codelogician 2.0.0b1__tar.gz

codelogician-2.0.0b1/.cl_server

@@ -0,0 +1 @@
+"{\"abs_path\":\"/Users/linhongyu/Documents/playground/code-logician/.cl_server\",\"strategy_paths\":[],\"config\":{\"debug\":true,\"host\":\"127.0.0.1\",\"port\":8000,\"mcp\":true,\"strategy_configs\":{}}}"

codelogician-2.0.0b1/.envrc

@@ -0,0 +1,5 @@
+# nix_direnv_manual_reload
+# use flake .
+set -a
+source .env
+set +a

codelogician-2.0.0b1/.github/workflows/main.yml

@@ -0,0 +1,87 @@
+name: "main"
+
+on:
+  workflow_dispatch:
+  push:
+
+permissions:
+  id-token: write
+  contents: read
+  statuses: write
+
+jobs:
+  format:
+    name: Format
+    runs-on: [self-hosted, Linux]
+    continue-on-error: true
+    env:
+      COLUMNS: 120
+    steps:
+    - uses: imandra-ai/imandra-build-config/actions/self-hosted-linux-runner-setup-ssh@46c4c21f5e783fc4b9bc172cf900a5f62ea285bf
+    - uses: actions/checkout@v4
+    - name: Checkout submodules
+      run: git submodule update --init -j 8 --recursive
+    - uses: rrbutani/use-nix-shell-action@v1
+      with:
+        extraNixOptions: --impure
+    - name: Install dependencies
+      run: uv sync
+    - name: Run format
+      run: make cicd-format
+
+  lint:
+    name: Lint
+    runs-on: [self-hosted, Linux]
+    continue-on-error: true
+    env:
+      COLUMNS: 120
+    steps:
+    - uses: imandra-ai/imandra-build-config/actions/self-hosted-linux-runner-setup-ssh@46c4c21f5e783fc4b9bc172cf900a5f62ea285bf
+    - uses: actions/checkout@v4
+    - name: Checkout submodules
+      run: git submodule update --init -j 8 --recursive
+    - uses: rrbutani/use-nix-shell-action@v1
+      with:
+        extraNixOptions: --impure
+    - name: Install dependencies
+      run: uv sync
+    - name: Run lint
+      run: make cicd-lint
+
+  type-check:
+    name: Type Check
+    runs-on: [self-hosted, Linux]
+    continue-on-error: true
+    env:
+      COLUMNS: 120
+    steps:
+    - uses: imandra-ai/imandra-build-config/actions/self-hosted-linux-runner-setup-ssh@46c4c21f5e783fc4b9bc172cf900a5f62ea285bf
+    - uses: actions/checkout@v4
+    - name: Checkout submodules
+      run: git submodule update --init -j 8 --recursive
+    - uses: rrbutani/use-nix-shell-action@v1
+      with:
+        extraNixOptions: --impure
+    - name: Install dependencies
+      run: uv sync
+    - name: Run type check
+      run: make cicd-type-check
+
+  tests:
+    name: Test
+    runs-on: [self-hosted, Linux]
+    continue-on-error: true
+    env:
+      COLUMNS: 120
+    steps:
+    - uses: imandra-ai/imandra-build-config/actions/self-hosted-linux-runner-setup-ssh@46c4c21f5e783fc4b9bc172cf900a5f62ea285bf
+    - uses: actions/checkout@v4
+    - name: Checkout submodules
+      run: git submodule update --init -j 8 --recursive
+    - uses: rrbutani/use-nix-shell-action@v1
+      with:
+        extraNixOptions: --impure
+    - name: Install dependencies
+      run: uv sync
+    - name: Run tests
+      run: make cicd-test

codelogician-2.0.0b1/.gitignore

@@ -0,0 +1,24 @@
+# Python
+__pycache__/
+*.py[oc]
+build/
+dist/
+wheels/
+*.egg-info
+*.ipynb
+.venv
+build/
+.env
+
+.history/
+.vscode/
+.DS_store
+
+scripts/local
+.claude/
+*local.*
+node_modules/
+
+data/*/cldata
+info.log
+formalization_graph_joblib_cache

codelogician-2.0.0b1/.python-version

@@ -0,0 +1 @@
+3.12

codelogician-2.0.0b1/LICENSE

@@ -0,0 +1,202 @@
+
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codelogician-2.0.0b1/Makefile

