Merge branch 'main' into python-312

.git-blame-ignore-revs

@@ -0,0 +1,3 @@
+# .git-blame-ignore-revs
+# Initial formatting with Ruff
+7c35332e15e8923992d77231fbcf2f19706bf625

.github/workflows/python-package.yml

@@ -33,9 +33,9 @@ jobs:
       run: |
         isort --check src
 
-    - name: Format check with black
+    - name: Format check with ruff
       run: |
-        black --check src
+        ruff format --check src
 
     - name: Security check with bandit
       run: |

.pre-commit-config.yaml

@@ -16,8 +16,8 @@ repos:
        entry: isort
        language: system
        types: [python]
-    -  id: black
-       name: black
-       entry: black
-       language: system
-       types: [python]
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.4.4
+  hooks:
+    - id: ruff-format
+      args: [ --check ]

Makefile

@@ -68,7 +68,7 @@ build: %:
 cqa:
 	flake8 src --count --select=E9,F63,F7,F82 --show-source --statistics
 	isort --profile black --check src
-	black --check src
+	ruff format --check src tests
 	bandit -ll -r src
 
 #=> test: execute tests
@@ -97,7 +97,7 @@ cqa:
 	flake8 src --show-source --statistics
 	pyright
 	isort --check src --profile black
-	black --check src
+	ruff format --check src
 	bandit -ll -r src
 
 #=> reformat: reformat code
@@ -108,13 +108,13 @@ reformat:
 ############################################################################
 #= UTILITY TARGETS
 
-#=> reformat: reformat code with yapf and commit
+#=> reformat: reformat code and commit
 .PHONY: reformat
 reformat:
 	@if ! git diff --cached --exit-code >/dev/null; then echo "Repository not clean" 1>&2; exit 1; fi
-	black src tests
+	ruff src tests
 	isort src tests
-	git commit -a -m "reformatted with black and isort"
+	git commit -a -m "reformatted with ruff and isort"
 
 #=> rename: rename files and substitute content for new repo name
 .PHONY: rename

docs/store.rst

@@ -24,9 +24,12 @@ To add a new sequence and/or aliases in a Python environment, construct a ``SeqR
    n_seqs_added, n_aliases_added = sr.store(sequence, nsaliases)
    print(n_seqs_added, n_aliases_added)
    # (1, 1)
+   sr.commit()
 
 ``store()`` returns a tuple containing the number of new sequences and aliases that were successfully added (the sha512t24u sequence hash is not counted as a new alias, because it is automatically added with a new sequence as the main sequence identifier).
 
+Note that the ``commit()`` method MUST be called before the end of an interpreter session for data to be durably committed to the database. ``store()`` only stages pending database additions, but only makes calls to ``commit()`` when the number of staged changes exceeds a (relatively large) threshold, for performance reasons.
+
 .. and this should be a "tip" admonition or something of that nature
 
 Load FASTA files

misc/docker/seqrepo.df

@@ -37,7 +37,6 @@ RUN pip3 install --upgrade \
     pygments \
     pysam \
     simplegeneric \
-    six \
     tqdm \
     traitlets \
     wcwidth \

pyproject.toml

@@ -12,7 +12,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
-    "License :: OSI Approved :: MIT License",
+    "License :: OSI Approved :: Apache Software License",
     "Operating System :: OS Independent",
 ]
 dynamic = ["version"]
@@ -22,7 +22,6 @@ dependencies = [
     "ipython ~= 8.4",
     "pysam ~= 0.22",
     "requests ~= 2.31",
-    "six ~= 1.16",
     "tqdm ~= 4.66",
     "yoyo-migrations ~= 8.2",
     "setuptools",  # pin until yoyo-migrations doesn't use pkg_resources
@@ -31,7 +30,6 @@ dependencies = [
 [project.optional-dependencies]
 dev = [
     "bandit ~= 1.7",
-    "black ~= 22.3",
     "build ~= 0.8",
     "flake8 ~= 4.0",
     "ipython ~= 8.4",
@@ -44,6 +42,7 @@ dev = [
     "pytest ~= 7.1",
     "pyright~=1.1",
     "requests_html ~= 0.10",
+    "ruff == 0.4.4",
     "tox ~= 3.25",
     "vcrpy",
 ]
@@ -118,9 +117,6 @@ exclude_lines = [
     "if __name__ == .__main__.:",
 ]
 
