Feature/slim automata and rebase (#139)

* unpatch np

* downgrade to python 3.8

* finish fix

* move tests, docs, and notebook out of automata

* add back samples

* update read the docs yaml

* slim automata directory down

* regenerate docs

.github/workflows/run_regressions.yml

@@ -22,6 +22,11 @@ jobs:
           python -m pip install --upgrade pip
           pip3 install -e .
 
+      - name: Setup Git LFS
+        run: |
+          git lfs install
+          git lfs pull
+
       - name: Run regression tests
         run: |
           pytest -m regression

.readthedocs.yaml

@@ -10,22 +10,12 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.9"
-    # You can also specify other tool versions:
-    # nodejs: "19"
-    # rust: "1.64"
-    # golang: "1.19"
 
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:
-  configuration: automata/docs/conf.py
-# Optionally build your docs in additional formats such as PDF and ePub
-# formats:
-#    - pdf
-#    - epub
+  configuration: docs/conf.py
 
-# Optional but recommended, declare the Python requirements required
-# to build your documentation
-# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+# Specify requirements
 python:
   install:
-    - requirements: automata/docs/requirements.txt
+    - requirements: docs/requirements.txt

README.md

@@ -3,8 +3,10 @@
 ![Banner](https://github.com/emrgnt-cmplxty/Automata/assets/68796651/61fe3c33-9b7a-4c1b-9726-a77140476b83)
 
 [![codecov](https://codecov.io/github/emrgnt-cmplxty/Automata/branch/main/graph/badge.svg?token=ZNE7RDUJQD)](https://codecov.io/github/emrgnt-cmplxty/Automata)
+  <a href="https://github.com/emrgnt-cmplxty/automata/blob/main/LICENSE" target="_blank">
+      <img src="https://img.shields.io/static/v1?label=license&message=Apache 2.0&color=white" alt="License">
+  </a> |
 [![Documentation Status](https://readthedocs.org/projects/automata/badge/?version=latest)](https://automata.readthedocs.io/en/latest/?badge=latest)
-[![Type Checking](https://github.com/emrgnt-cmplxty/Automata/actions/workflows/check-mypy.yml/badge.svg)](https://github.com/emrgnt-cmplxty/Automata/actions/workflows/check-mypy.yml)
 [![Discord](https://img.shields.io/discord/1120774652915105934?logo=discord)](https://discord.gg/j9GxfbxqAe)
 [![Twitter Follow](https://img.shields.io/twitter/follow/ocolegro?style=social)](https://twitter.com/ocolegro)
 
@@ -105,10 +107,10 @@ Sometimes the best way to understand a complicated system is to start by underst
 
 from automata.config.base import AgentConfigName
 from automata.config.openai_agent import OpenAIAutomataAgentConfigBuilder
-from automata.core.agent.providers import OpenAIAutomataAgent
-from automata.core.singletons.dependency_factory import dependency_factory
-from automata.core.singletons.py_module_loader import py_module_loader
-from automata.core.tools.factory import AgentToolFactory
+from automata.agent.providers import OpenAIAutomataAgent
+from automata.singletons.dependency_factory import dependency_factory
+from automata.singletons.py_module_loader import py_module_loader
+from automata.tools.factory import AgentToolFactory
 
 # Initialize the module loader to the local directory
 py_module_loader.initialize()
@@ -147,10 +149,10 @@ Code example for creating an instance of 'SymbolCodeEmbedding':
 
 ```python
 import numpy as np
-from automata.core.symbol_embedding.base import SymbolCodeEmbedding
-from automata.core.symbol.parser import parse_symbol
+from automata.symbol_embedding.base import SymbolCodeEmbedding
+from automata.symbol.parser import parse_symbol
 
-symbol_str = 'scip-python python automata 75482692a6fe30c72db516201a6f47d9fb4af065 `automata.core.agent.agent_enums`/ActionIndicator#'
+symbol_str = 'scip-python python automata 75482692a6fe30c72db516201a6f47d9fb4af065 `automata.agent.agent_enums`/ActionIndicator#'
 symbol = parse_symbol(symbol_str)
 source_code = 'symbol_source'
 vector = np.array([1, 0, 0, 0])
@@ -161,8 +163,8 @@ embedding = SymbolCodeEmbedding(symbol=symbol, source_code=source_code, vector=v
 Code example for creating an instance of 'SymbolDocEmbedding':
 
