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Clean up Regnum phylorefs#89

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gaurav wants to merge 24 commits intomasterphyloref/clade-ontology:masterfrom fix-specifier-authoritiesphyloref/clade-ontology:fix-specifier-authoritiesCopy head branch name to clipboard

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Commits on May 22, 2020

• Deleted unneeded phyloref_testcase.owl.

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Commits on Jun 30, 2020

• Imported some files from Anna's transcribed phylogenies.

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• Added phylogenies transcribed or obtained by Anna.

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Commits on Jul 13, 2020

• Standardized to file ID to seven digits rather than six.

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• Renamed from "REGNUM_" to "CLADO_".

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• Imported phylogenies curated by Anna.

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Commits on Jul 14, 2020

• Moved and renamed files with Newick errors.

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• Added expectation for Ascomycota.

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Commits on Aug 10, 2020

• Manually labeled one expected resolution.

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• Updated phylogenies with latest.

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• Improved debugging; removed two files with failing Newick strings.

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Commits on Aug 25, 2020

• Replaced generated filename from "REGNUM_" to "CLADO_".

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• Fix: specifier authorities now written correctly.

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• Removed folders named 'scripts/' from encryption.

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• Added a script for mass-converting Phyx files into OWL ontologies.

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• Changed default number of digits to 7.

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Commits on Aug 26, 2020

• Fixed author separators.

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• Added script to fix part of Phyx file.

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• Fixed specifier authorities in Phyx files.

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Commits on Jul 2, 2021

• Moved encrypted Phylonym Phyx out of encrypted/.

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• Deleted two test clade definitions.

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• Added a test for Newick strings in input files.

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Commits on Jul 11, 2021

• Add a GitHub action to test this repo.

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Commits on Jul 12, 2021

• Made some tests optional; fixed tests.

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