Ensure bots propagate through concat (#156)

Author: choldgraf

github_activity/github_activity.py

@@ -134,7 +134,8 @@ def get_activity(
     -------
     query_data : pandas DataFrame
         A munged collection of data returned from your query. This
-        will be a combination of issues and PRs.
+        will be a combination of issues and PRs. The DataFrame has a
+        `bot_users` attribute containing the set of detected bot usernames.
     """
 
     org, repo = _parse_target(target)
@@ -206,13 +207,16 @@ def get_activity(
     # Query for both opened and closed issues/PRs in this window
     print(f"Running search query:\n{search_query}\n\n", file=sys.stderr)
     query_data = []
+    all_bot_users = set()
     for activity_type in ["created", "closed"]:
         ii_search_query = (
             search_query + f" {activity_type}:{since_dt_str}..{until_dt_str}"
         )
         qu = GitHubGraphQlQuery(ii_search_query, auth=auth)
         qu.request()
         query_data.append(qu.data)
+        # Collect bot users from each query
+        all_bot_users.update(qu.data.attrs.get("bot_users", set()))
 
     query_data = (
         pd.concat(query_data).drop_duplicates(subset=["id"]).reset_index(drop=True)
@@ -223,9 +227,12 @@ def get_activity(
     query_data.until_dt_str = until_dt_str
     query_data.since_is_git_ref = since_is_git_ref
     query_data.until_is_git_ref = until_is_git_ref
+    # Restore bot_users in attrs (lost during concat)
+    query_data.attrs["bot_users"] = all_bot_users
 
     if cache:
         _cache_data(query_data, cache)
+
     return query_data
 
 
@@ -462,15 +469,34 @@ def generate_activity_md(
     data["contributors"] = [[]] * len(data)
 
     # Get bot users from GraphQL data (stored in DataFrame attrs)
-    bot_users = data.attrs.get("bot_users", set())
+    bot_users = data.attrs["bot_users"]
 
     def ignored_user(username):
-        if username in bot_users:
+        if not username:
+            return False
+
+        # First check against GraphQL-detected bot users
+        # It is common for a bot to have `username` in GitHub and `username[bot]` in commits.
+        # So this accounts for that.
+        normalized_username = username.replace("[bot]", "")
+        if normalized_username in bot_users:
+            return True
+
+        # Next use pattern-based fallback for bots not detected by GraphQL
+        username_lower = username.lower()
+        bot_patterns = [
+            "[bot]",  # e.g., github-actions[bot], codecov[bot]
+            "-bot",  # e.g., renovate-bot, release-bot, dependabot
+        ]
+        if any(pattern in username_lower for pattern in bot_patterns):
             return True
+
+        # Check against user-specified ignored contributors
         if ignored_contributors and any(
             fnmatch.fnmatch(username, user) for user in ignored_contributors
         ):
             return True
+
         return False
 
     def filter_ignored(userlist):
@@ -490,12 +516,19 @@ def filter_ignored(userlist):
         # - merger
         # - reviewers
 
-        item_contributors.author = row.author
+        # Only add author if they're not a bot
+        if not ignored_user(row.author):
+            item_contributors.author = row.author
 
         if row.kind == "pr":
             for committer in filter_ignored(row.committers):
                 item_contributors.add(committer)
-            if row.mergedBy and row.mergedBy != row.author:
+            # Only add merger if they're not a bot and not the author
+            if (
+                row.mergedBy
+                and row.mergedBy != row.author
+                and not ignored_user(row.mergedBy)
+            ):
                 item_contributors.add(row.mergedBy)
             for reviewer in filter_ignored(row.reviewers):
                 item_contributors.add(reviewer)

github_activity/graphql.py

@@ -47,13 +47,15 @@
                 committer {
                   user {
                     login
+                    __typename
                   }
                 }
                 authors(first: 10) {
                   edges {
                     node {
                       user {
                         login
+                        __typename
                       }
                     }
                   }
@@ -140,6 +142,7 @@ def __init__(self, query, display_progress=True, auth=None):
           variable `GITHUB_ACCESS_TOKEN` will be tried.
         """
         self.query = query
+        self.bot_users = set()  # Store detected bot usernames
 
         # Authentication
         token = auth or os.environ.get("GITHUB_ACCESS_TOKEN")
@@ -149,7 +152,7 @@ def __init__(self, query, display_progress=True, auth=None):
                 "--auth flag or must be used to pass a Personal Access Token "
                 "needed by the GitHub API. You can generate a token at "
                 "https://github.com/settings/tokens/new. Note that while "
-                "working with a public repository, you don’t need to set any "
+                "working with a public repository, you don't need to set any "
                 "scopes on the token you create."
             )
         self.auth = TokenAuth(token)
@@ -240,9 +243,7 @@ def request(self, n_pages=100, n_per_page=50):
         # Extract bot users from raw data before DataFrame conversion
         def is_bot(user_dict):
             """Check if a GraphQL user object represents a bot account."""
-            if not user_dict:
-                return False
-            return user_dict.get("__typename") == "Bot"
+            return user_dict and user_dict.get("__typename") == "Bot"
 
         bot_users = set()
         for item in self.issues_and_or_prs:
@@ -272,9 +273,26 @@ def is_bot(user_dict):
                     if is_bot(comment_author):
                         bot_users.add(comment_author["login"])
 
