fix(skills): exclude pull requests from GitHub issue research (#7516)

Co-authored-by: Willem Jiang <willem.jiang@gmail.com>

README.md

@@ -1729,6 +1729,8 @@ File reads accept raw repository-relative paths and preserve spaces, Unicode,
 `#`, `?`, and literal percent signs with either HTTP client.
 Directory listings ask for the repository's own default branch, so a repository that
 uses neither `main` nor `master` reports its current tree instead of a stale branch.
+The `issues` command excludes pull requests and follows additional pages to fill
+its requested issue limit; the `prs` command remains available for pull requests.
 
 Users can explicitly activate an enabled skill for a single turn by starting the request with `/skill-name`, for example `/data-analysis analyze uploads/foo.csv`. DeerFlow loads that skill's `SKILL.md` as hidden current-turn context while leaving the base prompt limited to skill metadata. Slash activation respects disabled skills, custom-agent skill whitelists, and existing channel commands such as `/new` and `/help`.
 

skills/public/github-deep-research/SKILL.md

@@ -56,6 +56,8 @@ python /path/to/skill/scripts/github_api.py <owner> <repo> tree
 - prs
 - releases
 
+The `issues` command returns repository issues only, excluding pull requests. It follows additional pages when needed to fill the requested issue limit; use `prs` to research pull requests separately.
+
 **Round 2 - Discovery (3-5 web_search)**
 - Get overview and identify key terms
 - Find official website/repo

skills/public/github-deep-research/scripts/github_api.py

@@ -172,16 +172,28 @@ class GitHubAPI:
         labels: Optional[str] = None,
     ) -> List[Dict]:
         """
-        Get repository issues.
+        Get repository issues, excluding pull requests.
 
         Args:
             state: 'open', 'closed', or 'all'
             labels: Comma-separated label names
         """
-        params = {"state": state, "per_page": min(limit, 100)}
+        limit = min(limit, 100)
+        if limit <= 0:
+            return []
+        params = {"state": state, "per_page": limit}
         if labels:
             params["labels"] = labels
-        return self._get(f"/repos/{owner}/{repo}/issues", params)
+        issues = []
+        page = 1
+        while len(issues) < limit:
+            items = self._get(f"/repos/{owner}/{repo}/issues", params)
+            issues.extend(item for item in items if "pull_request" not in item)
+            if len(items) < limit:
+                break
+            page += 1
+            params["page"] = page
+        return issues[:limit]
 
     def get_pull_requests(
         self, owner: str, repo: str, state: str = "all", limit: int = 30

tests/skills/test_github_deep_research.py

@@ -29,7 +29,7 @@ def fallback_client(monkeypatch):
         finally:
             connection.close()
         captured.update(url=request.full_url, timeout=timeout, headers=request.headers)
-        response = io.BytesIO(b'{"ok": true}')
+        response = io.BytesIO(captured.get("body", b'{"ok": true}'))
         response.status = 200
         return response
 
@@ -102,10 +102,11 @@ def test_fallback_search_preserves_query(fallback_client, query):
 
 def test_fallback_issues_preserves_filters(fallback_client):
     client, captured = fallback_client
+    captured["body"] = b'[{"number": 1}]'
 
     assert client.get_issues(
         "owner", "repo", state="open", limit=10, labels="bug,help wanted"
-    ) == {"ok": True}
+    ) == [{"number": 1}]
 
     assert parse_qs(urlsplit(captured["url"]).query) == {
         "state": ["open"],

