CHANGELOG.md

Changelog

Unreleased

[v1.11.1] - 2024-11-11 Mon

• Add: minor improvements in web-interface.
• Add: make web-interface remember nomenclatural code picked in the previous GET query.

[v1.11.0] - 2024-11-11 Mon

• Add #265: add optional nomenclatural code option to parse names with an ambiguity according to a particular code.

[v1.10.4] - 2024-11-07 Thu

• Add #269: switch to slog from zerologs.
• Fix [#271]: distinguish between ex and in.
• Fix #270: missing verbatim authorship for names that look similar to combination uninomial in ICZN.
• Fix #268: if botanical author looks like a combination uninomial, make sure its characters are not normalized.

v1.10.3 - 2024-10-11 Fri

• Fix #266: remove author from species detail for named hybrids.

v1.10.2 - 2024-07-30 Tue

• Add #264: more exceptions.

v1.10.1 - 2024-06-05 Wed

• Add #263: add more exceptions with speciific epithets like "complex", "do", "spec".

v1.10.0 - 2024-06-04 Tue

• Add #260: add candidatus field for parsed data.
• Add #232: parse names like subgen. Psammophrynopsis Koch, 1953.

v1.9.2 - 2024-05-01 Wed

• Add #261: a constructor to return a pool of a given size of gnparsers.

v1.9.1 - 2023-10-13 Fri

• Add: update modules.
• Fix #259: allow diacritics in any UTF-8 normalization form.
• Fix #258: allow authors with 2 dashes in the name.
• Fix #256: fix normalization where a misplacced year changes the year of original authors.

v1.9.0 - 2023-10-12 Thu

• Add: restore backward compatibility by creating a new flag --species-group-cut.

v1.8.0 - 2023-10-11 Wed

• Add #255: normalize stemmed canonical of Aus bus bus to Aus bus. WARNING this creates some backward incompatibility.
• Add: sorting uses slices package.

v1.7.5 - 2023-09-26 Tue

• Add: CSV and TSV files provide now verbatim authorship instead of normalized one.
• Add: a few more "termination words"
• Fix #254: treat fa as forma.
• Fix #253: process dem as an author word for Von dem Bush and like.
• Fix #251: do not process y as and for Rafael Arango y Molina.
• Fix #249: allow cf at the end of the strings, cf for infraspecies.
• Fix #248: do not escape double quotes for TSV output.
• Fix #246: ignore ms at the end of the strings.

v1.7.4 - 2023-08-22 Tue

• Fix #243: parse correctly Nassa pagoda var. acuta P. P. Carpenter, 1857.

v1.7.3 - 2023-06-17 Sat

• Add #241: allow comma before ex authors.

v1.7.2 - 2023-03-09 Thu

• Add #240: add tr. subtr. as ranks for combo-uninomials.

v1.7.1 - 2023-03-07 Tue

• Add: upgrade all modules.

v1.7.0 - 2023-03-07 Tue

• Add #238: stem takes in account -ii suffix, macdonaldii -> macdonald.

v1.6.9 - 2022-11-10 Thu

• Add #237: detect and normalize non-breaking hyphens. In case if other non-typical hythens will appear, they will be dealt the same way.

v1.6.8 - 2022-10-01 Sat

• Add: update all modules.

v1.6.7 - 2022-08-22 Mon

• Add #231: more edge cases.
• Add #230: Take into account mihi annotation.

v1.6.6 - 2022-05-15 Sun

• Add #224: Creation of Nix packages for gnparser.

v1.6.5 - 2022-03-21 Mon

• Add #223: Use PEG parser for preprocess instead of RegEx. This approach gives 15-17% speed increase.

v1.6.4 - 2022-03-19 Sat

• Add #224: Parse correctly italian authors with degli.

v1.6.3 - 2022-02-08 Tue

• Add #222: Improve logs for NSQ, switch to zerologs library.

v1.6.2 - 2022-02-04 Fri

• Fix #221: No parsing for names with cyanobacterium.
• Fix #220: Crenarchaeote enrichment culture clone should stop parsing at enrichment.
• Fix #219: filter out complex word during preprocessing for names like Aegla uruguayana complex.

v1.6.1 - 2022-02-01 Sat

• Add: use NSQ logger from sfgrp/lognsq

v1.6.0 - 2022-01-22 Sat

• Add #218: enable/disable logs for web-services, allow logs aggregation with NSQd.

v1.5.7 - 2021-11-26 Fri

• Fix: parsed.NormalizeByType preserves period char.

v1.5.6 - 2021-11-21 Sun

• Add #212: Set year from 'ex' authorship as a year of a name. Add 'ex' authors to list of all authors.

