Merge branch 'tanghaibao:main' into dev

.github/workflows/Black.yml

@@ -0,0 +1,28 @@
+name: Black Formatting
+on: [pull_request]
+jobs:
+  black:
+    if: ${{ github.actor != 'dependabot[bot]' }} # Do not run on commits created by dependabot
+    runs-on: ubuntu-latest
+    permissions:
+      # Give the default GITHUB_TOKEN write permission to commit and push the changed files.
+      contents: write # Allows reading and writing repository contents (e.g., commits)
+      pull-requests: write # Allows reading and writing pull requests
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ github.sha }}
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Black Code Formatter
+        uses: psf/black@stable
+        with:
+          options: "--verbose"
+          src: "."
+
+      - name: Commit changes
+        if: success()
+        uses: stefanzweifel/git-auto-commit-action@v5
+        id: auto-commit-action
+        with:
+          commit_message: 'Style fixes by Black'

jcvi/formats/gff.py

@@ -2850,9 +2850,7 @@ def note(args):
             continue
         if AED is not None and float(g.attributes["_AED"][0]) > AED:
             continue
-        keyval = [g.accn] + [
-            ",".join(g.attributes.get(x, ["nan"])) for x in attrib
-        ]
+        keyval = [g.accn] + [",".join(g.attributes.get(x, ["nan"])) for x in attrib]
         if exoncounts:
             nexons = exoncounts.get(g.accn, 0)
             keyval.append(str(nexons))

tests/formats/test_bed.py

@@ -3,6 +3,7 @@
 
 from jcvi.formats.bed import summary
 
+
 def test_summary():
     cwd = os.getcwd()
     os.chdir(op.join(op.dirname(__file__), "data"))

tests/formats/test_cblast_benchmark.py

@@ -5,6 +5,7 @@
 import pytest
 import time
 
+
 # Benchmark cblast vs blast module
 @pytest.mark.benchmark(
     group="CBlastLine vs PyBlastLine", timer=time.time, disable_gc=True, warmup=False

tests/graphics/test_grabseeds.py

@@ -17,7 +17,7 @@ def test_main():
     # Test calibrate
     json_file = "calibrate.json"
     cleanup(json_file, output_image)
-    json_file = calibrate(["calibrate.JPG", "1"]) # `1` for the boxsize arg
+    json_file = calibrate(["calibrate.JPG", "1"])  # `1` for the boxsize arg
     assert op.exists(json_file)
     seeds(["test.JPG", "--calibrate", json_file])
 

tests/utils/test_range.py

@@ -212,4 +212,4 @@ def test_range_conflict(ranges, expected):
 def test_range_chain(ranges, expected):
     from jcvi.utils.range import range_chain
 
-    assert range_chain(ranges) == expected
+    assert range_chain(ranges) == expected