Closed ielis closed 3 weeks ago
Split the repository into data (this repository) and code (Phenopacket Store Toolkit).
From now on, we use phenopacket-store-toolkit for Q/C, release, and access. The toolkit is versioned separately from the store.
phenopacket-store-toolkit
The toolkit can be installed from PyPi:
python3 -m pip install phenopacket-store-toolkit
The toolkit dramatically simplifies loading phenopackets, e.g. SUOX cohort of Phenopacket Store 0.1.18:
0.1.18
from ppktstore.registry import configure_phenopacket_registry() registry = configure_phenopacket_registry() with registry.open_phenopacket_store(release="0.1.18") as ps: phenopackets = list(ps.iter_cohort_phenopackets("SUOX")) assert len(phenopackets) == 35
The registry API is basically the same as HPO-toolkit's Ontology store.
For the release duties, the toolkit must be installed with a bunch of additional dependencies:
python3 -m pip install phenopacket-store-toolkit[release]
Then, the same CLI is available and we can use it to create the release ZIP and Q/C. The HOW_TO_RELEASE.md checklist has been updated.
HOW_TO_RELEASE.md
@pnrobinson this will require an update on your machine(s). I'll help with the setup.
Split the repository into data (this repository) and code (Phenopacket Store Toolkit).
From now on, we use
phenopacket-store-toolkit
for Q/C, release, and access. The toolkit is versioned separately from the store.The toolkit can be installed from PyPi:
Use to access Phenopacket Store
The toolkit dramatically simplifies loading phenopackets, e.g. SUOX cohort of Phenopacket Store
0.1.18
:The registry API is basically the same as HPO-toolkit's Ontology store.
Use for packaging and Q/C
For the release duties, the toolkit must be installed with a bunch of additional dependencies:
Then, the same CLI is available and we can use it to create the release ZIP and Q/C. The
HOW_TO_RELEASE.md
checklist has been updated.@pnrobinson this will require an update on your machine(s). I'll help with the setup.