Merge remote-tracking branch 'origin/main' into improve-readme

.github/static/get_dic2owl_deps.py

@@ -31,7 +31,7 @@ def main(argv_input: list = None) -> Set[str]:
     for file in args.requirements_files:
         if not file.exists():
             raise FileNotFoundError(f"Could not find {file} !")
-        with open(file.resolve(), "r") as handle:
+        with open(file.resolve(), "r", encoding="utf8") as handle:
             for line in handle.readlines():
                 match = requirements_regex.fullmatch(line)
                 if match is None:

.github/workflows/ci.yml

@@ -8,12 +8,12 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Set up Python 3.7
       uses: actions/setup-python@v4
       with:
-        python-version: 3.7
+        python-version: '3.7'
 
     - name: Install dependencies
       run: |

.github/workflows/ci_automerge_dependabot.yml

@@ -17,7 +17,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
         ref: ${{ github.event.pull_request.head.ref }}

.github/workflows/ci_cd_updated_main.yml

@@ -18,7 +18,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         ref: ${{ env.DEPENDABOT_BRANCH }}
         fetch-depth: 0

.github/workflows/ci_dependabot.yml

@@ -20,14 +20,14 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         ref: ${{ env.DEFAULT_REPO_BRANCH }}
 
     - name: Set up Python 3.7
       uses: actions/setup-python@v4
       with:
-        python-version: 3.7
+        python-version: '3.7'
 
     - name: Install `pre-commit` and dependencies
       run: |
@@ -69,7 +69,7 @@ jobs:
 
     - name: Fetch PR body
       id: pr_body
-      uses: chuhlomin/render-template@v1.6
+      uses: chuhlomin/render-template@v1.8
       with:
         template: .github/static/single_dependency_pr_body.txt
 

.github/workflows/dic2owl_ci.yml

@@ -13,12 +13,12 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Set up Python 3.7
       uses: actions/setup-python@v4
       with:
-        python-version: 3.7
+        python-version: '3.7'
 
     - name: Install dependencies
       run: |
@@ -35,12 +35,12 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Set up Python 3.7
       uses: actions/setup-python@v4
       with:
-        python-version: 3.7
+        python-version: '3.7'
 
     - name: Install dependencies
       run: |
@@ -53,21 +53,22 @@ jobs:
     - name: Run PyLint
       run: pylint --rcfile=dic2owl/pyproject.toml dic2owl/**/*.py
 
-      # Ignore ID 44715 for now.
-      # See this NumPy issue for more information: https://github.com/numpy/numpy/issues/19038
-      # Remove ignoring 48547 as soon as RDFLib/rdflib#1844 has been fixed and the fix
-      # has been released.
+      # Ignore ID 44715, 44716, and 44717 for now.
+      # See this NumPy issue for more information:
+      # https://github.com/numpy/numpy/issues/19038
+      # When dropping Python 3.7 support, these vulnerabilities are fixed and can be
+      # removed from the ignore list.
     - name: Run safety
-      run: pip freeze | safety check --stdin --ignore 44715 --ignore 44716 --ignore 44717 --ignore 48547
+      run: pip freeze | safety check --stdin --ignore 44715 --ignore 44716 --ignore 44717
 
   dic2owl-test:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ['3.7', '3.8', '3.9']
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4

.pre-commit-config.yaml

@@ -1,5 +1,9 @@
+default_language_version:
+  python: python3.7
+
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
+  # Keep at v4.4.0 to support Python 3.7
   rev: v4.4.0
   hooks:
   - id: check-symlinks
@@ -19,6 +23,7 @@ repos:
     exclude: ^.*(\.ttl|\.cif)$
 
 - repo: https://github.com/ambv/black
+  # Keep at 23.3.0 to support Python 3.7
   rev: 23.3.0
   hooks:
   - id: black
@@ -34,7 +39,8 @@ repos:
     files: ^dic2owl/.*$
 
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.1.1
+  # Keep at v1.4.1 to support Python 3.7
+  rev: v1.4.1
   hooks:
   - id: mypy
     exclude: ^tests/.*$

README.md

@@ -1,4 +1,6 @@
 [![CI tests](https://github.com/emmo-repo/CIF-ontology/workflows/CI/badge.svg)](https://github.com/emmo-repo/CIF-ontology/actions/)
+[![DOI](https://zenodo.org/badge/272473769.svg)](https://zenodo.org/badge/latestdoi/272473769)
+
 
 CIF Ontology
 ============

dic2owl/dic2owl/dic2owl.py

@@ -77,10 +77,6 @@ class Generator:
         "ontology/cif-ddl.ttl"
     )
 
-    # TODO:
-    # Should `comments` be replaced with a dict `annotations` for annotating
-    # the ontology itself?  If so, we should import Dublin Core.
-
     def __init__(
         self,
         dicfile: "StrPath",
@@ -187,10 +183,8 @@ def _add_data_value(self, item: dict) -> None:
         for ddl_name, value in item.items():
             if ddl_name.startswith("_type."):
                 if ddl_name == "_type.dimension":
-                    # TODO - fix special case
                     pass
                 elif value == "Implied":
-                    # TODO - fix special case
                     pass
                 else:
                     parents.append(self.ddl[value])
@@ -221,11 +215,6 @@ class `cls`.
 
     def _add_metadata(self) -> None:
         """Adds metadata to the generated ontology."""
-        # TODO:
-        # Is there a way to extract metadata from the dic object like
-        # _dictionary_audit.version?
-        # onto.set_version(version="XXX")
-
         for comment in self.comments:
             self.onto.metadata.comment.append(comment)
         self.onto.metadata.comment.append(
@@ -275,4 +264,4 @@ def main(
         overwrite=True,
     )
 
-    return gen  # XXX - just for debugging
+    return gen