More CI Cleanup (#742)

.github/workflows/python-linux.yml

@@ -54,7 +54,7 @@ jobs:
       - name: Run the tests
         if: ${{ matrix.python-version != 'pypy-3.7' }}
         run: |
-          pytest -vv --cov jupyter_server --cov-branch --cov-report term-missing:skip-covered || pytest -vv --cov jupyter_server --cov-branch --cov-report term-missing:skip-covered --lf
+          pytest -vv --cov jupyter_server --cov-branch --cov-report term-missing:skip-covered  --cov-fail-under 70 || pytest -vv --cov jupyter_server --cov-branch --cov-report term-missing:skip-covered --cov-fail-under 70 --lf
       - name: Run the tests on pypy
         if: ${{ matrix.python-version == 'pypy-3.7' }}
         run: |

.mailmap

@@ -26,7 +26,7 @@ David Hirschfeld <david.hirschfeld@gazprom-mt.com> dhirschfeld <david.hirschfeld
 David P. Sanders <dpsanders@gmail.com> David P. Sanders <dpsanders@ciencias.unam.mx>
 David Warde-Farley <wardefar@iro.umontreal.ca> David Warde-Farley <>
 Doug Blank <dblank@cs.brynmawr.edu> Doug Blank <doug.blank@gmail.com>
-Eugene Van den Bulke <eugene.van-den-bulke@gmail.com> Eugene Van den Bulke <eugene.vandenbulke@gmail.com> 
+Eugene Van den Bulke <eugene.van-den-bulke@gmail.com> Eugene Van den Bulke <eugene.vandenbulke@gmail.com>
 Evan Patterson <epatters@enthought.com> <epatters@EPattersons-MacBook-Pro.local>
 Evan Patterson <epatters@enthought.com> <epatters@evan-laptop.localdomain>
 Evan Patterson <epatters@enthought.com> <epatters@caltech.edu>

.pre-commit-config.yaml

@@ -15,10 +15,16 @@ repos:
     hooks:
       - id: prettier
 
-  - repo: https://gitlab.com/pycqa/flake8
+  - repo: https://github.com/pycqa/flake8
     rev: 4.0.1
     hooks:
       - id: flake8
+        additional_dependencies:
+          [
+            "flake8-bugbear==20.1.4",
+            "flake8-logging-format==0.6.0",
+            "flake8-implicit-str-concat==0.2.0",
+          ]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.1.0
@@ -33,6 +39,8 @@ repos:
       - id: check-yaml
       - id: debug-statements
       - id: forbid-new-submodules
+      - id: check-builtin-literals
+      - id: trailing-whitespace
 
   - repo: https://github.com/pre-commit/mirrors-eslint
     rev: v8.8.0

docs/Makefile

@@ -176,7 +176,7 @@ linkcheck:
 	@echo
 	@echo "Link check complete; look for any errors in the above output " \
 	      "or in $(BUILDDIR)/linkcheck/output.txt."
-		  
+
 spelling:
 	$(SPHINXBUILD) -b spelling $(ALLSPHINXOPTS) $(BUILDDIR)/spelling
 	@echo "Spell check complete; look for any errors in the above output " \

docs/autogen_config.py

@@ -37,7 +37,7 @@
 """
 try:
     destination = os.path.join(os.path.dirname(__file__), "source/other/full-config.rst")
-except:
+except BaseException:
     destination = os.path.join(os.getcwd(), "full-config.rst")
 
 with open(destination, "w") as f:

docs/source/conf.py

@@ -279,17 +279,6 @@
 
 # -- Options for LaTeX output ---------------------------------------------
 
-latex_elements = {
-    # The paper size ('letterpaper' or 'a4paper').
-    #'papersize': 'letterpaper',
-    # The font size ('10pt', '11pt' or '12pt').
-    #'pointsize': '10pt',
-    # Additional stuff for the LaTeX preamble.
-    #'preamble': '',
-    # Latex figure (float) alignment
-    #'figure_align': 'htbp',
-}
-
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).

