Add text annotator interface via Gilda (#159)

* Begin gilda framework * Add gilda implementation Co-Authored-By: Benjamin M. Gyori <[email protected]> * Update type hints * Add tests * Update poetry.lock * Add configuration * Update test_gilda.py * Add docs * Clean up code and better error messages * Update CLI command example Co-authored-by: Benjamin M. Gyori <[email protected]>
INCATools · Jul 12, 2022 · 85487aa · 85487aa
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diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
@@ -77,7 +77,7 @@ jobs:
       #    install your root project, if required 
       #----------------------------------------------      
       - name: Install library
-        run: poetry install --no-interaction
+        run: poetry install --no-interaction --extras gilda
 
       #----------------------------------------------
       #              run test suite   

diff --git a/docs/implementations/gilda.rst b/docs/implementations/gilda.rst
@@ -0,0 +1,25 @@
+.. _gilda_implementation:
+
+Gilda Endpoint
+==============
+Command Line Examples
+----------------------
+Use the :code:`gilda` selector:
+
+.. code:: shell
+
+    $ runoak -i gilda: COMMAND [COMMAND-ARGUMENTS-AND-OPTIONS]
+
+Currently ontology sub-selectors are not supported
+
+Annotation
+^^^^^^^^^^
+.. code:: shell
+
+   $ runoak -i gilda: annotate -W "cell cortex"
+
+Code
+----
+.. currentmodule:: oaklib.implementations.gilda
+
+.. autoclass:: GildaImplementation
diff --git a/docs/implementations/index.rst b/docs/implementations/index.rst
@@ -30,5 +30,5 @@ The most mature implementations are:
    ubergraph
    ontobee
    ols
+   gilda
    aggregator
-
-Original file line number
+Diff line change
@@ Expand Up / @@ -30,5 +30,5 @@ The most mature implementations are: @@
        ubergraph
        ontobee
        ols
+       gilda
        aggregator