switch to pytest

.pre-commit-config.yaml

@@ -1,13 +1,13 @@
 repos:
-  - repo: https://github.com/pre-commit/mirrors-yapf
-    rev: v0.30.0
+  - repo: https://github.com/google/yapf
+    rev: v0.40.2
     hooks:
       - id: yapf
   - repo: https://github.com/pycqa/flake8
-    rev: 3.9.0
+    rev: 6.1.0
     hooks:
       - id: flake8
   - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
       - id: isort

Makefile

@@ -2,11 +2,10 @@
 
 test:
 	rm -f .coverage
-	nosetests --verbose --with-coverage --cover-package ngs_tools tests/*
+	pytest -v --cov=ngs_tools tests
 
 check:
-	flake8 ngs_tools && echo OK
-	yapf -r --diff ngs_tools && echo OK
+	pre-commit run --all-files
 
 build:
 	python setup.py sdist

dev-requirements.txt

@@ -1,11 +1,12 @@
 bumpversion==0.6.0
-coverage==5.1
-flake8==3.9.0
-nose==1.3.7
-pre-commit==2.4.0
+coverage>=5.1
+flake8==6.1.0
+pre-commit>=2.4.0
+pytest>=7.4.3
+pytest-cov>=4.1.0
 sphinx>=3.3.1
 sphinx-autoapi>=1.5.1
 sphinx_rtd_theme>=0.5.0
 twine>=2.0.0
 wheel==0.34.2
-yapf==0.30.0
+yapf==0.40.2

ngs_tools/sequence.py

@@ -54,10 +54,11 @@
     'V': 'B',
 }
 NUCLEOTIDE_MASKS = {
-    n: np.array([
-        _n in NUCLEOTIDES_AMBIGUOUS.get(n, [n]) for _n in NUCLEOTIDES_STRICT
-    ],
-                dtype=bool)
+    n:
+        np.array([
+            _n in NUCLEOTIDES_AMBIGUOUS.get(n, [n]) for _n in NUCLEOTIDES_STRICT
+        ],
+                 dtype=bool)
     for n in NUCLEOTIDES
 }
 MASK_TO_NUCLEOTIDE = {tuple(mask): n for n, mask in NUCLEOTIDE_MASKS.items()}