 ```python
-from automata.core.symbol_embedding.base import SymbolDocEmbedding
-from automata.core.symbol.parser import parse_symbol
+from automata.symbol_embedding.base import SymbolDocEmbedding
+from automata.symbol.parser import parse_symbol
 import numpy as np
 
 symbol = parse_symbol('your_symbol_here')

automata/core/agent/agent.py → automata/agent/agent.py

@@ -6,11 +6,8 @@
 from pydantic import BaseModel
 
 from automata.config.base import AgentConfigName, LLMProvider
-from automata.core.llm.foundation import (
-    LLMConversationDatabaseProvider,
-    LLMIterationResult,
-)
-from automata.core.tools.base import Tool
+from automata.llm.foundation import LLMConversationDatabaseProvider, LLMIterationResult
+from automata.tools.base import Tool
 
 logger = logging.getLogger(__name__)
 

automata/core/agent/instances.py → automata/agent/instances.py

@@ -2,12 +2,12 @@
 
 from pydantic import BaseModel
 
+from automata.agent.agent import AgentInstance
 from automata.config.base import AgentConfigName
 from automata.config.openai_agent import OpenAIAutomataAgentConfigBuilder
-from automata.core.agent.agent import AgentInstance
 
 if TYPE_CHECKING:
-    from automata.core.agent.providers import OpenAIAutomataAgent
+    from automata.agent.providers import OpenAIAutomataAgent
 
 
 class OpenAIAutomataAgentInstance(AgentInstance, BaseModel):

automata/core/agent/providers.py → automata/agent/providers.py

@@ -2,30 +2,30 @@
 from abc import ABC, abstractmethod
 from typing import Dict, Final, List, Sequence
 
-from automata.config.base import ConfigCategory
-from automata.config.openai_agent import OpenAIAutomataAgentConfig
-from automata.core.agent.agent import Agent, AgentToolkitBuilder
-from automata.core.agent.error import (
+from automata.agent.agent import Agent, AgentToolkitBuilder
+from automata.agent.error import (
     AgentDatabaseError,
     AgentGeneralError,
     AgentMaxIterError,
     AgentResultError,
     AgentStopIteration,
 )
-from automata.core.llm.foundation import (
+from automata.config.base import ConfigCategory
+from automata.config.openai_agent import OpenAIAutomataAgentConfig
+from automata.core.utils import format_text, load_config
+from automata.llm.foundation import (
     LLMChatMessage,
     LLMConversationDatabaseProvider,
     LLMIterationResult,
 )
-from automata.core.llm.providers.openai import (
+from automata.llm.providers.openai import (
     FunctionCall,
     OpenAIChatCompletionProvider,
     OpenAIChatMessage,
     OpenAIConversation,
     OpenAIFunction,
     OpenAITool,
 )
-from automata.core.utils import format_text, load_config
 
 logger = logging.getLogger(__name__)
 

automata/cli/scripts/run_agent.py

@@ -1,14 +1,14 @@
 import logging
 from typing import List
 
+from automata.agent.providers import OpenAIAutomataAgent
 from automata.config import GITHUB_API_KEY, REPOSITORY_NAME
 from automata.config.base import AgentConfigName
 from automata.config.openai_agent import OpenAIAutomataAgentConfigBuilder
-from automata.core.agent.providers import OpenAIAutomataAgent
-from automata.core.github_management.client import GitHubClient
-from automata.core.singletons.dependency_factory import dependency_factory
-from automata.core.singletons.py_module_loader import py_module_loader
-from automata.core.tools.factory import AgentToolFactory
+from automata.github_management.client import GitHubClient
+from automata.singletons.dependency_factory import dependency_factory
+from automata.singletons.py_module_loader import py_module_loader
+from automata.tools.factory import AgentToolFactory
 
 logger = logging.getLogger(__name__)
 

automata/cli/scripts/run_agent_config_validation.py

@@ -8,7 +8,7 @@
 
 from automata.config.base import ConfigCategory
 
-# from automata.core.agent.action import AutomataActionExtractor
+# from automata.agent.action import AutomataActionExtractor
 from automata.core.utils import get_config_fpath, get_logging_config
 
 logger = logging.getLogger(__name__)

