ImperialCollegeLondon/safedata_validator issues and pull requests

#185 - Uploading a new dataset version to zenodo can cause old files to still appear

Issue - State: open - Opened by jacobcook1995 24 days ago

#184 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: open - Opened by pre-commit-ci[bot] 3 months ago - 1 comment

#183 - Checking that entry point arguments are of correct file type

Pull Request - State: closed - Opened by jacobcook1995 3 months ago - 1 comment

#182 - Changed all json outputs to use utf-8 encoding by default

Pull Request - State: closed - Opened by jacobcook1995 3 months ago - 1 comment

#182 - Changed all json outputs to use utf-8 encoding by default

Pull Request - State: closed - Opened by jacobcook1995 3 months ago - 1 comment

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

Pull Request - State: closed - Opened by jacobcook1995 3 months ago

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

Pull Request - State: closed - Opened by jacobcook1995 3 months ago

#180 - Publication process generates `UnicodeDecodeError` on windows

Issue - State: closed - Opened by jacobcook1995 3 months ago - 2 comments

#180 - Publication process generates `UnicodeDecodeError` on windows

Issue - State: closed - Opened by jacobcook1995 3 months ago - 2 comments

#179 - Updating zenodo and metadata server handling

Pull Request - State: closed - Opened by davidorme 4 months ago

#179 - Updating zenodo and metadata server handling

Pull Request - State: closed - Opened by davidorme 4 months ago

#178 - Add the SeqTaxa worksheet option and a high-trust, no validation handling

Pull Request - State: open - Opened by davidorme 4 months ago

#178 - Add the SeqTaxa worksheet option and a high-trust, no validation handling

Pull Request - State: open - Opened by davidorme 4 months ago

#177 - `safedata_zenodo publish_dataset` fails gracelessly if Zenodo credentials are not provided

Issue - State: closed - Opened by jacobcook1995 4 months ago

#177 - `safedata_zenodo publish_dataset` fails gracelessly if Zenodo credentials are not provided

Issue - State: closed - Opened by jacobcook1995 4 months ago

#176 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 4 months ago

#176 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 4 months ago

#175 - Parse and build taxon index from NCBI style taxon table without validation

Issue - State: open - Opened by davidorme 4 months ago

#175 - Parse and build taxon index from NCBI style taxon table without validation

Issue - State: open - Opened by davidorme 4 months ago

#174 - Handling of incertae sedis output from genbank

Pull Request - State: open - Opened by jacobcook1995 4 months ago - 2 comments

#174 - Handling of incertae sedis output from genbank

Pull Request - State: open - Opened by jacobcook1995 4 months ago - 2 comments

#173 - Proper handling of genus level synonyms for NCBITaxa

Issue - State: open - Opened by jacobcook1995 4 months ago

#173 - Proper handling of genus level synonyms for NCBITaxa

Issue - State: open - Opened by jacobcook1995 4 months ago

#172 - Handling of Incertae sedis output from genbank

Issue - State: open - Opened by jacobcook1995 4 months ago

#172 - Handling of Incertae sedis output from genbank

Issue - State: open - Opened by jacobcook1995 4 months ago

#171 - Fixed NCBI taxonomy building to catch all parents are child cases

Pull Request - State: closed - Opened by jacobcook1995 4 months ago

#170 - Release candidate 3.0.1 RC 7

Pull Request - State: open - Opened by davidorme 4 months ago - 1 comment

#170 - Release candidate 3.0.1 RC 7

Pull Request - State: open - Opened by davidorme 4 months ago - 1 comment

#169 - Make maximum embargo length configurable

Pull Request - State: closed - Opened by davidorme 4 months ago

#169 - Make maximum embargo length configurable

Pull Request - State: closed - Opened by davidorme 4 months ago

#168 - Handle missing xml configuration in dataset publication

Pull Request - State: closed - Opened by davidorme 4 months ago

#168 - Handle missing xml configuration in dataset publication

Pull Request - State: closed - Opened by davidorme 4 months ago

#167 - Make maximum embargo length configurable

Issue - State: closed - Opened by davidorme 4 months ago

#166 - Handle missing XML configuration in dataset publication.

Issue - State: closed - Opened by davidorme 5 months ago

#166 - Handle missing XML configuration in dataset publication.

Issue - State: closed - Opened by davidorme 5 months ago

#165 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 5 months ago

#165 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 5 months ago

#164 - Release 3.0.1 Release Candidate 4

Pull Request - State: closed - Opened by davidorme 5 months ago

#164 - Release 3.0.1 Release Candidate 4

Pull Request - State: closed - Opened by davidorme 5 months ago

#163 - Bump certifi from 2024.6.2 to 2024.7.4

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#163 - Bump certifi from 2024.6.2 to 2024.7.4

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#162 - Updating the Zenodo handling

