Merge pull request #3 from linkml/command-line

command line

.github/workflows/qc.yml

@@ -23,8 +23,9 @@ jobs:
 
       - name: Install Poetry
         uses: snok/[email protected]
+
       - name: Install dependencies
-        run: poetry install --no-interaction
+        run: poetry install --no-interaction --all-extras
 
       - name: Check common spelling errors
         run: poetry run tox -e codespell
@@ -33,4 +34,4 @@ jobs:
         run: poetry run tox -e lint
 
       - name: Test with pytest and generate coverage file
-        run: poetry run tox -e py
+        run: poetry run pytest

Makefile

@@ -5,6 +5,9 @@ CODE = src/linkml_data_browser
 test: pytest doctest
 test-full: test integration-tests
 
+install:
+	poetry install --extras "mongodb llm validation app"
+
 pytest:
 	$(RUN) pytest
 
@@ -25,7 +28,8 @@ doctest:
 	$(RUN) python -m doctest --option ELLIPSIS --option NORMALIZE_WHITESPACE $<
 
 app:
-	$(RUN) streamlit run $(CODE)/app.py --logger.level=debug
+	$(RUN) streamlit run $(CODE)/app.py
+#	$(RUN) streamlit run $(CODE)/app.py --logger.level=debug
 
 apidoc:
 	$(RUN) sphinx-apidoc -f -M -o docs/ src/linkml_store/ && cd docs && $(RUN) make html

README.md

@@ -1,7 +1,10 @@
 # linkml-store
 
-This is the project description.
+An integration layer for multiple database backends
 
-# Acknowledgements
+Currently this software is alpha, and has only been tested with DuckDB backends. See the Tutorial for more information.
 
-This [cookiecutter](https://cookiecutter.readthedocs.io/en/stable/README.html) project was developed from the [monarch-project-template](https://github.com/monarch-initiative/monarch-project-template) template and will be kept up-to-date using [cruft](https://cruft.github.io/cruft/).
+There is also experimental support for vector-based indexing using OpenAI test embedding via the `llm` library.
+
+The goals of this project are to provide high level access to data stored in heterogeneous databases,
+with optional schema management using LinkML.

docs/examples/Monarch-KG.ipynb

@@ -236,31 +236,6 @@
    },
    "id": "4b8c938384cd2550"
   },
-  {
-   "cell_type": "code",
-   "execution_count": 24,
-   "outputs": [
-    {
-     "data": {
-      "text/plain": "[DuckDBCollection(name='dangling_edges', parent=DuckDBDatabase(handle='duckdb:////Users/cjm/.data/linkml/store/monarch-kg.db', _schema_view=None, _collections={'dangling_edges': ..., 'denormalized_edges': DuckDBCollection(name='denormalized_edges', parent=..., _indexes=None, _table_created=None), 'edges': DuckDBCollection(name='edges', parent=..., _indexes=None, _table_created=None), 'nodes': DuckDBCollection(name='nodes', parent=..., _indexes=None, _table_created=None)}, _connection=None, _engine=Engine(duckdb:////Users/cjm/.data/linkml/store/monarch-kg.db)), _indexes=None, _table_created=None),\n DuckDBCollection(name='denormalized_edges', parent=DuckDBDatabase(handle='duckdb:////Users/cjm/.data/linkml/store/monarch-kg.db', _schema_view=None, _collections={'dangling_edges': DuckDBCollection(name='dangling_edges', parent=..., _indexes=None, _table_created=None), 'denormalized_edges': ..., 'edges': DuckDBCollection(name='edges', parent=..., _indexes=None, _table_created=None), 'nodes': DuckDBCollection(name='nodes', parent=..., _indexes=None, _table_created=None)}, _connection=None, _engine=Engine(duckdb:////Users/cjm/.data/linkml/store/monarch-kg.db)), _indexes=None, _table_created=None),\n DuckDBCollection(name='edges', parent=DuckDBDatabase(handle='duckdb:////Users/cjm/.data/linkml/store/monarch-kg.db', _schema_view=None, _collections={'dangling_edges': DuckDBCollection(name='dangling_edges', parent=..., _indexes=None, _table_created=None), 'denormalized_edges': DuckDBCollection(name='denormalized_edges', parent=..., _indexes=None, _table_created=None), 'edges': ..., 'nodes': DuckDBCollection(name='nodes', parent=..., _indexes=None, _table_created=None)}, _connection=None, _engine=Engine(duckdb:////Users/cjm/.data/linkml/store/monarch-kg.db)), _indexes=None, _table_created=None),\n DuckDBCollection(name='nodes', parent=DuckDBDatabase(handle='duckdb:////Users/cjm/.data/linkml/store/monarch-kg.db', _schema_view=None, _collections={'dangling_edges': DuckDBCollection(name='dangling_edges', parent=..., _indexes=None, _table_created=None), 'denormalized_edges': DuckDBCollection(name='denormalized_edges', parent=..., _indexes=None, _table_created=None), 'edges': DuckDBCollection(name='edges', parent=..., _indexes=None, _table_created=None), 'nodes': ...}, _connection=None, _engine=Engine(duckdb:////Users/cjm/.data/linkml/store/monarch-kg.db)), _indexes=None, _table_created=None)]"
-     },
-     "execution_count": 24,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "database.list_collections()"
-   ],
-   "metadata": {
-    "collapsed": false,
-    "ExecuteTime": {
-     "end_time": "2024-04-07T22:04:58.701820Z",
-     "start_time": "2024-04-07T22:04:58.694170Z"
-    }
-   },
-   "id": "c56b3475732f99b7"
-  },
   {
    "cell_type": "code",
    "execution_count": null,

docs/index.rst

@@ -13,6 +13,8 @@ Currently this is alpha, check back later for more docs
    :caption: Contents:
 
    examples/Tutorial
+   examples/Semantic-Search
+   examples/Monarch-KG
    modules
 
 Indices and tables