chore(deps-dev): bump ruff from 0.15.13 to 0.15.15 in /loculus-silo in the minorandpatch group (#6591)

Bumps the minorandpatch group in /loculus-silo with 1 update:
[ruff](https://github.com/astral-sh/ruff).

Updates `ruff` from 0.15.13 to 0.15.15
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/astral-sh/ruff/releases">ruff's
releases</a>.</em></p>
<blockquote>
<h2>0.15.15</h2>
<h2>Release Notes</h2>
<p>Released on 2026-05-28.</p>
<h3>Preview features</h3>
<ul>
<li>Fix Markdown closing fence handling (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25310">#25310</a>)</li>
<li>[<code>pyflakes</code>] Report duplicate imports in
<code>typing.TYPE_CHECKING</code> block (<code>F811</code>) (<a
href="https://redirect.github.com/astral-sh/ruff/pull/22560">#22560</a>)</li>
</ul>
<h3>Bug fixes</h3>
<ul>
<li>[<code>pyflakes</code>] Treat function-scope bare annotations as
locals per PEP 526 (<code>F821</code>) (<a
href="https://redirect.github.com/astral-sh/ruff/pull/21540">#21540</a>)</li>
</ul>
<h3>Performance</h3>
<ul>
<li>Avoid redundant <code>TokenValue</code> drops in the lexer (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25300">#25300</a>)</li>
<li>Reduce memory usage by dropping token-excess capacity and improve
performance by approximating the initial tokens <code>Vec</code> size
(<a
href="https://redirect.github.com/astral-sh/ruff/pull/25354">#25354</a>)</li>
<li>Use <code>ThinVec</code> in AST to shrink <code>Stmt</code> (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25361">#25361</a>)</li>
</ul>
<h3>Documentation</h3>
<ul>
<li>Fix <code>line-length</code> example for <code>--config</code>
option (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25389">#25389</a>)</li>
<li>[<code>flake8-comprehensions</code>] Document
<code>RecursionError</code> edge case in <code>__len__</code>
(<code>C416</code>) (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25286">#25286</a>)</li>
<li>[<code>mccabe</code>] Improve example (<code>C901</code>) (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25287">#25287</a>)</li>
<li>[<code>pyupgrade</code>] Clarify fix safety docs
(<code>UP007</code>, <code>UP045</code>) (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25288">#25288</a>)</li>
<li>[<code>refurb</code>] Document <code>FURB192</code> exception change
for empty sequences (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25317">#25317</a>)</li>
<li>[<code>ruff</code>] Document false negative for user-defined types
(<code>RUF013</code>) (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25289">#25289</a>)</li>
</ul>
<h3>Formatter</h3>
<ul>
<li>Fix formatting of lambdas nested within f-strings (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25398">#25398</a>)</li>
</ul>
<h3>Server</h3>
<ul>
<li>Return code action for <code>codeAction/resolve</code> requests that
contain no or no valid URL (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25365">#25365</a>)</li>
</ul>
<h3>Other changes</h3>
<ul>
<li>Expand semantic syntax errors for invalid walruses (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25415">#25415</a>)</li>
</ul>
<h3>Contributors</h3>
<ul>
<li><a
href="https://github.com/chirizxc"><code>@​chirizxc</code></a></li>
<li><a href="https://github.com/ntBre"><code>@​ntBre</code></a></li>
<li><a
href="https://github.com/adityasingh2400"><code>@​adityasingh2400</code></a></li>
<li><a
href="https://github.com/charliermarsh"><code>@​charliermarsh</code></a></li>
<li><a
href="https://github.com/fallintoplace"><code>@​fallintoplace</code></a></li>
<li><a
href="https://github.com/martin-schlossarek"><code>@​martin-schlossarek</code></a></li>
<li><a
href="https://github.com/MichaReiser"><code>@​MichaReiser</code></a></li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a
href="https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md">ruff's
changelog</a>.</em></p>
<blockquote>
<h2>0.15.15</h2>
<p>Released on 2026-05-28.</p>
<h3>Preview features</h3>
<ul>
<li>Fix Markdown closing fence handling (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25310">#25310</a>)</li>
<li>[<code>pyflakes</code>] Report duplicate imports in
<code>typing.TYPE_CHECKING</code> block (<code>F811</code>) (<a
href="https://redirect.github.com/astral-sh/ruff/pull/22560">#22560</a>)</li>
</ul>
<h3>Bug fixes</h3>
<ul>
<li>[<code>pyflakes</code>] Treat function-scope bare annotations as
locals per PEP 526 (<code>F821</code>) (<a
href="https://redirect.github.com/astral-sh/ruff/pull/21540">#21540</a>)</li>
</ul>
<h3>Performance</h3>
<ul>
<li>Avoid redundant <code>TokenValue</code> drops in the lexer (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25300">#25300</a>)</li>
<li>Reduce memory usage by dropping token-excess capacity and improve
performance by approximating the initial tokens <code>Vec</code> size
(<a
href="https://redirect.github.com/astral-sh/ruff/pull/25354">#25354</a>)</li>
<li>Use <code>ThinVec</code> in AST to shrink <code>Stmt</code> (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25361">#25361</a>)</li>
