chore(collection-seeding): bump all dependencies to latest versions (#1320)

## Summary

- `requests`: `>=2.33.1` → `>=2.34`
- `pytest`: `>=9.0.3` → `>=9.1`
- `responses`: `>=0.26.0` → `>=0.26.2`
- `ruff`: `>=0.9` → `>=0.15`
- Formatter applied after ruff update (line-length reformatting in
`rsv_nextclade_lineages.py` and its tests)

🤖 Generated with [Claude Code](https://claude.com/claude-code)

---------

Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: Fabian Engelniederhammer <92720311+fengelniederhammer@users.noreply.github.com>

Author: 4 people

collection-seeding/pixi.lock

@@ -8,7 +8,7 @@ platforms = ["linux-64", "osx-arm64", "osx-64", "linux-aarch64"]
 python = "3.13.*"
 
 [pypi-dependencies]
-requests = ">=2.33.1"
+requests = ">=2.34"
 
 [tasks]
 seed = "python seed.py"
@@ -17,9 +17,9 @@ seed-lineages-sample = "python seed.py --source covid-pango-lineages-sample"
 seed-resistance = "python seed.py --source covid-resistance-mutations"
 
 [feature.test.pypi-dependencies]
-pytest = ">=9.0.3"
-responses = ">=0.26.0"
-ruff = ">=0.9"
+pytest = ">=9.1"
+responses = ">=0.26.2"
+ruff = ">=0.15"
 
 [feature.test.tasks]
 test = "pytest"

collection-seeding/pixi.toml

@@ -162,7 +162,11 @@ def _extract_clades(node, parent_clade=None, accum_nuc=None, accum_aa=None):
     if "clade" in labels:
         # Flatten branch-level AA mutations into GENE:MUT strings for the "new" variant.
         branch_aa_flat = sorted(
-            [f"{gene}:{m}" for gene, gene_muts in branch_aa_by_gene.items() for m in gene_muts],
+            [
+                f"{gene}:{m}"
+                for gene, gene_muts in branch_aa_by_gene.items()
+                for m in gene_muts
+            ],
             key=lambda s: (s.split(":")[0], int(s.split(":")[1][1:-1])),
         )
         yield _CladeInfo(
@@ -272,7 +276,10 @@ def _format_accum_nuc(accum: dict[str, tuple[str, str]]) -> list[str]:
     E.g. {"982": ("A", "T")} → ["A982T"], meaning: at genome position 982 the reference
     has A and this clade (from root) has T.
     """
-    return [f"{ref}{pos}{cur}" for pos, (ref, cur) in sorted(accum.items(), key=lambda item: int(item[0]))]
+    return [
+        f"{ref}{pos}{cur}"
+        for pos, (ref, cur) in sorted(accum.items(), key=lambda item: int(item[0]))
+    ]
 
 
 def _format_accum_aa(accum: dict[tuple[str, str], tuple[str, str]]) -> list[str]:
@@ -281,4 +288,9 @@ def _format_accum_aa(accum: dict[tuple[str, str], tuple[str, str]]) -> list[str]
     E.g. {("F", "8"): ("T", "G")} → ["F:T8G"], meaning: in gene F at codon 8 the reference
     has T and this clade (from root) has G.
     """
-    return [f"{gene}:{ref}{pos}{cur}" for (gene, pos), (ref, cur) in sorted(accum.items(), key=lambda item: (item[0][0], int(item[0][1])))]
+    return [
+        f"{gene}:{ref}{pos}{cur}"
+        for (gene, pos), (ref, cur) in sorted(
+            accum.items(), key=lambda item: (item[0][0], int(item[0][1]))
+        )
+    ]

collection-seeding/sources/rsv_nextclade_lineages.py

@@ -479,7 +479,11 @@ def test_full_aa_sorted_by_gene_then_position():
     cols = _build_collections(SORT_TREE, "rsvA", "RSV-A", "#nextclade-lineage")
     a = next(c for c in cols if c["name"] == "A")
     full_aa = next(v for v in a["variants"] if v["name"] == "Amino acid substitutions")
-    assert full_aa["filterObject"]["aminoAcidMutations"] == ["F:T8A", "F:K124N", "G:T4N"]
+    assert full_aa["filterObject"]["aminoAcidMutations"] == [
+        "F:T8A",
+        "F:K124N",
+        "G:T4N",
+    ]
 
 
 # --- source class attributes ---