• Add #211: PR #214 by @tobymarsden, general approach for non-... specific epithets.

• Add #208: PR #210 by @tobymarsden, option to preserve diaereses.

• Fix #213: Stop generating space between Mc, Mac and the rest of an an author name.

v1.5.5 - 2021-11-17 Wed

• Add #207: PR #209 by @tobymarsden, fix parsing of names with nudum specific epithet.

v1.5.4 - 2021-11-14 Sun

• Add: different approach for normalize-by-type for words.
• Add #205: allow genera starting with De-, Eu-, Le-, Ne- (by @tobymarsden).
• Add #203: allow up to 2 dashes in genera (by @tobymarsden).

v1.5.3 - 2021-11-13 Sat

• Add #202: add NormalizeMore function for Word.

v1.5.2 - 2021-11-10 Wed

• Add #200: support for 'div.' rank in uninomial combinations.
• Add #199: fixes for several names that were not parsed correctly.
• Add #198: parse "Solanum tuberosum wila-k`oyu".
• Add #97: do not parse "Cyanophage".
• Add #85: parse names with a dagger character.
• Add #84: parse "Muscicapa randi Amadon & duPont, 1970".
• Add #83: parse authors like 'Laverde-R.'.

v1.5.1 - 2021-11-01 Mon

• Add #191: support for ambiguous specific epithets

v1.5.0 - 2021-10-22 Fri

• Add #194: support for cultivars' graft-chymeras (courtesy of @tobymarsden)

v1.4.2 - 2021-10-21 Thu

• Add #196: parse authors with prefix 'ver'

v1.4.1 - 2021-10-07 Thu

• Fix #195: parse multinomials where authorshp is not separated by space.

v1.4.0 - 2021-09-4 Sat

• Add #193: add TSV format for output.
• Add #190: support prefixes do and de los for authors.
• Add #187: support ter suffix for authors.
• Add #186: support non-ASCII apostrophe in authors.

v1.3.3 - 2021-09-11 Wed

• Add #176: refactoring of hybrid sign treatment (use PEG instead of RegEx for normalizing x, X, and ×.
• Add #183: stop parsing after nec, non, fide, vide, treat ms in as in or ex for exAuthors.
• Add #182: support for authors with prefixes ten, delle, dos.

v1.3.2 - 2021-08-02 Mon

• Add #182: support Do, Oo, Nu 2-letter genera.
• Add [#53]: exceptions to annotations (Bottaria nudum for example).
• Fix: names where sp epithet starts with cf can be parsed now.

v1.3.1 - 2021-07-17 Sat

• Add #180: Zenodo DOI.

v1.3.0 - 2021-06-29 Tue

• Add #179: cultivars info to README.

• Add #178: parse cultivars via REST API.

• Add #177: parse botanical cultivars via web.

• Add #173: cultivars parsing #174 @tobymarsden.

• Add #172: authors initials with a dash like "B.-E.van Wyk".

• Add: tests for cultivars (Toby Marsden)

• Fix #174: Hybrid character is missed or wrong in details' Words section.

v1.2.0 - 2021-04-08 Thu

• Add #169: option to capitalize first letter of name-strings.
• Add #166: support 'fm.' as 'forma'.

v1.1.0 - 2021-03-21 Sun

• Add #163: support bacterial Candidatus names.
• Add #162: show PEG AST tree for debugging.
• Add #161: add automatic tools dependency.
• Add #160: use embed feature of Go v1.16.

v1.0.13 - 2021-02-23 Tue

• Add: limit nightly builds to master only.
• Fix #159: POST method contains w18rong URL.

v1.0.12 - 2021-02-21 Sun

• Add #154: parse names with ambiguous f. as forma if there is a space between authr and f.. If there is no space, parse as filius. Give ambiguity warning in both cases.
• Add: PHP example from @barotto about using pipes with gnparser.

v1.0.11 - 2021-02-20 Sat

• Fix #153: flags csv=false and with_details=false trigger opposite behavior.

