move

docs/source/contributing.rst

@@ -56,3 +56,10 @@ The documentation is built with Sphinx, which is included as part of the ``docs`
     make html
 
 See the `Sphinx documentation <https://www.sphinx-doc.org/en/master/>`_ for more information.
+
+Generating examples
+-------------
+
+The fusion examples in ``src/fusor/examples`` can be generated by running the following: ::
+
+    python3 scripts/generate_examples.py

pyproject.toml

@@ -169,6 +169,7 @@ ignore = [
 # SLF001 - private-member-access
 "tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "B011", "INP001", "SLF001"]
 "src/fusor/models.py" = ["ANN201", "N803", "N805", "N815", "ANN001", "ANN2", "ANN102"]
+"scripts/*" = ["INP001"]
 
 [tool.ruff.format]
 docstring-code-format = true

src/fusor/examples/create_examples.py → scripts/generate_examples.py

@@ -1,4 +1,4 @@
-"""Script for creating JSON examples"""
+"""Script for creating JSON examples in src/fusor/examples"""
 
 import asyncio
 import json
@@ -17,7 +17,7 @@
     RegulatoryClass,
 )
 
-EXAMPLES_DIR = Path(__file__).resolve().parents[0]
+EXAMPLES_DIR = Path(__file__).resolve().parents[1] / "src" / "fusor" / "examples"
 
 
 async def _create_json(fn: str, model: BaseModel) -> None:

src/fusor/examples/README.md

@@ -7,9 +7,3 @@
 * `tpm3_ntrk1.json`: Example TPM3-NTRK1 assayed fusion drawn from previous VICC Fusion Curation draft material. Represented in nomenclature as `NM_152263.3(TPM3):e.1_8::NM_002529.3(NTRK1):e.10_22`.
 * `tpm3_pdgfrb.json`: Example TPM3-PDGFRB assayed fusion identified via RT-PCR. Represented in nomenclature as `NM_152263.3(TPM3):e.8::NM_002609.3(PDGFRB):e.11_22`.
 * `igh_myc.json`: Example of an enhancer-driven IGH-MYC categorical fusion. Represented in nomenclature as `reg_e_EH38E3121735@IGH(hgnc:5477)::MYC(hgnc:7553)`.
-
-To generate all examples from examples directory, run the following:
-
-```shell
-python3 create_examples.py
-```