add mypy type checking to actions

.github/workflows/python-package.yml

@@ -27,7 +27,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
+        python -m pip install flake8 pytest mypy
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Install package
       run: |
@@ -40,4 +40,7 @@ jobs:
         flake8 . --count --exit-zero --statistics
     - name: Test with pytest
       run: |
-        pytest
+        python -m pytest
+    - name: Type check with mypy
+      run: |
+        python -m mypy src/

src/fqfa/fastq/fastq.py

@@ -37,7 +37,8 @@ def parse_fastq_reads(handle: TextIO) -> Generator[FastqRead, None, None]:
             raise ValueError("incomplete FASTQ record")
         else:
             lines = [x.rstrip() for x in lines]  # remove trailing newlines
-            yield FastqRead(*lines)
+            # TODO: figure out why mypy doesn't like this
+            yield FastqRead(*lines)  # type: ignore[arg-type]
 
 
 def parse_fastq_pe_reads(
@@ -80,9 +81,9 @@ def parse_fastq_pe_reads(
     for fwd, rev in zip_longest(fwd_generator, rev_generator, fillvalue=None):
         if None in (fwd, rev):
             raise ValueError("mismatched FASTQ file lengths")
-        elif fwd.header.split()[0] != rev.header.split()[0]:
+        elif fwd.header.split()[0] != rev.header.split()[0]:  # type: ignore[union-attr]
             raise ValueError("forward and reverse read headers do not match")
         else:
             if revcomp:
-                rev.reverse_complement()
-            yield fwd, rev
+                rev.reverse_complement()  # type: ignore[union-attr]
+            yield fwd, rev  # type: ignore[misc]