+            # Check commit authors and committers
+            commits = item.get("commits")
+            if commits:
+                for commit_edge in commits.get("edges", []):
+                    commit = commit_edge["node"]["commit"]
+                    # Check committer
+                    committer = commit.get("committer")
+                    if committer and committer.get("user"):
+                        if is_bot(committer["user"]):
+                            bot_users.add(committer["user"]["login"])
+                    # Check authors
+                    authors = commit.get("authors")
+                    if authors:
+                        for author_edge in authors.get("edges", []):
+                            author_user = author_edge["node"].get("user")
+                            if author_user and is_bot(author_user):
+                                bot_users.add(author_user["login"])
+
         # Create a dataframe of the issues and/or PRs
         self.data = pd.DataFrame(self.issues_and_or_prs)
-        # Store bot users in DataFrame metadata (attrs dict)
         self.data.attrs["bot_users"] = bot_users
 
         # Add some extra fields

tests/test_cli.py

@@ -141,3 +141,34 @@ def test_contributor_sorting(tmpdir, file_regression):
     run(cmd.split(), check=True)
     md = path_output.read_text()
     file_regression.check(md, extension=".md")
+
+
+@mark.integration
+def test_bot_filtering(file_regression):
+    """Test that bot users are detected and filtered from output."""
+    from github_activity.github_activity import get_activity, generate_activity_md
+
+    # Use jupyter-book/mystmd because it's a small release, and know theres bot activity
+    data = get_activity(
+        target="jupyter-book/mystmd",
+        since="mystmd@1.6.5",
+        until="mystmd@1.6.6",
+    )
+
+    # Verify bot_users attrs exists and was preserved (catches the concat bug)
+    assert "bot_users" in data.attrs, "bot_users should be in DataFrame attrs"
+
+    # Verify we actually detected some bots
+    assert len(data.attrs["bot_users"]) > 0, (
+        "Should have detected bot users in this release"
+    )
+
+    # Generate markdown and save as regression baseline
+    md = generate_activity_md(
+        target="jupyter-book/mystmd",
+        since="mystmd@1.6.5",
+        until="mystmd@1.6.6",
+    )
+
+    # Use this regression test to make sure no bots are in the output
+    file_regression.check(md, extension=".md")

tests/test_cli/test_bot_filtering.md

@@ -0,0 +1,23 @@
+# mystmd@1.6.5...mystmd@1.6.6
+
+([full changelog](https://github.com/jupyter-book/mystmd/compare/mystmd@1.6.5...mystmd@1.6.6))
+
+## Bugs fixed
+
+- Fix execution bug: no need for kernelspec if no executable content [#2454](https://github.com/jupyter-book/mystmd/pull/2454) ([@choldgraf](https://github.com/choldgraf), [@stefanv](https://github.com/stefanv))
+
+## Other merged PRs
+
+- 🚀 Release [#2457](https://github.com/jupyter-book/mystmd/pull/2457) ([@stefanv](https://github.com/stefanv))
+- Pull in latest myst-execute [#2456](https://github.com/jupyter-book/mystmd/pull/2456) ([@stefanv](https://github.com/stefanv))
+- 🚀 Release [#2455](https://github.com/jupyter-book/mystmd/pull/2455) ([@stefanv](https://github.com/stefanv))
+- 🚀 Release [#2416](https://github.com/jupyter-book/mystmd/pull/2416) ([@bsipocz](https://github.com/bsipocz), [@choldgraf](https://github.com/choldgraf), [@stefanv](https://github.com/stefanv))
+
+## Contributors to this release
+
+The following people contributed discussions, new ideas, code and documentation contributions, and review.
+See [our definition of contributors](https://github-activity.readthedocs.io/en/latest/#how-does-this-tool-define-contributions-in-the-reports).
+
+([GitHub contributors page for this release](https://github.com/jupyter-book/mystmd/graphs/contributors?from=2025-11-18&to=2025-11-19&type=c))
+
+@bsipocz ([activity](https://github.com/search?q=repo%3Ajupyter-book%2Fmystmd+involves%3Absipocz+updated%3A2025-11-18..2025-11-19&type=Issues)) | @choldgraf ([activity](https://github.com/search?q=repo%3Ajupyter-book%2Fmystmd+involves%3Acholdgraf+updated%3A2025-11-18..2025-11-19&type=Issues)) | @jukent ([activity](https://github.com/search?q=repo%3Ajupyter-book%2Fmystmd+involves%3Ajukent+updated%3A2025-11-18..2025-11-19&type=Issues)) | @stefanv ([activity](https://github.com/search?q=repo%3Ajupyter-book%2Fmystmd+involves%3Astefanv+updated%3A2025-11-18..2025-11-19&type=Issues))