Pull Request - State: closed - Opened by davidorme 5 months ago - 3 comments

#162 - Updating the Zenodo handling

Pull Request - State: closed - Opened by davidorme 5 months ago - 3 comments

#161 - Cleaner error handling for `create_deposit` entry point

Issue - State: closed - Opened by jacobcook1995 5 months ago - 1 comment

#160 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 5 months ago

#160 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 5 months ago

#159 - Add publishing workflow and make CI workflow reusable

Pull Request - State: closed - Opened by davidorme 5 months ago - 1 comment

#158 - Add trusted publishing

Issue - State: closed - Opened by davidorme 5 months ago

#158 - Add trusted publishing

Issue - State: closed - Opened by davidorme 5 months ago

#157 - Bump urllib3 from 2.2.1 to 2.2.2

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#157 - Bump urllib3 from 2.2.1 to 2.2.2

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#156 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 5 months ago

#156 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 5 months ago

#155 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 6 months ago

#155 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 6 months ago

#154 - Add 3.12 to the CI

Pull Request - State: closed - Opened by jacobcook1995 6 months ago

#154 - Add 3.12 to the CI

Pull Request - State: closed - Opened by jacobcook1995 6 months ago

#153 - Added ruff specific formatting options

Pull Request - State: closed - Opened by jacobcook1995 6 months ago

#153 - Added ruff specific formatting options

Pull Request - State: closed - Opened by jacobcook1995 6 months ago

#152 - Add gazetteer creation guide

Pull Request - State: closed - Opened by jacobcook1995 6 months ago - 2 comments

#152 - Add gazetteer creation guide

Pull Request - State: closed - Opened by jacobcook1995 6 months ago - 2 comments

#151 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 6 months ago

#151 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 6 months ago

#150 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 6 months ago

#150 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 6 months ago

#149 - Bump requests from 2.31.0 to 2.32.0

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago - 1 comment
Labels: dependencies

#149 - Bump requests from 2.31.0 to 2.32.0

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago - 1 comment
Labels: dependencies

#148 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 6 months ago

#147 - Switched example file download links to point to develop

Pull Request - State: closed - Opened by jacobcook1995 6 months ago - 1 comment

#147 - Switched example file download links to point to develop

Pull Request - State: closed - Opened by jacobcook1995 6 months ago - 1 comment

#146 - Switching to using `ruff`

Pull Request - State: closed - Opened by jacobcook1995 6 months ago - 1 comment

#146 - Switching to using `ruff`

Pull Request - State: closed - Opened by jacobcook1995 6 months ago - 1 comment

#145 - Adding an example file to the documentation

Pull Request - State: closed - Opened by jacobcook1995 6 months ago - 1 comment

#145 - Adding an example file to the documentation

Pull Request - State: closed - Opened by jacobcook1995 6 months ago - 1 comment

#144 - Validation passes with no worksheets

Pull Request - State: closed - Opened by davidorme 6 months ago

#144 - Validation passes with no worksheets

Pull Request - State: closed - Opened by davidorme 6 months ago

#143 - Validation passes with no worksheets being described

Issue - State: closed - Opened by jacobcook1995 6 months ago - 1 comment

#143 - Validation passes with no worksheets being described

Issue - State: closed - Opened by jacobcook1995 6 months ago - 1 comment

#142 - Command line workflow updates

Pull Request - State: closed - Opened by davidorme 6 months ago

#142 - Command line workflow updates

Pull Request - State: closed - Opened by davidorme 6 months ago

#141 - Bump jinja2 from 3.1.3 to 3.1.4

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#141 - Bump jinja2 from 3.1.3 to 3.1.4

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#140 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 7 months ago

#140 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 7 months ago

#139 - Bump tqdm from 4.66.2 to 4.66.3

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#139 - Bump tqdm from 4.66.2 to 4.66.3

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#138 - Customisable Zenodo HTML

Pull Request - State: closed - Opened by davidorme 7 months ago

#138 - Customisable Zenodo HTML

Pull Request - State: closed - Opened by davidorme 7 months ago

#137 - Issues with command line workflow

Issue - State: closed - Opened by davidorme 7 months ago

#136 - Fix XML distribution flow

Pull Request - State: closed - Opened by davidorme 7 months ago - 4 comments

#136 - Fix XML distribution flow

Pull Request - State: closed - Opened by davidorme 7 months ago - 4 comments

#135 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 7 months ago

#135 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 7 months ago

#134 - Release/3.0.1

Pull Request - State: closed - Opened by davidorme 7 months ago

#133 - Provide example `.xlsx` file as a guide

Issue - State: closed - Opened by jacobcook1995 7 months ago - 2 comments

#133 - Provide example `.xlsx` file as a guide

Issue - State: closed - Opened by jacobcook1995 7 months ago - 2 comments

#132 - Fixing weird `Shapely` related test failures

Pull Request - State: closed - Opened by jacobcook1995 7 months ago

#132 - Fixing weird `Shapely` related test failures

Pull Request - State: closed - Opened by jacobcook1995 7 months ago

#131 - Added note to say that Unknown should be used for missing permit numbers

Pull Request - State: closed - Opened by jacobcook1995 7 months ago - 2 comments

#131 - Added note to say that Unknown should be used for missing permit numbers

Pull Request - State: closed - Opened by jacobcook1995 7 months ago - 2 comments

GitHub / ImperialCollegeLondon/safedata_validator issues and pull requests