v1.0.10 - 2021-02-19 Fri

• Add #152: change auto-prereleases from nightly to on master submit.
• Add #151: do not parse names with (endo|ecto)?symbiont.
• Add #150: ignore serovar/serotype in bacerital names.
• Add #149: support abbreviated subgenus (Aus (B.) cus).

v1.0.9 - 2021-02-17 Wed

• Add #146: unordered flag.
• Add #145: better CI/build actions, add nightly binaries.
• Fix #144: remove configuration file as it creates more problems than solves.

v1.0.8 - 2021-02-15 Mon

• Add: remove config message for CLI app.
• Add: ldflags -s -w to decrease binary size.
• Fix: header does not show in CSV format for stream.

v1.0.7 - 2021-02-14 Sun

• Add #143: quiet flag to suppress showing progress output.

• Fix #142: stream waits until certain names number is equal the batch size.

• Fix #141: config file is not created.

v1.0.6 - 2021-02-04 Thu

• Add: update version handling, readme.

v1.0.5 - 2021-02-01 Mon

• Add: remove gnlib package.
• Add #140: remove config package.

v1.0.4 - 2021-01-23 Sat

• Add: cleanup constructor methods names.

v1.0.3 - 2021-01-23 Sat

• Add #139: make package names less abstract.

v1.0.2 - 2021-01-22 Fri

• Fix #137: add correct VerbatimID for HTML-containing names.

v1.0.1 - 2021-01-20 Wed

• Add #136: Man page

• Add #100: Switch continuous integration to use GitHub Actions.

• Add #129: Make c-binding usable for biodiversity parser.

• Fix #135: Changes: SubGenus->Subgenus, InfraSpecies->Infraspecies

v1.0.0 - 2021-01-19 Tue

• Add #127: Update documentation to v1.0.0.
• Add #122: Implement parsing as a stream in addition to batch parsing.
• Add #126: Update c-binding to v1.0.0.
• Add #131: Add parameters "with_details" and "csv" to REST API.
• Add #134: Transoform "positions" section to "words" section.
• Add #128: Add more examples to OpenAPI specification.
• Add #125: Describe changes from v0.x to 1.x.
• Add #132: Add context.Context to control lifespan of go routines.
• Add #115: Migrate tests from ginkgo to plain tests.
• Add #109: Move web package to io.
• Add #124: Document warnings for each quality category.
• Add #121: Convert package parser to use interfaces.
• Add #120: CLI app for newly created functionality.
• Add #119: Formatted output for output.Parsed.
• Add #117: Convert failed parsing results to output.Parsed.
• Add #114: Convert parsing result to output.Parsed.
• Add #118: Add Verbatim and Year fields to the root of Authorship.
• Add #107: Move grammar package to entity and rename to parser.
• Add #110: Move stemmer to entity.
• Add #113: Move str package to entity.
• Add #112: Move preprocess package to entity.
• Add #105: Move fs package to io.
• Add #111: Move dict package to io.
• Add #106: Describe main use-case via interface.
• Add #104: Add configuration package.
• Add #103: Create an output.Parsed object that can be used in Go and as JSON.
• Add #101: Start using gnlib where it makes sense.
• Add #99: Move code to GitHub and change links accordingly.
• Add #95: Remove dependency on gRPC and protobuf.

v0.14.4 - 2020-12-15 Tue

• Add #96: Do not parse names starting with "Candidatus".
• Add #93: Parse 'y' (Spanish '&') as an author separator.

v0.14.3 - 2020-12-13 Sun

• Add #95: Remove make dependency on gRPC tooling.
• Add #94: Do not parse names with "bacterium" "epithet.

v0.14.2 - 2020-05-12 Tue

• Add #90: Allow ß in names.
• Add #89: Support subspec. as a rank.
• Add #82: Support authors with prefix zu.

v0.14.1 - 2020-05-07 Thu

• Fix: Change web API from default to Compact format to get correct API output.

v0.14.0 - 2020-05-07 Thu

• Add #81: Add year range in format "1888/89".
• Add #80: Add Cardinality to parser outputs.
• Add #79: Make CSV the default format for CLI.
• Add #78: Take into account non-virus names that look like virus names.

v0.13.1 - 2020-03-05 Thu

• Fix #77: Memory leak when used as clib.
• Fix #76: Non ASCII apostrophe does not show up in canonical.