</ul>
<h3>Documentation</h3>
<ul>
<li>Fix <code>line-length</code> example for <code>--config</code>
option (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25389">#25389</a>)</li>
<li>[<code>flake8-comprehensions</code>] Document
<code>RecursionError</code> edge case in <code>__len__</code>
(<code>C416</code>) (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25286">#25286</a>)</li>
<li>[<code>mccabe</code>] Improve example (<code>C901</code>) (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25287">#25287</a>)</li>
<li>[<code>pyupgrade</code>] Clarify fix safety docs
(<code>UP007</code>, <code>UP045</code>) (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25288">#25288</a>)</li>
<li>[<code>refurb</code>] Document <code>FURB192</code> exception change
for empty sequences (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25317">#25317</a>)</li>
<li>[<code>ruff</code>] Document false negative for user-defined types
(<code>RUF013</code>) (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25289">#25289</a>)</li>
</ul>
<h3>Formatter</h3>
<ul>
<li>Fix formatting of lambdas nested within f-strings (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25398">#25398</a>)</li>
</ul>
<h3>Server</h3>
<ul>
<li>Return code action for <code>codeAction/resolve</code> requests that
contain no or no valid URL (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25365">#25365</a>)</li>
</ul>
<h3>Other changes</h3>
<ul>
<li>Expand semantic syntax errors for invalid walruses (<a
href="https://redirect.github.com/astral-sh/ruff/pull/25415">#25415</a>)</li>
</ul>
<h3>Contributors</h3>
<ul>
<li><a
href="https://github.com/chirizxc"><code>@​chirizxc</code></a></li>
<li><a href="https://github.com/ntBre"><code>@​ntBre</code></a></li>
<li><a
href="https://github.com/adityasingh2400"><code>@​adityasingh2400</code></a></li>
<li><a
href="https://github.com/charliermarsh"><code>@​charliermarsh</code></a></li>
<li><a
href="https://github.com/fallintoplace"><code>@​fallintoplace</code></a></li>
<li><a
href="https://github.com/martin-schlossarek"><code>@​martin-schlossarek</code></a></li>
<li><a
href="https://github.com/MichaReiser"><code>@​MichaReiser</code></a></li>
<li><a
href="https://github.com/Ruchir28"><code>@​Ruchir28</code></a></li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/astral-sh/ruff/commit/db5aa0a5f1b92cb91d910bf0866a967554dd94f5"><code>db5aa0a</code></a>
Bump 0.15.15 (<a
href="https://redirect.github.com/astral-sh/ruff/issues/25431">#25431</a>)</li>
<li><a
href="https://github.com/astral-sh/ruff/commit/366fe21ba369ccdd01eb99c1043c9a969c99230b"><code>366fe21</code></a>
[ty] Improve diagnostics for syntax errors in forward annotations (<a
href="https://redirect.github.com/astral-sh/ruff/issues/25158">#25158</a>)</li>
<li><a
href="https://github.com/astral-sh/ruff/commit/e2e1e647d182b8567845039c9a65fb0608a4dcfc"><code>e2e1e64</code></a>
[ty] Remove excess capacity from more Salsa cached collections (<a
href="https://redirect.github.com/astral-sh/ruff/issues/25411">#25411</a>)</li>
<li><a
href="https://github.com/astral-sh/ruff/commit/1bd77e1646f2213d86b8da215f08279187867d72"><code>1bd77e1</code></a>
[ty] Use diagnostic message as tie breaker when sorting (<a
href="https://redirect.github.com/astral-sh/ruff/issues/25424">#25424</a>)</li>
<li><a
href="https://github.com/astral-sh/ruff/commit/7e1bc1e75f15795f12c846294b13df4535f2abbf"><code>7e1bc1e</code></a>
Add agent skills for working on ty (<a
href="https://redirect.github.com/astral-sh/ruff/issues/25422">#25422</a>)</li>
<li><a
href="https://github.com/astral-sh/ruff/commit/574e10752f8cfa9e0cdbe3b01e96c4380950469b"><code>574e107</code></a>
Expand semantic syntax errors for invalid walruses (<a
href="https://redirect.github.com/astral-sh/ruff/issues/25415">#25415</a>)</li>
<li><a
href="https://github.com/astral-sh/ruff/commit/4a7ca062fccd80443a43aa61e5dc7e5858e88dc1"><code>4a7ca06</code></a>
[ty] Display docs for matching parameter when hovering over the name of
an ar...</li>
<li><a
href="https://github.com/astral-sh/ruff/commit/54327092dbfe455040690d63bb1e5e4b5f551239"><code>5432709</code></a>
Refine a few agents instructions (<a
href="https://redirect.github.com/astral-sh/ruff/issues/25423">#25423</a>)</li>
<li><a
href="https://github.com/astral-sh/ruff/commit/3cb09eba689ebb49e799131092121928cc789c18"><code>3cb09eb</code></a>
[ty] Support <code>typing.TypeForm</code> (<a
href="https://redirect.github.com/astral-sh/ruff/issues/25334">#25334</a>)</li>
<li><a
href="https://github.com/astral-sh/ruff/commit/c8cd59f189f2b6f55d542b29bddb953622add6fc"><code>c8cd59f</code></a>
[ty] Infer class attributes assigned by metaclass initialization (<a
href="https://redirect.github.com/astral-sh/ruff/issues/25342">#25342</a>)</li>
<li>Additional commits viewable in <a
href="https://github.com/astral-sh/ruff/compare/0.15.13...0.15.15">compare
view</a></li>
</ul>
</details>
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loculus-silo/pyproject.toml

