Skip to content

Commit

Permalink
Merge pull request #60 from linkml/ready_release
Browse files Browse the repository at this point in the history
Ready release
  • Loading branch information
sierra-moxon authored Dec 19, 2023
2 parents 80fadb9 + ce528e8 commit 9cc516a
Show file tree
Hide file tree
Showing 13 changed files with 452 additions and 1,406 deletions.
4 changes: 2 additions & 2 deletions .github/workflows/main.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,9 @@ jobs:
matrix:
python-version: [ "3.11", "3.7" ]
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
uses: actions/setup-python@v3
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
Expand Down
38 changes: 15 additions & 23 deletions .github/workflows/pypi-publish.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -2,37 +2,29 @@ name: Publish Python Package

on:
release:
types: [created]
types: [ created ]

jobs:
build-n-publish:
name: Build and publish Python 🐍 distributions 📦 to PyPI
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v3

- name: Set up Python
uses: actions/setup-python@v3
with:
python-version: 3.9
- name: Set up Python
uses: actions/setup-python@v3

- name: Install Poetry
uses: snok/[email protected]
with:
virtualenvs-create: true
virtualenvs-in-project: true
- name: Install Poetry
run: |
pip install poetry
poetry self add "poetry-dynamic-versioning[plugin]"
- name: Install dependencies
run: poetry install --no-interaction
- name: Build source and wheel archives
run: poetry build

- name: Build source and wheel archives
run: |
poetry version $(git describe --tags --abbrev=0)
poetry build
- name: Publish distribution 📦 to PyPI
uses: pypa/[email protected]
with:
user: __token__
password: ${{ secrets.pypi_password }}
- name: Publish distribution 📦 to PyPI
uses: pypa/[email protected]
with:
user: __token__
password: ${{ secrets.pypi_password }}
2 changes: 1 addition & 1 deletion .github/workflows/refresh.yml
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ jobs:
with:
persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
- uses: actions/setup-python@v2
- uses: actions/setup-python@v3
with:
python-version: "3.10"

Expand Down
1,546 changes: 197 additions & 1,349 deletions poetry.lock

Large diffs are not rendered by default.

12 changes: 8 additions & 4 deletions pyproject.toml
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[tool.poetry]
name = "prefixmaps"
version = "0.1.8"
version = "0.0.0"
description = "A python library for retrieving semantic prefix maps"
readme = "README.md"
authors = ["cmungall <[email protected]>"]
Expand Down Expand Up @@ -39,10 +39,14 @@ curies = ">=0.5.3"
tox = "^4.11.3"
pydantic = "^2.5"

[tool.poetry-dynamic-versioning]
enable = true
vcs = "git"
style = "pep440"


[tool.poetry.dev-dependencies]
pytest = ">=6.2"
linkml = ">=1.3.1"
coverage = ">=6.4.4"
typing-extensions = ">=4.4.0"

Expand All @@ -65,8 +69,8 @@ line-length = 100
target-version = ["py39", "py310"]

[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"
requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
build-backend = "poetry_dynamic_versioning.backend"

