Bump the pip group with 7 updates (#16270)

* Bump the pip group with 7 updates

Updates the requirements on [sphinx](https://github.com/sphinx-doc/sphinx), [matplotlib](https://github.com/matplotlib/matplotlib), [pandas](https://github.com/pandas-dev/pandas), [scipy](https://github.com/scipy/scipy), [ruff](https://github.com/astral-sh/ruff), [pyyaml-include](https://github.com/tanbro/pyyaml-include) and [pydantic](https://github.com/pydantic/pydantic) to permit the latest version.

Updates `sphinx` to 7.3.7
- [Release notes](https://github.com/sphinx-doc/sphinx/releases)
- [Changelog](https://github.com/sphinx-doc/sphinx/blob/master/CHANGES.rst)
- [Commits](sphinx-doc/sphinx@v1.8.0...v7.3.7)

Updates `matplotlib` from 3.8.3 to 3.8.4
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](matplotlib/matplotlib@v3.8.3...v3.8.4)

Updates `pandas` from 2.2.1 to 2.2.2
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Commits](pandas-dev/pandas@v2.2.1...v2.2.2)

Updates `scipy` from 1.12.0 to 1.13.0
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](scipy/scipy@v1.12.0...v1.13.0)

Updates `ruff` from 0.3.5 to 0.4.2
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@v0.3.5...v0.4.2)

Updates `pyyaml-include` to 2.0.2.post1
- [Changelog](https://github.com/tanbro/pyyaml-include/blob/main/CHANGELOG.md)
- [Commits](tanbro/pyyaml-include@0.1a1...v2.0.2.post1)

Updates `pydantic` to 2.7.1
- [Release notes](https://github.com/pydantic/pydantic/releases)
- [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md)
- [Commits](pydantic/pydantic@v0.0.2...v2.7.1)

---
updated-dependencies:
- dependency-name: sphinx
  dependency-type: direct:production
  dependency-group: pip
- dependency-name: matplotlib
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: pandas
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: scipy
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: ruff
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: pyyaml-include
  dependency-type: direct:production
  dependency-group: pip
- dependency-name: pydantic
  dependency-type: direct:production
  dependency-group: pip
...

Signed-off-by: dependabot[bot] <support@github.com>

* Fix ruff UP031

* More lint fixes

* Ignore UP031 for milestone_check.py

* Format

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Frédéric Collonval <fcollonval@gmail.com>
Co-authored-by: Frédéric Collonval <fcollonval@users.noreply.github.com>

.pre-commit-config.yaml

@@ -33,7 +33,7 @@ repos:
 
   # Check ruff version is aligned with the one in pyproject.toml
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.5
+    rev: v0.4.2
     hooks:
       - id: ruff
         args: ["--fix"]

examples/test_examples.py

@@ -33,14 +33,14 @@ def main():
     parser.add_argument("--testPath", help="paths containing this string are tested")
     args = parser.parse_args()
 
-    paths = [i for i in glob.glob("%s/*" % here) if osp.isdir(i)]
+    paths = [i for i in glob.glob(f"{here}/*") if osp.isdir(i)]
 
     services_dir = osp.abspath(osp.join(here, "../packages/services/examples"))
-    paths += list(glob.glob("%s/*" % services_dir))
+    paths += list(glob.glob(f"{services_dir}/*"))
     if args.testPath:
         paths = [p for p in paths if args.testPath in p]
 
-    print("Testing %s" % paths)
+    print(f"Testing {paths}")
     count = 0
     failed = []
     for path in sorted(paths):
@@ -64,7 +64,7 @@ def main():
         msg = "The following examples failed:\n-{}".format("\n-".join(failed))
         raise AssertionError(msg)
 
-    print("\n\n%s tests complete!" % count)
+    print(f"\n\n{count} tests complete!")
 