-[tool.black]
-line-length = 100
-
 [tool.isort]
 profile = "black"
 src_paths = ["src", "tests"]
@@ -135,3 +131,7 @@ disable = "R0913"
 
 [tool.pylint.format]
 max-line-length = 100
+
+[tool.ruff]
+src = ["src", "tests"]
+line-length = 100

src/biocommons/seqrepo/cli.py

@@ -11,8 +11,6 @@
 
 """
 
-from __future__ import division, print_function
-
 import argparse
 import datetime
 import gzip
@@ -527,7 +525,10 @@ def load(opts: argparse.Namespace) -> None:
             fh = io.open(fn, mode="rt", encoding="ascii")
         _logger.info("Opened " + fn)
         seq_bar = tqdm.tqdm(
-            FastaIter(fh), unit=" seqs", disable=disable_bar, leave=False  # type: ignore noqa: E501
+            FastaIter(fh),  # type: ignore
+            unit=" seqs",
+            disable=disable_bar,
+            leave=False,
         )
         for defline, seq in seq_bar:  # type: ignore
             n_seqs_seen += 1

src/biocommons/seqrepo/fastadir/bases.py

@@ -1,11 +1,8 @@
 import abc
 from typing import Optional
 
-import six
 
-
-@six.add_metaclass(abc.ABCMeta)
-class BaseReader:
+class BaseReader(metaclass=abc.ABCMeta):
     @abc.abstractmethod
     def fetch(self, seq_id: str, start: Optional[int] = None, end: Optional[int] = None) -> str:
         raise NotImplementedError
@@ -14,8 +11,7 @@ def __getitem__(self, ac: str) -> str:
         return self.fetch(ac)
 
 
-@six.add_metaclass(abc.ABCMeta)
-class BaseWriter:
+class BaseWriter(metaclass=abc.ABCMeta):
     @abc.abstractmethod
     def store(self, seq_id: str, seq: str) -> str:
         pass  # pragma: no cover

src/biocommons/seqrepo/fastadir/fabgz.py

@@ -6,8 +6,6 @@
 
 """
 
-from __future__ import unicode_literals
-
 import io
 import logging
 import os
@@ -19,7 +17,6 @@
 from types import TracebackType
 from typing import Optional, Type
 
-import six
 from pysam import FastaFile
 from typing_extensions import Self
 
@@ -48,15 +45,14 @@ def _get_bgzip_version(exe: str) -> str:
 
 def _find_bgzip() -> str:
     """return path to bgzip if found and meets version requirements, else exception"""
-    missing_file_exception = OSError if six.PY2 else FileNotFoundError
     min_bgzip_version = ".".join(map(str, min_bgzip_version_info))
     exe = os.environ.get("SEQREPO_BGZIP_PATH", shutil.which("bgzip") or "/usr/bin/bgzip")
 
     try:
         bgzip_version = _get_bgzip_version(exe)
     except AttributeError:
         raise RuntimeError("Didn't find version string in bgzip executable ({exe})".format(exe=exe))
-    except missing_file_exception:
+    except FileNotFoundError:
         raise RuntimeError(
             "{exe} doesn't exist; you need to install htslib and tabix "
             "(See https://github.com/biocommons/biocommons.seqrepo#requirements)".format(exe=exe)
@@ -119,7 +115,7 @@ def __init__(self, filename: str) -> None:
         super(FabgzWriter, self).__init__()
 
         self.filename = filename
-        self.fh = None
+        self._fh = None
         self._basepath, suffix = os.path.splitext(self.filename)
         if suffix != ".bgz":
             raise RuntimeError("Path must end with .bgz")

src/biocommons/seqrepo/fastadir/fastadir.py

@@ -81,9 +81,7 @@ def __init__(
         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:
@@ -142,9 +140,7 @@ def fetch(self, seq_id: str, start: Optional[int] = None, end: Optional[int] = N
         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
+                )
             )
 
