lint/deps

.github/workflows/ci.yml

@@ -1,12 +1,11 @@
 name: CI Pipeline (PRs and pushes main)
 run-name: Merged to main by ${{ github.actor }}
+
 on:
   push:
-    branches:
-      - main
+    branches: [main]
   pull_request:
-    branches:
-      - main
+    branches: [main]
 
 permissions:
   contents: read
@@ -23,16 +22,16 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          cache: pip
 
-      - name: Install package with pip
-        run: |
-          python -m pip install --upgrade pip
-          pip install .[dev]
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+
+      - name: Install dependencies
+        run: uv sync --group dev
 
       - name: Run tests
-        run: pytest
+        run: uv run pytest

.github/workflows/publish_pypi.yml

@@ -51,4 +51,4 @@ jobs:
           name: python-package-distributions
           path: dist/
       - name: Publish distribution package to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@release/v1

.pre-commit-config.yaml

@@ -1,19 +1,58 @@
 fail_fast: true
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v6.0.0
   hooks:
+    - id: check-ast
+    - id: check-builtin-literals
+    - id: check-case-conflict
+    - id: check-docstring-first
+    - id: check-illegal-windows-names
+    - id: check-merge-conflict
+    - id: check-shebang-scripts-are-executable
+    - id: check-symlinks
+    - id: check-toml
     - id: check-yaml
-- repo: https://github.com/astral-sh/uv-pre-commit
-  rev: 0.9.5
+    - id: debug-statements
+    - id: end-of-file-fixer
+    - id: mixed-line-ending
+    - id: trailing-whitespace
+- repo: https://github.com/fpgmaas/deptry
+  rev: 0.24.0
   hooks:
-    - id: uv-lock
+    - id: deptry
+      language: python
+      additional_dependencies: [deptry]
+      exclude: '^(?!.*\.py$).*$'
+- repo: https://github.com/asottile/pyupgrade
+  rev: v3.21.2
+  hooks:
+    - id: pyupgrade
+- repo: https://github.com/asottile/add-trailing-comma
+  rev: v4.0.0
+  hooks:
+      - id: add-trailing-comma
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.5.0
+  rev: v0.14.14
   hooks:
-    - id: ruff
-      args: [ --fix ]
+    - id: ruff-check
+      args:
+        - --fix
     - id: ruff-format
+- repo: https://github.com/astral-sh/uv-pre-commit
+  rev: 0.9.28
+  hooks:
+    - id: uv-lock
+- repo: https://github.com/tombi-toml/tombi-pre-commit
+  rev: v0.7.25
+  hooks:
+    - id: tombi-format
+    - id: tombi-lint
+- repo: https://github.com/crate-ci/typos
+  rev: v1
+  hooks:
+  - id: typos
+    exclude: "^tests/"
 - repo: local
   hooks:
     - id: uv-upgrade
@@ -25,4 +64,4 @@ repos:
       name: pytest
       entry: uv run pytest
       language: system
-      pass_filenames: false
+      pass_filenames: false

CHANGELOG.md

@@ -42,7 +42,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ### Changed
 
 - In html_json generation, changed substrate from tuple to list of tuples to visualize substrates separately
-- Changed Wikidata QID checking from raise errror to log warning (frequent 403 errors)
+- Changed Wikidata QID checking from raise error to log warning (frequent 403 errors)
 
 ## [1.5.1] 26-07-2025
 
@@ -75,7 +75,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 - Bumped `mite_schema` version to `1.7.0`
 - Reworked `ValidationManager`
 - Implemented option for intramolecular reactions (recognized from reaction SMARTS)
-- Pinned RDkit version to `2024.3.6` 
+- Pinned RDkit version to `2024.3.6`
 
 ## [1.3.1] 02-12-2024
 
@@ -142,4 +142,4 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ### Added
 
-- Initial version of `mite_extras`
+- Initial version of `mite_extras`

CODE_OF_CONDUCT.md

@@ -1,3 +1,3 @@
 # CODE OF CONDUCT
 
-See our organization-level [Code of Conduct](https://github.com/mite-standard/.github/blob/main/CODE_OF_CONDUCT.md).
+See our organization-level [Code of Conduct](https://github.com/mite-standard/.github/blob/main/CODE_OF_CONDUCT.md).