examples/simple/jupyter_server_config.py

@@ -2,5 +2,5 @@
 # ------------------------------------------------------------------------------
 # Application(SingletonConfigurable) configuration
 # ------------------------------------------------------------------------------
-## The date format used by logging formatters for %(asctime)s
+# The date format used by logging formatters for %(asctime)s
 c.Application.log_datefmt = "%Y-%m-%d %H:%M:%S Simple_Extensions_Example"

examples/simple/pytest.ini

@@ -1,3 +1,3 @@
 [pytest]
 # Disable any upper exclusion.
-norecursedirs = 
+norecursedirs =

examples/simple/simple_ext11/application.py

@@ -57,7 +57,7 @@ def simple11_dir_formatted(self):
 
     def initialize_settings(self):
         self.log.info("hello: {}".format(self.hello))
-        if self.hello == True:
+        if self.hello is True:
             self.log.info(
                 "Hello Simple11: You have launched with --hello flag or defined 'c.SimpleApp1.hello == True' in your config file"
             )

jupyter_server/auth/login.py

@@ -229,10 +229,10 @@ def validate_security(cls, app, ssl_options=None):
         if not app.ip:
             warning = "WARNING: The Jupyter server is listening on all IP addresses"
             if ssl_options is None:
-                app.log.warning(warning + " and not using encryption. This " "is not recommended.")
+                app.log.warning(f"{warning} and not using encryption. This is not recommended.")
             if not app.password and not app.token:
                 app.log.warning(
-                    warning + " and not using authentication. "
+                    f"{warning} and not using authentication. "
                     "This is highly insecure and not recommended."
                 )
         else:

jupyter_server/auth/logout.py

@@ -11,7 +11,7 @@ def get(self):
         if self.login_available:
             message = {"info": "Successfully logged out."}
         else:
-            message = {"warning": "Cannot log out. Jupyter Server authentication " "is disabled."}
+            message = {"warning": "Cannot log out. Jupyter Server authentication is disabled."}
         self.write(self.render_template("logout.html", message=message))
 
 

jupyter_server/auth/security.py

@@ -48,7 +48,7 @@ def passwd(passphrase=None, algorithm="argon2"):
 
     """
     if passphrase is None:
-        for i in range(3):
+        for _ in range(3):
             p0 = getpass.getpass("Enter password: ")
             p1 = getpass.getpass("Verify password: ")
             if p0 == p1:
@@ -161,7 +161,7 @@ def persist_config(config_file=None, mode=0o600):
 
     try:
         os.chmod(config_file, mode)
-    except Exception as e:
+    except Exception:
         tb = traceback.format_exc()
         warnings.warn("Failed to set permissions on %s:\n%s" % (config_file, tb), RuntimeWarning)
 

jupyter_server/base/handlers.py

@@ -454,7 +454,7 @@ def check_xsrf_cookie(self):
             return
         try:
             return super(JupyterHandler, self).check_xsrf_cookie()
-        except web.HTTPError as e:
+        except web.HTTPError:
             if self.request.method in {"GET", "HEAD"}:
                 # Consider Referer a sufficient cross-origin check for GET requests
                 if not self.check_referer():

jupyter_server/extension/application.py

@@ -543,7 +543,7 @@ def load_classic_server_extension(cls, serverapp):
         extension.initialize()
 
     @classmethod
-    def initialize_server(cls, argv=[], load_other_extensions=True, **kwargs):
+    def initialize_server(cls, argv=None, load_other_extensions=True, **kwargs):
         """Creates an instance of ServerApp and explicitly sets
         this extension to enabled=True (i.e. superceding disabling
         found in other config from files).
@@ -560,7 +560,7 @@ def initialize_server(cls, argv=[], load_other_extensions=True, **kwargs):
         serverapp = ServerApp.instance(jpserver_extensions=jpserver_extensions, **kwargs)
         serverapp.aliases.update(cls.aliases)
         serverapp.initialize(
-            argv=argv,
+            argv=argv or [],
             starter_extension=cls.name,
             find_extensions=find_extensions,
         )

jupyter_server/extension/manager.py

@@ -39,7 +39,7 @@ def _valid_metadata(self, proposed):
             self._module_name = metadata["module"]
         except KeyError:
             raise ExtensionMetadataError(
-                "There is no 'module' key in the extension's " "metadata packet."
+                "There is no 'module' key in the extension's metadata packet."
             )
 
         try:

