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Fix specifier authorities and other bugs in Regnum to Phyx generation #80

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34 changes: 34 additions & 0 deletions .github/workflows/test.yaml
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name: Test

on: [push, pull_request, workflow_dispatch]

jobs:
build:
runs-on: ubuntu-latest

strategy:
matrix:
node-version: [10.x, 12.x, 14.x]

steps:
- uses: actions/checkout@v2
- name: Use Node.js ${{ matrix.node-version }}
uses: actions/setup-node@v2
with:
node-version: ${{ matrix.node-version }}
- name: Cache Node modules
uses: actions/cache@v2
env:
cache-name: cache-node-modules
with:
# npm cache files are stored in `~/.npm` on Linux/macOS
path: ~/.npm
key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('**/package-lock.json') }}
restore-keys: |
${{ runner.os }}-build-${{ env.cache-name }}-
${{ runner.os }}-build-
${{ runner.os }}-
- name: Install dependencies
run: npm install
- name: Test
run: npm test
1 change: 1 addition & 0 deletions phyx/encrypted/.gitattributes
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* filter=git-crypt diff=git-crypt
.gitattributes !filter !diff
README.md !filter !diff
scripts/** !filter !diff
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{
"@context": "http://www.phyloref.org/phyx.js/context/v0.2.0/phyx.json",
"phylogenies": [
{
"primaryPhylogenyCitation": {
"type": "article",
"title": "Higher level phylogeny and evolutionary trends in Campanulaceae subfam. Lobelioideae: Molecular signal overshadows morphology.",
"year": 2008,
"authors": [
{
"name": "A. Antonelli",
"alternate": [
"Antonelli, A."
],
"firstname": "A.",
"lastname": "Antonelli"
}
],
"editors": [],
"series_editors": [],
"figure": "2",
"identifier": [
{
"type": "doi",
"id": "10.1016/j.ympev.2007.06.015"
}
],
"link": [],
"journal": {
"name": "Molecular Phylogenetics and Evolution",
"volume": "46",
"identifier": []
}
}
}
],
"phylorefs": [
{
"regnumId": 2,
"label": "Lobelioideae",
"dwc:scientificNameAuthorship": "Cellinese, N.",
"dwc:namePublishedIn": [
{
"type": "book",
"title": "Outlines of botany",
"year": 1835,
"authors": [
{
"name": "G. T. Burnett",
"alternate": [
"Burnett, G. T."
],
"firstname": "G.",
"lastname": "Burnett",
"middlename": "T."
}
],
"editors": [],
"series_editors": [],
"publisher": "Renshaw",
"city": "London",
"identifier": [],
"link": []
}
],
"obo:IAO_0000119": [],
"cladeDefinition": "The crown clade originating in the most recent common ancestor of Lobelia cardinalis Linnaeus 1753 and Lobelia coronopifolia Linnaeus 1753.",
"internalSpecifiers": [
{
"@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept",
"hasName": {
"@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName",
"nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000109",
"label": "Lobelia cardinalis Linnaeus, 1753",
"nameComplete": "Lobelia cardinalis"
}
},
{
"@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept",
"hasName": {
"@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName",
"nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000109",
"label": "Lobelia coronopifolia Linnaeus, 1753",
"nameComplete": "Lobelia coronopifolia"
}
}
],
"externalSpecifiers": []
}
]
}
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