README.md

@@ -1,7 +1,7 @@
 mite_extras
 ==========
 
-[![DOI](https://zenodo.org/badge/804997522.svg)](https://doi.org/10.5281/zenodo.13941745) 
+[![DOI](https://zenodo.org/badge/804997522.svg)](https://doi.org/10.5281/zenodo.13941745)
 [![PyPI version](https://badge.fury.io/py/mite-extras.svg)](https://badge.fury.io/py/mite-extras)
 
 
@@ -59,7 +59,7 @@ Dependencies including exact versions are specified in the [pyproject.toml](./py
 
 ## Quick Start
 
-To validate MITE entries or update them to a new schema versiom, run:
+To validate MITE entries or update them to a new schema version, run:
 
 - `mite_extras -i <input/> -o <output/>`
 
@@ -87,7 +87,7 @@ This work was supported by the Netherlands Organization for Scientific Research
 
 ### With `uv` from GitHub
 
-*Note: assumes that `uv` is installed locally - see the methods described [here](https://docs.astral.sh/uv/getting-started/installation/).* 
+*Note: assumes that `uv` is installed locally - see the methods described [here](https://docs.astral.sh/uv/getting-started/installation/).*
 
 ```commandline
 git clone https://github.com/mite-standard/mite_extras

src/mite_extras/main.py → mite_extras/main.py

@@ -46,8 +46,8 @@ def config_logger(verboseness: str) -> logging.Logger:
     console_handler = logging.StreamHandler(sys.stdout)
     console_handler.setFormatter(
         coloredlogs.ColoredFormatter(
-            "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
-        )
+            "%(asctime)s - %(name)s - %(levelname)s - %(message)s",
+        ),
     )
     logger.addHandler(console_handler)
     return logger

src/mite_extras/processing/data_classes.py → mite_extras/processing/data_classes.py

@@ -168,7 +168,7 @@ def to_json(self: Self) -> dict:
 
         if self.databaseIds.to_json() == {}:
             raise RuntimeError(
-                "At least one of 'uniprot' and 'genpept' IDs must be provided."
+                "At least one of 'uniprot' and 'genpept' IDs must be provided.",
             )
         else:
             json_dict["databaseIds"] = self.databaseIds.to_json()
@@ -271,7 +271,8 @@ def validate_ids(self):
         try:
             if self.uniprot and self.genpept:
                 self._id_validator.cleanup_ids(
-                    genpept=self.genpept, uniprot=self.uniprot
+                    genpept=self.genpept,
+                    uniprot=self.uniprot,
                 )
             elif self.uniprot:
                 data = self._id_validator.cleanup_ids(uniprot=self.uniprot)
@@ -336,8 +337,8 @@ def cleanup_smarts(self):
             cleaned_smarts = (
                 self._reaction_validator.reaction_cleaner.clean_ketcher_format(
                     self._reaction_validator.molecule_validator._clean_string(
-                        self.reactionSMARTS
-                    )
+                        self.reactionSMARTS,
+                    ),
                 )
             )
 
@@ -372,7 +373,7 @@ def validate_reactions(self):
                 )
             except Exception as e:
                 raise ValueError(
-                    f"Reaction SMARTS #{reaction_id} - reaction example #{reaction}: Validation failed for substrate {reaction.substrate}: {e!s}"
+                    f"Reaction SMARTS #{reaction_id} - reaction example #{reaction}: Validation failed for substrate {reaction.substrate}: {e!s}",
                 ) from e
         return self
 
@@ -460,13 +461,13 @@ def validate_smiles(self):
         try:
             # Clean substrate SMILES
             self.substrate = self._molecule_validator.canonicalize_smiles(
-                self._molecule_validator._clean_string(self.substrate)
+                self._molecule_validator._clean_string(self.substrate),
             )
 
             # Clean product SMILES
             self.products = [
                 self._molecule_validator.canonicalize_smiles(
-                    self._molecule_validator._clean_string(prod)
+                    self._molecule_validator._clean_string(prod),
                 )
                 for prod in self.products
             ]
@@ -476,7 +477,7 @@ def validate_smiles(self):