jupyter_server/extension/serverextension.py

@@ -337,7 +337,7 @@ def list_server_extensions(self):
                     version = extension.version
                     self.log.info("      {} {} {}".format(name, version, GREEN_OK))
                 except Exception as err:
-                    self.log.warn("      {} {}".format(RED_X, err))
+                    self.log.warning("      {} {}".format(RED_X, err))
             # Add a blank line between paths.
             self.log.info("")
 

jupyter_server/extension/utils.py

@@ -26,9 +26,9 @@ def get_loader(obj, logger=None):
     underscore prefix.
     """
     try:
-        func = getattr(obj, "_load_jupyter_server_extension")
+        func = getattr(obj, "_load_jupyter_server_extension")  # noqa B009
     except AttributeError:
-        func = getattr(obj, "load_jupyter_server_extension")
+        func = getattr(obj, "load_jupyter_server_extension", None)
         warnings.warn(
             "A `_load_jupyter_server_extension` function was not "
             "found in {name!s}. Instead, a `load_jupyter_server_extension` "

jupyter_server/gateway/managers.py

@@ -125,9 +125,11 @@ async def list_kernels(self, **kwargs):
         # Remove any of our kernels that may have been culled on the gateway server
         our_kernels = self._kernels.copy()
         culled_ids = []
-        for kid, km in our_kernels.items():
+        for kid, _ in our_kernels.items():
             if kid not in kernel_models:
-                self.log.warn(f"Kernel {kid} no longer active - probably culled on Gateway server.")
+                self.log.warning(
+                    f"Kernel {kid} no longer active - probably culled on Gateway server."
+                )
                 self._kernels.pop(kid, None)
                 culled_ids.append(kid)  # TODO: Figure out what do with these.
         return list(kernel_models.values())
@@ -606,7 +608,7 @@ async def start_channels(self, shell=True, iopub=True, stdin=True, hb=True, cont
             "channels",
         )
         # Gather cert info in case where ssl is desired...
-        ssl_options = dict()
+        ssl_options = {}
         ssl_options["ca_certs"] = GatewayClient.instance().ca_certs
         ssl_options["certfile"] = GatewayClient.instance().client_cert
         ssl_options["keyfile"] = GatewayClient.instance().client_key

jupyter_server/i18n/__init__.py

@@ -52,7 +52,7 @@ def parse_accept_lang_header(accept_lang):
         by_q[qvalue].append(lang)
 
     res = []
-    for qvalue, langs in sorted(by_q.items()):
+    for _, langs in sorted(by_q.items()):
         res.extend(sorted(langs))
     return res
 

jupyter_server/i18n/babel_nbui.cfg

@@ -1,4 +1,4 @@
 [jinja2: notebook/templates/**.html]
  encoding = utf-8
-[extractors] 
+[extractors]
  jinja2 = jinja2.ext:babel_extract

jupyter_server/nbconvert/handlers.py

@@ -30,7 +30,7 @@
 
 def find_resource_files(output_files_dir):
     files = []
-    for dirpath, dirnames, filenames in os.walk(output_files_dir):
+    for dirpath, _, filenames in os.walk(output_files_dir):
         files.extend([os.path.join(dirpath, f) for f in filenames])
     return files
 

jupyter_server/serverapp.py

@@ -132,7 +132,6 @@
     url_path_join,
     check_pid,
     url_escape,
-    pathname2url,
     unix_socket_in_use,
     urlencode_unix_socket_path,
     fetch,
@@ -198,7 +197,7 @@ def random_ports(port, n):
     """
     for i in range(min(5, n)):
         yield port + i
-    for i in range(n - 5):
+    for _ in range(n - 5):
         yield max(1, port + random.randint(-2 * n, 2 * n))
 
 
@@ -292,11 +291,7 @@ def init_settings(
         )
         sys_info = get_sys_info()
 
-        # If the user is running the server in a git directory, make the assumption
-        # that this is a dev install and suggest to the developer `npm run build:watch`.
         base_dir = os.path.realpath(os.path.join(__file__, "..", ".."))
-        dev_mode = os.path.exists(os.path.join(base_dir, ".git"))
-
         nbui = gettext.translation(
             "nbui",
             localedir=os.path.join(base_dir, "jupyter_server/i18n"),
@@ -423,7 +418,7 @@ def init_handlers(self, default_services, settings):
             # for each handler required for gateway, locate its pattern
             # in the current list and replace that entry...
             gateway_handlers = load_handlers("jupyter_server.gateway.handlers")
-            for i, gwh in enumerate(gateway_handlers):
+            for _, gwh in enumerate(gateway_handlers):
                 for j, h in enumerate(handlers):
                     if gwh[0] == h[0]:
                         handlers[j] = (gwh[0], gwh[1])
@@ -517,7 +512,7 @@ def shutdown_server(server_info, timeout=5, log=None):
     if log:
         log.debug("POST request to %sapi/shutdown", url)
 