 
 if __name__ == "__main__":

jupyterlab/extensions/manager.py

@@ -207,7 +207,7 @@ def __init__(
     ) -> None:
         super().__init__(parent=parent)
         self.log.debug(
-            "Plugins in %s will managed on the %s level", self.__class__.__name__, self.level
+            f"Plugins in {self.__class__.__name__} will managed on the {self.level} level"
         )
         self.app_options = _ensure_options(app_options)
         plugin_options_field = {f.name for f in fields(PluginManagerOptions)}

jupyterlab/federated_labextensions.py

@@ -102,7 +102,7 @@ def develop_labextension(  # noqa
     full_dest = normpath(pjoin(labext, destination))
     if overwrite and os.path.lexists(full_dest):
         if logger:
-            logger.info("Removing: %s" % full_dest)
+            logger.info(f"Removing: {full_dest}")
         if os.path.isdir(full_dest) and not os.path.islink(full_dest):
             shutil.rmtree(full_dest)
         else:
@@ -129,15 +129,16 @@ def develop_labextension(  # noqa
                 raise
 
         elif not os.path.islink(full_dest):
-            raise ValueError("%s exists and is not a symlink" % full_dest)
+            msg = f"{full_dest} exists and is not a symlink"
+            raise ValueError(msg)
 
     elif os.path.isdir(path):
         path = pjoin(os.path.abspath(path), "")  # end in path separator
         for parent, _, files in os.walk(path):
             dest_dir = pjoin(full_dest, parent[len(path) :])
             if not os.path.exists(dest_dir):
                 if logger:
-                    logger.info("Making directory: %s" % dest_dir)
+                    logger.info(f"Making directory: {dest_dir}")
                 os.makedirs(dest_dir)
             for file_name in files:
                 src = pjoin(parent, file_name)
@@ -202,7 +203,7 @@ def build_labextension(
     ext_path = str(Path(path).resolve())
 
     if logger:
-        logger.info("Building extension in %s" % path)
+        logger.info(f"Building extension in {path}")
 
     builder = _ensure_builder(ext_path, core_path)
 
@@ -225,7 +226,7 @@ def watch_labextension(
     ext_path = str(Path(path).resolve())
 
     if logger:
-        logger.info("Building extension in %s" % path)
+        logger.info(f"Building extension in {path}")
 
     # Check to see if we need to create a symlink
     federated_extensions = get_federated_extensions(labextensions_path)
@@ -268,9 +269,8 @@ def _ensure_builder(ext_path, core_path):
     dep_version2 = ext_data.get("devDependencies", {}).get("@jupyterlab/builder")
     dep_version2 = dep_version2 or ext_data.get("dependencies", {}).get("@jupyterlab/builder")
     if dep_version2 is None:
-        raise ValueError(
-            "Extensions require a devDependency on @jupyterlab/builder@%s" % dep_version1
-        )
+        msg = f"Extensions require a devDependency on @jupyterlab/builder@{dep_version1}"
+        raise ValueError(msg)
 
     # if we have installed from disk (version is a path), assume we know what
     # we are doing and do not check versions.
@@ -331,10 +331,10 @@ def _should_copy(src, dest, logger=None):
         # we add a fudge factor to work around a bug in python 2.x
         # that was fixed in python 3.x: https://bugs.python.org/issue12904
         if logger:
-            logger.warning("Out of date: %s" % dest)
+            logger.warning(f"Out of date: {dest}")
         return True
     if logger:
-        logger.info("Up to date: %s" % dest)
+        logger.info(f"Up to date: {dest}")
     return False
 
 

jupyterlab/handlers/error_handler.py

@@ -16,7 +16,7 @@
 </head>
 <body>
 <h1>JupyterLab Error<h1>
-%s
+{messages}
 </body>
 """
 
@@ -29,5 +29,5 @@ def initialize(self, messages=None, name=None):
     @web.authenticated
     @web.removeslash
     def get(self):
-        msgs = ["<h2>%s</h2>" % msg for msg in self.messages]
-        self.write(TEMPLATE % "\n".join(msgs))
+        msgs = [f"<h2>{msg}</h2>" for msg in self.messages]
+        self.write(TEMPLATE.format(messages="\n".join(msgs)))