[tool.poetry.scripts]
slurp-prefixmaps = "prefixmaps.ingest.etl_runner:cli"
Expand Down
39 changes: 39 additions & 0 deletions src/prefixmaps/data/bioregistry.csv
Original file line number Diff line number Diff line change
Expand Up @@ -350,6 +350,7 @@ bioregistry,APOLLO_SV,https://bioregistry.io/apollosv:,prefix_alias
bioregistry,APOLLO_SV,https://purl.obolibrary.org/obo/APOLLO_SV_,prefix_alias
bioregistry,APOLLO_SV,https://purl.obolibrary.org/obo/apollo_sv/dev/apollo_sv.owl#APOLLO_SV_,prefix_alias
bioregistry,APOLLO_SV,https://www.ebi.ac.uk/ols/ontologies/apollo_sv/terms?iri=http://purl.obolibrary.org/obo/APOLLO_SV_,prefix_alias
bioregistry,apollosv,http://purl.obolibrary.org/obo/APOLLO_SV_,namespace_alias
bioregistry,arachnoserver,http://identifiers.org/arachnoserver/,canonical
bioregistry,arachnoserver,http://bio2rdf.org/arachnoserver:,prefix_alias
bioregistry,arachnoserver,http://bioregistry.io/arachnoserver:,prefix_alias
Expand Down Expand Up @@ -1416,6 +1417,10 @@ bioregistry,cbioportal,https://identifiers.org/cbioportal/,prefix_alias
bioregistry,cbioportal,https://identifiers.org/cbioportal:,prefix_alias
bioregistry,cbioportal,https://n2t.net/cbioportal:,prefix_alias
bioregistry,cbioportal,https://www.cbioportal.org/study/summary?id=,prefix_alias
bioregistry,cc,https://creativecommons.org/ns#,canonical
bioregistry,cc,http://bioregistry.io/cc:,prefix_alias
bioregistry,cc,http://creativecommons.org/ns#,prefix_alias
bioregistry,cc,https://bioregistry.io/cc:,prefix_alias
bioregistry,ccdc,http://identifiers.org/ccdc/,canonical
bioregistry,ccdc,http://bioregistry.io/ccdc:,prefix_alias
bioregistry,ccdc,http://identifiers.org/ccdc:,prefix_alias
Expand Down Expand Up @@ -1844,6 +1849,7 @@ bioregistry,civic.vid,https://identifiers.org/civic.vid:,prefix_alias
bioregistry,CL,http://purl.obolibrary.org/obo/CL_,canonical
bioregistry,CL,http://bio2rdf.org/cl:,prefix_alias
bioregistry,CL,http://bioregistry.io/CL:,prefix_alias
bioregistry,CL,http://cellxgene.cziscience.com/cellguide/CL_,prefix_alias
bioregistry,CL,http://identifiers.org/CL/,prefix_alias
bioregistry,CL,http://identifiers.org/CL:,prefix_alias
bioregistry,CL,http://identifiers.org/cl/CL:,prefix_alias
Expand All @@ -1853,6 +1859,7 @@ bioregistry,CL,http://purl.bioontology.org/ontology/CL/CL:,prefix_alias
bioregistry,CL,http://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http://purl.obolibrary.org/obo/CL_,prefix_alias
bioregistry,CL,https://bio2rdf.org/cl:,prefix_alias
bioregistry,CL,https://bioregistry.io/CL:,prefix_alias
bioregistry,CL,https://cellxgene.cziscience.com/cellguide/CL_,prefix_alias
bioregistry,CL,https://identifiers.org/CL/,prefix_alias
bioregistry,CL,https://identifiers.org/CL:,prefix_alias
bioregistry,CL,https://identifiers.org/cl/CL:,prefix_alias
Expand Down Expand Up @@ -4966,6 +4973,7 @@ bioregistry,gramene.gene,https://identifiers.org/gramene.gene/,prefix_alias
bioregistry,gramene.gene,https://identifiers.org/gramene.gene:,prefix_alias
bioregistry,gramene.gene,https://n2t.net/gramene.gene:,prefix_alias
bioregistry,gramene.gene,https://www.gramene.org/db/genes/search_gene?acc=,prefix_alias
bioregistry,gramene.growthstage,http://purl.obolibrary.org/obo/GRO_,namespace_alias
bioregistry,gramene.protein,http://identifiers.org/gramene.protein/,canonical
bioregistry,gramene.protein,http://bioregistry.io/GR_PROTEIN:,prefix_alias
bioregistry,gramene.protein,http://bioregistry.io/gramene.protein:,prefix_alias
Expand Down Expand Up @@ -6090,11 +6098,13 @@ bioregistry,interlex,http://bioregistry.io/ILX:,prefix_alias
