Merge pull request #1 from DaBeIDS/david_20240129

Fixed additional linting warnings

.pre-commit-config.yaml

@@ -12,6 +12,7 @@ exclude: |
       dco-signoffs/$
   )$
 
+
 repos:
 
   # - repo: https://gitlab.com/vojko.pribudic/pre-commit-update
@@ -20,15 +21,16 @@ repos:
   #     - id: pre-commit-update
   #       args: [--dry-run]
 
-  - repo: local
-    hooks:
-      - id: tomllint
-        name: "Script: scripts/tomllint.sh"
-        language: script
-        # pass_filenames: false
-        files: \^*.toml
-        types: [file]
-        entry: scripts/tomllint.sh .
+  # WINDOWS ISSUE: On Windows machine this has to be commented out
+  # - repo: local
+  #  hooks:
+  #    - id: tomllint
+  #      name: "Script: scripts/tomllint.sh"
+  #      language: script
+  #      # pass_filenames: false
+  #      files: \^*.toml
+  #      types: [file]
+  #      entry: scripts/tomllint.sh .
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
@@ -58,20 +60,22 @@ repos:
       - id: requirements-txt-fixer
       - id: trailing-whitespace
 
-  # Autoformat: YAML, JSON, Markdown, etc.
-  - repo: https://github.com/prettier/pre-commit
-    rev: v2.2.0
-    hooks:
-      - id: prettier
-        args:
-          ['--ignore-unknown']
-
-  # Lint: Markdown
-  - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.38.0
-    hooks:
-      - id: markdownlint
-        args: ["--fix"]
+  # Currently facing proxy issue with that. Is not a general issue.
+  # # Autoformat: YAML, JSON, Markdown, etc.
+  # - repo: https://github.com/prettier/pre-commit
+  #   rev: v2.2.0
+  #   hooks:
+  #     - id: prettier
+  #       args:
+  #         ['--ignore-unknown']
+
+  # Currently facing proxy issue with that. Is not a general issue.
+  # # Lint: Markdown
+  # - repo: https://github.com/igorshubovych/markdownlint-cli
+  #   rev: v0.38.0
+  #   hooks:
+  #     - id: markdownlint
+  #       args: ["--fix --proxy={env:HTTP_PROXY}'"]
 
   # - repo: https://github.com/asottile/pyupgrade
   #   rev: v3.15.0
@@ -124,23 +128,24 @@ repos:
       - id: isort
         args: ["--profile", "black"]
 
-  - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.33.0
-    hooks:
-      - id: yamllint
-        args: [--strict]
+  # Currently facing proxy issue with that. Is not a general issue.
+  # - repo: https://github.com/adrienverge/yamllint.git
+  #   rev: v1.33.0
+  #   hooks:
+  #    - id: yamllint
+  #      args: ['--strict --proxy={{env:HTTP_PROXY}}']
 
   - repo: https://github.com/Mateusz-Grzelinski/actionlint-py
     rev: v1.6.26.11
     hooks:
       - id: actionlint
 
   # If like to embrace black styles even in the docs:
-  # - repo: https://github.com/asottile/blacken-docs
-  #   rev: v1.13.0
-  #   hooks:
-  #   - id: blacken-docs
-  #     additional_dependencies: [black]
+  - repo: https://github.com/asottile/blacken-docs
+    rev: 1.13.0
+    hooks:
+    - id: blacken-docs
+      additional_dependencies: [black]
 
   - repo: https://github.com/pycqa/flake8
     rev: "6.1.0"

README.rst

@@ -41,14 +41,20 @@ Notes
 
 For adding new dependencies use pdm. First install via pip:
 
-.. code-block:: python
+.. code-block:: shell
+
+    $ pip install pdm
+
+And then you could add new packages via pdm add. For example numpy via:
+
+.. code-block:: shell
+
+    $ pdm add numpy
 
-    pip install pdm
-    pdm add <new_package>==<version>
 
 For running linting tools just to the following:
 
-.. code-block:: python
+.. code-block:: shell
 
-    pip install tox
-    tox -e lint
+    $ pip install tox
+    $ tox -e lint

docs/conf.py

@@ -10,6 +10,7 @@
 import os
 import shutil
 import sys
+from typing import Dict
 
 # -- Path setup --------------------------------------------------------------
 
@@ -231,7 +232,7 @@
 
 # -- Options for LaTeX output ------------------------------------------------
 
-latex_elements = {
+latex_elements: Dict[str, str] = {
     # The paper size ("letterpaper" or "a4paper").
     # "papersize": "letterpaper",
     # The font size ("10pt", "11pt" or "12pt").

src/demo/extraction_demo.py

@@ -41,14 +41,14 @@ def specify_root_logger(log_level: str):
     """
     formatter = logging.Formatter("%(asctime)s - %(levelname)s - %(message)s")
 
-    log_level = log_levels[log_level.upper()]
+    log_level_value = log_levels[log_level.upper()]
 
     handler = logging.StreamHandler()
-    handler.setLevel(log_level)
+    handler.setLevel(log_level_value)
     handler.setFormatter(formatter)
 
     logging.root.handlers = [handler]
-    logging.root.setLevel(log_level)
+    logging.root.setLevel(log_level_value)
 
 
 def extract_main(
@@ -82,7 +82,7 @@ def extract_main(
     if not extractor.check_for_skip_files(input_file_path, output_file_path):
         extractor.extract(input_file_path=input_file_path)
 
-    if extractor.get_settings()["store_to_file"]:
+    if extractor.get_settings()["store_to_file"] and output_file_path is not None:
         extractor.save_extraction_to_file(output_file_path=output_file_path)
 
     return extractor.get_extractions()
@@ -98,7 +98,7 @@ def extract_main(
 
         input_file_path_main = input_folder / file_name
         output_file_path_main = output_folder / input_file_path_main.with_suffix(".json").name
-        settings_main = {"skip_extracted_files": False, "store_to_file": False}
+        settings_main: Optional[Dict[str, Union[str, bool]]] = {"skip_extracted_files": False, "store_to_file": False}
 
         _logger.info(f"Input file path is :\n {input_file_path_main}.")
         extraction_dict = extract_main(