aiagents4pharma 1.39.2__py3-none-any.whl → 1.39.4__py3-none-any.whl

aiagents4pharma/talk2biomodels/configs/tools/get_annotation/default.yaml

@@ -3,4 +3,6 @@ prompt: >
   Given the user question, extract the relevant species names.
   If the user aks for a specific species, extract that species.
   If none of the species match the user question, return None.
-  If the user asks for all species, return all species.
+  If the user asks for all species, return all species.
+  If the user does not specify any species or simpley asks for
+  model annotations, return all species.

{aiagents4pharma-1.39.2.dist-info → aiagents4pharma-1.39.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aiagents4pharma
-Version: 1.39.2
+Version: 1.39.4
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -114,18 +114,19 @@ _We now have all the agents available on Docker Hub._
 
 Both agents require [Ollama](https://ollama.com/) to run embedding models like `nomic-embed-text`. We use a **single startup script** that automatically detects your hardware (NVIDIA, AMD, or CPU) and handles container startup, model loading, and service orchestration.
 
-##### **1. Clone the repository and navigate to the agent directory**
+##### **1. Download docker-compose.yml, .env.example and startup.sh from GitHub**
 
-```sh
-git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
+###### Talk2Agents4Pharma
 
-cd AIAgents4Pharma/aiagents4pharma/<agent>
+```sh
+mkdir talk2aiagents4pharma && cd talk2aiagents4pharma && wget https://raw.githubusercontent.com/VirtualPatientEngine/AIAgents4Pharma/main/aiagents4pharma/talk2aiagents4pharma/docker-compose.yml https://raw.githubusercontent.com/VirtualPatientEngine/AIAgents4Pharma/main/aiagents4pharma/talk2aiagents4pharma/.env.example https://raw.githubusercontent.com/VirtualPatientEngine/AIAgents4Pharma/main/aiagents4pharma/talk2aiagents4pharma/startup.sh
 ```
 
-Replace `<agent>` with either:
+###### Talk2KnowledgeGraphs
 
-- `talk2aiagents4pharma`
-- `talk2knowledgegraphs`
+```sh
+mkdir talk2knowledgegraphs && cd talk2knowledgegraphs && wget https://raw.githubusercontent.com/VirtualPatientEngine/AIAgents4Pharma/main/aiagents4pharma/talk2knowledgegraphs/docker-compose.yml https://raw.githubusercontent.com/VirtualPatientEngine/AIAgents4Pharma/main/aiagents4pharma/talk2knowledgegraphs/.env.example https://raw.githubusercontent.com/VirtualPatientEngine/AIAgents4Pharma/main/aiagents4pharma/talk2knowledgegraphs/startup.sh
+```
 
 ##### **2. Setup environment variables**
 
@@ -209,8 +210,7 @@ If you are using docker on Windows, please follow these [Windows Setup Notes](ht
 1. **Clone the repository:**
 
 ```sh
-git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
-cd AIAgents4Pharma
+git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma && cd AIAgents4Pharma
 ```
 
 2. **Install dependencies:**
@@ -321,9 +321,10 @@ git push origin feat/your-feature-name
 
 #### Contacts for contributions
 
-- **Talk2Biomodels / Talk2Cells**: [@gurdeep330](https://github.com/gurdeep330), [@lilijap](https://github.com/lilijap), [@dmccloskey](https://github.com/dmccloskey)
-- **Talk2KnowledgeGraphs**: [@awmulyadi](https://github.com/awmulyadi), [@dmccloskey](https://github.com/dmccloskey)
-- **Talk2Scholars**: [@ansh-info](https://github.com/ansh-info), [@gurdeep330](https://github.com/gurdeep330), [@dmccloskey](https://github.com/dmccloskey)
+- **Talk2Biomodels**: [@lilijap](https://github.com/lilijap), [@gurdeep330](https://github.com/gurdeep330)
+- **Talk2Cells**: [@gurdeep330](https://github.com/gurdeep330)
+- **Talk2KnowledgeGraphs**: [@awmulyadi](https://github.com/awmulyadi)
+- **Talk2Scholars**: [@ansh-info](https://github.com/ansh-info), [@gurdeep330](https://github.com/gurdeep330)
 
 Please refer to our [CONTRIBUTING.md](CONTRIBUTING.md) for more detailed contribution guidelines.
 

{aiagents4pharma-1.39.2.dist-info → aiagents4pharma-1.39.4.dist-info}/RECORD

@@ -28,7 +28,7 @@ aiagents4pharma/talk2biomodels/configs/tools/ask_question/default.yaml,sha256=7k
 aiagents4pharma/talk2biomodels/configs/tools/custom_plotter/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
 aiagents4pharma/talk2biomodels/configs/tools/custom_plotter/default.yaml,sha256=14Aic9IDr1eOyeLo_YGMwZL40CYsgqOXix2j9ucB4EA,464
 aiagents4pharma/talk2biomodels/configs/tools/get_annotation/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
-aiagents4pharma/talk2biomodels/configs/tools/get_annotation/default.yaml,sha256=o5kqLJ5QGJsLMUhAqotudIMhxxNfPUVcDVH1tdRIutU,304
+aiagents4pharma/talk2biomodels/configs/tools/get_annotation/default.yaml,sha256=Dx6afMdafUEZjN4LWEFQWkjXHw7DChSpQeb_wlQXRUo,408
 aiagents4pharma/talk2biomodels/models/__init__.py,sha256=5fTHHm3PVloYPNKXbgNlcPgv3-u28ZquxGydFYDfhJA,122
 aiagents4pharma/talk2biomodels/models/basico_model.py,sha256=4LjeHKGcXsdm1gFxs9SGVNDerajZ7REvCeNch0s2pDg,5242
 aiagents4pharma/talk2biomodels/models/sys_bio_model.py,sha256=JeoiGQAvQABHnG0wKR2XBmmxqQdtgO6kxaLDUTUmr1s,2001
@@ -251,8 +251,8 @@ aiagents4pharma/talk2scholars/tools/zotero/utils/review_helper.py,sha256=IPD1V9y
 aiagents4pharma/talk2scholars/tools/zotero/utils/write_helper.py,sha256=ALwLecy1QVebbsmXJiDj1GhGmyhq2R2tZlAyEl1vfhw,7410
 aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_path.py,sha256=oIrfbOySgts50ksHKyjcWjRkPRIS88g3Lc0v9mBkU8w,6375
 aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_pdf_downloader.py,sha256=ERBha8afU6Q1EaRBe9qB8tchOzZ4_KfFgDW6EElOJoU,4816
-aiagents4pharma-1.39.2.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
-aiagents4pharma-1.39.2.dist-info/METADATA,sha256=Gc44kyTHU3VlsH8ZqKwPJvZId36XWFRHAlLTpLShCNg,14775
-aiagents4pharma-1.39.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-aiagents4pharma-1.39.2.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
-aiagents4pharma-1.39.2.dist-info/RECORD,,
+aiagents4pharma-1.39.4.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
+aiagents4pharma-1.39.4.dist-info/METADATA,sha256=0vzjxCMHm4xhDVEZoMhq68SJBox2dvrEV8GEJNcLvLY,15462
+aiagents4pharma-1.39.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+aiagents4pharma-1.39.4.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
+aiagents4pharma-1.39.4.dist-info/RECORD,,