jupyterlab/labapp.py

@@ -188,12 +188,12 @@ def start(self):
             core_config=self.core_config,
             splice_source=self.splice_source,
         )
-        self.log.info("JupyterLab %s", version)
+        self.log.info(f"JupyterLab {version}")
         with self.debug_logging():
             if self.pre_clean:
-                self.log.info("Cleaning %s" % app_dir)
+                self.log.info(f"Cleaning {app_dir}")
                 clean(app_options=app_options)
-            self.log.info("Building in %s", app_dir)
+            self.log.info(f"Building in {app_dir}")
             try:
                 production = None if self.dev_build is None else not self.dev_build
                 build(
@@ -216,7 +216,7 @@ def start(self):
 clean_flags = dict(base_flags)
 clean_flags["extensions"] = (
     {"LabCleanApp": {"extensions": True}},
-    "Also delete <app-dir>/extensions.\n%s" % ext_warn_msg,
+    f"Also delete <app-dir>/extensions.\n{ext_warn_msg}",
 )
 clean_flags["settings"] = (
     {"LabCleanApp": {"settings": True}},
@@ -228,7 +228,7 @@ def start(self):
 )
 clean_flags["all"] = (
     {"LabCleanApp": {"all": True}},
-    "Delete the entire contents of the app directory.\n%s" % ext_warn_msg,
+    f"Delete the entire contents of the app directory.\n{ext_warn_msg}",
 )
 
 
@@ -257,9 +257,7 @@ class LabCleanApp(JupyterApp):
 
     app_dir = Unicode("", config=True, help="The app directory to clean")
 
-    extensions = Bool(
-        False, config=True, help="Also delete <app-dir>/extensions.\n%s" % ext_warn_msg
-    )
+    extensions = Bool(False, config=True, help=f"Also delete <app-dir>/extensions.\n{ext_warn_msg}")
 
     settings = Bool(False, config=True, help="Also delete <app-dir>/settings")
 
@@ -268,7 +266,7 @@ class LabCleanApp(JupyterApp):
     all = Bool(
         False,
         config=True,
-        help="Delete the entire contents of the app directory.\n%s" % ext_warn_msg,
+        help=f"Delete the entire contents of the app directory.\n{ext_warn_msg}",
     )
 
     def start(self):
@@ -300,9 +298,9 @@ class LabPathApp(JupyterApp):
     """
 
     def start(self):
-        print("Application directory:   %s" % get_app_dir())
-        print("User Settings directory: %s" % get_user_settings_dir())
-        print("Workspaces directory: %s" % get_workspaces_dir())
+        print(f"Application directory:   {get_app_dir()}")
+        print(f"User Settings directory: {get_user_settings_dir()}")
+        print(f"Workspaces directory: {get_workspaces_dir()}")
 
 
 class LabWorkspaceExportApp(WorkspaceExportApp):
@@ -742,8 +740,8 @@ def initialize_handlers(self):  # noqa
         # Client-side code assumes notebookVersion is a JSON-encoded string
         page_config["notebookVersion"] = json.dumps(jpserver_version_info)
 
-        self.log.info("JupyterLab extension loaded from %s" % HERE)
-        self.log.info("JupyterLab application directory is %s" % self.app_dir)
+        self.log.info(f"JupyterLab extension loaded from {HERE!s}")
+        self.log.info(f"JupyterLab application directory is {self.app_dir!s}")
 
         if self.custom_css:
             handlers.append(

jupyterlab/labextensions.py

@@ -187,7 +187,7 @@ def run_task(self):
 
     def deprecation_warning(self, msg):
         return self.log.warning(
-            "\033[33m(Deprecated) %s\n\n%s \033[0m", msg, LABEXTENSION_COMMAND_WARNING
+            f"\033[33m(Deprecated) {msg}\n\n{LABEXTENSION_COMMAND_WARNING} \033[0m"
         )
 
     def _log_format_default(self):
@@ -589,7 +589,7 @@ def start(self):
         # The above should have called a subcommand and raised NoStart; if we
         # get here, it didn't, so we should self.log.info a message.
         subcmds = ", ".join(sorted(self.subcommands))
-        self.exit("Please supply at least one subcommand: %s" % subcmds)
+        self.exit(f"Please supply at least one subcommand: {subcmds}")
 
 
 main = LabExtensionApp.launch_instance

jupyterlab/utils.py

@@ -36,12 +36,13 @@ def __init__(self, alt_func=None, behavior="warn", removed_version=None):
     def __call__(self, func):
         alt_msg = ""
         if self.alt_func is not None:
-            alt_msg = " Use ``%s`` instead." % self.alt_func
+            alt_msg = f" Use ``{self.alt_func}`` instead."
         rmv_msg = ""
         if self.removed_version is not None:
-            rmv_msg = " and will be removed in version %s" % self.removed_version
+            rmv_msg = f" and will be removed in version {self.removed_version}"
 