-    r = fetch(url, method="POST", headers={"Authorization": "token " + server_info["token"]})
+    fetch(url, method="POST", headers={"Authorization": "token " + server_info["token"]})
     # Poll to see if it shut down.
     for _ in range(timeout * 10):
         if not check_pid(pid):
@@ -581,7 +576,7 @@ def _shutdown_or_exit(self, target_endpoint, server):
     def _maybe_remove_unix_socket(socket_path):
         try:
             os.unlink(socket_path)
-        except (OSError, IOError):
+        except OSError:
             pass
 
     def start(self):
@@ -1293,7 +1288,7 @@ def _default_allow_remote(self):
     tornado_settings = Dict(
         config=True,
         help=_i18n(
-            "Supply overrides for the tornado.web.Application that the " "Jupyter server uses."
+            "Supply overrides for the tornado.web.Application that the Jupyter server uses."
         ),
     )
 
@@ -1948,7 +1943,6 @@ def init_webapp(self):
             )
             if self.ssl_options.get("ca_certs", False):
                 self.ssl_options.setdefault("cert_reqs", ssl.CERT_REQUIRED)
-            ssl_options = self.ssl_options
 
         self.login_handler_class.validate_security(self, ssl_options=self.ssl_options)
 
@@ -2655,8 +2649,10 @@ def launch_browser(self):
 
         assembled_url, _ = self._prepare_browser_open()
 
-        b = lambda: browser.open(assembled_url, new=self.webbrowser_open_new)
-        threading.Thread(target=b).start()
+        def target():
+            browser.open(assembled_url, new=self.webbrowser_open_new)
+
+        threading.Thread(target=target).start()
 
     def start_app(self):
         super(ServerApp, self).start()

jupyter_server/services/contents/fileio.py

@@ -113,7 +113,7 @@ def atomic_writing(path, text=True, encoding="utf-8", log=None, **kwargs):
 
     try:
         yield fileobj
-    except:
+    except BaseException:
         # Failed! Move the backup file back to the real path to avoid corruption
         fileobj.close()
         replace_file(tmp_path, path)
@@ -161,7 +161,7 @@ def _simple_writing(path, text=True, encoding="utf-8", log=None, **kwargs):
 
     try:
         yield fileobj
-    except:
+    except BaseException:
         fileobj.close()
         raise
 
@@ -219,7 +219,7 @@ def perm_to_403(self, os_path=""):
         """context manager for turning permission errors into 403."""
         try:
             yield
-        except (OSError, IOError) as e:
+        except OSError as e:
             if e.errno in {errno.EPERM, errno.EACCES}:
                 # make 403 error message without root prefix
                 # this may not work perfectly on unicode paths on Python 2,

jupyter_server/services/contents/filemanager.py

@@ -500,7 +500,7 @@ def is_non_empty_dir(os_path):
                 return
             else:
                 self.log.warning(
-                    "Skipping trash for %s, on different device " "to home directory",
+                    "Skipping trash for %s, on different device to home directory",
                     os_path,
                 )
 
@@ -833,7 +833,7 @@ async def is_non_empty_dir(os_path):
                 return
             else:
                 self.log.warning(
-                    "Skipping trash for %s, on different device " "to home directory",
+                    "Skipping trash for %s, on different device to home directory",
                     os_path,
                 )
 

jupyter_server/services/contents/manager.py

@@ -505,7 +505,7 @@ def validate_notebook_model(self, model, validation_error=None):
                 validate_nb(model["content"])
         except ValidationError as e:
             model["message"] = "Notebook validation failed: {}:\n{}".format(
-                e.message,
+                str(e),
                 json.dumps(e.instance, indent=1, default=lambda obj: "<UNKNOWN>"),
             )
         return model