Version 3.1.0

This release retires the NCBITaxa system of taxonomic validation in favour of a higher-trust, more flexible system of taxonomic validation for taxa found by sequencing

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #197
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #199
• Removing safedata_zenodo amend_metadata subcommand by @jacobcook1995 in #200
• Added python 3.13 testing to the CI by @jacobcook1995 in #198
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #202
• Bump jinja2 from 3.1.5 to 3.1.6 by @dependabot[bot] in #201
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #203
• Add the SeqTaxa worksheet option and a high-trust, no validation handling by @davidorme in #178
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #206
• Retire NCBI code by @jacobcook1995 in #207
• Bump requests from 2.32.3 to 2.32.4 by @dependabot[bot] in #210
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #208
• Allowing multiple SeqTaxa sheets to be provided with appropriate metadata by @jacobcook1995 in #209
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #212
• Bump urllib3 from 2.3.0 to 2.5.0 by @dependabot[bot] in #211
• Improve rendering of Zenodo metadata for sequenced taxonomy sheets by @jacobcook1995 in #214

Full Changelog: 3.0.2...3.1.0

Version 3.0.2

What's Changed

• Catching develop up with changes from the release branch by @jacobcook1995 in #189
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #184
• Bump configobj from 5.0.8 to 5.0.9 by @dependabot in #186
• Bump jinja2 from 3.1.4 to 3.1.5 by @dependabot in #187
• Bump virtualenv from 20.26.3 to 20.26.6 by @dependabot in #188
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #191
• Saving embargo dates in the metadata JSON in date format rather than datetime format by @jacobcook1995 in #192
• Fix file synchronisation issue with new versions of embargoed datasets by @jacobcook1995 in #194
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #193
• Bumping package version ready for 3.0.2 patch by @jacobcook1995 in #195

Full Changelog: 3.0.1...3.0.2

Version 3.0.1

What's Changed

• Updating safedata_server to safedata_metadata by @davidorme in #99
• Bump jinja2 from 3.1.2 to 3.1.3 by @dependabot in #101
• Updating server resources upload by @davidorme in #103
• Add args list to cli entry points to facilitate debugging by @davidorme in #108
• Fix broken HTML and XML local generation by @davidorme in #111
• Fixing OS specific issues with logging by @davidorme in #114
• Update taxon builder tools by @davidorme in #115
• Release 3.0.1rc1 by @davidorme in #116
• Bump black from 22.12.0 to 24.3.0 by @dependabot in #118
• Bump idna from 3.6 to 3.7 by @dependabot in #119
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #117
• Making 3.10 the minimum version by @jacobcook1995 in #121
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #122
• Bugfix/summary whitespace by @jacobcook1995 in #129
• Bug fix/sheet name docs by @jacobcook1995 in #130
• Fixing weird Shapely related test failures by @jacobcook1995 in #132
• Added note to say that Unknown should be used for missing permit numbers by @jacobcook1995 in #131
• Release/3.0.1 by @davidorme in #134
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #135
• Fix XML distribution flow by @davidorme in #136
• Bump tqdm from 4.66.2 to 4.66.3 by @dependabot in #139
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #140
• Bump jinja2 from 3.1.3 to 3.1.4 by @dependabot in #141
• Customisable Zenodo HTML by @davidorme in #138
• Command line workflow updates by @davidorme in #142
• Switching to using ruff by @jacobcook1995 in #146
• Adding an example file to the documentation by @jacobcook1995 in #145
• Bump requests from 2.31.0 to 2.32.0 by @dependabot in #149
• Validation passes with no worksheets by @davidorme in #144
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #148
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #150
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #151
• Added ruff specific formatting options by @jacobcook1995 in #153
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #155
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #156
• Bump urllib3 from 2.2.1 to 2.2.2 by @dependabot in #157
• Add 3.12 to the CI by @jacobcook1995 in #154
• Add publishing workflow and make CI workflow reusable by @davidorme in #159
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #160
• Bump certifi from 2024.6.2 to 2024.7.4 by @dependabot in #163
• Updating the Zenodo handling by @davidorme in #162
• Switched example file download links to point to develop by @jacobcook1995 in #147
• Add gazetteer creation guide by @jacobcook1995 in #152
• Make maximum embargo length configurable by @davidorme in #169
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #165
• Handle missing xml configuration in dataset publication by @davidorme in #168
• Fixed NCBI taxonomy building to catch all parents are child cases by @jacobcook1995 in #171
• changed entry points so that json is always read in using utf-8 encoding by @jacobcook1995 in #181
• Changed all json outputs to use utf-8 encoding by default by @jacobcook1995 in #182
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #176
• Updating zenodo and metadata server handling by @davidorme in #179
• Checking that entry point arguments are of correct file type by @jacobcook1995 in #183
• Release candidate 3.0.1 RC 7 by @davidorme in #170

New Contributors

• @dependabot made their first contribution in #101
• @pre-commit-ci made their first contribution in #117

Full Changelog: 3.0.0...3.0.1

Version 3.0.1 release candidate 7

What's Changed

• Changed all json outputs to use utf-8 encoding by default by @jacobcook1995 in #182

Full Changelog: 3.0.1rc6...3.0.1rc7

Release v3.0.1 release candidate 6

What's Changed

• changed entry points so that json is always read in using utf-8 encoding by @jacobcook1995 in #181

Full Changelog: 3.0.1rc5...3.0.1rc6

Release v3.0.1 release candidate 5

What's Changed

• Release 3.0.1rc1 by @davidorme in #116
• Make maximum embargo length configurable by @davidorme in #169
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #165
• Handle missing xml configuration in dataset publication by @davidorme in #168

Full Changelog: 3.0.1rc4...3.0.1rc5

Version 3.0.1 release candidate 4

This is Release Candidate 4 of version 3.0.1, following feedback and usage notes from Samuel Lee at SEARPP.

