Merge pull request #93 from monarch-initiative/name_change

Rename main module from curate_gpt to curategpt
monarch-initiative · Oct 7, 2024 · 1a9c248 · 1a9c248
2 parents f859122 + deaa948
commit 1a9c248
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Showing 147 changed files with 546 additions and 514 deletions.
diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml
@@ -25,11 +25,11 @@ jobs:
 
     - name: Build documentation.
       run: |
-        echo ${{ secrets.GH_TOKEN }} >> src/curate_gpt/token.txt
+        echo ${{ secrets.GH_TOKEN }} >> src/curategpt/token.txt
         mkdir gh-pages
         touch gh-pages/.nojekyll
         cd docs/
-        poetry run sphinx-apidoc -o . ../src/curate_gpt/ --ext-autodoc -f
+        poetry run sphinx-apidoc -o . ../src/curategpt/ --ext-autodoc -f
         poetry run sphinx-build -b html . _build
         cp -r _build/* ../gh-pages/
 

diff --git a/Makefile b/Makefile
@@ -22,13 +22,13 @@ ont-%:
 
 
 app:
-	$(RUN) streamlit run src/curate_gpt/app/app.py --logger.level=debug
+	$(RUN) streamlit run src/curategpt/app/app.py --logger.level=debug
 
 ## -- Docs --
 
 
 apidoc:
-	$(RUN) sphinx-apidoc -f -M -o docs/ src/curate_gpt/ && cd docs && $(RUN) make html
+	$(RUN) sphinx-apidoc -f -M -o docs/ src/curategpt/ && cd docs && $(RUN) make html
 
 %-doctest: %
 	$(RUN) python -m doctest --option ELLIPSIS --option NORMALIZE_WHITESPACE $<

diff --git a/adhoc.Makefile b/adhoc.Makefile
@@ -2,7 +2,7 @@ RUN = poetry run
 DB_PATH = db
 
 data/nmdc.json:
-	$(RUN) python -m curate_gpt.adhoc.nmdc_sample_downloader --no-stream  --format json > $@
+	$(RUN) python -m curategpt.adhoc.nmdc_sample_downloader --no-stream  --format json > $@
 
 
 data/clingen.json:

diff --git a/docs/conf.py b/docs/conf.py
@@ -5,12 +5,12 @@
 import os
 from datetime import date
 
-from curate_gpt import __version__
+from curategpt import __version__
 
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'curate_gpt'
+project = 'curategpt'
 copyright = f"{date.today().year}, Author 1 <cjmungall@lbl.gov>"
 author = 'Author 1 <cjmungall@lbl.gov>'
 release = __version__

diff --git a/docs/index.rst b/docs/index.rst
@@ -10,12 +10,12 @@ Welcome to curategpt's documentation!
    :maxdepth: 2
    :caption: Contents:
 
-   curate_gpt.store
-   curate_gpt.wrappers
-   curate_gpt.agents
-   curate_gpt.extract
-   curate_gpt.utils
-   curate_gpt.formatters
+   curategpt.store
+   curategpt.wrappers
+   curategpt.agents
+   curategpt.extract
+   curategpt.utils
+   curategpt.formatters
 
    modules
 

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "curategpt"
-version = "0.2.0"
+version = "0.2.1"
 description = "CurateGPT"
 authors = ["Author 1 <cjmungall@lbl.gov>"]
 license = "BSD-3"

diff --git a/src/curate_gpt/wrappers/__init__.py b/src/curate_gpt/wrappers/__init__.py
diff --git a/src/curate_gpt/__init__.py → src/curategpt/__init__.py b/src/curate_gpt/__init__.py → src/curategpt/__init__.py
@@ -22,7 +22,7 @@
     # package is not installed
     __version__ = "0.0.0"  # pragma: no cover
 
-from curate_gpt.extract import BasicExtractor, Extractor
-from curate_gpt.store import ChromaDBAdapter, DBAdapter
+from curategpt.extract import BasicExtractor, Extractor
+from curategpt.store import ChromaDBAdapter, DBAdapter
 