v0.13.0 - 2020-02-12 Wed

• Add #74: Simple format output is now in CSV format.
• Add #73: Improve speed by using ragel's FSM instead of regex.
• Fix #75: Normalize subspecies to subsp. instead of ssp..
• Fix #72: Surrogate detection by gnparser.ParseToObject method.

v0.12.0 - 2019-11-18 Mon

• Add #71: do not parse 'Unnamed clade...'.
• Add #69: gnparser as a shared C library.
• Add: Make dynamic version using ldflags.
• Fix #70: parse 'Remera cvancarai' correctly.

v0.11.0 - 2019-10-24 Thu

• Add #68: add stemmed version of canonical form to outputs.
• Add: benchmarks to gnparser_test.go

v0.10.0 - 2019-09-10 Tue

• Add #67: field authorship of the name for JSON output
• Add #66: remove HTML tags during parsing instead of a separate step.
• Add #61: handle authors that end with a word "bis".
• Add #60: handle correctly deprecated ranks with Greek letters.
• Fix #62: parser breaks on Drepanolejeunea (Spruce) (Steph.).

v0.9.0 - 2019-08-16 Fri

• Add #65: gRPC is able to return a protobuf object now instead of JSON. string (only for ParseArray function so far). The same protobuf object is now also used by gnparser.ParseToObject function.
• Add #64: gRPC method ParseArray that cleans and parses an input from an array of names instead of a stream.
• Add #63: abbreviation for form or forma is now f. instead of fm..

v0.8.0 - 2019-04-10 Wed

• Add [#51]: strings like Aus (Bus) are parsed differently for ICN and ICZN names. If string inside of parenthesis matches known ICN author name is parsed as Uninomial (Author), otherwise it is parsed as Aus subgen. Bus.

v0.7.5 - 2019-03-31 Sun

• Add #59: method ParseToObject to avoid JSON in Go programs.
• Add #58: parse Aus (Bus) as Uninomial (Author) to prevent botanical authors appear as subgenera. We need a better solution for this.
• Add #57: warning in cases of an ambiguous filius.
• Fix #56: bug Ambrysus-Stål, 1862 breaks parser.

v0.7.4 - 2019-02-12 Tue

• Add #48: transliteration of diacriticals.
• Add #43: notho- (hybrids) rank supported.
• Add #52: genera with hyphens with lower or upper char after hyphen.
• Add #49: multiple hyphens in specific epithet.

v0.7.3 - 2019-02-04 Mon

• Add #54: add cleaning functions to gRPC
• Add #46: add supg. rank
• Add #45: add natio rank (deprecated ICZN rank)
• Add #44: documentation for canonicalName fields
• Add #42: tests for command line app

v0.7.2 - 2019-02-01 Fri

• Add #41: parse/clean multiple names from standard input.

v0.7.1 - 2019-01-24 Thu

• Add #40: add names with missing parenthesis for combination authors.
• Fix: remove typo for Scala parser URL on the parser web-page.

v0.7.0 - 2019-01-23 Wed

• Add #38: docker image can do gRPC, REST, CLI
• Add #37: flag for cleanup HTML entities and tags, underscores are part of parsing.
• Add #39: documentation for contributors.
• Add #31: continuous integration.
• Add #36: substitute underscores to spaces for Newick format.
• Add #34: escape HTML entities, remove common tags.
• Add #33: Web-based user interface and REST API.

v0.6.0 - 2019-01-16 Wed

• Add #35: gRPC method to preserve order in output according to input
• Add #30: write inline and README documentation.
• Add #29: docker and dockerhub support.
• Add #26: get all parser rules to CamelCase format.

v0.5.1 - 2019-01-15 Tue

• Add: fix Makefile
• Add #28: non-ASCII apostrophe support.
• Add #27: agamosp. agamossp. agamovar. ranks.
• Add #25: reorganize output to be more readable and logical.
• Add #24: gRPC server for receiving name-strings and streaming back the parsed results.
• Add #23: Remove multiple years. Now name can have only one year.
• Add #22: Run the parser against 24 million names from global names index and fix found problems.
• Add #21: Rebuilds tests into test_data_new.txt file. It is important for making global changes in tests.
• Add #20: Pass all tests made for Scala gnparser. Tickets 1-19 are about approaching #20.

Footnotes

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