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change log for taxtastic

1.0.0

  • Migrated setup.py to pyproject.toml [GH-172]
  • New subcommand taxit append that adds rank tax_id or tax_name to csv file
  • Updated tox.ini to support Python 3.8-3.12, removed obsolete setup.py and pysqlite commands
  • Added GitHub Actions workflows for unittests and PyPI publishing

0.12.0

  • Fixed updated NCBI taxonomoy update for lineages_table subcommand [GH-176]
  • Added another new NCBI rank plus ability to set unknown ranks to no_rank [GH-175]

0.11.1

  • Updated taxonomy ranks to include cellular_root and acellular_root [GH-171]

0.11.0

  • Updated NCBI taxdmp.zip download protocol from ftp to https [GH-156]
  • New subcommand taxit named that filters unclassified, unnamed taxonomy ids
  • Subcommand update_taxids can now process a tab delimited headerless file
  • Subcommand taxtable has option to continue if unknown taxids
  • Added Dockerfile support for execution on cirro.app
  • Updated taxonomy ranks to replace superkingdom with domain [GH-171]

0.10.1

  • Fixed broken GH-Pages build

0.10.0

  • drop support for Python versions before 3.8
  • works with sqlalchemy 2+, drop support for sqlalchemy 1.x series
  • drop indexes and constraints before creating Postgresql database
  • restructure Dockerfile, uses python:3.11-slim-bullseye base image
  • simplify setup.py and remove deprecated features
  • major speed improvements to subcommand namelookup
  • added support text file support for update_taxids

0.9.4

  • general improvements and updates to Github Actions Workflows

0.9.3

  • migrated docker/* into Dockerfile and GH Actions automatic container build (.github/workflows/docker-publish.yml)

0.9.2

  • Support for parsing RAxML-ng v1.0.2 log file [GH-132]
  • Support for RAxML-ng/epa-ng .bestModel using taxit create

0.9.1

  • Bug fix [GH-134]

0.9.0

  • New ordered ranks: biotype, genotype, morph, pathogroup, serogroup and subvariety [GH-133]
  • New unordered ranks: clade, isolate, forma specialis, serotype and strain [GH-133]
  • Python 3 only support
  • Bug fixes

0.8.11

  • adding section, subsection, series and subseries to ncbi.py ranks

0.8.10

  • adding subcohort to ncbi.py ranks

0.8.9

  • prevent unique constraint violation when file in taxdmp contains duplicate lines [GH-124].

0.8.8

  • new taxit get_descendants that returns given and descendant taxids [GH-126]

0.8.7

  • fixed psycopg2 library warning
  • updated Docker and Singularity build files to use Python 3.6.7

0.8.6

  • recognize LG-model in Fasttree stats file
  • bugfix to prevent error reading NCBI taxonomy [GH-124]

0.8.5

  • add taxit lineage_table [GH-117]

0.8.4

  • python3.4+ compatibility
  • logging messages write to stderr
  • add subcommand taxit namelookup

0.8.3

  • add_nodes prints traceback on error
  • Taxonomy.add_node() tolerates extra fields
  • create additional mount points in Docker image

0.8.2

  • add psycopg2 as a requirement (support for postgresql from a docker image)

0.8.1

  • major speedups (> 30x) for new_database and taxtable
  • sql expressions for calculating lineages require sqlite 3.8.3+; include script for installing pysqlite and updated sqlite3 library.
  • names.is_classified is set to true only for scientific names at rank species
  • nodes.is_valid is true for all ranks above species
  • remove names.id and ranks.is_below from schema
  • taxtable renames "no rank" intermediate ranks by appending "_" to parent rank name (instead of prepending "below_")
  • intermediate ranks are renamed on the fly when creating the taxtable rather than on database creation.
  • add Taxonomy.get_source()
  • add Taxonomy.add_name() and Taxonomy.add_names()
  • Taxonomy.add_node() takes a list of dicts representing tax_names
  • adding nodes or names occur within a transaction
  • removed subcommands merge_taxtables, merge, count_taxids
  • remove numpy, pandas, BioPython as dependencies, add Dendropy
  • taxit add_nodes requires input in YAML format (replaces csv) and can add names as well

0.7.0

  • All commands can read from a specified .conf or .ini configuration file
  • taxit --ranked now takes one of two arguments {rows, columns}
  • Records containing the word "group" in taxonomic name are no longer flagged as unclassified/invalid [GH-93]
  • fix missing parent_id column in taxtable
  • include docker build

