Ruff cutover

.github/workflows/ci.yaml

@@ -32,7 +32,8 @@ jobs:
       - name: Run sqlfluff on jinja templates
         run: |
           sqlfluff lint
-      - name: Run black
-        if: success() || failure() # still run black if above checks fails
+            - name: Run ruff
+        if: success() || failure() # still run ruff if above checks fails
         run: |
-          black --check --verbose .
+          ruff check
+          ruff format --check

cumulus_library_covid/counts.py

@@ -1,6 +1,7 @@
 from pathlib import Path
-from cumulus_library.statistics.counts import CountsBuilder
+
 from cumulus_library import base_utils, study_manifest
+from cumulus_library.statistics.counts import CountsBuilder
 
 
 class CovidCountsBuilder(CountsBuilder):
@@ -100,10 +101,7 @@ def count_symptom(self, duration="week"):
         return self.count_encounter(view_name, from_table, cols)
 
     def prepare_queries(
-        self, 
-        config:base_utils.StudyConfig,
-        manifest:study_manifest.StudyManifest,
-        **kwargs
+        self, config: base_utils.StudyConfig, manifest: study_manifest.StudyManifest, **kwargs
     ):
         self.queries = [
             self.count_dx("month"),

cumulus_library_covid/define_symptom.py

@@ -1,4 +1,4 @@
-""" util for sql view creation"""
+"""util for sql view creation"""
 
 import ctakesclient
 
@@ -15,7 +15,7 @@ def main():
 
     table_cols = "AS t (cui, tui, code, system, text, pref);"
     create_view = (
-        "create or replace view covid_symptom__define_symptom as "
+        "create or replace view covid_symptom__define_symptom as "  # noqa: S608
         f"select * from (VALUES \n {values_sql}) \n {table_cols}"
     )
 

cumulus_library_covid/table_study_period.sql

@@ -17,7 +17,9 @@ WITH documented_encounter AS (
         ce.encounter_ref,
         ce.status,
         cdr.documentreference_ref,
-        date_diff('day', ce.period_start_day, date(cdr.author_day)) AS diff_enc_note_days,
+        date_diff(
+            'day', ce.period_start_day, date(cdr.author_day)
+        ) AS diff_enc_note_days,
         coalesce(ce.class_code, 'None') AS enc_class_code,
         coalesce(ce.class_display, 'None') AS enc_class_display,
         coalesce(cdr.type_code, 'None') AS doc_type_code,
@@ -33,33 +35,34 @@ WITH documented_encounter AS (
         AND (ce.period_start_day BETWEEN date('2016-06-01') AND current_date)
         AND (ce.period_end_day BETWEEN date('2016-06-01') AND current_date)
 ),
+
 encounter_with_note AS (
-SELECT
-    de.period_start_day,
-    de.period_start_week,
-    de.period_start_month,
-    de.period_end_day,
-    de.age_at_visit,
-    de.author_day,
-    de.author_week,
-    de.author_month,
-    de.author_year,
-    de.gender,
-    de.race_display,
-    de.ethnicity_display,
-    de.subject_ref,
-    de.encounter_ref,
-    de.status,
-    de.documentreference_ref,
-    de.diff_enc_note_days,
-    de.enc_class_code,
-    de.enc_class_display,
-    de.doc_type_code,
-    de.doc_type_display,
-    coalesce(ed.code IS NOT NULL, FALSE) AS ed_note
-FROM documented_encounter AS de
-LEFT JOIN core__ed_note AS ed
-    ON de.doc_type_code = ed.from_code
+    SELECT
+        de.period_start_day,
+        de.period_start_week,
+        de.period_start_month,
+        de.period_end_day,
+        de.age_at_visit,
+        de.author_day,
+        de.author_week,
+        de.author_month,
+        de.author_year,
+        de.gender,
+        de.race_display,
+        de.ethnicity_display,
+        de.subject_ref,
+        de.encounter_ref,
+        de.status,
+        de.documentreference_ref,
+        de.diff_enc_note_days,
+        de.enc_class_code,
+        de.enc_class_display,
+        de.doc_type_code,
+        de.doc_type_display,
+        coalesce(ed.code IS NOT NULL, FALSE) AS ed_note
+    FROM documented_encounter AS de
+    LEFT JOIN core__ed_note AS ed
+        ON de.doc_type_code = ed.from_code
 )
 
 SELECT DISTINCT
@@ -83,7 +86,7 @@ SELECT DISTINCT
     e.enc_class_display,
     e.doc_type_code,
     e.doc_type_display,
-    e.ed_note, 
+    e.ed_note,
     a.age_group,
     e.status
 FROM encounter_with_note AS e,

pyproject.toml

@@ -28,9 +28,26 @@ build-backend = "flit_core.buildapi"
 
 [project.optional-dependencies]
 dev = [
-    "black >= 24.3, <25",
+    # if you update the ruff version, also update .pre-commit-config.yaml
+    "ruff < 0.6",
     "pylint",    
 ]
 
 [tool.flit.sdist]
 include = ["covid_symptom/"]
+
+[tool.ruff]
+line-length = 100
+
+[tool.ruff.lint]
+allowed-confusables = ["’"]  # allow proper apostrophes
+select = [
+    "A",  # prevent using keywords that clobber python builtins
+    "E",  # pycodestyle
+    "F",  # pyflakes
+    "I",  # isort
+    "PLE",  # pylint errors
+    "RUF",  # the ruff developer's own rules
+    "S",  # bandit security warnings
+    "UP",  # alert you when better syntax is available in your python version
+]