add p-dt git submodule

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "predict-drug-target"]
+	path = predict-drug-target
+	url = https://github.com/MaastrichtU-IDS/predict-drug-target.git

CONTRIBUTING.md

@@ -28,6 +28,16 @@ To work with translator-openpredict locally:
    hatch env create
    ```
 
+> [!WARNING]
+>
+> For the project to take into account the code changes in dependencies you will need to activate the virtual environment yourself and install all packages that will changes in edit mode:
+>
+> ```bash
+> pip install -e ./predict-drug-target .
+> ```
+>
+>
+
 ### 🚀 Start the API
 
 Start the API in development with docker, the API will automatically reload when you make changes in the code:

README.md

@@ -20,10 +20,10 @@ The data used by the models in this repository is versionned using `dvc` in the
 
 Requirements: Python 3.8+ and `pip` installed
 
-1. Clone the repository:
+1. Clone the repository with submodule:
 
    ```bash
-   git clone https://github.com/MaastrichtU-IDS/translator-openpredict.git
+   git clone --recursive https://github.com/MaastrichtU-IDS/translator-openpredict.git
    cd translator-openpredict
    ```
 

pyproject.toml

@@ -35,18 +35,18 @@ dependencies = [
     "scikit-learn",
     "gensim", # For word2vec
     "scipy ==1.10.1", # https://stackoverflow.com/questions/78279136/importerror-cannot-import-name-triu-from-scipy-linalg-gensim
-
     "requests >=2.23.0",
     "rdflib >=6.1.1",
     "SPARQLWrapper >=2.0.0,<3.0.0",
     "reasoner-pydantic >=4.1.4",
+
     # "trapi-predict-kit[web,opentelemetry] >=0.2.3",
     "trapi-predict-kit[web,opentelemetry] @ git+https://github.com/MaastrichtU-IDS/trapi-predict-kit.git",
     # "trapi-predict-kit @ {root:uri}/trapi-predict-kit",
-    "predict-drug-target @ git+https://github.com/MaastrichtU-IDS/predict-drug-target.git",
-    # "predict-drug-target", # Load from workspace
 
-    # "pydantic >=1.9",
+    # "predict-drug-target @ git+https://github.com/MaastrichtU-IDS/predict-drug-target.git", # Uncomment for prod
+    "predict-drug-target", # Uncomment if you want to run locally in dev
+    # "predict-drug-target @ {root:uri}/predict-drug-target",
 ]
 
 [project.optional-dependencies]