-        msg = "Function ``%s`` is deprecated" % func.__name__ + rmv_msg + "." + alt_msg
+        function_description = func.__name__ + rmv_msg + "." + alt_msg
+        msg = f"Function ``{function_description}`` is deprecated"
 
         @functools.wraps(func)
         def wrapped(*args, **kwargs):

pyproject.toml

@@ -76,7 +76,7 @@ Pypi = "https://pypi.org/project/jupyterlab"
 
 [project.optional-dependencies]
 docs = [
-    "sphinx>=1.8,<7.3.0",
+    "sphinx>=1.8,<7.4.0",
     "sphinx-copybutton",
     "pydata-sphinx-theme>=0.13.0",
     "pytest",
@@ -91,10 +91,10 @@ docs-screenshots = [
     "ipywidgets==8.1.2",
     "jupyterlab-geojson==3.4.0",
     "jupyterlab-language-pack-zh-CN==4.1.post2",
-    "matplotlib==3.8.3",
+    "matplotlib==3.8.4",
     "nbconvert>=7.0.0",
-    "pandas==2.2.1",
-    "scipy==1.12.0",
+    "pandas==2.2.2",
+    "scipy==1.13.0",
     "vega_datasets==0.9.0",
 ]
 test = [
@@ -118,13 +118,13 @@ dev = [
     "coverage",
     "hatch",
     "bump2version",
-    "ruff==0.3.5",
+    "ruff==0.4.2",
 ]
 upgrade-extension = [
-    "pyyaml-include<2.0",
+    "pyyaml-include<3.0",
     "copier>=8,<10",
     "jinja2-time<0.3",
-    "pydantic<2.0",
+    "pydantic<3.0",
     "tomli-w<2.0"
 ]
 
@@ -303,7 +303,7 @@ lint.ignore = [
 # RUF012 Mutable class attributes should be annotated with `typing.ClassVar`
 "jupyterlab/tests/echo_kernel.py" = ["RUF012"]
 # T201 `print` found
-"scripts/milestone_check.py" = ["T201"]
+"scripts/milestone_check.py" = ["T201", "UP031"]
 # N806 Variable `tM` in function should be lowercase
 # N816 Variable `comparatorTrimReplace` in global scope should not be mixedCase
 # PLC1901 test can be simplified as an empty string is falsey

scripts/ci_script.sh

@@ -82,7 +82,7 @@ if [[ $GROUP == lint ]]; then
 
     # Python checks
     ruff format .
-    ruff .
+    ruff check .
     pipx run 'validate-pyproject[all]' pyproject.toml
 fi
 

scripts/milestone_check.py

@@ -95,7 +95,7 @@
 }
 
 
-headers = {"Authorization": "token %s" % api_token}
+headers = {"Authorization": f"token {api_token}"}
 # construct a commit to PR dictionary
 prs = {}
 large_prs = []
@@ -170,9 +170,9 @@
 
     prs[prnumber] = {"mergeCommit": pr["mergeCommit"]["oid"], "commits": pr_commits}
     if total_commits > len(pr_commits):
+        oid = pr["mergeCommit"]["oid"]
         print(
-            "WARNING: PR %d (merge %s) has %d commits, but GitHub is only giving us %d of them"
-            % (prnumber, pr["mergeCommit"]["oid"], total_commits, len(pr_commits))
+            f"WARNING: PR {prnumber} (merge {oid}) has {total_commits} commits, but GitHub is only giving us {len(pr_commits)} of them"
         )
 
 
@@ -197,7 +197,7 @@
 
 prs_not_represented = set(prs.keys()) - good
 
-print("Milestone: %s, %d merged PRs, %d commits in history" % (MILESTONE, total_prs, len(commits)))
+print(f"Milestone: {MILESTONE}, {total_prs} merged PRs, {len(commits)} commits in history")
 
 print()
 print("-" * 40)
@@ -211,9 +211,7 @@
 """
     )
     print(
-        "\n".join(
-            "https://github.com/jupyterlab/jupyterlab/pull/%d" % i for i in prs_not_represented
-        )
+        "\n".join(f"https://github.com/jupyterlab/jupyterlab/pull/{i}" for i in prs_not_represented)
     )
 else:
     print(