Introduce typo checker to pre-commit and fix typos

.pre-commit-config.yaml

@@ -1,3 +1,4 @@
+exclude: (quetz/migrations)
 repos:
   - repo: https://github.com/pycqa/isort
     rev: 5.12.0
@@ -41,3 +42,8 @@ repos:
     rev: v1.1.314
     hooks:
       - id: pyright
+  - repo: https://github.com/Quantco/pre-commit-mirrors-typos
+    rev: 1.16.26
+    hooks:
+      - id: typos-conda
+        exclude: (quetz/tests/authentification/test_oauth.py)

_typos.toml

@@ -0,0 +1,5 @@
+[default.extend-words]
+fo = "fo"
+
+[files]
+extend-exclude = ["quetz/migrations/*.po", "quetz/tests/authentification/test_oauth.py"]

docker/jupyterhub_config.py

@@ -1161,7 +1161,7 @@
 #
 #  This function is called after the user has passed all authentication checks
 #  and is ready to successfully authenticate. This function must return the
-#  authentication dict reguardless of changes to it.
+#  authentication dict regardless of changes to it.
 #
 #  This maybe a coroutine.
 #

docs/source/deploying/authenticators.rst

@@ -98,7 +98,7 @@ For example, the custom authenticator might be:
 Registering authenticator
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The standard way to register an authenticator with Quetz, is to distibute it as a plugin
+The standard way to register an authenticator with Quetz, is to distribute it as a plugin
 (see :ref:`plugins_section`). 
 To automatize the creation of a plugin, check out our cookiecutter `template`_.
 

docs/source/deploying/configuration.rst

@@ -72,14 +72,14 @@ Configure default user permissions, creating default channel and super-admin per
    admins = ["github:admin_user"]
    # users with maintainer role
    maintainers = ["google:other_user"]
-   # users with memeber role
+   # users with member role
    members = ["github:some", "github:random", "github:name"]
    # default role assigned to new users
    # leave out if role should be null
    default_role = "member"
    # create a default channel for new users named {username}
    create_default_channel = false
-   # wether to collect email addresses when users register
+   # whether to collect email addresses when users register
    collect_emails = false
 
 You can use one of the following options to configure privileged users:
@@ -193,7 +193,7 @@ Quetz can store packages in Google Cloud Storage. To configure, use the followin
     region="..."
 
 :project: The Google Cloud Project ID to work under
-:token: A token to pass the `gcsfs`. See the `gcsfs documention <https://gcsfs.readthedocs.io/en/latest/index.html#credentials>`_ for valid values.
+:token: A token to pass the `gcsfs`. See the `gcsfs documentation <https://gcsfs.readthedocs.io/en/latest/index.html#credentials>`_ for valid values.
 :bucket_prefix:
 :bucket_suffix: channel buckets on GCS are created with the following semantics: ``{bucket_prefix}{channel_name}{bucket_suffix}``
 :cache_timeout: Timeout in s after which local GCS cache entries are invalidated. Set to a value <=0 to disable caching completely. Default is that entries are never invalidated.
@@ -270,9 +270,9 @@ You can also use a couple of environment variables to configure the behaviour of
 Variable                 description                             values                       default
 =======================  ======================================  ===========================  ===================
 ``QUETZ_LOG_LEVEL``      log level                               ERROR, INFO, WARNING, DEBUG  INFO or config file
-``QUETZ_API_KEY``        api key used by quetz-client log level  string  
+``QUETZ_API_KEY``        api key used by quetz-client            string  
 ``QUETZ_TEST_DATABASE``  uri to the database used in tests       string                       sqlite:///:memory:
-``QUETZ_TEST_DBINIT``    method to create db tabels in tests     "create-tables" or           "create-tables"
+``QUETZ_TEST_DBINIT``    method to create db tables in tests     "create-tables" or           "create-tables"
                                                                  "use-migrations" 
 ``S3_ACCESS_KEY``        access key to s3 (used in tests)        string                                         
 ``S3_SECRET_KEY``        secret key to s3 (used in tests)        string                                         

docs/source/deploying/index.rst

@@ -2,7 +2,7 @@ Deploying
 =========
 
 There are many options for deploying a package repository with Quetz. You can deploy Quetz either locally for 
-testing, on a production server or in the cloud. The process can be tailored to your needs and exisiting
+testing, on a production server or in the cloud. The process can be tailored to your needs and existing
 infrastructure.
 
