pre-commit update and extension

.pre-commit-config.yaml

@@ -1,8 +1,9 @@
 exclude: '^docs/conf.py'
 
+minimum_pre_commit_version: 3.2.0
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
+  rev: v5.0.0
   hooks:
   - id: trailing-whitespace
   - id: check-added-large-files
@@ -17,24 +18,25 @@ repos:
   - id: mixed-line-ending
     args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
 
-## If you want to avoid flake8 errors due to unused vars or imports:
-# - repo: https://github.com/myint/autoflake
-#   rev: v1.4
-#   hooks:
-#   - id: autoflake
-#     args: [
-#       --in-place,
-#       --remove-all-unused-imports,
-#       --remove-unused-variables,
-#     ]
+# If you want to avoid flake8 errors due to unused vars or imports:
+- repo: https://github.com/myint/autoflake
+  rev: v2.3.1
+  hooks:
+  - id: autoflake
+    args: [
+#      --in-place,  # Use this to modify the files in place, without printing diffs, as opposed to --stdout
+      --stdout,
+      --remove-all-unused-imports,
+      --remove-unused-variables,
+    ]
 
 - repo: https://github.com/pycqa/isort
   rev: 5.13.2
   hooks:
   - id: isort
 
 - repo: https://github.com/psf/black
-  rev: 24.3.0
+  rev: 24.10.0
   hooks:
   - id: black
     language_version: python3
@@ -47,8 +49,8 @@ repos:
 #     additional_dependencies: [black]
 
 - repo: https://github.com/PyCQA/flake8
-  rev: 7.0.0
+  rev: 7.1.1
   hooks:
   - id: flake8
   ## You can add flake8 plugins via `additional_dependencies`:
-  #  additional_dependencies: [flake8-bugbear]
+    additional_dependencies: [flake8-bugbear]

examples/device_inventory.py

@@ -68,7 +68,9 @@
     OSW.StoreEntityParam(
         entities=[new_category],
         namespace="Category",
-        # meta_category_title="Category:OSWd845b96813a344458f140e48c4d063fd" # usage of MetaDeviceCategory not yet supported
+        # meta_category_title= (
+        # "Category:OSWd845b96813a344458f140e48c4d063fd")
+        # usage of MetaDeviceCategory not yet supported
     )
 )
 

examples/gui_local_slot_editing.py

@@ -352,7 +352,7 @@ def save_as_page_package(
             with open(settings["settings_file_path"], "r") as f:
                 settings = json.load(f)
             # update GUI
-            window["-CREDENTIALS-"].update(settings["credentials_file_path"]),
+            window["-CREDENTIALS-"].update(settings["credentials_file_path"])
             window["-LWD-"].update(settings["local_working_directory"])
             window["-DOMAIN-"].update(settings["domain"])
             window["-ADDRESS-"].update(settings["target_page"])

examples/ontology_import emmo.py

@@ -28,54 +28,61 @@
 ontology_name = "BVCO"
 
 # Define ontology metadata
-emmo = model.Ontology(
+emmo = model.OwlOntology(
     name="EMMO",
+    label=[model.Label(text="EMMO", lang="en")],
     iri="http://emmo.info/emmo",
     prefix="http://emmo.info/emmo#",
     prefix_name="emmo",
-    link="https://github.com/emmo-repo/EMMO",
+    see_also=["https://github.com/emmo-repo/EMMO"],
 )
-dc = model.Ontology(
+dc = model.OwlOntology(
     name="DC",
+    label=[model.Label(text="Dublin Core", lang="en")],
     iri="http://purl.org/dc/elements/1.1",
     prefix="http://purl.org/dc/elements/1.1/",
     prefix_name="dc",
-    link="http://purl.org/dc",
+    see_also=["http://purl.org/dc"],
 )
-battinfo = model.Ontology(
+battinfo = model.OwlOntology(
     name="EMMO BattINFO",
+    label=[model.Label(text="EMMO BattINFO", lang="en")],
     iri="http://emmo.info/battery",
     prefix="http://emmo.info/battery#",
     prefix_name="battinfo",
-    link="https://github.com/BIG-MAP/BattINFO",
+    see_also=["https://github.com/BIG-MAP/BattINFO"],
 )
-electrochemistry = model.Ontology(
+electrochemistry = model.OwlOntology(
     name="EMMO Electrochemistry",
+    label=[model.Label(text="EMMO Electrochemistry", lang="en")],
     iri="http://emmo.info/electrochemistry",
     prefix="http://emmo.info/electrochemistry#",
     prefix_name="electrochemistry",
-    link="https://github.com/emmo-repo/EMMO",
+    see_also=["https://github.com/emmo-repo/EMMO"],
 )
-periodictable = model.Ontology(
+periodictable = model.OwlOntology(
     name="EMMO Periodic Table",
+    label=[model.Label(text="EMMO Periodic Table", lang="en")],
     iri="http://emmo.info/emmo/domain/periodic-table",
     prefix="http://emmo.info/emmo/domain/periodic-table#",
     prefix_name="periodictable",
-    link="https://github.com/emmo-repo/EMMO",
+    see_also=["https://github.com/emmo-repo/EMMO"],
 )
-gpo = model.Ontology(
+gpo = model.OwlOntology(
     name="GPO",
+    label=[model.Label(text="General Process Ontology", lang="en")],
     iri="https://gpo.ontology.link",
     prefix="https://gpo.ontology.link/",
     prefix_name="gpo",
-    link="https://github.com/General-Process-Ontology/ontology",
+    see_also=["https://github.com/General-Process-Ontology/ontology"],
 )
-bvco = model.Ontology(
+bvco = model.OwlOntology(
     name="BVCO",
+    label=[model.Label(text="Battery Value Chain Ontology", lang="en")],
     iri="https://bvco.ontology.link",
     prefix="https://bvco.ontology.link/",
     prefix_name="bvco",
-    link="https://github.com/Battery-Value-Chain-Ontology/ontology",
+    see_also=["https://github.com/Battery-Value-Chain-Ontology/ontology"],
 )
 