0.6.4

  • rank cohort has been added as an official rank
  • taxit taxtable --taxtable has been added back to work from a pre-built taxtable. This switch used to be called --from-table

0.6.3

  • root is now a valid node

0.6.2

  • bug fixes

0.6.1

  • bug fixes

0.6.0

  • taxit update_taxids --taxid-column allows updating of any tax_id column [GH-84]
  • taxit update_taxids --ignore-unknowns allows unknown tax_ids to remain in final output [GH-84]
  • taxit new_database adds ncbi as the only entry in the source table [GH-91]
  • taxit new_database adds a ranks table with all ranks appearing in the nodes table [GH-86]
  • Any flavor of database can used with Taxtastic. But only sqlite and Postgres have been tested.
  • Numerous new features and performance improvements.

0.5.7

  • taxit update_taxids is significantly faster but can still use some optimizations [GH-78]

0.5.6

  • remove support for reading excel spreadsheets (GH-71)
  • requirements.txt identifies all direct dependencies
  • add taxit merge_taxtables
  • New taxit new_database --taxdump and taxit new_database--taxdump-url arguments for flexibility on taxdump.zip location(s)
  • New function taxtable.remove_subtree() (GH-80)

0.5.5

  • new taxit count_taxids counts every tax_id occurance in a taxit taxtable lineage [GH-75]
  • new taxit taxid_classified decides if a tax_id is primary and valid (True/False)
  • taxit update_taxids will halt on unknown tax_ids unless --unknowns FILE is specified
  • taxit update_taxids only requires a csv file with 'tax_id' column
  • taxit update_taxids takes an optional --name-column to assist in assigning tax_ids
  • taxit update_taxids will read stdin if csv file is not provided as argument

0.5.4

  • Add taxit taxtable --full for outputing all ranks in header.
  • Update subcommand help text
  • Generate Sphinx docs using help text emitted by subcommands (GH-70)

0.5.3

  • Suppress warning when updating refpkg tree_stats file via taxit update.

0.5.2

  • Fix GH-63: "empirical_frequencies" now set to false when parsing FastTree AA statistics files
  • Close GH-64: "empirical_frequencies" is now available as a flag for PhyML statistics files
  • Fixed bug that prevented temporary files from being deleted

0.5.1

  • Fix GH-62: "empirical_frequencies" was not set when parsing PhyML AA statistics files.

0.5.0

  • Add .drop() .collapse() methods to taxtastic.taxtable.TaxNode
  • Change is_classified column in taxonomy database: now does not mark below species as unclassified if the species-level classification is valid. [GH-59]
  • Add taxit composition - shows the taxonomic composition of a reference package at a given rank
  • Fix broken taxit lonelynodes
  • Add taxit merge - Identifies tax_ids which have been merged, suggests new tax_ids.
  • Add taxit add_to_taxtable - adds nodes to a taxonomy [GH-60]
  • Fix support for newer versions of PhyML [GH-61]
  • Updates for compatibility with RAxML 7.7.2

0.4

  • 'names' table in the taxonomy database has a new column 'is_classified' indicating whether 'tax_name' should be considered "classified".
  • Bugfix in taxit findcompany
  • Support stdin as a source for taxit findcompany
  • Taxonomy objects use NCBI ranks by default
  • Reference packages are created optionally (fixes creation of empty reference packages for commands like taxit info nonexisting.refpkg)
  • Support zipped reference packages
  • Add a taxtable API: taxtastic.taxtable
  • Remove some tests requiring a full taxonomy database
  • Rerooting reference packages on creation [GH-57]
  • More intelligent file name generation on clash
  • Deprecate the default create=True in taxtastic.refpkg.Refpkg
  • Some PEP8 fixes

0.3.2

  • version number contains abbreviated git sha identifying the commit.
  • Initial release to PyPI
  • Add findcompany subcommand
  • Add refpkg_intersection subcommand
  • Remove some obsolete components
  • Check required fields in seqinfo file [GH-46]
  • Add option to build taxtable from seqinfo file [GH-55]
  • Add subcommand to update taxids [GH-56]
  • Support FastTree AA and DNA log files
  • Fix rank order bug (infraorder was below parvorder)
  • Documentation updates