@@ -13,7 +13,7 @@ silo-import = "silo_import.__main__:main"
 
 [project.optional-dependencies]
 test = ["pytest", "mypy",
-    "ruff==0.15.13",]
+    "ruff==0.15.15",]
 
 [build-system]
 requires = ["hatchling"]

loculus-silo/src/silo_import/config.py

@@ -32,7 +32,7 @@ def from_env(cls) -> ImporterConfig:
         lineage_definitions_raw = env.get("LINEAGE_DEFINITIONS")
         lineage_definitions: dict[str, dict[int, str]] | None = None
         if lineage_definitions_raw:
-            try:
+            try:  # noqa: PLW0717
                 data = json.loads(lineage_definitions_raw)
                 lineage_definitions = {}
                 for key, value in data.items():

loculus-silo/src/silo_import/decompressor.py

@@ -47,7 +47,7 @@ def analyze_ndjson(
         {name: set() for name in hierarchical_filters} if hierarchical_filters else {}
     )
 
-    try:
+    try:  # noqa: PLW0717
         for record in orjsonl.stream(path):
             record_count += 1
             metadata = record.get("metadata", {})  # type: ignore

loculus-silo/src/silo_import/download_manager.py

@@ -106,7 +106,7 @@ def _download_file(
     if etag and etag != "0":
         headers["If-None-Match"] = etag
 
-    try:
+    try:  # noqa: PLW0717
         session = requests.Session()
         session.headers.update(headers)
         response = session.get(url, timeout=timeout, stream=True)
@@ -167,7 +167,7 @@ def download_release(
         data_path = download_dir / DATA_FILENAME
         transformed_path = download_dir / TRANSFORMED_DATA_FILENAME
 
-        try:
+        try:  # noqa: PLW0717
             # Download data from backend
             logger.info("Requesting released data from %s", config.released_data_endpoint)
             response = self.download_func(

loculus-silo/src/silo_import/instruct_silo.py

@@ -14,7 +14,7 @@ def __init__(self, silo_binary: Path, preprocessing_config: Path) -> None:
 
     def run_preprocessing(self, timeout_seconds: int) -> None:
         logger.info("Starting SILO preprocessing")
-        try:
+        try:  # noqa: PLW0717
             result = subprocess.run(  # noqa: S603
                 [str(self._silo_binary), "preprocessing"],
                 env={"SILO_PREPROCESSING_CONFIG": str(self._preprocessing_config)},

loculus-silo/src/silo_import/lineage.py

@@ -81,7 +81,7 @@ def fetch_updated_hierarchy(
     url = f"{service_url.rstrip('/')}/silo-lineage"
     logger.info("Fetching %s hierarchy over %d values", file_base, len(values))
     sorted_values = sorted(values)
-    try:
+    try:  # noqa: PLW0717
         response = _post_silo_lineage(url, sorted_values)
         if response.status_code == codes.request_entity_too_large:
             logger.warning(