 import_config = ImportConfig(

examples/ontology_import.py

@@ -27,12 +27,13 @@
 
 ontology_name = "example_ontology"
 
-ex = model.Ontology(
+ex = model.OwlOntology(
     name="Example",
+    label=[model.Label(text="Example", lang="en")],
     iri="http://example.com",
     prefix="http://example.com/",
     prefix_name="example",
-    link="http://example.com",
+    see_also=["http://example.com"],
 )
 
 import_config = ImportConfig(

examples/page_manipulation.py

@@ -124,7 +124,8 @@ def slot_default_values():
     def modify(wtpage: WtPage):
         edit = True
         # print(wtpage.get_last_changed_time())
-        # if wtpage.get_last_changed_time() > datetime.fromisoformat('2023-01-15T12:00:00+00:00'):
+        # if (wtpage.get_last_changed_time() >
+        #     datetime.fromisoformat('2023-01-15T12:00:00+00:00')):
         #    print("new")
         # else:
         #    print("old")

examples/prefect/hello_world.py

@@ -28,14 +28,16 @@ class ConnectionSettings(model.OswBaseModel):
 
 
 @task
-def connect(settings: Optional[ConnectionSettings] = ConnectionSettings()):
+def connect(settings: Optional[ConnectionSettings] = None):
     """Initiates the connection to the OSW instance
 
     Parameters
     ----------
     settings
         see ConnectionSetttings dataclass
     """
+    if settings is None:
+        settings = ConnectionSettings()
     global wtsite
     # define username
     if environ.get("OSW_USER") is not None and environ.get("OSW_USER") != "":

setup.cfg

@@ -84,6 +84,7 @@ S3 = boto3
 
 # Add here dev requirements (semicolon/line-separated)
 dev =
+    pre-commit>=3.2.0
     tox
 
 # Add here test requirements (semicolon/line-separated)

src/osw/auth.py

@@ -289,7 +289,7 @@ def save_credentials_to_file(
         with open(write_to_fp, "r") as stream:
             content = stream.read()
         comment_set = False
-        for ii, fp in enumerate(filepath_):
+        for _ii, fp in enumerate(filepath_):
             if fp.name not in content:
                 print(f"Adding '{fp.name}' to gitignore file '{write_to_fp}'.")
                 with open(write_to_fp, "a") as stream:

src/osw/controller/__init__.py

@@ -1,16 +1,18 @@
-# This file is required to make Python treat directories containing the file as packages.
-# Additionally, classes from multiple files are imported to allow easy access via 'osw.controller.<ClassName>
+# This file is required to make Python treat directories containing the file as
+#  packages.
+# Additionally, classes from multiple files are imported to allow easy access via
+#  'osw.controller.<ClassName>
 
 import inspect
-from pprint import pprint
 
 import osw.model.entity as model
 
 # imports of controllers for always present models
-from osw.controller.entity import Entity
+# note: to keep this import auto-removal per pre-commit hook is disabled
+from osw.controller.entity import Entity  # noqa: F401
 
