Add support for protein alphabets in `lightmotif-py` module

lightmotif-py/Cargo.toml

@@ -14,6 +14,7 @@ keywords = ["bioinformatics", "python", "bindings", "pssm"]
 [lib]
 crate-type = ["cdylib", "rlib"]
 path = "lightmotif/lib.rs"
+doctest = false
 
 [dependencies.lightmotif]
 path = "../lightmotif"

lightmotif-py/lightmotif/tests/__init__.py

-from . import test_pipeline, test_sequence, test_pvalue
+from . import test_doctest, test_pipeline, test_sequence, test_pvalue
 
 
 def load_tests(loader, suite, pattern):
     suite.addTests(loader.loadTestsFromModule(test_pipeline))
     suite.addTests(loader.loadTestsFromModule(test_sequence))
     suite.addTests(loader.loadTestsFromModule(test_pvalue))
+    suite.addTests(loader.loadTestsFromModule(test_doctest))
     return suite

lightmotif-py/lightmotif/tests/test_doctest.py

+# coding: utf-8
+"""Test doctest contained tests in every file of the module.
+"""
+
+import doctest
+import importlib
+import pkgutil
+import re
+import shutil
+import sys
+import types
+import warnings
+from unittest import mock
+
+import lightmotif
+
+def _load_tests_from_module(tests, module, globs, setUp=None, tearDown=None):
+    """Load tests from module, iterating through submodules."""
+    for attr in (getattr(module, x) for x in dir(module) if not x.startswith("_")):
+        if isinstance(attr, types.ModuleType):
+            suite = doctest.DocTestSuite(
+                attr,
+                globs,
+                setUp=setUp,
+                tearDown=tearDown,
+                optionflags=+doctest.ELLIPSIS,
+            )
+            tests.addTests(suite)
+    return tests
+
+
+def load_tests(loader, tests, ignore):
+    """`load_test` function used by unittest to find the doctests."""
+
+    def setUp(self):
+        warnings.simplefilter("ignore")
+
+    def tearDown(self):
+        warnings.simplefilter(warnings.defaultaction)
+        
+    # doctests are not compatible with `green`, so we may want to bail out
+    # early if `green` is running the tests
+    if sys.argv[0].endswith("green"):
+        return tests
+
+    # recursively traverse all library submodules and load tests from them
+    packages = [None, lightmotif]
+    for pkg in iter(packages.pop, None):
+        for (_, subpkgname, subispkg) in pkgutil.walk_packages(pkg.__path__):
+            # do not import __main__ module to avoid side effects!
+            if subpkgname == "__main__" or subpkgname.startswith("tests") or subpkgname.startswith("cli"):
+                continue
+            # import the submodule and add it to the tests
+            module = importlib.import_module(".".join([pkg.__name__, subpkgname]))
+            globs = dict(lightmotif=lightmotif, **module.__dict__)
+            tests.addTests(
+                doctest.DocTestSuite(
+                    module,
+                    globs=globs,
+                    setUp=setUp,
+                    tearDown=tearDown,
+                    optionflags=+doctest.ELLIPSIS,
+                )
+            )
+            # if the submodule is a package, we need to process its submodules
+            # as well, so we add it to the package queue
+            if subispkg and subpkgname != "tests":
+                packages.append(module)
+
+    return tests

lightmotif-py/lightmotif/tests/test_pvalue.py

@@ -6,7 +6,7 @@ class TestMA0045(unittest.TestCase):
     
     @classmethod
     def setUpClass(cls):
-        cls.ma0045 = lightmotif.CountMatrix("ACTG", {
+        cls.ma0045 = lightmotif.CountMatrix({
             "A": [3, 7, 9, 3, 11, 11, 11, 3, 4, 3, 8, 8, 9, 9, 11, 2],
             "C": [5, 0, 1, 6, 0, 0, 0, 3, 1, 4, 5, 1, 0, 5, 0, 7],
             "T": [2, 4, 3, 1, 0, 1, 1, 6, 1, 1, 0, 1, 3, 0, 0, 5],
@@ -18,4 +18,4 @@ class TestMA0045(unittest.TestCase):
         self.assertAlmostEqual(self.ma0045.pvalue(8.7708), 0.00032910, places=5)
 
     def test_score(self):
-        self.assertAlmostEqual(self.ma0045.score(0.00033), 8.756855, places=5)
\ No newline at end of file
+        self.assertAlmostEqual(self.ma0045.score(0.00033), 8.756855, places=5)