automata/cli/scripts/run_code_embedding.py

@@ -4,13 +4,13 @@
 from tqdm import tqdm
 
 from automata.config.base import ConfigCategory
-from automata.core.llm.providers.openai import OpenAIEmbeddingProvider
-from automata.core.memory_store.symbol_code_embedding import SymbolCodeEmbeddingHandler
-from automata.core.singletons.dependency_factory import dependency_factory
-from automata.core.singletons.py_module_loader import py_module_loader
-from automata.core.symbol.graph import SymbolGraph
-from automata.core.symbol.symbol_utils import get_rankable_symbols
 from automata.core.utils import get_config_fpath
+from automata.llm.providers.openai import OpenAIEmbeddingProvider
+from automata.memory_store.symbol_code_embedding import SymbolCodeEmbeddingHandler
+from automata.singletons.dependency_factory import dependency_factory
+from automata.singletons.py_module_loader import py_module_loader
+from automata.symbol.graph import SymbolGraph
+from automata.symbol.symbol_utils import get_rankable_symbols
 
 logger = logging.getLogger(__name__)
 

automata/cli/scripts/run_doc_embedding.py

@@ -4,18 +4,18 @@
 from tqdm import tqdm
 
 from automata.config.base import ConfigCategory
-from automata.core.context_providers.symbol_synchronization import (
+from automata.context_providers.symbol_synchronization import (
     SymbolProviderSynchronizationContext,
 )
-from automata.core.llm.providers.openai import OpenAIEmbeddingProvider
-from automata.core.memory_store.symbol_code_embedding import SymbolCodeEmbeddingHandler
-from automata.core.memory_store.symbol_doc_embedding import SymbolDocEmbeddingHandler
-from automata.core.singletons.dependency_factory import dependency_factory
-from automata.core.singletons.py_module_loader import py_module_loader
-from automata.core.symbol.graph import SymbolGraph
-from automata.core.symbol.symbol_utils import get_rankable_symbols
-from automata.core.symbol_embedding.base import JSONSymbolEmbeddingVectorDatabase
 from automata.core.utils import get_config_fpath
+from automata.llm.providers.openai import OpenAIEmbeddingProvider
+from automata.memory_store.symbol_code_embedding import SymbolCodeEmbeddingHandler
+from automata.memory_store.symbol_doc_embedding import SymbolDocEmbeddingHandler
+from automata.singletons.dependency_factory import dependency_factory
+from automata.singletons.py_module_loader import py_module_loader
+from automata.symbol.graph import SymbolGraph
+from automata.symbol.symbol_utils import get_rankable_symbols
+from automata.symbol_embedding.base import JSONSymbolEmbeddingVectorDatabase
 
 logger = logging.getLogger(__name__)
 

automata/cli/scripts/run_doc_post_process.py

@@ -1,10 +1,10 @@
 import logging
 import os
 
+from automata.code_handling.py.writer import PyDocWriter
 from automata.config.base import ConfigCategory
-from automata.core.code_handling.py.writer import PyDocWriter
-from automata.core.symbol_embedding.base import JSONSymbolEmbeddingVectorDatabase
-from automata.core.utils import get_config_fpath, get_root_py_fpath
+from automata.core.utils import get_config_fpath, get_root_fpath
+from automata.symbol_embedding.base import JSONSymbolEmbeddingVectorDatabase
 
 logger = logging.getLogger(__name__)
 
@@ -13,7 +13,7 @@ def main(*args, **kwargs) -> str:
     """
     Update the symbol code embedding based on the specified SCIP index file.
     """
-    doc_writer = PyDocWriter(get_root_py_fpath())
+    doc_writer = PyDocWriter(get_root_fpath())
 
     embedding_path = os.path.join(
         get_config_fpath(), ConfigCategory.SYMBOL.value, "symbol_doc_embedding_l2.json"
@@ -25,5 +25,5 @@ def main(*args, **kwargs) -> str:
 
     docs = {symbol: embedding_db.get(symbol.dotpath) for symbol in symbols}
 
-    doc_writer.write_documentation(docs, symbols, os.path.join(get_root_py_fpath(), "docs"))  # type: ignore
+    doc_writer.write_documentation(docs, symbols, os.path.join(get_root_fpath(), "docs"))  # type: ignore
     return "Success"

automata/core/code_handling/py/reader.py → automata/code_handling/py/reader.py

@@ -5,8 +5,8 @@
 
 from redbaron import ClassNode, DefNode, Node, RedBaron, StringNode
 
-from automata.core.navigation.py.navigation_utils import find_syntax_tree_node
-from automata.core.singletons.py_module_loader import py_module_loader
+from automata.navigation.py.navigation_utils import find_syntax_tree_node
+from automata.singletons.py_module_loader import py_module_loader
 
 logger = logging.getLogger(__name__)
 FSTNode = Union[Node, RedBaron]

automata/core/code_handling/py/writer.py → automata/code_handling/py/writer.py

@@ -8,17 +8,17 @@
 import pypandoc
 from redbaron import ClassNode, DefNode, Node, NodeList, RedBaron
 
