Update ontoenv (#120)

* poetry -> uv, fix dependencies for ontoenv

* working on tests

* ci: Migrate GitHub Actions workflow to uv

Co-authored-by: aider (gemini/gemini-2.5-flash) <[email protected]>

* fix install

* nolock

* fix python?

* add pytest

* extras, python versions

---------

Co-authored-by: aider (gemini/gemini-2.5-flash) <[email protected]>

Author: gtfierro

.github/workflows/builds.yml

@@ -13,40 +13,26 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@v6
         with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-          installer-parallel: true
+          python-version: ${{ matrix.python-version }}
+          # Enable caching for uv
+          enable-cache: true
       - name: Set up Java
         uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
           java-version: '17'
-      - name: Load cached venv
-        id: cached-poetry-dependencies
-        uses: actions/cache@v4
-        with:
-          path: .venv
-          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
-      - name: Install dependencies for Python 3.11
-        # we do *not* install the dedupe extra because its dependency on PyLBFGS requires an older version
-        # of Cython that is not available in python 3.11
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' && matrix.python-version == '3.11'
-        run: poetry install --no-interaction --no-root -E allegro -E brickify -E web -E orm -E reasonable -E persistence -E bacnet -E networkx
       - name: Install all dependencies for other Python versions
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' && matrix.python-version != '3.11'
-        run: poetry install --no-interaction --no-root --all-extras
+        run: uv sync --all-extras
       - name: Run tests
-        run: |
-          source .venv/bin/activate
-          pytest -s -vvvv
+        run: uv run pytest -s -vvvv
 

brickschema/graph.py

@@ -127,15 +127,7 @@ def validate(
                 allow_warnings=True,
             )
         elif engine == "topquadrant":
-            # check if 'java' is in the path
-            import shutil
-
-            if shutil.which("java") is None:
-                raise Exception(
-                    "TopQuadrant SHACL validation requires Java to be installed and in the PATH"
-                )
-            from brickschema.topquadrant_shacl import validate
-
+            from brick_tq_shacl.pyshacl import validate
             if shape_graphs is not None and isinstance(shape_graphs, list):
                 for sg in shape_graphs:
                     shapes += sg
@@ -263,21 +255,12 @@ def expand(
             return
         elif profile == "shacl":
             if backend == "topquadrant":
-                # check if 'java' is in the path
-                import shutil
-
-                if shutil.which("java") is None:
-                    raise Exception(
-                        "TopQuadrant SHACL validation requires Java to be installed and in the PATH"
-                    )
-                from brickschema.topquadrant_shacl import infer
-
+                from brick_tq_shacl.pyshacl import infer
                 # 'res' is a de-skolemized graph. We want to replace the contents
                 # of this graph with the de-skolemized version because topquadrant requires
                 # that skolemization is applied to the input graph in order to preserve
                 # identity of inferred subject/objects
                 res = infer(self, og or rdflib.Graph())
-                self.remove((None, None, None))
                 self += res
                 return self
             valid, _, report = pyshacl.validate(