bioregistry,interlex,http://bioregistry.io/interlex:,prefix_alias
bioregistry,interlex,http://identifiers.org/ilx:,prefix_alias
bioregistry,interlex,http://scicrunch.org/scicrunch/interlex/view/ilx_,prefix_alias
bioregistry,interlex,http://uri.interlex.org/base/,prefix_alias
bioregistry,interlex,https://bioregistry.io/ILX:,prefix_alias
bioregistry,interlex,https://bioregistry.io/interlex:,prefix_alias
bioregistry,interlex,https://identifiers.org/ilx/,prefix_alias
bioregistry,interlex,https://identifiers.org/ilx:,prefix_alias
bioregistry,interlex,https://scicrunch.org/scicrunch/interlex/view/ilx_,prefix_alias
bioregistry,interlex,https://uri.interlex.org/base/,prefix_alias
bioregistry,interpro,http://purl.obolibrary.org/obo/IPR_,canonical
bioregistry,interpro,http://bio2rdf.org/interpro:,prefix_alias
bioregistry,interpro,http://bioregistry.io/IP:,prefix_alias
Expand Down Expand Up @@ -6875,6 +6885,14 @@ bioregistry,macie,https://identifiers.org/macie:,prefix_alias
bioregistry,macie,https://n2t.net/macie:,prefix_alias
bioregistry,macie,https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=,prefix_alias
bioregistry,macie,https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/getPage.pl?id=,prefix_alias
bioregistry,maggot,http://identifiers.org/maggot/,canonical
bioregistry,maggot,http://bioregistry.io/maggot:,prefix_alias
bioregistry,maggot,http://identifiers.org/maggot:,prefix_alias
bioregistry,maggot,http://pmb-bordeaux.fr/maggot/metadata/,prefix_alias
bioregistry,maggot,https://bioregistry.io/maggot:,prefix_alias
bioregistry,maggot,https://identifiers.org/maggot/,prefix_alias
bioregistry,maggot,https://identifiers.org/maggot:,prefix_alias
bioregistry,maggot,https://pmb-bordeaux.fr/maggot/metadata/,prefix_alias
bioregistry,MaizeGDB,http://identifiers.org/maizegdb.locus/,namespace_alias
bioregistry,maizegdb.locus,http://identifiers.org/maizegdb.locus/,canonical
bioregistry,maizegdb.locus,http://bio2rdf.org/maizegdb:,prefix_alias
Expand Down Expand Up @@ -8562,12 +8580,15 @@ bioregistry,niaest,https://identifiers.org/niaest/,prefix_alias
bioregistry,niaest,https://identifiers.org/niaest:,prefix_alias
bioregistry,niaest,https://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=,prefix_alias
bioregistry,niaest,https://n2t.net/niaest:,prefix_alias
bioregistry,nif.cell,http://purl.obolibrary.org/obo/NIF_CELL_,namespace_alias
bioregistry,nif.dysfunction,http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_,namespace_alias
bioregistry,nif.ext,http://uri.neuinfo.org/nif/nifstd/nifext_,canonical
bioregistry,nif.ext,http://bioregistry.io/NIFEXT:,prefix_alias
bioregistry,nif.ext,http://bioregistry.io/nif.ext:,prefix_alias
bioregistry,nif.ext,https://bioregistry.io/NIFEXT:,prefix_alias
bioregistry,nif.ext,https://bioregistry.io/nif.ext:,prefix_alias
bioregistry,nif.ext,https://uri.neuinfo.org/nif/nifstd/nifext_,prefix_alias
bioregistry,nif.grossanatomy,http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_,namespace_alias
bioregistry,nif.std,http://uri.neuinfo.org/nif/nifstd/,canonical
bioregistry,nif.std,http://bioregistry.io/NIFSTD:,prefix_alias
bioregistry,nif.std,http://bioregistry.io/nif.std:,prefix_alias
Expand Down Expand Up @@ -9230,6 +9251,10 @@ bioregistry,openalex,https://openalex.org/,canonical
bioregistry,openalex,http://bioregistry.io/openalex:,prefix_alias
bioregistry,openalex,http://openalex.org/,prefix_alias
bioregistry,openalex,https://bioregistry.io/openalex:,prefix_alias
bioregistry,openwemi,https://dcmi.github.io/openwemi/ns#,canonical