tests/skills/test_github_research_issues.py

@@ -0,0 +1,127 @@
+"""Keep pull requests out of repository issue research, across both transports."""
+
+import io
+import json
+import runpy
+import sys
+import urllib.error
+import urllib.request
+from pathlib import Path
+from urllib.parse import parse_qs, urlsplit
+
+import pytest
+
+
+@pytest.fixture(params=["requests", "urllib"])
+def issue_client(request, monkeypatch):
+    if request.param == "urllib":
+        monkeypatch.setitem(sys.modules, "requests", None)
+    script = (
+        Path(__file__).resolve().parents[2]
+        / "skills/public/github-deep-research/scripts/github_api.py"
+    )
+    module = runpy.run_path(str(script))
+    pages = []
+    calls = []
+
+    if request.param == "urllib":
+
+        def fake_urlopen(prepared, timeout):
+            calls.append(prepared.full_url)
+            payload, status = pages.pop(0)
+            data = json.dumps(payload).encode()
+            if status >= 400:
+                raise urllib.error.HTTPError(prepared.full_url, status, "error", {}, io.BytesIO(data))
+            response = io.BytesIO(data)
+            response.status = status
+            return response
+
+        monkeypatch.setattr(urllib.request, "urlopen", fake_urlopen)
+    else:
+        requests = pytest.importorskip("requests")
+
+        def fake_send(session, prepared, **kwargs):
+            calls.append(prepared.url)
+            payload, status = pages.pop(0)
+            response = requests.Response()
+            response.status_code = status
+            response._content = json.dumps(payload).encode()
+            return response
+
+        monkeypatch.setattr(requests.Session, "send", fake_send)
+
+    return module["GitHubAPI"](), pages, calls
+
+
+def test_issue_limit_counts_issues_instead_of_pull_requests(issue_client):
+    client, pages, calls = issue_client
+    pages.extend([
+        ([{"number": 10, "pull_request": {}}, {"number": 9}], 200),
+        ([{"number": 8, "pull_request": {}}, {"number": 7}], 200),
+    ])
+
+    assert client.get_issues("owner", "repo", state="open", limit=2, labels="bug,help wanted") == [{"number": 9}, {"number": 7}]
+    assert len(calls) == 2
+    for index, url in enumerate(calls):
+        assert urlsplit(url).path == "/repos/owner/repo/issues"
+        parameters = parse_qs(urlsplit(url).query)
+        assert parameters["state"] == ["open"]
+        assert parameters["labels"] == ["bug,help wanted"]
+        assert parameters["per_page"] == ["2"]
+        assert parameters.get("page", ["1"]) == [str(index + 1)]
+
+
+def test_issue_search_continues_after_a_page_of_only_pull_requests(issue_client):
+    client, pages, calls = issue_client
+    pages.extend([
+        ([{"number": 5, "pull_request": {}}, {"number": 4, "pull_request": {}}], 200),
+        ([{"number": 3}], 200),
+    ])
+
+    assert client.get_issues("owner", "repo", limit=2) == [{"number": 3}]
+    assert len(calls) == 2
+
+
+def test_issue_search_stops_at_an_empty_page(issue_client):
+    client, pages, calls = issue_client
+    pages.extend([([{"number": 2, "pull_request": {}}], 200), ([], 200)])
+
+    assert client.get_issues("owner", "repo", limit=1) == []
+    assert len(calls) == 2
+
+
+def test_issue_search_does_not_fetch_an_unneeded_page(issue_client):
+    client, pages, calls = issue_client
+    pages.append(([{"number": 2}, {"number": 1}], 200))
+
+    assert client.get_issues("owner", "repo", limit=2) == [{"number": 2}, {"number": 1}]
+    assert len(calls) == 1
+
+
+def test_last_page_does_not_exceed_the_requested_issue_limit(issue_client):
+    client, pages, calls = issue_client
+    pages.extend([
+        ([{"number": 4}, {"number": 3, "pull_request": {}}], 200),
+        ([{"number": 2}, {"number": 1}], 200),
+    ])
+
+    assert client.get_issues("owner", "repo", limit=2) == [{"number": 4}, {"number": 2}]
+    assert len(calls) == 2
+
+
+@pytest.mark.parametrize("limit", [0, -1])
+def test_nonpositive_issue_limit_does_not_make_a_request(issue_client, limit):
+    client, pages, calls = issue_client
+    pages.append(([], 200))
+
+    assert client.get_issues("owner", "repo", limit=limit) == []
+    assert calls == []
+
+
+def test_later_page_failure_is_not_returned_as_partial_research(issue_client):
+    client, pages, calls = issue_client
+    pages.extend([([{"number": 3}, {"number": 2, "pull_request": {}}], 200), ({"message": "rate limited"}, 403)])
+
+    with pytest.raises(Exception, match="403"):
+        client.get_issues("owner", "repo", limit=2)
+    assert len(calls) == 2