Add CodeQL workflow for GitHub code scanning and fix few bugs it detected

.github/workflows/codeql.yml

@@ -0,0 +1,42 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+  schedule:
+    - cron: "31 5 * * 5"
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ python ]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v2
+        with:
+          languages: ${{ matrix.language }}
+          queries: +security-and-quality
+          config-file: codeql.yml
+
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v2
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v2
+        with:
+          category: "/language:${{ matrix.language }}"

codeql.yml

@@ -0,0 +1,4 @@
+paths-ignore:
+  - dandi/_version.py
+  - dandi/due.py
+  - versioneer.py

dandi/cli/tests/test_command.py

@@ -46,9 +46,11 @@ def test_no_heavy_imports():
         [
             sys.executable,
             "-c",
-            "import sys; "
-            "import dandi.cli.command; "
-            "print(','.join(set(m.split('.')[0] for m in sys.modules)));",
+            (
+                "import sys; "
+                "import dandi.cli.command; "
+                "print(','.join(set(m.split('.')[0] for m in sys.modules)));"
+            ),
         ],
         env=env,
         stdout=PIPE,

dandi/cli/tests/test_ls.py

@@ -91,8 +91,10 @@ def test_ls_path_url():
         [
             "-f",
             "yaml",
-            "https://api.dandiarchive.org/api/dandisets/000027/versions/draft"
-            "/assets/?path=sub-RAT123/",
+            (
+                "https://api.dandiarchive.org/api/dandisets/000027/versions/draft"
+                "/assets/?path=sub-RAT123/"
+            ),
         ],
     )
     assert r.exit_code == 0, r.output

dandi/dandiapi.py

@@ -1250,7 +1250,7 @@ def __str__(self) -> str:
 
     @classmethod
     def from_base_data(
-        self,
+        cls,
         client: "DandiAPIClient",
         data: Dict[str, Any],
         metadata: Optional[Dict[str, Any]] = None,

dandi/support/pyout.py

@@ -36,11 +36,11 @@ def naturalsize(v):
     return humanize.naturalsize(v)
 
 
-def datefmt(v, fmt=u"%Y-%m-%d/%H:%M:%S"):
+def datefmt(v, fmt="%Y-%m-%d/%H:%M:%S"):
     if isinstance(v, datetime.datetime):
         return v.strftime(fmt)
     else:
-        time.strftime(fmt, time.localtime(v))
+        return time.strftime(fmt, time.localtime(v))
 
 
 # def empty_for_none(v):
@@ -71,8 +71,8 @@ def counts(values):
     color=dict(
         interval=[
             [0, 1024, "blue"],
-            [1024, 1024 ** 2, "green"],
-            [1024 ** 2, None, "red"],
+            [1024, 1024**2, "green"],
+            [1024**2, None, "red"],
         ]
     ),
     aggregate=lambda x: naturalsize(sum(x)),

dandi/tests/fixtures.py

@@ -8,7 +8,6 @@
 import re
 import shutil
 from subprocess import DEVNULL, check_output, run
-import tempfile
 from time import sleep
 from typing import TYPE_CHECKING, Any, Callable, Dict, Iterator, List, Optional, Union
 from uuid import uuid4
@@ -246,30 +245,19 @@ def get_gitrepo_fixture(
     url: str,
     committish: Optional[str] = None,
     scope: Scope = "session",
-) -> Callable[[], Iterator[str]]:
+) -> Callable[[pytest.TempPathFactory], str]:
 
     if committish:
         raise NotImplementedError()
 
     @pytest.fixture(scope=scope)
-    def fixture() -> Iterator[str]:
+    def fixture(tmp_path_factory: pytest.TempPathFactory) -> str:
         skipif.no_network()
         skipif.no_git()
-
-        path = tempfile.mktemp()  # not using pytest's tmpdir fixture to not
-        # collide in different scopes etc. But we
-        # would need to remove it ourselves
+        path = str(tmp_path_factory.mktemp("gitrepo"))
         lgr.debug("Cloning %r into %r", url, path)
-        try:
-            runout = run(["git", "clone", "--depth=1", url, path])
-            if runout.returncode:
-                raise RuntimeError(f"Failed to clone {url} into {path}")
-            yield path
-        finally:
-            try:
-                shutil.rmtree(path)
-            except BaseException as exc:
-                lgr.warning("Failed to remove %s - using Windows?: %s", path, exc)
+        run(["git", "clone", "--depth=1", url, path], check=True)
+        return path
 
     return fixture