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SISTR v1.1.3 release#59

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kbessonov1984 merged 40 commits intomasterphac-nml/sistr_cmd:masterfrom v1.1.3phac-nml/sistr_cmd:v1.1.3Copy head branch name to clipboardNov 26, 2024

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Commits

Commits on Aug 29, 2024

• first SISTR v1.1.3 commit with serovar around O24/25 antigen update

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Commits on Aug 30, 2024

• fixed empty subspecies value for reverse antigen to serovar lookup feature and removed some serovars that will no longer be detected and reported in Salmonella-serotype_serogroup_antigen_table-WHO_…

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• added Database section to README

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Commits on Sep 4, 2024

• CI tests, list of serovars -l option

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• CI tests running on pytest

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• pycurl added in CI and fixed regex for O24 and O25

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• pycurl added in CI and fixed regex for O24 and O25

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• pycurl added in CI and fixed regex for O24 and O25

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• python 3.10 for CI

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• python 3.10 for CI

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• python 3.10 for CI

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• python 3.10 for CI

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• numpy no upper limit requirement

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• pycurl more relaxed conditions

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• building

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• building

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• numpy <2

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• numpy <2

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• Databases init more transparent

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• Databases init more transparent

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• Databases init more transparent

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• pre-release v1.1.3 commit tested against test dataset with O24 and O25 antigens from PulseNet and EnteroBase

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Commits on Sep 5, 2024

• Updated README.md with urls to Databases on Zenodo.org and constants.py SISTR_DB_URL global varibale with new url

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Commits on Sep 6, 2024

• Updated the CHANGELOG.md and README.md

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Commits on Sep 23, 2024

• The O24 and O25 collapsed serovars antigenic formula now corrected in sistr/data/Salmonella-serotype_serogroup_antigen_table-WHO_2007.csv and not via o_antigen value parsing in infer_o_antigen() si…

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Commits on Sep 25, 2024

• serovar list feature unit tested and new tests written, changelog updated

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• fixed 'sistr_cmd/sistr/data' directory initalization for database init. Does not delete directory anymore

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Commits on Sep 26, 2024

• Updaetd the list-of-serovars field and fixed some log level messages

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• updated README with updated usage data

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• updated README with updated usage data

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Commits on Oct 1, 2024

• Updated README.md and CHANGELOG.md

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• Updated README.md and CHANGELOG.md

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• Updated README.md and CHANGELOG.md

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• Updated README.md and CHANGELOG.md

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Commits on Nov 22, 2024

• Updated serovar list log message to indicate which list is used for a given job

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• improved IIIb O:61:k:1,5,7 reporting by removing O: from overall serovar output

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Commits on Nov 26, 2024

• Added d-tartrate qc message for Paratyphi B, Paratyphi B var. Java and I 1,4,[5],12:i:-

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• fixed test_serotyping - KeyError: 'serovar_in_serovar_list' error

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• Update CHANGELOG.md

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• Updated CHANGELOG.md

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