@@ -0,0 +1,160 @@
+venv:
+	python -m venv venv
+
+.PHONY: helm-template-dev
+helm-template-dev:
+	helm template langgraph-agents dep/charts/langgraph-agents --values dep/values/dev.yaml --set image.tag="COMMIT_SHA"
+
+FDB_INSTANCE_NAME := imandra-dev-db-master
+
+.env:
+	echo FIX_NEO4J_URI="neo4j+s://a589fffb.databases.neo4j.io" >> .env
+	echo FIX_NEO4J_USERNAME=neo4j >> .env
+	echo FIX_NEO4J_PASSWORD=$$(gcloud secrets versions access latest --project imandra-dev --secret "neo4j-at-dev-neo4j-01") >> .env
+	echo NEO4J_URI="neo4j+s://d05597fd.databases.neo4j.io" >> .env
+	echo NEO4J_USERNAME=universe_dev_ro >> .env
+	echo NEO4J_PASSWORD=$$(gcloud secrets versions access latest --project imandra-dev --secret "universe-neo4j-password-universe_dev_ro") >> .env
+	echo OPENAI_API_KEY=$$(gcloud secrets versions access latest --secret "langgraph-cogito-openai-api-key-dev" --project imandra-dev) >> .env
+	echo ANTHROPIC_API_KEY=$$(gcloud secrets versions access latest --secret "langgraph-agents-anthropic-api-key-dev" --project imandra-dev) >> .env
+	echo LANGGRAPH_CLOUD_LICENSE_KEY=$$(gcloud secrets versions access latest --project imandra-dev --secret "langgraph-cloud-license-key") >> .env
+	echo IMANDRA_U_URL=https://api.dev.imandracapital.com >> .env
+	echo IMANDRAX_URL=https://api.dev.imandracapital.com/internal/imandrax >> .env
+	echo IMANDRAX_API_KEY=$$(cat ~/.config/imandrax/api_key) >> .env
+	echo IMANDRA_API_KEY=$$(cat ~/.config/imandrax/api_key) >> .env
+	echo OLLAMA_URL=http://localhost:11434/v1 >> .env
+	echo CLOUD_SQL_INSTANCE=imandra-dev:europe-west1:imandra-dev-db-master >> .env
+	echo IU_FDB_DB_USER=$$(gcloud auth list --filter=status:ACTIVE --format="value(account)") >> .env
+	echo IU_OAUTH_DB_USER=$$(gcloud auth list --filter=status:ACTIVE --format="value(account)") >> .env
+	echo OAUTH_CODES_KMS_KEY=projects/imandra-dev/locations/global/keyRings/universe-oauth/cryptoKeys/oauth-codes >> .env
+	echo OAUTH_TOKEN_ISSUER=https://api.dev.imandracapital.com/oauth >> .env
+	echo FASTMCP_JSON_RESPONSE="true" >> .env
+	echo FASTMCP_STREAMABLE_HTTP_PATH=/ >> .env
+	echo FASTMCP_STATELESS_HTTP="true" >> .env
+
+# Same as above but with the imandra(x) api keys removed
+cicd-env:
+	echo FIX_NEO4J_URI="neo4j+s://a589fffb.databases.neo4j.io" >> .env
+	echo FIX_NEO4J_USERNAME=neo4j >> .env
+	echo FIX_NEO4J_PASSWORD=$$(gcloud secrets versions access latest --project imandra-dev --secret "neo4j-at-dev-neo4j-01") >> .env
+	echo NEO4J_URI="neo4j+s://d05597fd.databases.neo4j.io" >> .env
+	echo NEO4J_USERNAME=universe_dev_ro >> .env
+	echo NEO4J_PASSWORD=$$(gcloud secrets versions access latest --project imandra-dev --secret "universe-neo4j-password-universe_dev_ro") >> .env
+	echo OPENAI_API_KEY=$$(gcloud secrets versions access latest --secret "langgraph-agents-openai-api-key-cicd" --project imandra-dev) >> .env
+	echo ANTHROPIC_API_KEY=$$(gcloud secrets versions access latest --secret "langgraph-agents-anthropic-api-key-cicd" --project imandra-dev) >> .env
+	echo LANGGRAPH_CLOUD_LICENSE_KEY=$$(gcloud secrets versions access latest --project imandra-dev --secret "langgraph-cloud-license-key") >> .env
+	echo IMANDRA_U_URL=https://api.dev.imandracapital.com >> .env
+	echo IMANDRAX_URL=https://api.dev.imandracapital.com/internal/imandrax >> .env
+	echo IMANDRAX_API_KEY=$$(gcloud secrets versions access latest --secret "imandrax-dev-api-key" --project imandra-dev) >> .env
+	echo IMANDRA_API_KEY=$$(gcloud secrets versions access latest --secret "imandrax-dev-api-key" --project imandra-dev) >> .env
+	echo OLLAMA_URL=http://localhost:11434/v1 >> .env