-from automata.core.code_handling.py.reader import PyReader
-from automata.core.navigation.directory import DirectoryManager
-from automata.core.navigation.py.navigation_utils import (
+from automata.code_handling.py.reader import PyReader
+from automata.navigation.directory import DirectoryManager
+from automata.navigation.py.navigation_utils import (
     find_all_function_and_class_syntax_tree_nodes,
     find_import_syntax_tree_node_by_name,
     find_import_syntax_tree_nodes,
     find_syntax_tree_node,
 )
-from automata.core.singletons.py_module_loader import py_module_loader
-from automata.core.symbol.base import Symbol
-from automata.core.symbol_embedding.base import SymbolDocEmbedding
+from automata.singletons.py_module_loader import py_module_loader
+from automata.symbol.base import Symbol
+from automata.symbol_embedding.base import SymbolDocEmbedding
 
 logger = logging.getLogger(__name__)
 

automata/config/base.py

@@ -6,8 +6,8 @@
 import yaml
 from pydantic import BaseModel, PrivateAttr
 
-from automata.core.tools.base import Tool
 from automata.core.utils import convert_kebab_to_snake
+from automata.tools.base import Tool
 
 
 class ConfigCategory(Enum):

automata/config/openai_agent.py

@@ -10,8 +10,8 @@
     InstructionConfigVersion,
     LLMProvider,
 )
-from automata.core.experimental.search.rank import SymbolRank
-from automata.core.singletons.dependency_factory import dependency_factory
+from automata.experimental.search.rank import SymbolRank
+from automata.singletons.dependency_factory import dependency_factory
 
 
 class OpenAIAutomataAgentConfig(AgentConfig):

automata/config/prompt/doc_generation.py

@@ -40,9 +40,9 @@
     ## Related Symbols
 
     - `config.config_enums.AgentConfigName`
-    - `automata.core.agent.agent.AutomataAgent`
+    - `automata.agent.agent.AutomataAgent`
     - `config.automata_agent_config_utils.AutomataAgentConfigBuilder`
-    - `automata.core.coordinator.automata_instance.AutomataInstance`
+    - `automata.coordinator.automata_instance.AutomataInstance`
 
     ## Example
 

automata/core/context_providers/symbol_synchronization.py → automata/context_providers/symbol_synchronization.py

@@ -1,6 +1,6 @@
 from typing import List, Set
 
-from automata.core.symbol.base import ISymbolProvider, Symbol
+from automata.symbol.base import ISymbolProvider, Symbol
 
 
 class SymbolProviderRegistry:

automata/core/utils.py

@@ -9,7 +9,7 @@
 import openai
 import yaml
 
-from automata.core.symbol.base import Symbol
+from automata.symbol.base import Symbol
 
 
 def set_openai_api_key(override_key: Optional[str] = None) -> None:

automata/core/embedding/base.py → automata/embedding/base.py

@@ -6,7 +6,7 @@
 import numpy as np
 
 from automata.core.base.database.vector import VectorDatabaseProvider
-from automata.core.symbol.base import Symbol
+from automata.symbol.base import Symbol
 
 logger = logging.getLogger(__name__)
 
@@ -54,7 +54,7 @@ def build(self, source_text: str, symbol: Symbol) -> Any:
 
     def fetch_embedding_source_code(self, symbol: Symbol) -> str:
         """An abstract method for embedding the context is the source code itself."""
-        from automata.core.symbol.symbol_utils import (  # imported late for mocking
+        from automata.symbol.symbol_utils import (  # imported late for mocking
             convert_to_fst_object,
         )
 

automata/core/experimental/search/rank.py → automata/experimental/search/rank.py

@@ -4,7 +4,7 @@
 from networkx.exception import NetworkXError
 from pydantic import BaseModel
 
-from automata.core.symbol.base import Symbol
+from automata.symbol.base import Symbol
 
 
 class SymbolRankConfig(BaseModel):