 __all__ = ["DBAdapter", "ChromaDBAdapter", "Extractor", "BasicExtractor"]
diff --git a/src/curate_gpt/adhoc/__init__.py → src/curategpt/adhoc/__init__.py b/src/curate_gpt/adhoc/__init__.py → src/curategpt/adhoc/__init__.py
diff --git a/src/curate_gpt/adhoc/gocam_predictor.py → src/curategpt/adhoc/gocam_predictor.py b/src/curate_gpt/adhoc/gocam_predictor.py → src/curategpt/adhoc/gocam_predictor.py
@@ -10,11 +10,11 @@
 import click
 import yaml
 
-from curate_gpt import BasicExtractor, DBAdapter
-from curate_gpt.store import get_store
-from curate_gpt.utils.eval_utils import Outcome, score_prediction
-from curate_gpt.utils.llm_utils import query_model
-from curate_gpt.wrappers.bio.gocam_wrapper import GOCAMWrapper
+from curategpt import BasicExtractor, DBAdapter
+from curategpt.store import get_store
+from curategpt.utils.eval_utils import Outcome, score_prediction
+from curategpt.utils.llm_utils import query_model
+from curategpt.wrappers.bio.gocam_wrapper import GOCAMWrapper
 
 logger = logging.getLogger(__name__)
 

diff --git a/src/curate_gpt/agents/__init__.py → src/curategpt/agents/__init__.py b/src/curate_gpt/agents/__init__.py → src/curategpt/agents/__init__.py
diff --git a/src/curate_gpt/agents/agent_utils.py → src/curategpt/agents/agent_utils.py b/src/curate_gpt/agents/agent_utils.py → src/curategpt/agents/agent_utils.py
@@ -6,8 +6,8 @@
 import yaml
 from llm import Model
 
-from curate_gpt.store.db_adapter import SEARCH_RESULT
-from curate_gpt.utils.tokens import estimate_num_tokens, max_tokens_by_model
+from curategpt.store.db_adapter import SEARCH_RESULT
+from curategpt.utils.tokens import estimate_num_tokens, max_tokens_by_model
 
 logger = logging.getLogger(__name__)
 

diff --git a/src/curate_gpt/agents/base_agent.py → src/curategpt/agents/base_agent.py b/src/curate_gpt/agents/base_agent.py → src/curategpt/agents/base_agent.py
@@ -4,8 +4,8 @@
 from dataclasses import dataclass
 from typing import Union
 
-from curate_gpt import DBAdapter, Extractor
-from curate_gpt.wrappers import BaseWrapper
+from curategpt import DBAdapter, Extractor
+from curategpt.wrappers import BaseWrapper
 
 
 @dataclass

diff --git a/src/curate_gpt/agents/bootstrap_agent.py → src/curategpt/agents/bootstrap_agent.py b/src/curate_gpt/agents/bootstrap_agent.py → src/curategpt/agents/bootstrap_agent.py
@@ -5,9 +5,9 @@
 from jinja2 import Template
 from pydantic import BaseModel, ConfigDict
 
-from curate_gpt.agents.base_agent import BaseAgent
-from curate_gpt.conf.prompts import PROMPTS_DIR
-from curate_gpt.extract import AnnotatedObject
+from curategpt.agents.base_agent import BaseAgent
+from curategpt.conf.prompts import PROMPTS_DIR
+from curategpt.extract import AnnotatedObject
 
 
 class KnowledgeBaseSpecification(BaseModel):

diff --git a/src/curate_gpt/agents/chat_agent.py → src/curategpt/agents/chat_agent.py b/src/curate_gpt/agents/chat_agent.py → src/curategpt/agents/chat_agent.py
@@ -9,9 +9,9 @@
 from llm import Conversation
 from pydantic import BaseModel, ConfigDict
 
-from curate_gpt.agents.base_agent import BaseAgent
-from curate_gpt.utils.tokens import estimate_num_tokens, max_tokens_by_model
-from curate_gpt.wrappers import BaseWrapper
+from curategpt.agents.base_agent import BaseAgent
+from curategpt.utils.tokens import estimate_num_tokens, max_tokens_by_model
+from curategpt.wrappers import BaseWrapper
 
 logger = logging.getLogger(__name__)
 

diff --git a/...e_gpt/agents/concept_recognition_agent.py → ...tegpt/agents/concept_recognition_agent.py b/...e_gpt/agents/concept_recognition_agent.py → ...tegpt/agents/concept_recognition_agent.py
@@ -7,7 +7,7 @@
 
 from pydantic import BaseModel, ConfigDict
 
-from curate_gpt.agents.base_agent import BaseAgent
+from curategpt.agents.base_agent import BaseAgent
 
 logger = logging.getLogger(__name__)
 

diff --git a/src/curate_gpt/agents/dase_agent.py → src/curategpt/agents/dase_agent.py b/src/curate_gpt/agents/dase_agent.py → src/curategpt/agents/dase_agent.py
@@ -6,10 +6,10 @@
 
 from pydantic import BaseModel, ConfigDict
 
-from curate_gpt.agents.base_agent import BaseAgent
-from curate_gpt.agents.chat_agent import ChatResponse
-from curate_gpt.extract import AnnotatedObject
-from curate_gpt.store import DBAdapter
+from curategpt.agents.base_agent import BaseAgent
+from curategpt.agents.chat_agent import ChatResponse
+from curategpt.extract import AnnotatedObject
+from curategpt.store import DBAdapter
 
 logger = logging.getLogger(__name__)
 

diff --git a/src/curate_gpt/agents/dragon_agent.py → src/curategpt/agents/dragon_agent.py b/src/curate_gpt/agents/dragon_agent.py → src/curategpt/agents/dragon_agent.py
@@ -7,9 +7,9 @@
 import yaml
 from pydantic import BaseModel, ConfigDict
 
-from curate_gpt.agents.base_agent import BaseAgent
-from curate_gpt.extract import AnnotatedObject
-from curate_gpt.store import DBAdapter
+from curategpt.agents.base_agent import BaseAgent
+from curategpt.extract import AnnotatedObject
+from curategpt.store import DBAdapter
 
 logger = logging.getLogger(__name__)
 

diff --git a/src/curate_gpt/agents/evidence_agent.py → src/curategpt/agents/evidence_agent.py b/src/curate_gpt/agents/evidence_agent.py → src/curategpt/agents/evidence_agent.py
@@ -5,12 +5,12 @@
 
 import yaml
 
-from curate_gpt import BasicExtractor
-from curate_gpt.agents.base_agent import BaseAgent
-from curate_gpt.agents.chat_agent import ChatAgent, ChatResponse
-from curate_gpt.formatters.format_utils import object_as_yaml
-from curate_gpt.utils.tokens import estimate_num_tokens, max_tokens_by_model
-from curate_gpt.wrappers import BaseWrapper
+from curategpt import BasicExtractor
+from curategpt.agents.base_agent import BaseAgent
+from curategpt.agents.chat_agent import ChatAgent, ChatResponse
+from curategpt.formatters.format_utils import object_as_yaml
+from curategpt.utils.tokens import estimate_num_tokens, max_tokens_by_model
+from curategpt.wrappers import BaseWrapper
 
 logger = logging.getLogger(__name__)
 

diff --git a/src/curate_gpt/agents/huggingface_agent.py → src/curategpt/agents/huggingface_agent.py b/src/curate_gpt/agents/huggingface_agent.py → src/curategpt/agents/huggingface_agent.py
diff --git a/src/curate_gpt/agents/mapping_agent.py → src/curategpt/agents/mapping_agent.py b/src/curate_gpt/agents/mapping_agent.py → src/curategpt/agents/mapping_agent.py
@@ -12,10 +12,10 @@
 import yaml
 from pydantic import BaseModel, ConfigDict
 
-from curate_gpt.agents.base_agent import BaseAgent
-from curate_gpt.formatters.format_utils import remove_formatting
-from curate_gpt.store.db_adapter import SEARCH_RESULT
-from curate_gpt.utils.tokens import estimate_num_tokens, max_tokens_by_model
+from curategpt.agents.base_agent import BaseAgent
+from curategpt.formatters.format_utils import remove_formatting
+from curategpt.store.db_adapter import SEARCH_RESULT
+from curategpt.utils.tokens import estimate_num_tokens, max_tokens_by_model
 
 logger = logging.getLogger(__name__)
 

diff --git a/src/curate_gpt/agents/summarization_agent.py → src/curategpt/agents/summarization_agent.py b/src/curate_gpt/agents/summarization_agent.py → src/curategpt/agents/summarization_agent.py
@@ -2,8 +2,8 @@
 from dataclasses import dataclass
 from typing import List
 
-from curate_gpt.agents.base_agent import BaseAgent
-from curate_gpt.wrappers import BaseWrapper
+from curategpt.agents.base_agent import BaseAgent
+from curategpt.wrappers import BaseWrapper
 
 logger = logging.getLogger(__name__)
 

diff --git a/src/curate_gpt/app/__init__.py → src/curategpt/app/__init__.py b/src/curate_gpt/app/__init__.py → src/curategpt/app/__init__.py
diff --git a/src/curate_gpt/app/app.py → src/curategpt/app/app.py b/src/curate_gpt/app/app.py → src/curategpt/app/app.py
@@ -9,24 +9,24 @@
 import yaml
 from scipy.spatial import distance_matrix
 
-from curate_gpt import BasicExtractor
-from curate_gpt.agents import MappingAgent
-from curate_gpt.agents.chat_agent import ChatAgent, ChatResponse
-from curate_gpt.agents.dase_agent import DatabaseAugmentedStructuredExtraction
-from curate_gpt.agents.dragon_agent import DragonAgent
-from curate_gpt.agents.evidence_agent import EvidenceAgent
-from curate_gpt.app.components import (
+from curategpt import BasicExtractor
+from curategpt.agents import MappingAgent
+from curategpt.agents.chat_agent import ChatAgent, ChatResponse
+from curategpt.agents.dase_agent import DatabaseAugmentedStructuredExtraction
+from curategpt.agents.dragon_agent import DragonAgent
+from curategpt.agents.evidence_agent import EvidenceAgent
+from curategpt.app.components import (
     DimensionalityReductionOptions,
     limit_slider_component,
     vectors_to_fig,
 )
-from curate_gpt.app.helper import get_applicable_examples, get_case_collection
-from curate_gpt.app.state import get_state
-from curate_gpt.extract import OpenAIExtractor, RecursiveExtractor
-from curate_gpt.wrappers import BaseWrapper
-from curate_gpt.wrappers.investigation.jgi_wrapper import JGIWrapper
-from curate_gpt.wrappers.literature import WikipediaWrapper
-from curate_gpt.wrappers.literature.pubmed_wrapper import PubmedWrapper
+from curategpt.app.helper import get_applicable_examples, get_case_collection
+from curategpt.app.state import get_state
+from curategpt.extract import OpenAIExtractor, RecursiveExtractor
+from curategpt.wrappers import BaseWrapper
+from curategpt.wrappers.investigation.jgi_wrapper import JGIWrapper
+from curategpt.wrappers.literature import WikipediaWrapper
+from curategpt.wrappers.literature.pubmed_wrapper import PubmedWrapper
 
 PUBMED = "PubMed (via API)"
 WIKIPEDIA = "Wikipedia (via API)"

diff --git a/src/curate_gpt/app/cart.py → src/curategpt/app/cart.py b/src/curate_gpt/app/cart.py → src/curategpt/app/cart.py
diff --git a/src/curate_gpt/app/components.py → src/curategpt/app/components.py b/src/curate_gpt/app/components.py → src/curategpt/app/components.py
diff --git a/src/curate_gpt/app/helper.py → src/curategpt/app/helper.py b/src/curate_gpt/app/helper.py → src/curategpt/app/helper.py
@@ -4,7 +4,7 @@
 
 import yaml
 
-from curate_gpt.conf import EXAMPLES_DIR
+from curategpt.conf import EXAMPLES_DIR
 
 HELP_CASES = EXAMPLES_DIR / "bio.yaml"
 

diff --git a/src/curate_gpt/app/state.py → src/curategpt/app/state.py b/src/curate_gpt/app/state.py → src/curategpt/app/state.py
@@ -1,10 +1,10 @@
 from dataclasses import dataclass, field
 from typing import Any, Dict, List, Optional
 
-from curate_gpt import BasicExtractor, ChromaDBAdapter, DBAdapter, Extractor
-from curate_gpt.agents.chat_agent import ChatResponse
-from curate_gpt.app.cart import Cart
-from curate_gpt.extract import AnnotatedObject
+from curategpt import BasicExtractor, ChromaDBAdapter, DBAdapter, Extractor
+from curategpt.agents.chat_agent import ChatResponse
+from curategpt.app.cart import Cart
+from curategpt.extract import AnnotatedObject
 
 
 @dataclass