Merge branch 'main' into improve-readme

.github/workflows/ci.yml

@@ -19,14 +19,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install -U setuptools wheel
-
-        while IFS="" read -r line || [ -n "${line}" ]; do
-          if [[ "${line}" =~ ^pre-commit.*$ ]]; then
-            pre_commit="${line}"
-          fi
-        done < dic2owl/requirements_dev.txt
-
-        pip install ${pre_commit}
+        pip install pre-commit
 
     - name: Run pre-commit
       run: SKIP=pylint,mypy,black,bandit,requirements-txt-fixer pre-commit run --all-files

.github/workflows/ci_dependabot.yml

@@ -33,14 +33,7 @@ jobs:
       run: |
         python -m pip install -U pip
         pip install -U setuptools wheel
-
-        while IFS="" read -r line || [ -n "${line}" ]; do
-          if [[ "${line}" =~ ^pre-commit.*$ ]]; then
-            pre_commit="${line}"
-          fi
-        done < dic2owl/requirements_dev.txt
-
-        pip install ${pre_commit}
+        pip install pre-commit
 
     - name: Set up git user info
       run: |
@@ -82,7 +75,7 @@ jobs:
 
     - name: Create PR
       id: cpr
-      uses: peter-evans/create-pull-request@v4
+      uses: peter-evans/create-pull-request@v5
       with:
         token: ${{ secrets.RELEASE_PAT_CWA }}
         commit-message: New @dependabot-fueled updates

.github/workflows/dic2owl_ci.yml

@@ -24,14 +24,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install -U setuptools wheel
-
-        while IFS="" read -r line || [ -n "${line}" ]; do
-          if [[ "${line}" =~ ^pre-commit.*$ ]]; then
-            pre_commit="${line}"
-          fi
-        done < dic2owl/requirements_dev.txt
-
-        pip install ${pre_commit}
+        pip install pre-commit
 
     - name: Run pre-commit
       run: SKIP=pylint pre-commit run --all-files

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.3.0
+  rev: v4.4.0
   hooks:
   - id: check-symlinks
   - id: check-xml
@@ -19,22 +19,22 @@ repos:
     exclude: ^.*(\.ttl|\.cif)$
 
 - repo: https://github.com/ambv/black
-  rev: 22.10.0
+  rev: 23.3.0
   hooks:
   - id: black
     args:
       - --config=dic2owl/pyproject.toml
 
 - repo: https://github.com/PyCQA/bandit
-  rev: '1.7.4'
+  rev: '1.7.5'
   hooks:
   - id: bandit
     args: [-r]
     exclude: ^tests/.*$
     files: ^dic2owl/.*$
 
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v0.982
+  rev: v1.1.1
   hooks:
   - id: mypy
     exclude: ^tests/.*$

dic2owl/dic2owl/cli.py

@@ -5,17 +5,21 @@
 ontology-generation tool for CIF `.dic`-files.
 """
 import argparse
+from typing import TYPE_CHECKING
 
 # import logging
 from pathlib import Path
 
+if TYPE_CHECKING:  # pragma: no cover
+    from typing import List, Optional
+
 
 # LOGGING_LEVELS = [
 #     logging.getLevelName(level).lower() for level in range(0, 51, 10)
 # ]
 
 
-def main(argv: list = None) -> None:
+def main(argv: "Optional[List[str]]" = None) -> None:
     """Ontologize CIF dictionaries (`.dic`) using OWL.
 
     Produce an OWL Turtle (`.ttl`) file from a CIF dictionary (`.dic`) file.

dic2owl/dic2owl/dic2owl.py

@@ -211,7 +211,6 @@ class `cls`.
 
         """
         for annotation_name, value in item.items():
-
             # Add new annotation to generated ontology
             if annotation_name not in self.ddl:
                 raise MissingAnnotationError(annotation_name)

dic2owl/requirements_dev.txt

@@ -1,4 +1,5 @@
-pre-commit~=2.20
-pylint~=2.15
-pytest~=7.1
+pre-commit~=2.21; python_version<"3.8"
+pre-commit~=3.2; python_version>="3.8"
+pylint~=2.17
+pytest~=7.2
 pytest-cov~=4.0