+	echo CLOUD_SQL_INSTANCE=imandra-dev:europe-west1:imandra-dev-db-master >> .env
+	echo DISABLE_LLM_FALLBACK=true >> .env
+
+cicd-prod-env:
+	echo FIX_NEO4J_URI="neo4j+s://a589fffb.databases.neo4j.io" >> .env
+	echo FIX_NEO4J_USERNAME=neo4j >> .env
+	echo FIX_NEO4J_PASSWORD=$$(gcloud secrets versions access latest --project imandra-dev --secret "neo4j-at-dev-neo4j-01") >> .env
+	echo NEO4J_URI="neo4j+s://d05597fd.databases.neo4j.io" >> .env
+	echo NEO4J_USERNAME=universe_dev_ro >> .env
+	echo NEO4J_PASSWORD=$$(gcloud secrets versions access latest --project imandra-dev --secret "universe-neo4j-password-universe_dev_ro") >> .env
+	echo OPENAI_API_KEY=$$(gcloud secrets versions access latest --secret "langgraph-agents-openai-api-key-cicd" --project imandra-dev) >> .env
+	echo ANTHROPIC_API_KEY=$$(gcloud secrets versions access latest --secret "langgraph-agents-anthropic-api-key-cicd" --project imandra-dev) >> .env
+	echo LANGGRAPH_CLOUD_LICENSE_KEY=$$(gcloud secrets versions access latest --project imandra-dev --secret "langgraph-cloud-license-key") >> .env
+	echo IMANDRA_U_URL=https://api.imandra.ai >> .env
+	echo IMANDRAX_URL=https://api.imandra.ai/internal/imandrax >> .env
+	echo IMANDRAX_API_KEY=$$(gcloud secrets versions access latest --secret "imandrax-prod-api-key" --project imandra-dev) >> .env
+	echo IMANDRA_API_KEY=$$(gcloud secrets versions access latest --secret "imandrax-prod-api-key" --project imandra-dev) >> .env
+	echo IMANDRA_ORGANIZATION=d818cc33-609a-4f9c-bea6-825e683f06c6 >> .env
+	echo OLLAMA_URL=http://localhost:11434/v1 >> .env
+	echo CLOUD_SQL_INSTANCE=imandra-dev:europe-west1:imandra-dev-db-master >> .env
+	echo DISABLE_LLM_FALLBACK=true >> .env
+
+neo4j-home:
+	echo NEO4J_HOME=./.neo4j >> .env
+
+reload-env:  ## Populate .env file
+	rm -f .env
+	make .env
+
+.PHONY: test
+test:
+	uv run pytest -vvv
+
+.PHONY: cicd-test
+cicd-test:
+	uv run pytest -vvv --inline-snapshot=disable
+
+.PHONY: try-tui
+try-tui:
+	uv run python src/code_logician/tui/cl.py data
+
+.PHONY: textual-console
+textual-console:
+	uv run textual console -x EVENT
+
+.PHONY: format
+format:
+	uv tool run ruff@latest format .
+
+.PHONY: cicd-format
+cicd-format:
+	uv tool run ruff@latest format src/ --check
+
+.PHONY: lint
+lint:
+	uv tool run ruff@latest check .
+
+.PHONY: cicd-lint
+cicd-lint:
+	uv tool run ruff@latest check src/ --no-fix --output-format=github
+
+.PHONY: help
+help: ## Show this help (usage: make help)
+	@echo "Usage: make [recipe]"
+	@echo "Recipes:"
+	@awk '/^[a-zA-Z0-9_-]+:.*?##/ { \
+		helpMessage = match($$0, /## (.*)/); \
+		if (helpMessage) { \
+			recipe = $$1; \
+			sub(/:/, "", recipe); \
+			printf "  \033[36m%-20s\033[0m %s\n", recipe, substr($$0, RSTART + 3, RLENGTH); \
+		} \
+	}' $(MAKEFILE_LIST)
+
+ty-paths := src/
+
+.PHONY: type-check
+type-check:
+	uv run ty check $(ty-paths)
+
+.PHONY: type-check-watch
+type-check-watch:
+	uv run ty check $(ty-paths) -W
+
+.PHONY: cicd-type-check
+cicd-type-check:
+	uv tool run ty@latest check $(ty-paths) --output-format=concise
+
+.PHONY: update-submodules
+update-submodules:
+	git submodule update --init --recursive
+
+.PHONY: build
+build:
+	rm -rf dist && uv build --no-sources
+
+.PHONY: publish-testpypi
+publish-testpypi: build
+	uv publish \
+	--index testpypi \
+	-u __token__ \
+	-p $$(gcloud secrets versions access --project imandra-dev --secret pypi-test-imandrax-api-api-token latest) \
+	./dist/codelogician-*
+
+.PHONY: publish-pypi
+publish-pypi: build
+	uv publish \
+	--index pypi \
+	-u __token__ \
+	-p $$(gcloud secrets versions access --project imandra-dev --secret pypi-imandrax-api-api-token latest) \
+	./dist/codelogician-*

codelogician-2.0.0b1/PKG-INFO

@@ -0,0 +1,42 @@
+Metadata-Version: 2.4
+Name: codelogician
+Version: 2.0.0b1
+Summary: CodeLogician applies neurosymbolic AI to translate source code into precise mathematical logic, striving to create a formal model of the program's behavior that's functionally equivalent to the original source code.
+Author-email: hongyu <hongyu@imandra.ai>, samer <samer@imandra.ai>, denis <denis@imandra.ai>
+License-File: LICENSE
+Requires-Python: >=3.12
+Requires-Dist: chromadb>=1.0.12
+Requires-Dist: fastapi-mcp>=0.4.0
+Requires-Dist: fastapi>=0.116.1
+Requires-Dist: imandra[universe]>=2.1.1
+Requires-Dist: iml-query==0.3.4
+Requires-Dist: joblib>=1.5.1
+Requires-Dist: matplotlib>=3.10.3
+Requires-Dist: networkx-mermaid>=0.1.7
+Requires-Dist: networkx>=3.5
+Requires-Dist: pydantic-yaml>=1.6.0
+Requires-Dist: pydantic>=2.11.5
+Requires-Dist: rich>=14.0.0
+Requires-Dist: termcolor>=3.1.0
+Requires-Dist: textual-dev>=1.7.0
+Requires-Dist: textual-image>=0.8.3
+Requires-Dist: watchdog>=6.0.0
+Description-Content-Type: text/markdown
+
+# CodeLogician 2.0 (Server) 
+
+CodeLogician v2.0 now contains a server for performing asynchronous formalization strategies for entire directories, interacting with the CodeLogician Agent (and soon, other agents) ito formalize the code, fix issues, generate test cases and perform formally verified modifications. 
+
+**Note: CodeLogician requires `IMANDRA_UNI_KEY` to be set to a valid Imandra Universe API key. Get yours at https://www.imandra.ai**
+
+
+To run the server for a starting directory:
+
+```shell
+codelogician start -d PATH_TO_DIRECTORY 
+```
+
+To run server in 'oneshot' mode:
+```shell
+codelogician oneshot -d PATH_TO_DIRECTORY
+```

codelogician-2.0.0b1/cl.log

@@ -0,0 +1,22 @@
+2025-10-14 15:56:21,833 - textual_image.renderable - DEBUG - Sixel support detected
+2025-10-14 15:57:10,164 - textual_image.renderable - DEBUG - Sixel support detected
+2025-10-14 15:57:32,534 - textual_image.renderable - DEBUG - Sixel support detected
+2025-10-14 15:58:00,766 - textual_image.renderable - DEBUG - Not connected to a terminal, falling back to unicode
+2025-10-14 15:58:06,297 - textual_image.renderable - DEBUG - Not connected to a terminal, falling back to unicode
+2025-10-14 15:58:18,572 - textual_image.renderable - DEBUG - Sixel support detected
+2025-10-14 15:58:25,951 - textual_image.renderable - DEBUG - Sixel support detected
+2025-10-14 16:00:19,064 - textual_image.renderable - DEBUG - Sixel support detected
+2025-10-14 16:00:24,228 - textual_image.renderable - DEBUG - Sixel support detected
+2025-10-14 16:00:24,272 - codelogician.server.config - ERROR - Failed to read in the YAML configuration: [Errno 2] No such file or directory: 'config/server_config.yaml'
+2025-10-14 16:00:24,272 - codelogician.server.main - WARNING - Failed to create server state file: Failed to read in state file: [/Users/linhongyu/Documents/playground/code-logician/.cl_server]; [Errno 2] No such file or directory: '/Users/linhongyu/Documents/playground/code-logician/.cl_server'
+2025-10-14 16:00:24,273 - codelogician.server.cl_server - INFO - Will now instantiate server strategies. I have 0 paths!
+2025-10-14 16:00:24,273 - codelogician.server.cl_server - INFO - Starting to mount MCP server...
+2025-10-14 16:00:24,273 - mcp.server.lowlevel.server - DEBUG - Initializing server 'CodeLogician Server'
+2025-10-14 16:00:24,273 - mcp.server.lowlevel.server - DEBUG - Registering handler for ListToolsRequest
+2025-10-14 16:00:24,273 - mcp.server.lowlevel.server - DEBUG - Registering handler for CallToolRequest
+2025-10-14 16:00:24,273 - fastapi_mcp.server - INFO - No auth config provided, skipping auth setup
+2025-10-14 16:00:24,273 - fastapi_mcp.server - INFO - MCP HTTP server listening at /mcp
+2025-10-14 16:00:24,273 - codelogician.server.cl_server - INFO - MCP server mounted!
+2025-10-14 16:00:24,480 - codelogician.server.cl_server - INFO - File system observer started!
+2025-10-14 16:01:57,815 - codelogician.server.cl_server - INFO - Sending `None` event to strategies to shut them down!
+2025-10-14 16:01:57,815 - codelogician.server.cl_server - INFO - Will save server state now.

codelogician-2.0.0b1/data/code1/account.py

@@ -0,0 +1,93 @@
+#
+#   Imandra Bank
+#
+#   account.py
+#
+
+from .transaction import CreditTransaction, DebitTransaction
+
+
+class Account:
+    """Account class to represent a bank account"""
+
+    LIABILITY = 0
+    ASSET = 1
+
+    def __init__(
+        self,
+        customer: str,
+        name: str,
+        currency: int,
+        account_type: int,
+        account_number: str,
+        starting_balance: float = 0.0,
+    ):
+        """Initialize an account with account number and balance"""
+
+        self._account_type = account_type  # type of account (liability or asset)
+        self._customer = customer  # customer name
+        self._name = name  # account name
+        self._number = account_number  # account number
+        self._balance = starting_balance  # current balance
+        self._transactions = []  # list of transactions
+
+    def account_type(self):
+        """Get the type of the account"""
+        return self._account_type
+
+    def customer(self):
+        """Get the customer associated with the account"""
+        return self._customer
+
+    def name(self):
+        """Get the name of the account"""
+        return self._name
+
+    def number(self):
+        """Get the account number"""
+        return self._number
+
+    def currency(self):
+        """Get the currency of the account"""
+        return self._currency
+
+    def balance(self):
+        """return the current balance of the account"""
+        return self._balance
+
+    def transactions(self):
+        """Get the list of transactions in the account"""
+        return self._transactions
+
+    def add_transaction(self, transaction):
+        """Add a transaction to the account"""
+
+        if isinstance(transaction, DebitTransaction):
+            if self._type() == Account.ASSET and self._balance >= transaction.amount:
+                self._balance -= transaction.amount
+            else:
+                raise ValueError("Insufficient balance for debit transaction")
+
+        elif isinstance(transaction, CreditTransaction):
+            if self._type() == Account.LIABILITY:
+                self._balance += transaction.amount
+            elif self._type() == Account.ASSET:
+                self._balance -= transaction.amount
+            else:
+                raise ValueError("Invalid account type for credit transaction")
+
+        else:
+            raise ValueError("Invalid transaction type")
+
+        self._transactions.append(transaction)
+
+        def __repr__(self):
+            """String representation of the account"""
+            return (
+                f"Account(account_number={self.account_number}, balance={self.balance})"
+            )
+
+
+if __name__ == "__main__":
+    # Example usage
+    account = Account("base_account", "123456789", 1000.0)