bioregistry,openwemi,http://bioregistry.io/openwemi:,prefix_alias
bioregistry,openwemi,http://dcmi.github.io/openwemi/ns#,prefix_alias
bioregistry,openwemi,https://bioregistry.io/openwemi:,prefix_alias
bioregistry,OPL,http://purl.obolibrary.org/obo/OPL_,canonical
bioregistry,OPL,http://bioregistry.io/OPL:,prefix_alias
bioregistry,OPL,http://www.ebi.ac.uk/ols/ontologies/opl/terms?iri=http://purl.obolibrary.org/obo/OPL_,prefix_alias
Expand Down Expand Up @@ -10825,6 +10850,10 @@ bioregistry,rdf,http://www.w3.org/1999/02/22-rdf-syntax-ns#,canonical
bioregistry,rdf,http://bioregistry.io/rdf:,prefix_alias
bioregistry,rdf,https://bioregistry.io/rdf:,prefix_alias
bioregistry,rdf,https://www.w3.org/1999/02/22-rdf-syntax-ns#,prefix_alias
bioregistry,rdfa,http://www.w3.org/ns/rdfa#,canonical
bioregistry,rdfa,http://bioregistry.io/rdfa:,prefix_alias
bioregistry,rdfa,https://bioregistry.io/rdfa:,prefix_alias
bioregistry,rdfa,https://www.w3.org/ns/rdfa#,prefix_alias
bioregistry,rdfs,http://www.w3.org/2000/01/rdf-schema#,canonical
bioregistry,rdfs,http://bioregistry.io/rdfs:,prefix_alias
bioregistry,rdfs,https://bioregistry.io/rdfs:,prefix_alias
Expand Down Expand Up @@ -12344,6 +12373,14 @@ bioregistry,treefam,https://identifiers.org/treefam:,prefix_alias
bioregistry,treefam,https://n2t.net/treefam:,prefix_alias
bioregistry,treefam,https://www.treefam.org/cgi-bin/TFinfo.pl?ac=,prefix_alias
bioregistry,treefam,https://www.treefam.org/family/,prefix_alias
bioregistry,tricdb,http://identifiers.org/tricdb/,canonical
bioregistry,tricdb,http://biomeddb.org/Disease/Details?DISEASEID=,prefix_alias
bioregistry,tricdb,http://bioregistry.io/tricdb:,prefix_alias
bioregistry,tricdb,http://identifiers.org/tricdb:,prefix_alias
bioregistry,tricdb,https://biomeddb.org/Disease/Details?DISEASEID=,prefix_alias
bioregistry,tricdb,https://bioregistry.io/tricdb:,prefix_alias
bioregistry,tricdb,https://identifiers.org/tricdb/,prefix_alias
bioregistry,tricdb,https://identifiers.org/tricdb:,prefix_alias
bioregistry,trichdb,http://identifiers.org/trichdb/,canonical
bioregistry,trichdb,http://bioregistry.io/trichdb:,prefix_alias
bioregistry,trichdb,http://identifiers.org/trichdb:,prefix_alias
Expand Down Expand Up @@ -12405,6 +12442,7 @@ bioregistry,Uber-anatomy ontology,http://purl.obolibrary.org/obo/UBERON_,namespa
bioregistry,UBERON,http://purl.obolibrary.org/obo/UBERON_,canonical
bioregistry,UBERON,http://bioregistry.io/UBERON:,prefix_alias
bioregistry,UBERON,http://bioregistry.io/Uber-anatomy ontology:,prefix_alias
bioregistry,UBERON,http://cellxgene.cziscience.com/cellguide/tissues/UBERON_,prefix_alias
bioregistry,UBERON,http://identifiers.org/UBERON/,prefix_alias
bioregistry,UBERON,http://identifiers.org/UBERON:,prefix_alias
bioregistry,UBERON,http://identifiers.org/uberon/UBERON:,prefix_alias
Expand All @@ -12415,6 +12453,7 @@ bioregistry,UBERON,http://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http://p
bioregistry,UBERON,http://www.ebi.ac.uk/ols4/ontologies/uberon/terms?obo_id=UBERON:,prefix_alias
bioregistry,UBERON,https://bioregistry.io/UBERON:,prefix_alias
bioregistry,UBERON,https://bioregistry.io/Uber-anatomy ontology:,prefix_alias
bioregistry,UBERON,https://cellxgene.cziscience.com/cellguide/tissues/UBERON_,prefix_alias
bioregistry,UBERON,https://identifiers.org/UBERON/,prefix_alias
bioregistry,UBERON,https://identifiers.org/UBERON:,prefix_alias
bioregistry,UBERON,https://identifiers.org/uberon/UBERON:,prefix_alias
Expand Down
Loading

0 comments on commit 9cc516a

Please sign in to comment.