Merge branch 'release-0.9.1' into support-0.9.x

Author: ajnelson-nist

.github/workflows/cicd.yml

@@ -13,13 +13,15 @@ name: Continuous Integration
 
 on:
   push:
-    branches: 
+    branches:
       - main
       - develop
+      - support-*
   pull_request:
-    branches: 
+    branches:
       - main
       - develop
+      - support-*
   release:
     types:
       - published
@@ -30,8 +32,8 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: 
-          - '3.7'
+        python-version:
+          - '3.8'
           - '3.11'
 
     steps:
@@ -52,7 +54,7 @@ jobs:
       run: make clean
     - name: Run tests
       run: make PYTHON3=python check
-    
+
     # Build the binary wheel as well as the source tar
     - name: Build Objects
       run: |

.pre-commit-config.yaml

@@ -1,14 +1,14 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 22.10.0
+    rev: 23.12.0
     hooks:
       - id: black
   - repo: https://github.com/pycqa/flake8
-    rev: 5.0.4
+    rev: 6.1.0
     hooks:
       - id: flake8
   - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+    rev: 5.13.2
     hooks:
       - id: isort
         name: isort (python)

case_utils/__init__.py

@@ -11,6 +11,6 @@
 #
 # We would appreciate acknowledgement if the software is used.
 
-__version__ = "0.9.0"
+__version__ = "0.9.1"
 
 from . import local_uuid  # noqa: F401

case_utils/case_file/__init__.py

@@ -39,6 +39,7 @@
 
 DEFAULT_PREFIX = "http://example.org/kb/"
 
+
 # Shortcut syntax for defining an immutable named tuple is noted here:
 # https://docs.python.org/3/library/typing.html#typing.NamedTuple
 # via the "See also" box here: https://docs.python.org/3/library/collections.html#collections.namedtuple

case_utils/case_sparql_construct/__init__.py

@@ -98,7 +98,7 @@ def main() -> None:
     construct_query_result = in_graph.query(construct_query_object)
     _logger.debug("type(construct_query_result) = %r." % type(construct_query_result))
     _logger.debug("len(construct_query_result) = %d." % len(construct_query_result))
-    for (row_no, row) in enumerate(construct_query_result):
+    for row_no, row in enumerate(construct_query_result):
         if row_no == 0:
             _logger.debug("row[0] = %r." % (row,))
         out_graph.add(row)

case_utils/case_sparql_select/__init__.py

@@ -86,10 +86,10 @@ def graph_and_query_to_data_frame(
     select_query_object = rdflib.plugins.sparql.processor.prepareQuery(
         select_query_text, initNs=nsdict
     )
-    for (row_no, row) in enumerate(_graph.query(select_query_object)):
+    for row_no, row in enumerate(_graph.query(select_query_object)):
         tally = row_no + 1
         record = []
-        for (column_no, column) in enumerate(row):
+        for column_no, column in enumerate(row):
             if column is None:
                 column_value = ""
             elif (

case_utils/local_uuid.py

@@ -32,9 +32,25 @@
 _logger = logging.getLogger(pathlib.Path(__file__).name)
 
 
+def _is_relative_to(p1: pathlib.Path, p2: pathlib.Path) -> bool:
+    """
+    This function provides pathlib.is_relative_to to Pythons before 3.9.  After the End of Life of Python 3.8, this function can be removed.
+    """
+    if sys.version_info < (3, 9):
+        try:
+            _ = p1.relative_to(p2)
+            return True
+        except ValueError:
+            return False
+    else:
+        return p1.is_relative_to(p2)
+
+
 def configure() -> None:
     global DEMO_UUID_BASE
 
+    # _logger.debug("sys.argv = %r.", sys.argv)
+
     if os.getenv("DEMO_UUID_REQUESTING_NONRANDOM") == "NONRANDOM_REQUESTED":
         warnings.warn(
             "Environment variable DEMO_UUID_REQUESTING_NONRANDOM is deprecated.  See case_utils.local_uuid.demo_uuid for usage notes on its replacement, CASE_DEMO_NONRANDOM_UUID_BASE.  Proceeding with random UUIDs.",
@@ -84,18 +100,23 @@ def configure() -> None:
         demo_uuid_base_parts.append(sys.argv[0])
     else:
         command_original_path = pathlib.Path(sys.argv[0])
+        # _logger.debug("command_original_path = %r.", command_original_path)
         command_resolved_path = command_original_path.resolve()
+        # _logger.debug("command_resolved_path = %r.", command_resolved_path)
+
+        # The command could be a command embedded in a virtual
+        # environment, or it could be a script external to any virtual
+        # environment.
         venv_original_path = pathlib.Path(env_venv_name)
         venv_resolved_path = venv_original_path.resolve()
-        try:
+        if _is_relative_to(command_resolved_path, venv_resolved_path):
             command_relative_path = command_resolved_path.relative_to(
                 venv_resolved_path
             )
             # _logger.debug("command_relative_path = %r.", command_relative_path)
             demo_uuid_base_parts.append(str(command_relative_path))
-        except ValueError:
-            # _logger.debug("Command path is not relative to virtual environment path.")
-            demo_uuid_base_parts.append(str(command_resolved_path))
+        else:
+            demo_uuid_base_parts.append(str(command_original_path))
 
     if len(sys.argv) > 1:
         # Component: Arguments of argument vector.

case_utils/ontology/src/ontology_and_version_iris.py

@@ -28,7 +28,8 @@
 
 def concept_is_cdo_concept(n_concept: rdflib.URIRef) -> bool:
     """
-    This function is purposefully distinct from the function used in case_validate.  Within this script, the publishing history of CASE and UCO is reviewed."""
+    This function is purposefully distinct from the function used in case_validate.  Within this script, the publishing history of CASE and UCO is reviewed.
+    """
     concept_iri = str(n_concept)
     return (
         concept_iri.startswith("https://ontology.unifiedcyberontology.org/")

setup.cfg

@@ -19,13 +19,13 @@ license_files =
 [options]
 include_package_data = true
 install_requires =
-    pandas
+    pandas < 2.1.0
     pyshacl
-    rdflib >= 6.2.0
+    rdflib >= 6.2.0, < 6.3.0
     requests
     tabulate
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8
 
 [options.entry_points]
 console_scripts =

tests/case_utils/case_sparql_select/test_data_frame_to_table_text_json.py

@@ -36,9 +36,9 @@
 )
 
 
-def make_data_frame_to_json_table_text_parameters() -> typing.Iterator[
-    typing.Tuple[str, str, bool, bool]
-]:
+def make_data_frame_to_json_table_text_parameters() -> (
+    typing.Iterator[typing.Tuple[str, str, bool, bool]]
+):
     for use_header in [False, True]:
         for use_index in [False, True]:
             for output_mode in ["csv", "html", "json", "md", "tsv"]: