Merge pull request #146 from casework/release-0.5.1

Release 0.5.1

.github/workflows/cicd.yml

@@ -13,24 +13,35 @@ name: Continuous Integration
 
 on:
   push:
-    branches: [ main, develop ]
+    branches:
+      - main
+      - develop
+      - support-*
   pull_request:
-    branches: [ main, develop ]
+    branches:
+      - main
+      - develop
+      - support-*
+  release:
+    types:
+      - published
 
 jobs:
   build:
 
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.7', '3.10' ]
+        python-version:
+          - '3.8'
+          - '3.10'
 
     steps:
     - uses: actions/checkout@v2
-    - uses: actions/setup-java@v2
+    - uses: actions/setup-java@v3
       with:
-        distribution: 'adopt'
-        java-version: '8'
+        distribution: 'temurin'
+        java-version: '11'
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
@@ -43,7 +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: |
@@ -65,5 +76,5 @@ jobs:
     # If this commit is the result of a Git tag, push the wheel and tar packages
     # to the PyPi registry
     - name: Publish to PyPI
-      if: startsWith(github.ref, 'refs/tags')
+      if: github.event_name == 'release' && github.event.action == 'published'
       run: twine upload --repository-url https://upload.pypi.org/legacy/ -u __token__ -p ${{ secrets.PYPI_API_TOKEN }} --skip-existing --verbose dist/*

.pre-commit-config.yaml

@@ -1,5 +1,5 @@
 repos:
 -   repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 23.12.0
     hooks:
     -   id: black

case_utils/__init__.py

@@ -11,6 +11,6 @@
 #
 # We would appreciate acknowledgement if the software is used.
 
-__version__ = "0.5.0"
+__version__ = "0.5.1"
 
 from . import local_uuid

case_utils/case_file/__init__.py

@@ -32,6 +32,7 @@
 
 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

@@ -96,7 +96,7 @@ 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

@@ -109,10 +109,10 @@ def main() -> None:
     select_query_object = rdflib.plugins.sparql.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.",
@@ -82,18 +98,23 @@ 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.

setup.cfg

@@ -21,11 +21,11 @@ include_package_data = true
 install_requires =
     pandas
     pyshacl
-    rdflib >= 6.0.2
+    rdflib >= 6.0.2, < 6.3.0
     requests
     tabulate
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8
 
 [options.entry_points]
 console_scripts =

tests/Makefile

@@ -22,6 +22,7 @@ all: \
 
 .PHONY: \
   all-case_utils \
+  all-lib \
   check-case_utils \
   check-isomorphic_diff \
   check-mypy \
@@ -53,10 +54,15 @@ all: \
 	touch $@
 
 all-case_utils: \
-  .venv.done.log
+  .venv.done.log \
+  all-lib
 	$(MAKE) \
 	  --directory case_utils
 
+all-lib:
+	$(MAKE) \
+	  --directory lib
+
 # These check calls are provided in preferred run-order.
 check: \
   check-mypy \
@@ -68,7 +74,8 @@ check: \
 	    --log-level=DEBUG
 
 check-case_utils: \
-  .venv.done.log
+  .venv.done.log \
+  all-lib
 	$(MAKE) \
 	  --directory case_utils \
 	  check

tests/case_utils/case_file/Makefile

@@ -17,9 +17,7 @@ top_srcdir := $(shell cd ../../.. ; pwd)
 
 tests_srcdir := $(top_srcdir)/tests
 
-case_srcdir := $(top_srcdir)/dependencies/CASE
-
-RDF_TOOLKIT_JAR := $(case_srcdir)/lib/rdf-toolkit.jar
+RDF_TOOLKIT_JAR := $(tests_srcdir)/lib/rdf-toolkit.jar
 
 all: \
   kb.json \

tests/case_utils/case_validate/case_test_examples/Makefile

@@ -15,13 +15,11 @@ SHELL := /bin/bash
 
 top_srcdir := $(shell cd ../../../.. ; pwd)
 
