PyPI - aiagents4pharma - Versions diffs - 1.47.0__py3-none-any.whl → 1.48.0__py3-none-any.whl - Mend

aiagents4pharma 1.47.0py3-none-any.whl → 1.48.0py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (11) hide show

aiagents4pharma/talk2aiagents4pharma/Dockerfile CHANGED Viewed

@@ -58,6 +58,7 @@ LABEL description="AI Agents for Pharma - Streamlit Application"
 RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
   ca-certificates \
   curl \
+  gnupg \
   libmagic1 \
   libopenblas0 \
   libomp5 \
@@ -66,6 +67,23 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-ins
   && update-alternatives --install /usr/bin/python3 python3 /usr/bin/python${PYTHON_VERSION} 1 \
   && update-alternatives --install /usr/bin/python python /usr/bin/python${PYTHON_VERSION} 1
+# Install CUDA runtime libraries required by cudf/cupy
+RUN curl -fsSL https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/3bf863cc.pub \
+    | gpg --dearmor -o /usr/share/keyrings/nvidia-cuda-keyring.gpg \
+  && echo "deb [signed-by=/usr/share/keyrings/nvidia-cuda-keyring.gpg] https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/ /" \
+    > /etc/apt/sources.list.d/nvidia-cuda.list \
+  && apt-get update \
+  && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+    cuda-cudart-12-6 \
+    cuda-cudart-dev-12-6 \
+    cuda-nvrtc-12-6 \
+    cuda-nvrtc-dev-12-6 \
+    libcublas-12-6 \
+    libcusparse-12-6 \
+  && rm -rf /var/lib/apt/lists/*
+ENV LD_LIBRARY_PATH=/usr/local/cuda/lib64
 # Copy UV virtual environment from build stage
 COPY --from=uv-install /opt/venv /opt/venv

aiagents4pharma/talk2aiagents4pharma/docker-compose/cpu/.env.example CHANGED Viewed

@@ -15,7 +15,7 @@ MILVUS_HOST=localhost
 MILVUS_PORT=19530
 MILVUS_USER=root
 MILVUS_PASSWORD=Milvus
-MILVUS_DATABASE=your_database_name_here
+MILVUS_DATABASE=t2kg_primekg
 # Specify the data directory for multimodal data to your own data directory
 # DATA_DIR=/your_absolute_path_to_your_data_dir/

aiagents4pharma/talk2aiagents4pharma/docker-compose/gpu/.env.example CHANGED Viewed

@@ -15,7 +15,7 @@ MILVUS_HOST=localhost
 MILVUS_PORT=19530
 MILVUS_USER=root
 MILVUS_PASSWORD=Milvus
-MILVUS_DATABASE=your_database_name_here
+MILVUS_DATABASE=t2kg_primekg
 # Specify the data directory for multimodal data to your own data directory
 # DATA_DIR=/your_absolute_path_to_your_data_dir/

aiagents4pharma/talk2knowledgegraphs/Dockerfile CHANGED Viewed

@@ -58,6 +58,7 @@ LABEL description="AI Agents for Pharma - Knowledge Graphs Application"
 RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
   ca-certificates \
   curl \
+  gnupg \
   libmagic1 \
   libopenblas0 \
   libomp5 \
@@ -66,6 +67,23 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-ins
   && update-alternatives --install /usr/bin/python3 python3 /usr/bin/python${PYTHON_VERSION} 1 \
   && update-alternatives --install /usr/bin/python python /usr/bin/python${PYTHON_VERSION} 1
+# Install CUDA runtime libraries required by cudf/cupy
+RUN curl -fsSL https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/3bf863cc.pub \
+  | gpg --dearmor -o /usr/share/keyrings/nvidia-cuda-keyring.gpg \
+  && echo "deb [signed-by=/usr/share/keyrings/nvidia-cuda-keyring.gpg] https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/ /" \
+  > /etc/apt/sources.list.d/nvidia-cuda.list \
+  && apt-get update \
+  && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+  cuda-cudart-12-6 \
+  cuda-cudart-dev-12-6 \
+  cuda-nvrtc-12-6 \
+  cuda-nvrtc-dev-12-6 \
+  libcublas-12-6 \
+  libcusparse-12-6 \
+  && rm -rf /var/lib/apt/lists/*
+ENV LD_LIBRARY_PATH=/usr/local/cuda/lib64
 # Copy UV virtual environment from build stage
 COPY --from=uv-install /opt/venv /opt/venv

aiagents4pharma/talk2knowledgegraphs/docker-compose/cpu/.env.example CHANGED Viewed

@@ -15,7 +15,7 @@ MILVUS_HOST=localhost
 MILVUS_PORT=19530
 MILVUS_USER=root
 MILVUS_PASSWORD=Milvus
-MILVUS_DATABASE=your_database_name_here
+MILVUS_DATABASE=t2kg_primekg
 # Specify the data directory for multimodal data to your own data directory
 # DATA_DIR=/your_absolute_path_to_your_data_dir/

aiagents4pharma/talk2knowledgegraphs/docker-compose/gpu/.env.example CHANGED Viewed

@@ -15,7 +15,7 @@ MILVUS_HOST=localhost
 MILVUS_PORT=19530
 MILVUS_USER=root
 MILVUS_PASSWORD=Milvus
-MILVUS_DATABASE=your_database_name_here
+MILVUS_DATABASE=t2kg_primekg
 # Specify the data directory for multimodal data to your own data directory
 # DATA_DIR=/your_absolute_path_to_your_data_dir/

aiagents4pharma/talk2knowledgegraphs/milvus_data_dump.py CHANGED Viewed

@@ -150,6 +150,7 @@ class DynamicDataLoader:
         self.normalize_vectors = self.use_gpu  # Only normalize for GPU (original logic)
         self.vector_index_type = "GPU_CAGRA" if self.use_gpu else "HNSW"
         self.metric_type = "IP" if self.use_gpu else "COSINE"
+        self.vector_index_params = self._build_vector_index_params()
         logger.info("Loader Configuration:")
         logger.info("  Using GPU acceleration: %s", self.use_gpu)
@@ -284,6 +285,29 @@ class DynamicDataLoader:
             else:
                 return list(data)
+    def _build_vector_index_params(self) -> dict[str, Any]:
+        """Return index params tuned for the selected backend."""
+        base_params: dict[str, Any] = {
+            "index_type": self.vector_index_type,
+            "metric_type": self.metric_type,
+        }
+        if self.vector_index_type == "GPU_CAGRA":
+            base_params["params"] = {
+                "graph_degree": int(os.getenv("CAGRA_GRAPH_DEGREE", "32")),
+                "intermediate_graph_degree": int(
+                    os.getenv("CAGRA_INTERMEDIATE_GRAPH_DEGREE", "40")
+                ),
+                "search_width": int(os.getenv("CAGRA_SEARCH_WIDTH", "64")),
+            }
+        elif self.vector_index_type == "HNSW":
+            base_params["params"] = {
+                "M": int(os.getenv("HNSW_M", "16")),
+                "efConstruction": int(os.getenv("HNSW_EF_CONSTRUCTION", "200")),
+            }
+        return base_params
     def connect_to_milvus(self):
         """Connect to Milvus and setup database."""
         logger.info("Connecting to Milvus at %s:%s", self.milvus_host, self.milvus_port)
@@ -442,10 +466,7 @@ class DynamicDataLoader:
         )
         collection.create_index(
             field_name="desc_emb",
-            index_params={
-                "index_type": self.vector_index_type,
-                "metric_type": self.metric_type,
-            },
+            index_params=self.vector_index_params.copy(),
             index_name="desc_emb_index",
         )
@@ -569,18 +590,12 @@ class DynamicDataLoader:
             )
             collection.create_index(
                 field_name="desc_emb",
-                index_params={
-                    "index_type": self.vector_index_type,
-                    "metric_type": self.metric_type,
-                },
+                index_params=self.vector_index_params.copy(),
                 index_name="desc_emb_index",
             )
             collection.create_index(
                 field_name="feat_emb",
-                index_params={
-                    "index_type": self.vector_index_type,
-                    "metric_type": self.metric_type,
-                },
+                index_params=self.vector_index_params.copy(),
                 index_name="feat_emb_index",
             )
@@ -706,10 +721,7 @@ class DynamicDataLoader:
         )
         collection.create_index(
             field_name="feat_emb",
-            index_params={
-                "index_type": self.vector_index_type,
-                "metric_type": self.metric_type,
-            },
+            index_params=self.vector_index_params.copy(),
             index_name="feat_emb_index",
         )
@@ -796,8 +808,7 @@ class DynamicDataLoader:
                 logger.info("  %s: %d entities", coll, collection.num_entities)
         except Exception:
-            logger.error("Error occurred during data loading")
-            logger.debug("Detailed error information available in debug mode")
+            logger.exception("Error occurred during data loading")
             raise
@@ -867,8 +878,7 @@ def main():
         logger.info("Data loading interrupted by user")
         sys.exit(1)
     except Exception:
-        logger.error("Fatal error occurred during data loading")
-        logger.debug("Detailed error information available in debug mode")
+        logger.exception("Fatal error occurred during data loading")
         sys.exit(1)

{aiagents4pharma-1.47.0.dist-info → aiagents4pharma-1.48.0.dist-info}/METADATA RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aiagents4pharma
-Version: 1.47.0
+Version: 1.48.0
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 License-File: LICENSE
 Classifier: License :: OSI Approved :: MIT License

{aiagents4pharma-1.47.0.dist-info → aiagents4pharma-1.48.0.dist-info}/RECORD RENAMED Viewed

@@ -1,6 +1,6 @@
 aiagents4pharma/__init__.py,sha256=B-tLRCbWgti-jlCnW_qknNKrG4j1t9nhBb-gXaz0Wtg,187
 aiagents4pharma/talk2aiagents4pharma/.dockerignore,sha256=-hAM7RzkGbjDeU411-kXOmYzNfl3Z9OlLWvN9zMDAXE,89
-aiagents4pharma/talk2aiagents4pharma/Dockerfile,sha256=J2QvwifcCxtz9EzPaq99zhSygHV9ADsB5ZQ_cmiwATI,3533
+aiagents4pharma/talk2aiagents4pharma/Dockerfile,sha256=DScrZujkLc5OY79XP5KSAfxiniQlZ5MWHkbtw534JY4,4295
 aiagents4pharma/talk2aiagents4pharma/README.md,sha256=0eGxj7jxi_LrCvX-4I4KrQv-7T2ivo3pqLslG7suaCk,74
 aiagents4pharma/talk2aiagents4pharma/__init__.py,sha256=gjVTAhBHKPEFBbv_2T-MWuDdwHhAKfWIo-lQSrcsLNE,97
 aiagents4pharma/talk2aiagents4pharma/install.md,sha256=5oyy9P8fd03x3f_jOFZTGg2G1AzxMIOrH2vVd8ZS4Iw,4201
@@ -13,9 +13,9 @@ aiagents4pharma/talk2aiagents4pharma/configs/agents/main_agent/default.yaml,sha2
 aiagents4pharma/talk2aiagents4pharma/configs/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 aiagents4pharma/talk2aiagents4pharma/configs/app/frontend/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 aiagents4pharma/talk2aiagents4pharma/configs/app/frontend/default.yaml,sha256=BpDv_Bau0F7xDPzMHVYxedKpZQAPdo0rAsRnfH32-U8,3470
-aiagents4pharma/talk2aiagents4pharma/docker-compose/cpu/.env.example,sha256=twsuiEN-FczXfka40_bVoSQXaMDR_3J3ESKCqU4qSkg,585
+aiagents4pharma/talk2aiagents4pharma/docker-compose/cpu/.env.example,sha256=mfwCKG0bv6_IjEfIdQlEb6cnXsbaeAqC_U4kcIa03o0,574
 aiagents4pharma/talk2aiagents4pharma/docker-compose/cpu/docker-compose.yml,sha256=2I8jyzaFXSGsBMMFOZ4Hz7hAH3A-ELpoYCphkpT_8rA,2631
-aiagents4pharma/talk2aiagents4pharma/docker-compose/gpu/.env.example,sha256=twsuiEN-FczXfka40_bVoSQXaMDR_3J3ESKCqU4qSkg,585
+aiagents4pharma/talk2aiagents4pharma/docker-compose/gpu/.env.example,sha256=mfwCKG0bv6_IjEfIdQlEb6cnXsbaeAqC_U4kcIa03o0,574
 aiagents4pharma/talk2aiagents4pharma/docker-compose/gpu/docker-compose.yml,sha256=bZwpaLynxyY6YOj2Sdz3MEVKgBY-FFXTC_K_KmZrMuM,3001
 aiagents4pharma/talk2aiagents4pharma/states/__init__.py,sha256=VuVAFmoH8p2erE-mYiaa0uoqTuFynBcXia5Y8lmjI34,109
 aiagents4pharma/talk2aiagents4pharma/states/state_talk2aiagents4pharma.py,sha256=ahquXi8hg6Bk1ttskl9QaYdHq4rDWa_bK7hu81E75M4,468
@@ -94,12 +94,12 @@ aiagents4pharma/talk2cells/tools/scp_agent/__init__.py,sha256=DAJp26kugSdVHfFyVR
 aiagents4pharma/talk2cells/tools/scp_agent/display_studies.py,sha256=nQltO147j1cFWUJ9mxg3JlWBLsqFivhJ93g1G7gWZko,602
 aiagents4pharma/talk2cells/tools/scp_agent/search_studies.py,sha256=xjsgYJ8Bn8RIzIu_bgn8D_2I8wzLOJeu9evT_vF15mM,2647
 aiagents4pharma/talk2knowledgegraphs/.dockerignore,sha256=-hAM7RzkGbjDeU411-kXOmYzNfl3Z9OlLWvN9zMDAXE,89
-aiagents4pharma/talk2knowledgegraphs/Dockerfile,sha256=qGy6I4oBvQonpDEANQaCW-5JMtHPdd2HKc-JJgoCyYQ,3384
+aiagents4pharma/talk2knowledgegraphs/Dockerfile,sha256=0Do2gcsbEeh07xnPNuApTV77bfEbhAYSdMEwE3U0CKU,4130
 aiagents4pharma/talk2knowledgegraphs/README.md,sha256=0eGxj7jxi_LrCvX-4I4KrQv-7T2ivo3pqLslG7suaCk,74
 aiagents4pharma/talk2knowledgegraphs/__init__.py,sha256=ZztaRzRlovSXtVX3i9Rvf84ivIjPn8RMPiYRkbkEJ0E,114
 aiagents4pharma/talk2knowledgegraphs/entrypoint.sh,sha256=EK_jGau1VuW1uTmFWZcKhLMK9VanC5l3q9axF4ZYgmI,5758
 aiagents4pharma/talk2knowledgegraphs/install.md,sha256=1rCv2e6ywb-kZOxtqFJ25qpWHl2MCa9bW6nHYHfxJMI,5555
-aiagents4pharma/talk2knowledgegraphs/milvus_data_dump.py,sha256=D5BB700QshEhY6paByXNLyMjOYyO4Csm4ODgbeeWfmc,35616
+aiagents4pharma/talk2knowledgegraphs/milvus_data_dump.py,sha256=RyPYjtF49DxL7MIWmVUprw0Wpu4HErHOAOQ2_wLUfVI,36095
 aiagents4pharma/talk2knowledgegraphs/agents/__init__.py,sha256=ugUvVYEdjbZ3y_dogfF5hpQ3lFPFrAvLSydlcpbkGo0,93
 aiagents4pharma/talk2knowledgegraphs/agents/t2kg_agent.py,sha256=GDeSjJNhAqQWagZOxAWUKqDhzUohHViSsu444W9SzRQ,3240
 aiagents4pharma/talk2knowledgegraphs/configs/__init__.py,sha256=H-yhTbJ_RXBLe3XSto5x6FmVrgbi7y1WKEfiwmKzLAk,87
@@ -129,9 +129,9 @@ aiagents4pharma/talk2knowledgegraphs/datasets/biobridge_primekg.py,sha256=M6NtpM
 aiagents4pharma/talk2knowledgegraphs/datasets/dataset.py,sha256=ls0e15uudIbb4zwHMHxjEovmH145RJ_hPeZni89KSnM,411
 aiagents4pharma/talk2knowledgegraphs/datasets/primekg.py,sha256=1WHlQCAyKjpBiX3JnIsSohUZe8Yi5pY-VDP4tCugxkg,7709
 aiagents4pharma/talk2knowledgegraphs/datasets/starkqa_primekg.py,sha256=JtP-jNIFDA3xQbzy5DkK2OHin5NnbWUGa_EJ_1OH6vE,7483
-aiagents4pharma/talk2knowledgegraphs/docker-compose/cpu/.env.example,sha256=twsuiEN-FczXfka40_bVoSQXaMDR_3J3ESKCqU4qSkg,585