 .. toctree::

docs/source/deploying/migrations.rst

@@ -5,7 +5,7 @@ When the data classes in Quetz are modified (for example, a column is added, rem
 
 .. note::
 
-   Before running any of the commands below, you need to make sure that your database is backed up. The backup process depends on the infrastrcuture, but in the simplest case it may involve the dump of the whole database (using ``pg_dump`` for example).
+   Before running any of the commands below, you need to make sure that your database is backed up. The backup process depends on the infrastructure, but in the simplest case it may involve the dump of the whole database (using ``pg_dump`` for example).
 
 Migrating database
 ------------------

docs/source/qeps/qep-001-user-permissions.rst

@@ -61,7 +61,7 @@ Roles can be configure with a config file:
    admins = ["wolfv"]
    # users with maintainer role
    maintainers = ["btel"]
-   # users with memeber role
+   # users with member role
    members = ["some", "random", "name"]
    # default role assigned to new users
    # leave out if role should be null

quetz/authentication/azuread.py

@@ -16,7 +16,7 @@ class AzureADAuthenticator(OAuthAuthenticator):
       tenant_id = "tenant-name or id"
 
     You can obtain ``client_id`` and ``client_secret`` by registering your
-    application with AzureAD platfrom at this URL:
+    application with AzureAD platform at this URL:
     `https://portal.azure.com/#blade/Microsoft_AAD_IAM/ActiveDirectoryMenuBlade/RegisteredApps`
 
     The ``tenant_id`` can either be a specific tenant's GUID identifier or one of three

quetz/authentication/google.py

@@ -18,7 +18,7 @@ class GoogleAuthenticator(OAuthAuthenticator):
       client_secret = "03728444a12abff17e9444fd231b4379d58f0b"
 
     You can obtain ``client_id`` and ``client_secret`` by registering your
-    application with Google platfrom at this URL:
+    application with Google platform at this URL:
     `<https://console.developers.google.com/apis/credentials>`_.
     """
 

quetz/authentication/jupyterhub.py

@@ -60,7 +60,7 @@ def register(cls, config: Config):
 
 
 class JupyterhubAuthenticator(OAuthAuthenticator):
-    """Use Oauth2 protcol to authenticate with jupyterhub server, which acts
+    """Use OAuth2 protocol to authenticate with jupyterhub server, which acts
     as identity provider.
 
     To activate add the following section to the ``config.toml`` (see :ref:`configfile`):
@@ -74,13 +74,13 @@ class JupyterhubAuthenticator(OAuthAuthenticator):
       client_id = "quetz_client"
       client_secret = "super-secret"
 
-      # token enpoint of Jupyterhub, needs to be accessible from Quetz server
+      # token endpoint of Jupyterhub, needs to be accessible from Quetz server
       access_token_url = "http://JUPYTERHUB_HOST:PORT/hub/api/oauth2/token"
 
       # authorize endpoint of JupyterHub, needs to be accessible from users' browser
       authorize_url = "http://JUPYTERHUB_HOST:PORT/hub/api/oauth2/authorize"
 
-      # API root, needs to be accesible from Quetz server
+      # API root, needs to be accessible from Quetz server
       api_base_url = "http://JUPYTERHUB_HOST:PORT/hub/api/"
 
     To configure quetz as an oauth client in JupyterHub, you will need to define

quetz/authentication/oauth2.py

@@ -40,18 +40,18 @@ class OAuthAuthenticator(BaseAuthenticator):
     """Base class for authenticators using Oauth2 protocol and its variants.
 
     The :py:meth:`authenticate` method is already implemented, but you will need to
-    override some of the following variables in sublasses to make it work:
+    override some of the following variables in subclasses to make it work:
 
     :var str provider: name of the provider (it will be used in the url)
     :var handler_cls: class with handlers for all oauth2
       relevant endpoints in Quetz server
-    :type handler_cls: sublass of :py:class:`OauthHandlers`
+    :type handler_cls: subclass of :py:class:`OauthHandlers`
     :var client_id: required, client id registered with the provider
     :var client_secret: required, likewise
     :var bool is_enabled: True if authenticator is enabled, can be configured in
       :py:meth:`configure` method
 
-    :var access_token_url: URL of the OAuth2 endpoint ot request a token
+    :var access_token_url: URL of the OAuth2 endpoint to request a token
     :var authorize_url: URL of the OAuth2 ``authorize`` endpoint
     :var api_base_url: URL of the API root of the provider server
     :var validate_token_url: path of endpoint to validate the token

quetz/authorization.py

@@ -262,7 +262,7 @@ def assert_create_api_key_roles(self, roles):
                 )
                 self.assert_channel_roles(role.channel, required_channel_roles)
             else:
-                # create key without assigning special channel/package privilages
+                # create key without assigning special channel/package privileges
                 return True
 
     def assert_delete_api_key(self, api_key):

quetz/channel_data.py

@@ -81,7 +81,7 @@ def export(dao, channel_name):
     packages = channeldata["packages"]
     subdirs = set(['noarch'])
 
-    for name, info in dao.get_channel_datas(channel_name):
+    for name, info in dao.get_channel_data(channel_name):
         if info is not None:
             data = json.loads(info)
             packages[name] = data

quetz/config.py

@@ -401,18 +401,18 @@ def _get_environ_config(self) -> Dict[str, Any]:
             if key.startswith(_env_prefix)
         }
         for var, value in quetz_var.items():
-            splitted_key = var.split('_')
-            config_key = splitted_key[1].lower()
+            split_key = var.split('_')
+            config_key = split_key[1].lower()
             idx = 2
 
             # look for the first level of config_map.
             # It must be done in loop as the key itself can contains '_'.
             first_level = None
-            while idx < len(splitted_key):
+            while idx < len(split_key):
                 first_level = self._find_first_level_config(config_key)
                 if first_level:
                     break
-                config_key += f"_{ splitted_key[idx].lower()}"
+                config_key += f"_{ split_key[idx].lower()}"
                 idx += 1
 
             # no first_level found, the variable is useless.
@@ -423,7 +423,7 @@ def _get_environ_config(self) -> Dict[str, Any]:
                 config[first_level.name] = value
             # the first level is a section.
             elif isinstance(first_level, ConfigSection):
-                entry = "_".join(splitted_key[idx:]).lower()
+                entry = "_".join(split_key[idx:]).lower()
                 # the entry does not exist in section, the variable is useless.
                 if entry not in [
                     section_entry.name for section_entry in first_level.entries
@@ -432,7 +432,7 @@ def _get_environ_config(self) -> Dict[str, Any]:
                 # add the entry to the config.
                 if first_level.name not in config:
                     config[first_level.name]: Dict[str, Any] = {}
-                config[first_level.name]["_".join(splitted_key[idx:]).lower()] = value
+                config[first_level.name]["_".join(split_key[idx:]).lower()] = value
 
         return config
 
@@ -499,7 +499,7 @@ def configured_section(self, section: str) -> bool:
         Returns
         -------
         bool
-            Wether or not the given section is configured
+            Whether or not the given section is configured
         """
 
         return bool(self.config.get(section))

quetz/dao.py

@@ -165,9 +165,9 @@ def _parse_sort_by(query, model, sortstr: str):
     sorts = sortstr.split(',')
 
     for s in sorts:
-        splitted = s.split(':')
-        if len(splitted) == 2:
-            field, order = splitted
+        split_result = s.split(':')
+        if len(split_result) == 2:
+            field, order = split_result
         else:
             field = s
             order = 'desc'
@@ -1000,7 +1000,7 @@ def get_package_infos(self, channel_name: str, subdir: str):
             .order_by(PackageVersion.filename)
         )
 
-    def get_channel_datas(self, channel_name: str):
+    def get_channel_data(self, channel_name: str):
         # Returns iterator
         return (
             self.db.query(Package.name, Package.channeldata)

quetz/hooks.py

@@ -22,7 +22,7 @@ def register_router() -> 'fastapi.APIRouter':
 def post_add_package_version(
     version: 'quetz.db_models.PackageVersion', condainfo: 'quetz.condainfo.CondaInfo'
 ) -> None:
-    """hook for post-processsing after adding a package file.
+    """hook for post-processing after adding a package file.
 
     :param quetz.db_models.PackageVersion version:
         package version model that was added in to the database
@@ -42,7 +42,7 @@ def post_package_indexing(
     files: dict,
     packages: dict,
 ) -> None:
-    """hook for post-processsing after building indexes.
+    """hook for post-processing after building indexes.
 
     :param quetz.pkgstores.PackageStore pkgstore:
         package store used to store/retrieve packages
@@ -70,7 +70,7 @@ def post_index_creation(
     channel_name: str,
     subdir: str,
 ) -> None:
-    """hook for post-processsing after creating package index.
+    """hook for post-processing after creating package index.
 