 # conditional imports
 models = [m[0] for m in inspect.getmembers(model)]
 
 if "Database" in models:
-    from osw.controller.database import DatabaseController
+    from osw.controller.database import DatabaseController  # noqa: F401

src/osw/controller/file/base.py

@@ -16,7 +16,6 @@ def get(self) -> IO:
         -------
             the IO object of the opened file
         """
-        pass
 
     @abstractmethod
     def put(self, file: IO, **kwargs: Dict[str, Any]):
@@ -27,7 +26,6 @@ def put(self, file: IO, **kwargs: Dict[str, Any]):
             file
                 the IO object to read from
         """
-        pass
 
     def put_from(self, other: "FileController", **kwargs: Dict[str, Any]):
         """Writes or uploads a file from another file controller

src/osw/controller/file/remote.py

@@ -7,8 +7,9 @@
 # TODO: add addional remove file with https://docs.prefect.io/2.11.4/concepts/filesystems/
 
 
-# note: the order of the base classes is important
-# the data class must be the first base class, otherwise subclass controllers fall back to the data model of the controller superclass
+# Note: the order of the base classes is important
+# The data class must be the first base class, otherwise subclass controllers fall back
+#  to the data model of the controller superclass
 class RemoteFileController(model.RemoteFile, FileController):
     @abstractmethod
     def get(self) -> IO:

src/osw/controller/file/wiki.py

@@ -42,7 +42,12 @@ def get(self) -> IO:
         web_api_failed = False
         response = None
         try:
-            url = f"{self.osw.site._site.scheme}://{self.osw.site._site.host}{self.osw.site._site.path}api.php?action=download&format=json&title={full_title}"
+            url = (
+                f"{self.osw.site._site.scheme}://"
+                f"{self.osw.site._site.host}"
+                f"{self.osw.site._site.path}"
+                f"api.php?action=download&format=json&title={full_title}"
+            )
             # print("Use web api: ", url)
             response = self.osw.site._site.connection.get(url, stream=True)
             api_error = response.headers.get("Mediawiki-Api-Error")
@@ -63,20 +68,22 @@ def get(self) -> IO:
             # fallback: use direct download
             url = file.imageinfo["url"]
             print(
-                "Extension FileApi not installed on the server. Fallback: use direct download from ",
+                "Extension FileApi not installed on the server. Fallback: use direct "
+                "download from ",
                 url,
             )
             response = self.osw.site._site.connection.get(url, stream=True)
 
         if response.status_code != 200:
             raise Exception(
-                "Download failed. Please note that bot or OAuth logins have in general no permission for direct downloads. Error: "
-                + response.text
+                "Download failed. Please note that bot or OAuth logins have in general "
+                "no permission for direct downloads. Error: " + response.text
             )
 
         # for chunk in response.iter_content(1024):
         #    destination.write(chunk)
-        # see https://stackoverflow.com/questions/16694907/download-large-file-in-python-with-requests
+        # See https://stackoverflow.com/questions/16694907/
+        #  download-large-file-in-python-with-requests
         response.raw.read = functools.partial(response.raw.read, decode_content=True)
         return response.raw
 
@@ -90,7 +97,8 @@ def get_to(self, other: "FileController"):
         ) as response:
             # for chunk in response.iter_content(1024):
             #    destination.write(chunk)
-            # see https://stackoverflow.com/questions/16694907/download-large-file-in-python-with-requests
+            # See https://stackoverflow.com/questions/16694907/
+            #  download-large-file-in-python-with-requests
             response.raw.read = functools.partial(
                 response.raw.read, decode_content=True
             )

src/osw/controller/page_package.py

@@ -200,15 +200,13 @@ def read_package_script_file(script_fp: Path, package_name: str = None) -> dict:
 def get_listed_pages_from_package_script(package_script: dict) -> List[str]:
     """Takes in the output of read_package_script_file and returns a list of
     pages listed in the package"""
-    return getattr(package_script["package_meta_data"], "page_titles")
+    return getattr(package_script["package_meta_data"], "page_titles", [])
 
 
 def get_required_packages_from_package_script(package_script: dict) -> List[str]:
     """Takes in the output of read_package_script_file and returns a list of
     packages listed in the package"""
-    if getattr(package_script["package_meta_data"], "requiredPackages"):
-        return getattr(package_script["package_meta_data"], "requiredPackages")
-    return []
+    return getattr(package_script["package_meta_data"], "requiredPackages", [])
 
 
 def read_package_info_file(