-case_srcdir := $(top_srcdir)/dependencies/CASE
-
-examples_srcdir := $(case_srcdir)/tests/examples
+examples_srcdir := $(top_srcdir)/dependencies/CASE/tests/examples
 
 tests_srcdir := $(top_srcdir)/tests
 
-RDF_TOOLKIT_JAR := $(case_srcdir)/lib/rdf-toolkit.jar
+RDF_TOOLKIT_JAR := $(tests_srcdir)/lib/rdf-toolkit.jar
 
 all: \
   investigative_action_PASS_validation.ttl \

tests/case_utils/case_validate/cli/Makefile

@@ -21,7 +21,7 @@ examples_srcdir := $(case_srcdir)/tests/examples
 
 tests_srcdir := $(top_srcdir)/tests
 
-RDF_TOOLKIT_JAR := $(case_srcdir)/lib/rdf-toolkit.jar
+RDF_TOOLKIT_JAR := $(tests_srcdir)/lib/rdf-toolkit.jar
 
 files_to_generate := \
   format_human_output_jsonld.jsonld \

tests/case_utils/case_validate/uco_test_examples/Makefile

@@ -15,15 +15,11 @@ SHELL := /bin/bash
 
 top_srcdir := $(shell cd ../../../.. ; pwd)
 
-case_srcdir := $(top_srcdir)/dependencies/CASE
-
-uco_srcdir := $(case_srcdir)/dependencies/UCO
-
-examples_srcdir := $(uco_srcdir)/tests/examples
+examples_srcdir := $(top_srcdir)/dependencies/CASE/dependencies/UCO/tests/examples
 
 tests_srcdir := $(top_srcdir)/tests
 
-RDF_TOOLKIT_JAR := $(case_srcdir)/lib/rdf-toolkit.jar
+RDF_TOOLKIT_JAR := $(tests_srcdir)/lib/rdf-toolkit.jar
 
 all: \
   action_inheritance_PASS_validation.ttl \

tests/lib/.gitignore

@@ -0,0 +1 @@
+*.jar

tests/lib/Makefile

@@ -0,0 +1,38 @@
+#!/usr/bin/make -f
+
+# Portions of this file contributed by NIST are governed by the
+# following statement:
+#
+# This software was developed at the National Institute of Standards
+# and Technology by employees of the Federal Government in the course
+# of their official duties. Pursuant to Title 17 Section 105 of the
+# United States Code, this software is not subject to copyright
+# protection within the United States. NIST assumes no responsibility
+# whatsoever for its use by other parties, and makes no guarantees,
+# expressed or implied, about its quality, reliability, or any other
+# characteristic.
+#
+# We would appreciate acknowledgement if the software is used.
+
+# This Makefile is incorporated to support versions of case-utils since
+# 0.5.0 that had not yet incorporated rdf-toolkit-1.11.0.jar into their
+# testing process.  The Makefile is adapted from the `/lib` directory of
+# UCO at version 1.2.0.
+
+SHELL := /bin/bash
+
+all: \
+  rdf-toolkit.jar
+
+rdf-toolkit.jar:
+	test -r rdf-toolkit.jar.sha512
+	rm -f $@_
+	# Try retrieval from files.caseontology.org.
+	wget \
+	  --output-document $@_ \
+	  https://files.caseontology.org/rdf-toolkit-1.11.0.jar
+	test \
+	  "x$$(openssl dgst -sha512 $@_ | awk '{print($$NF)}')" \
+	  == \
+	  "x$$(head -n1 rdf-toolkit.jar.sha512)"
+	mv $@_ $@

tests/lib/rdf-toolkit.jar.sha512

@@ -0,0 +1 @@
+8131e5515da63f099a89a3ce2c7587fb6b228f1ec7c5eb49ff35710509e8511921bfc847e182ee994e575b1f7895c04ae5bed7e1b7826bb32c9475b43b74dc17