     :param dict raw_repodata:
         the package index

quetz/jobs/runner.py

@@ -334,14 +334,14 @@ def _update_running_jobs(self):
             .outerjoin(Job)
             .filter(running_job)
             .group_by(Task.job_id)
-            # select jobs where all tasks are finsihed
+            # select jobs where all tasks are finished
             .having(all_true(task_done))
             .all()
         )
         for job_id, repeat, failed in results:
             if repeat:
                 # job with repeat non-null repeat column should be
-                # kept runing until cancelled
+                # kept running until cancelled
                 status = JobStatus.pending
             elif failed:
                 status = JobStatus.failed

quetz/main.py

@@ -1770,7 +1770,7 @@ async def task():
 
 
 @app.on_event("shutdown")
-async def stop_sync_donwload_counts():
+async def stop_sync_download_counts():
     app.sync_download_task.cancel()
     try:
         await app.sync_download_task

quetz/metrics/tasks.py

@@ -57,7 +57,7 @@ def synchronize_metrics_from_mirrors(
             packages = response_data["packages"]
         except KeyError:
             logger.error(
-                f"malfromated respose received from {metrics_url}: "
+                f"malfromated response received from {metrics_url}: "
                 "missing 'packages' key"
             )
             continue

quetz/tasks/indexing.py

@@ -123,7 +123,7 @@ def validate_packages(dao, pkgstore, channel_name):
         in_ls_not_db = ls_result_set - db_result_set
         in_db_not_ls = db_result_set - ls_result_set
 
-        valid, inexistant, wrong_size = 0, 0, 0
+        valid, inexistent, wrong_size = 0, 0, 0
 
         # remove all files that are in database and not uploaded
         for f in in_db_not_ls:
@@ -138,7 +138,7 @@ def validate_packages(dao, pkgstore, channel_name):
                 .one()
             )
             dao.db.delete(db_pkg_to_delete)
-            inexistant += 1
+            inexistent += 1
 
         db_dict = dict(db_result)
         for f in ls_result:
@@ -173,7 +173,7 @@ def validate_packages(dao, pkgstore, channel_name):
 
         logger.info(f"Valid files: {valid}")
         logger.info(f"Wrong size: {wrong_size}")
-        logger.info(f"Not uploaded: {inexistant}")
+        logger.info(f"Not uploaded: {inexistent}")
 
     update_indexes(dao, pkgstore, channel_name)
 

quetz/testing/fixtures.py

@@ -120,10 +120,10 @@ def auto_rollback():
 @pytest.fixture
 def session_maker(sql_connection, create_tables, auto_rollback):
     # run the tests with a separate external DB transaction
-    # so that we can easily rollback all db changes (even if commited)
+    # so that we can easily rollback all db changes (even if committed)
     # done by the test client
 
-    # Note: when rollback is explictly called in the implementation,
+    # Note: when rollback is explicitly called in the implementation,
     #       it will remove all objects created in the test even the ones
     #       that were already committed!
 
@@ -255,7 +255,7 @@ def get_session_mock(*args, **kwargs):
 
     mocker.patch("quetz.database.get_session", get_session_mock)
 
-    # overiding dependency works with all requests handlers that
+    # overriding dependency works with all requests handlers that
     # depend on quetz.deps.get_db
     app.dependency_overrides[get_db] = lambda: db
 

quetz/tests/api/test_channels.py

@@ -275,7 +275,7 @@ def remove_jobs(db):
 def test_channel_names_are_case_insensitive(
     auth_client, maintainer, remove_package_versions
 ):
-    channel_name = "MyChanneL"
+    channel_name = "MyChannel"
 
     response = auth_client.post(
         "/api/channels", json={"name": channel_name, "private": False}
@@ -348,7 +348,7 @@ def test_channel_names_are_case_insensitive(
 
 
 def test_unique_channel_names_are_case_insensitive(auth_client, maintainer):
-    channel_name = "MyChanneL"
+    channel_name = "MyChannel"
 
     response = auth_client.post(
         "/api/channels", json={"name": channel_name, "private": False}

quetz/tests/api/test_main_packages.py

@@ -901,7 +901,7 @@ def api_key(db, dao: Dao, owner, private_channel):
                 ],
             )
         ),
-        "API key with role restruction",
+        "API key with role restriction",
     )
 
     yield key