     # ############################################################################

tests/test_cli.py

@@ -1,6 +1,4 @@
 # -*- coding: utf-8 -*-
-from __future__ import unicode_literals
-
 import io
 import os
 import tempfile

tests/test_fabgz.py

@@ -3,7 +3,6 @@
 import tempfile
 
 import pytest
-import six
 
 from biocommons.seqrepo.fastadir.fabgz import FabgzReader, FabgzWriter
 
@@ -19,18 +18,18 @@ def test_write_reread():
 
     # write sequences
     faw = FabgzWriter(fabgz_fn)
-    for seq_id, seq in six.iteritems(sequences):
+    for seq_id, seq in sequences.items():
         faw.store(seq_id, seq)
     # add twice to demonstrate non-redundancy
-    for seq_id, seq in six.iteritems(sequences):
+    for seq_id, seq in sequences.items():
         faw.store(seq_id, seq)
     faw.close()
 
     # now read them back
     far = FabgzReader(fabgz_fn)
-    assert far.filename.startswith(tmpdir.encode())
+    assert far.filename.startswith(tmpdir.encode())  # type: ignore
     assert set(far.keys()) == set(sequences.keys())
-    assert 5 == len(far), "expected 5 sequences"
+    assert 5 == len(far), "expected 5 sequences"  # type: ignore
     assert "l10" in far.keys()
     assert far["l10"] == seed * 10
     for seq_id in far.keys():

tests/test_fastaiter.py

@@ -1,6 +1,6 @@
+from io import StringIO
+
 import pytest
-import six
-from six.moves import StringIO
 
 from biocommons.seqrepo.fastaiter import FastaIter
 
@@ -12,7 +12,7 @@ def test_empty():
 
     # should return an empty generator
     with pytest.raises(StopIteration):
-        six.next(iterator)
+        next(iterator)
 
 
 def test_noheader():
@@ -22,54 +22,54 @@ def test_noheader():
 
     # should return an empty generator
     with pytest.raises(StopIteration):
-        six.next(iterator)
+        next(iterator)
 
 
 def test_single():
     data = StringIO(">seq1\nACGT\n")
 
     iterator = FastaIter(data)
 
-    header, seq = six.next(iterator)
+    header, seq = next(iterator)
     assert header == "seq1"
     assert seq == "ACGT"
 
     # should be empty now
     with pytest.raises(StopIteration):
-        six.next(iterator)
+        next(iterator)
 
 
 def test_multiple():
     data = StringIO(">seq1\nACGT\n>seq2\nTGCA\n\n>seq3\nTTTT")
 
     iterator = FastaIter(data)
 
-    header, seq = six.next(iterator)
+    header, seq = next(iterator)
     assert header == "seq1"
     assert seq == "ACGT"
 
-    header, seq = six.next(iterator)
+    header, seq = next(iterator)
     assert header == "seq2"
     assert seq == "TGCA"
 
-    header, seq = six.next(iterator)
+    header, seq = next(iterator)
     assert header == "seq3"
     assert seq == "TTTT"
 
     # should be empty now
     with pytest.raises(StopIteration):
-        six.next(iterator)
+        next(iterator)
 
 
 def test_multiline():
     data = StringIO(">seq1\nACGT\nTGCA")
 
     iterator = FastaIter(data)
 
-    header, seq = six.next(iterator)
+    header, seq = next(iterator)
     assert header == "seq1"
     assert seq == "ACGTTGCA"
 
     # should be empty now
     with pytest.raises(StopIteration):
-        six.next(iterator)
+        next(iterator)