From 98294edceb433ad3d4060fa771105bdd2e1c6605 Mon Sep 17 00:00:00 2001
From: James Stevenson <james.stevenson@nationwidechildrens.org>
Date: Mon, 13 Nov 2023 14:04:35 -0600
Subject: [PATCH] cicd: use ruff for autoformatting (#292)

---
 .github/workflows/github-actions.yml | 13 +++++++++----
 .pre-commit-config.yaml              |  9 ++-------
 Pipfile                              |  3 +--
 pyproject.toml                       |  3 ++-
 src/gene/database/postgresql.py      | 10 +++++++---
 src/gene/schemas.py                  |  3 +--
 6 files changed, 22 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/github-actions.yml b/.github/workflows/github-actions.yml
index da38a429..da14c709 100644
--- a/.github/workflows/github-actions.yml
+++ b/.github/workflows/github-actions.yml
@@ -6,11 +6,16 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - name: black
-        uses: psf/black@stable
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies
+        run: python3 -m pip install ".[dev]"
 
-      - name: ruff
-        uses: chartboost/ruff-action@v1
+      - name: Check style
+        run: python3 -m ruff check . && python3 -m ruff format --check .
 
   test:
     runs-on: ubuntu-latest
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 6767f6cb..2b0ba8a9 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,13 +7,8 @@ repos:
   - id: detect-private-key
   - id: trailing-whitespace
   - id: end-of-file-fixer
-- repo: https://github.com/psf/black
-  rev: 23.7.0
-  hooks:
-    - id: black
-      language_version: python3.11
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.0.290
+  rev: v0.1.2
   hooks:
     - id: ruff
-      args: [ --fix, --exit-non-zero-on-fix ]
+    - id: ruff-format
diff --git a/Pipfile b/Pipfile
index aed3a8de..5ed5972f 100644
--- a/Pipfile
+++ b/Pipfile
@@ -18,8 +18,7 @@ gffutils = "*"
 psycopg = {version = "*", extras=["binary"]}
 pytest = "*"
 pre-commit = "*"
-black = "*"
-ruff = "*"
+ruff = ">=0.1.2"
 pytest-cov = "*"
 httpx = "*"
 mock = "*"
diff --git a/pyproject.toml b/pyproject.toml
index ca67c218..8f54c725 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -41,7 +41,7 @@ etl = ["gffutils", "biocommons.seqrepo"]
 
 test = ["pytest>=6.0", "pytest-cov", "mock", "httpx"]
 
-dev = ["pre-commit", "black", "ruff"]
+dev = ["pre-commit", "ruff>=0.1.2"]
 
 docs = [
     "sphinx==6.1.3",
@@ -92,6 +92,7 @@ extend-exclude = "^/docs/source/conf.py"
 
 [tool.ruff]
 src = ["src"]
+exclude = ["docs/source/conf.py"]
 # pycodestyle (E, W)
 # Pyflakes (F)
 # flake8-annotations (ANN)
diff --git a/src/gene/database/postgresql.py b/src/gene/database/postgresql.py
index c699cd20..f62a1819 100644
--- a/src/gene/database/postgresql.py
+++ b/src/gene/database/postgresql.py
@@ -546,12 +546,16 @@ def add_source_metadata(self, src_name: SourceName, meta: SourceMeta) -> None:
     VALUES (%s, %s, %s, %s, %s, %s, %s, %s);
     """
     _ins_symbol_query = (
-        b"INSERT INTO gene_symbols (symbol, concept_id) VALUES (%s, %s);"  # noqa: E501
+        b"INSERT INTO gene_symbols (symbol, concept_id) VALUES (%s, %s);"
+    )
+    _ins_prev_symbol_query = (
+        b"INSERT INTO gene_previous_symbols (prev_symbol, concept_id) VALUES (%s, %s);"
     )
-    _ins_prev_symbol_query = b"INSERT INTO gene_previous_symbols (prev_symbol, concept_id) VALUES (%s, %s);"  # noqa: E501
     _ins_alias_query = b"INSERT INTO gene_aliases (alias, concept_id) VALUES (%s, %s);"
     _ins_xref_query = b"INSERT INTO gene_xrefs (xref, concept_id) VALUES (%s, %s);"
-    _ins_assoc_query = b"INSERT INTO gene_associations (associated_with, concept_id) VALUES (%s, %s);"  # noqa: E501
+    _ins_assoc_query = (
+        b"INSERT INTO gene_associations (associated_with, concept_id) VALUES (%s, %s);"
+    )
 
     def add_record(self, record: Dict, src_name: SourceName) -> None:
         """Add new record to database.
diff --git a/src/gene/schemas.py b/src/gene/schemas.py
index ab49faab..6f85b1bc 100644
--- a/src/gene/schemas.py
+++ b/src/gene/schemas.py
@@ -94,8 +94,7 @@ class BaseGene(BaseModel):
     strand: Optional[Strand] = None
     location_annotations: List[StrictStr] = []
     locations: Union[
-        List[models.SequenceLocation],
-        List[GeneSequenceLocation]
+        List[models.SequenceLocation], List[GeneSequenceLocation]
         # List[Union[SequenceLocation, ChromosomeLocation]],
         # List[Union[GeneSequenceLocation, GeneChromosomeLocation]]  # dynamodb
     ] = []