                 cleaned_forbidden = []
                 for prod in self.forbidden_products:
                     cleaned = self._molecule_validator.canonicalize_smiles(
-                        self._molecule_validator._clean_string(prod)
+                        self._molecule_validator._clean_string(prod),
                     )
                     # Split composite SMILES into individual molecules
                     cleaned_forbidden.extend(cleaned.split("."))
@@ -505,7 +506,7 @@ def to_json(self: Self) -> dict:
 
     def to_html(self: Self) -> dict:
         def _smiles_to_svg(smiles: str) -> str:
-            """Generates a base64 encoded SVG strin"""
+            """Generates a base64 encoded SVG string"""
             m = MolFromSmiles(smiles)
 
             for atom in m.GetAtoms():
@@ -538,7 +539,7 @@ def _smiles_to_svg(smiles: str) -> str:
             ]
         except Exception as e:
             logger.warning(
-                f"Error during splitting substrate SMILES for rendering: {e!s}"
+                f"Error during splitting substrate SMILES for rendering: {e!s}",
             )
             html_dict["substrate"] = [(self.substrate, _smiles_to_svg(self.substrate))]
 

src/mite_extras/processing/file_manager.py → mite_extras/processing/file_manager.py

@@ -60,19 +60,19 @@ def validate_exists(self):
     def read_files_indir(self: Self) -> None:
         """Read files in the indir, store to self"""
         logger.debug(
-            f"FileManager: started reading file in input directory '{self.indir.name}'."
+            f"FileManager: started reading file in input directory '{self.indir.name}'.",
         )
 
         for infile in self.indir.iterdir():
             if infile.suffix != ".json":
                 logger.warning(
-                    f"FileManager: file '{infile.name}' does not apprear to be in .json-format - SKIP."
+                    f"FileManager: file '{infile.name}' does not appear to be in .json-format - SKIP.",
                 )
                 continue
             self.infiles.append(infile)
 
         logger.debug(
-            f"FileManager: completed reading file in input directory '{self.indir.name}'."
+            f"FileManager: completed reading file in input directory '{self.indir.name}'.",
         )
 
     def write_json(self: Self, outfile_name: str, payload: dict) -> None:

src/mite_extras/processing/mite_parser.py → mite_extras/processing/mite_parser.py

@@ -123,7 +123,7 @@ def get_databaseids_reaction(
             return ReactionDatabaseIds(**data)
 
     def get_reactions(self: Self, reactions: list) -> list:
-        """Extract reactions infor and converts into internal data structure
+        """Extract reactions info and converts into internal data structure
 
         Args:
             reactions: list with reaction data
@@ -166,19 +166,19 @@ def parse_mite_json(self: Self, data: dict):
                     description=data.get("enzyme", {}).get("description"),
                     databaseIds=EnyzmeDatabaseIds(**data["enzyme"]["databaseIds"]),
                     auxiliaryEnzymes=self.get_auxenzymes(
-                        auxenzymes=data.get("enzyme", {}).get("auxiliaryEnzymes")
+                        auxenzymes=data.get("enzyme", {}).get("auxiliaryEnzymes"),
                     ),
                     references=data.get("enzyme", {}).get("references"),
                     cofactors=self.get_cofactors(
-                        cofactors=data.get("enzyme", {}).get("cofactors")
+                        cofactors=data.get("enzyme", {}).get("cofactors"),
                     ),
                 ),
                 reactions=self.get_reactions(reactions=data.get("reactions")),
                 comment=data.get("comment"),
             )
         except Exception as e:
             msg = str(e).split("For further information visit")[0].rstrip()
-            msg = f"Error in parsing entry {data.get("accession")}: {msg}"
+            msg = f"Error in parsing entry {data.get('accession')}: {msg}"
             raise ValueError(msg) from e
 
         logger.debug("MiteParser: completed creating Entry object.")