style: add ruff formatting

.gitignore

@@ -1,3 +1,4 @@
+*.DS_Store
 *.bak
 *.egg
 *.egg-info

docs/utils.py

@@ -7,7 +7,7 @@
 
 def _format_time(timespan, precision=3):
     """Formats the timespan in a human readable form
-    
+
     >>> _format_time(0.35)
     '350 ms'
 
@@ -26,31 +26,31 @@ def _format_time(timespan, precision=3):
     if timespan >= 60.0:
         # we have more than a minute, format that in a human readable form
         # Idea from http://snipplr.com/view/5713/
-        parts = [("d", 60*60*24),("h", 60*60),("min", 60), ("s", 1)]
+        parts = [("d", 60 * 60 * 24), ("h", 60 * 60), ("min", 60), ("s", 1)]
         time = []
         leftover = timespan
         for suffix, length in parts:
             value = int(leftover / length)
             if value > 0:
                 leftover = leftover % length
-                time.append(u'%s%s' % (str(value), suffix))
+                time.append("%s%s" % (str(value), suffix))
             if leftover < 1:
                 break
         return " ".join(time)
 
-    units = [u"s", u"ms", u"us", u"ns"]  # the save value   
+    units = ["s", "ms", "us", "ns"]  # the save value
     scaling = [1, 1e3, 1e6, 1e9]
-        
+
     if timespan > 0.0:
         order = min(-int(math.floor(math.log10(timespan)) // 3), 3)
     else:
         order = 3
-    return u"%.*g %s" % (precision, timespan * scaling[order], units[order])
+    return "%.*g %s" % (precision, timespan * scaling[order], units[order])
 
 
 def hex_to_base64url(s):
     return urlsafe_b64encode(unhexlify(s)).decode("ascii")
 
+
 def base64url_to_hex(s):
     return hexlify(urlsafe_b64decode(s)).decode("ascii")
-

misc/threading-tests/threading-verification.py

@@ -30,14 +30,12 @@
 
 
 def fetch_in_thread(sr, nsa):
-    """fetch a sequence in a thread
-
-    """
+    """fetch a sequence in a thread"""
 
     def fetch_seq(q, nsa):
         pid, ppid = os.getpid(), os.getppid()
         q.put((pid, ppid, sr[nsa]))
-    
+
     q = Queue()
     p = Process(target=fetch_seq, args=(q, nsa))
     p.start()
@@ -46,11 +44,13 @@ def fetch_seq(q, nsa):
 
     assert pid != ppid, "sequence was not fetched from thread"
     return pid, ppid, seq
-
 
-def make_seqrepo(writeable):    
+
+def make_seqrepo(writeable):
     sr = SeqRepo("/tmp/sr", writeable=True)
-    sr.store("SMELLASSWEET", [{"namespace": "en", "alias": "rose"}, {"namespace": "fr", "alias": "rose"}])
+    sr.store(
+        "SMELLASSWEET", [{"namespace": "en", "alias": "rose"}, {"namespace": "fr", "alias": "rose"}]
+    )
 
     if writeable is False:
         del sr
@@ -70,6 +70,6 @@ def _test(sr):
     print("sys.platform: " + sys.platform)
     print("sys.version: " + sys.version.replace("\n", " "))
     print("sqlite3.sqlite_version: " + sqlite3.sqlite_version)
-    
+
     _test(make_seqrepo(writeable=False))
     _test(make_seqrepo(writeable=True))

pyproject.toml

@@ -29,20 +29,16 @@ dependencies = [
 
 [project.optional-dependencies]
 dev = [
-    "bandit ~= 1.7",
-    "black ~= 22.3",
     "build ~= 0.8",
-    "flake8 ~= 4.0",
     "ipython ~= 8.4",
-    "isort ~= 5.10",
     "mypy-extensions ~= 1.0",
     "pre-commit ~= 3.4",
-    "pylint ~= 2.14",
     "pytest-cov ~= 4.1",
     "pytest-optional-tests",
     "pytest ~= 7.1",
     "pyright~=1.1",
     "requests_html ~= 0.10",
+    "ruff ~= 0.4.4",
     "tox ~= 3.25",
     "vcrpy",
 ]
@@ -117,20 +113,68 @@ exclude_lines = [
     "if __name__ == .__main__.:",
 ]
 
-[tool.black]
-line-length = 100
-
-[tool.isort]
-profile = "black"
-src_paths = ["src", "tests"]
-
 [tool.pyright]
 include = ["src", "tests"]
 
+[tool.ruff]
+src = ["src", "test"]
+line-length = 100
 
-[tool.pylint.'MESSAGES CONTROL']
-disable = "R0913"
+[tool.ruff.lint]
+select = [
+    "F",
+    "E",
+    "W",
+    "I",
+    "N",
+    "UP",
+    "YTT",
+    "S",
+    "B",
+    "A",
+    "C4",
+    "DTZ",
+    "EM",
+    "LOG",
+    "G",
+    "PIE",
+    "PT",
+    "RSE",
+    "RET",
+    "SIM",
+    "ARG",
+    "PTH",
+    "PL",
+    "TRY",
+    "PERF",
+    "FURB",
+    "RUF",
+]
+fixable = [
+    "F401",
+    "F541",
+    "I",
+    "D",
+    "UP",
+    "B",
+    "C4",
+    "EM",
+    "PIE",
+    "PT",
+    "RSE",
+    "RET",
+    "SIM",
+    "PERF",
+    "FURB",
+    "RUF",
+]
+ignore = [
+    # ignore for compatibility with formatter
+    "W191", "E111", "E114", "E117", "S321",
+    # other
+    "PLR0913",
+]
 
+[tool.ruff.lint.per-file-ignores]
+"tests/*" = ["S101"]
 
-[tool.pylint.format]
-max-line-length = 100

setup.py

@@ -1,2 +1,3 @@
 from setuptools import setup
+
 setup(use_scm_version=True)

src/biocommons/seqrepo/fastadir/fastadir.py

@@ -75,9 +75,7 @@ def __init__(self, root_dir, writeable=False, check_same_thread=True, fd_cache_s
         if schema_version != expected_schema_version:
             raise RuntimeError(
                 """Upgrade required: Database schema
-            version is {} and code expects {}""".format(
-                    schema_version, expected_schema_version
-                )
+            version is {} and code expects {}""".format(schema_version, expected_schema_version)
             )
 
         if fd_cache_size == 0:
@@ -136,9 +134,7 @@ def fetch(self, seq_id, start=None, end=None):
         if self._writing and self._writing["relpath"] == rec["relpath"]:
             _logger.warning(
                 """Fetching from file opened for writing;
-            closing first ({})""".format(
-                    rec["relpath"]
-                )
+            closing first ({})""".format(rec["relpath"])
             )
             self.commit()
 

src/biocommons/seqrepo/seqaliasdb/seqaliasdb.py

@@ -53,8 +53,9 @@ def __init__(
         # if we're not at the expected schema version for this code, bail
         if schema_version != expected_schema_version:  # pragma: no cover
             raise RuntimeError(
-                "Upgrade required: Database schema"
-                "version is {} and code expects {}".format(schema_version, expected_schema_version)
+                "Upgrade required: Database schema" "version is {} and code expects {}".format(
+                    schema_version, expected_schema_version
+                )
             )
 
     # ############################################################################