From 2780e0c20d99b03e1fc87c33c01d27fac925316c Mon Sep 17 00:00:00 2001
From: Vincent Emonet <vincent.emonet@gmail.com>
Date: Thu, 11 Apr 2024 12:31:34 +0200
Subject: [PATCH] add p-dt git submodule

---
 .gitmodules         |  3 +++
 CONTRIBUTING.md     | 10 ++++++++++
 README.md           |  4 ++--
 predict-drug-target |  1 +
 pyproject.toml      |  8 ++++----
 5 files changed, 20 insertions(+), 6 deletions(-)
 create mode 100644 .gitmodules
 create mode 160000 predict-drug-target

diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000..783bbaa
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "predict-drug-target"]
+	path = predict-drug-target
+	url = https://github.com/MaastrichtU-IDS/predict-drug-target.git
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 4360b30..d39f238 100644
--- a/CONTRIBUTING.md
+++ b/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:
diff --git a/README.md b/README.md
index a3a0354..196579f 100644
--- a/README.md
+++ b/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
    ```
 
diff --git a/predict-drug-target b/predict-drug-target
new file mode 160000
index 0000000..ace2287
--- /dev/null
+++ b/predict-drug-target
@@ -0,0 +1 @@
+Subproject commit ace2287f315caa66ece4082fe32d6c54188495c9
diff --git a/pyproject.toml b/pyproject.toml
index 94498c5..2dd6f4f 100644
--- a/pyproject.toml
+++ b/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]