long
2024-09-13 - E501 line too long
2024-09-13 - E302 expected 2 blank lines, found 1
2024-09-13 - E501 line too long
2024-09-13 - W292 no newline at end of file
2024-09-13 - attempting to reuse conda environment
2024-09-13 - adding tests and example config file
2024-09-13 - adding tests and example config file
2024-09-08 - adding tests and example config file
2024-09-08 - adding tests and example config file
2024-09-08 - Adding logger factory
2024-09-08 - Adding config object, which commonly needs pyyaml
2024-09-03 - Merge branch 'minioS3' into 'main'
2024-09-02 - fix-test: add docker service to fix the test
2024-09-02 - fix: use Optional
2024-09-02 - fix: remove logger instance
2024-09-01 - fix: edit comment and remove print
2024-09-01 - - removed unused imports - added default logger - added (more) type hints - added :param and :return: documentation
2024-09-01 - reformatted with black
2024-09-01 - feat: add minioS3 service
2024-08-21 - retaining existing tip for further annotation
2024-08-20 - E303 too many blank lines
2024-08-20 - Taxon.guids now stores processid => sampleid mapping to represent multiple processes for the same species
2024-08-20 - Parser must only annotate terminal from lineage
2024-08-20 - Previous initialization created global dict
2024-08-20 - updated BOLD BGE export
2024-08-20 - reformatted by black
2024-08-20 - capturing stdout from ete3
2024-08-20 - path corrected for linters
2024-08-20 - updated README.md
2024-08-20 - moving to match package name for PyPI
2024-08-20 - updating package name for PyPI
2024-08-20 - updated pipeline
2024-08-20 - applies version number from git tags and commit hash
2024-08-20 - added publish stage to push to PyPI when tagged
2024-08-19 - needs hashing impl to add to sets
2024-08-19 - changed stringification
2024-08-19 - reformatted for black
2024-08-19 - added comparator of Taxon objects
2024-08-19 - rank more informative than common name
2024-08-16 - removing py3.9 type hint
2024-08-16 - debugging pip from gitlab
2024-08-16 - debugging pip from gitlab
2024-08-16 - debugging pip from gitlab
2024-08-15 - adding tests for NCBI taxonomy dump parser
2024-08-15 - adding ncbi taxonomy dump parser
2024-08-15 - adding ete3, requests for ncbi taxonomy
2024-08-15 - adding skip pattern for osx stuff
2024-08-15 - reformatted for black
2024-08-15 - removed trailing whitespace
2024-08-15 - adding BOLD Excel parser and unit tests
2024-08-15 - adding BGE's BOLD excel sheet
2024-08-15 - added defaults, only name is needed
2024-08-15 - added requirements for reading XLSX and pandas
2024-08-15 - taxon now subclasses Clade
2024-08-15 - refolded pydoc for flake8
2024-08-15 - no common name in stringification
2024-08-15 - added explanation, reformatted, ignoring F401
2024-08-15 - added explanation, reformatted, ignoring F401
2024-08-15 - adding a taxon based on dendropy
2024-08-15 - changed single to double quotes to make black happy
2024-08-15 - tests passing
2024-08-15 - factored out into separate subclasses for TSV and JSON-L
2024-08-15 - added line break
2024-08-15 - added skip pattern for pycache
2024-08-15 - updating _FormatToIterator directly
2024-08-15 - attempting to register with SeqIO
2024-08-15 - requirements reinstalled during testing
2024-08-15 - pytest not in requirements but installed in the test phase
2024-08-15 - adding skip patterns for pycharm
2024-08-15 - updated gitlab CI configuration
2024-08-15 - adding pip requirements.txt
2024-08-15 - adding config files for linters
2024-08-15 - adding first unit tests with example data
2024-08-15 - adding first class: BCDM parser for SeqIO
2024-08-13 - Add CHANGELOG
2024-08-13 - Add CONTRIBUTING
2024-08-13 - Update README.md
2024-08-13 - Update README.md
2024-08-13 - updated readme
2024-08-13 - Update .gitlab-ci.yml file
2024-08-13 - Add LICENSE
2024-08-13 - Initial commit