Rewrite `auto_correlation` and `hydrophobicity` using vectorized code

peptides/__init__.py

@@ -344,12 +344,12 @@ class Peptide(typing.Sequence[str]):
             mu = statistics.mean(table.values())
             sigma = statistics.stdev(table.values())
             table = {k: (v - mu) / sigma for k, v in table.items()}
-        # compute using Cruciani formula
-        s = 0.0
-        for aa1, aa2 in zip(self.sequence, self.sequence[lag:]):
-            s += table.get(aa1, 0.0) * table.get(aa2, 0.0)
-        # return correlation
-        return s / len(self.sequence)
+        # build the lookup table
+        lut = array([table.get(aa, 0.0) for aa in self._CODE1])
+        # compute correlation using Cruciani formula
+        v1 = take(lut, self.encoded[:-lag])
+        v2 = take(lut, self.encoded[lag:])
+        return sum(v1 * v2) / len(self.sequence)
 
     def cross_covariance(
         self,
@@ -903,7 +903,8 @@ class Peptide(typing.Sequence[str]):
         table = tables.HYDROPHOBICITY.get(scale)
         if table is None:
             raise ValueError(f"Invalid hydrophobicity scale: {scale!r}")
-        return sum(table.get(aa, 0.0) for aa in self.sequence) / len(self.sequence)
+        lut = array([table.get(aa, 0.0) for aa in self._CODE1], dtype="d")
+        return sumtake(lut, self.encoded) / len(self.sequence)
 
     def instability_index(self) -> float:
         """Compute the instability index of a protein sequence.

peptides/_npcompat.py

@@ -11,6 +11,16 @@ class array(array.array):
     def __new__(cls, values, dtype='f'):
         return super().__new__(cls, dtype, values)
 
+    def __mul__(self, other):
+        if not isinstance(other, array):
+            return NotImplemented
+        if len(self) != len(other):
+            raise ValueError("Cannot pairwise multiply arrays of different lengths")
+        return array(
+            [x1 * x2 for x1, x2 in zip(self, other)],
+            dtype=self.typecode
+        )
+
 
 def take(a, indices):
     """Take elements from an array.

tests/test_doctest.py

@@ -53,17 +53,12 @@ def load_tests(loader, tests, ignore):
     if sys.argv[0].endswith("green"):
         return tests
 
-    # doctests require `numpy` to run, which may not be available because
-    # it is a pain to get to work out-of-the-box on OSX
-    # if numpy is None:
-    #     return tests
-
     # recursively traverse all library submodules and load tests from them
     packages = [None, peptides]
 
     for pkg in iter(packages.pop, None):
         # import the base module and add it to the tests
-        globs = dict(numpy=numpy, peptides=peptides, **pkg.__dict__)
+        globs = dict(peptides=peptides, **pkg.__dict__)
         tests.addTests(
             doctest.DocTestSuite(
                 pkg,