Merge pull request #29 from PennChopMicrobiomeProgram/28-use-fmt-cont…

…rollers

Use `#fmt` controllers for test_align.py linting

.github/workflows/test.yml

@@ -40,7 +40,10 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ['3.12']
-        os: [ubuntu-latest, macos-latest]
+        os: [ubuntu-latest]
+        # Windows runners can take way too long to be available
+        # and the setup-conda action isn't compatible with macOS and python 3.12
+        # os: [ubuntu-latest, windows-latest, macos-latest]
         include:
           - python-version: '3.11'
             os: ubuntu-latest
@@ -85,17 +88,9 @@ jobs:
       - name: Install Dependencies
         run: pip install black
 
-      # test_align.py includes tests that have weird formatting because we want to be able to line 
-      # up the expected and actual alignments in the test output. I've found it's really easy to 
-      # run 'black .' and forget about it, so I'm including this check to make sure it FAILS the 
-      # formatting check. If this trips you up, probably just revert the changes to that file.
       - name: Lint Code Base
         run: |
-          black --check --exclude="test_align.py" .
-
-          if black --check --include="test_align.py" . ; then
-            exit 1
-          fi
+          black --check .
 
   codacy-analysis-cli:
     name: Codacy Analysis CLI

tests/unit/test_align.py

@@ -19,43 +19,55 @@ def test_no_endgaps(self):
         self.assertEqual(align_semiglobal(qseq, sseq), (qseq, sseq))
 
     def test_endgaps_both_sides_query(self):
+        # fmt: off
         qseq =      "GATGAACGCTAGCTTCAGGCTTAAC"
         sseq = "CTCAGGATGAACGCTAGCTACAGGCTTAACACATGCAAGT"
+        # fmt: on
         aligned_qseq, aligned_sseq = align_semiglobal(qseq, sseq)
         self.assertEqual(aligned_qseq, "-----" + qseq + "----------")
         self.assertEqual(aligned_sseq, sseq)
 
     def test_endgaps_left_query(self):
+        # fmt: off
         qseq =      "GATGAACGCTAGCTTCAGGCTTAAC"
         sseq = "CTCAGGATGAACGCTAGCTACAGGCTTAAC"
+        # fmt: on
         aligned_qseq, aligned_sseq = align_semiglobal(qseq, sseq)
         self.assertEqual(aligned_qseq, "-----" + qseq)
         self.assertEqual(aligned_sseq, sseq)
 
     def test_endgaps_right_query(self):
+        # fmt: off
         qseq = "GATGAACGCTAGCTTCAGGCTTAAC"
         sseq = "GATGAACGCTAGCTACAGGCTTAACACATGCAAGT"
+        # fmt: on
         aligned_qseq, aligned_sseq = align_semiglobal(qseq, sseq)
         self.assertEqual(aligned_qseq, qseq + "----------")
         self.assertEqual(aligned_sseq, sseq)
 
     def test_ragged_left_subject(self):
+        # fmt: off
         qseq = "CTCAGGATGAACGCTAGCTACAGGCTTAAC"
         sseq =      "GATGAACGCTAGCTTCAGGCTTAACACATG"
+        # fmt: on
         aligned_qseq, aligned_sseq = align_semiglobal(qseq, sseq)
         self.assertEqual(aligned_qseq, qseq + "-----")
         self.assertEqual(aligned_sseq, "-----" + sseq)
 
     def test_ragged_right_subject(self):
+        # fmt: off
         qseq =      "GATGAACGCTAGCTACAGGCTTAACACATG"
         sseq = "CTCAGGATGAACGCTAGCTTCAGGCTTAAC"
+        # fmt: on
         aligned_qseq, aligned_sseq = align_semiglobal(qseq, sseq)
         self.assertEqual(aligned_qseq, "-----" + qseq)
         self.assertEqual(aligned_sseq, sseq + "-----")
 
     def test_funky_query_left(self):
+        # fmt: off
         qseq =  "TTTTGATGAACGCTAGCTACAGGCTTA"
         sseq = "CTCAGGATGAACGCTAGCTTCAGGCTTAAC"
+        # fmt: on
         aligned_qseq, aligned_sseq = align_semiglobal(qseq, sseq)
         self.assertEqual(aligned_qseq, "-" + qseq + "--")
         self.assertEqual(aligned_sseq, sseq)