This candidate adds:

A data manager guide to gazetteer creation.
Fixes the workflow for Zenodo publication following a change in the API
Simplifies the configuration file to move static API URLs into the code.
Fixes a mkdocs pre-build hook issue

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #160
• Bump certifi from 2024.6.2 to 2024.7.4 by @dependabot in #163
• Updating the Zenodo handling by @davidorme in #162
• Switched example file download links to point to develop by @jacobcook1995 in #147
• Add gazetteer creation guide by @jacobcook1995 in #152

Full Changelog: 3.0.1rc3...3.0.1rc4

Candidate release v3.0.1rc3

No new content vs 3.0.1rc2. The point of this version is to publish on PyPI rather than just Test PyPI so that it can be more easily downloaded by people testing it.

Full Changelog: 3.0.1rc2...3.0.1rc3

Candidate release v.3.0.1rc2 [test-pypi-only]

What's Changed

• Updating get_taxa to more stringent checking by @davidorme in #1
• Updated taxon checking to allow users to flag new taxa with an asteri… by @davidorme in #2
• Taxon checking by @davidorme in #3
• GBIF validation by @davidorme in #4
• Integrating NCBI functionality by @jacobcook1995 in #8
• Restructure of dataworksheet logging to give cleaner output, tests re… by @davidorme in #9
• Ncbi config by @jacobcook1995 in #10
• Combined binomial and trinomial into a single function by @jacobcook1995 in #11
• Feature/fixing zenodo workflow by @davidorme in #12
• Feature/taxa mypy by @jacobcook1995 in #13
• Feature/mypy fixing by @davidorme in #21
• Feature/ncbi taxa tree by @jacobcook1995 in #17
• Feature/fix taxa tree by @jacobcook1995 in #23
• Added mocked test of status codes by @jacobcook1995 in #19
• Feature/taxon timestamps by @davidorme in #24
• Fixes typos that Vivienne noticed by @jacobcook1995 in #30
• Remove remote/online taxon validation option by @davidorme in #32
• Feature/zenodo workflow fixes by @davidorme in #37
• Updating location data setup by @davidorme in #38
• Bug/taxa in descriptions by @davidorme in #40
• Fixes to a couple of documentation problems by @jacobcook1995 in #41
• Removing old files/folders and updating .gitignore by @davidorme in #42
• Feature/cleaning for 300 by @davidorme in #43
• Added release branch and poetry details to the README by @jacobcook1995 in #44
• Feature/cleanup publication docs by @jacobcook1995 in #45
• Fixing precommit isort config by @davidorme in #55
• Allow unverified metadata servers by @davidorme in #56
• mypy fixes + improved CI procedure by @jacobcook1995 in #59
• Handle metadata for trailing empty fields by @davidorme in #61
• Added taxon header validation by @jacobcook1995 in #62
• Make project IDs optional by @jacobcook1995 in #65
• Fixes a couple of security venerabilities for release 3.0 by @jacobcook1995 in #68
• Update of mkdocs system and docs content by @davidorme in #71
• Add docs build step to the CI by @jacobcook1995 in #72
• Prevent Exception on empty data sheets by @davidorme in #73
• Exception with GBIF 2016-07-25 database by @davidorme in #74
• Updated certifi version by @jacobcook1995 in #82
• Fix bug for entirely empty chunks of rows by @jacobcook1995 in #83
• Assorted minor bugfixes by @davidorme in #92
• Update logging to allow output to text file. by @davidorme in #93
• Big restructure of data manager documentation by @davidorme in #95
• Documentation check + update by @jacobcook1995 in #79
• Implements the project database configuration by @davidorme in #96
• Restructure of taxa worksheet handling by @davidorme in #97
• Updating safedata_server to safedata_metadata by @davidorme in #99
• Bump jinja2 from 3.1.2 to 3.1.3 by @dependabot in #101
• Updating server resources upload by @davidorme in #103
• Add args list to cli entry points to facilitate debugging by @davidorme in #108
• Fix broken HTML and XML local generation by @davidorme in #111
• Fixing OS specific issues with logging by @davidorme in #114
• Update taxon builder tools by @davidorme in #115
• Bump black from 22.12.0 to 24.3.0 by @dependabot in #118
• Bump idna from 3.6 to 3.7 by @dependabot in #119
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #117
• Making 3.10 the minimum version by @jacobcook1995 in #121
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #122
• Bugfix/summary whitespace by @jacobcook1995 in #129
• Bug fix/sheet name docs by @jacobcook1995 in #130
• Fixing weird Shapely related test failures by @jacobcook1995 in #132
• Added note to say that Unknown should be used for missing permit numbers by @jacobcook1995 in #131
• Release/3.0.1 by @davidorme in #134
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #135
• Fix XML distribution flow by @davidorme in #136
• Bump tqdm from 4.66.2 to 4.66.3 by @dependabot in #139
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #140
• Bump jinja2 from 3.1.3 to 3.1.4 by @dependabot in #141
• Customisable Zenodo HTML by @davidorme in #138
• Command line workflow updates by @davidorme in #142
• Switching to using ruff by @jacobcook1995 in #146
• Adding an example file to the documentation by @jacobcook1995 in #145
• Bump requests from 2.31.0 to 2.32.0 by @dependabot in #149
• Validation passes with no worksheets by @davidorme in #144
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #148
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #150
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #151
• Added ruff specific formatting options by @jacobcook1995 in #153
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #155
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #156
• Bump urllib3 from 2.2.1 to 2.2.2 by @dependabot in #157
• Add 3.12 to the CI by @ja...