+aiagents4pharma/talk2knowledgegraphs/docker-compose/cpu/.env.example,sha256=mfwCKG0bv6_IjEfIdQlEb6cnXsbaeAqC_U4kcIa03o0,574
 aiagents4pharma/talk2knowledgegraphs/docker-compose/cpu/docker-compose.yml,sha256=7BNUIkwP0cAUH1jznun5-RgsIAZisegLFGiiUZG9F1Y,2631
-aiagents4pharma/talk2knowledgegraphs/docker-compose/gpu/.env.example,sha256=twsuiEN-FczXfka40_bVoSQXaMDR_3J3ESKCqU4qSkg,585
+aiagents4pharma/talk2knowledgegraphs/docker-compose/gpu/.env.example,sha256=mfwCKG0bv6_IjEfIdQlEb6cnXsbaeAqC_U4kcIa03o0,574
 aiagents4pharma/talk2knowledgegraphs/docker-compose/gpu/docker-compose.yml,sha256=MVWmuxTmTTq3g4MFi9HtvHY0F4MegtprZ7FGIt-60Ms,3001
 aiagents4pharma/talk2knowledgegraphs/states/__init__.py,sha256=9X3zHxvtAJFQ0s0VLZ_-iBn4rMVfZWk5CQiWEKJkr0c,109
 aiagents4pharma/talk2knowledgegraphs/states/state_talk2knowledgegraphs.py,sha256=QECNXd8IWDh3WlMvePcd2T6G5XqjOI9EkZdWmICcCT0,1088
@@ -330,7 +330,7 @@ aiagents4pharma/talk2scholars/tools/zotero/utils/review_helper.py,sha256=-q-UuzP
 aiagents4pharma/talk2scholars/tools/zotero/utils/write_helper.py,sha256=K1EatPfC-riGyFmkOAS3ReNBaGPY-znne1KqOnFahkI,7339
 aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_path.py,sha256=sKkfJu3u4LKSZjfoQRfeqz26IESHRwBtcSDzLMLlJMo,6311
 aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_pdf_downloader.py,sha256=DBrF5IiF7VRP58hUK8T9LST3lQWLFixLUfnpMSTccoQ,4614
-aiagents4pharma-1.47.0.dist-info/METADATA,sha256=Y7cHyuKy8HAGhEa-9SoqF6XxouOfe0RQxDDDCaqRdQI,17035
-aiagents4pharma-1.47.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-aiagents4pharma-1.47.0.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
-aiagents4pharma-1.47.0.dist-info/RECORD,,
+aiagents4pharma-1.48.0.dist-info/METADATA,sha256=LAfYILDy3HPzU2RdU1icFrP6s1N9pooLdFtRSaRzmfE,17035
+aiagents4pharma-1.48.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+aiagents4pharma-1.48.0.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
+aiagents4pharma-1.48.0.dist-info/RECORD,,

{aiagents4pharma-1.47.0.dist-info → aiagents4pharma-1.48.0.dist-info}/WHEEL RENAMED Viewed

File without changes

{aiagents4pharma-1.47.0.dist-info → aiagents4pharma-1.48.0.dist-info}/licenses/LICENSE RENAMED Viewed

File without changes

aiagents4pharma 1.47.0__py3-none-any.whl → 1.48.0__py3-none-any.whl

aiagents4pharma 1.47.0py3-none-any.whl → 1.48.0py3-none-any.whl