mcli-framework 8.0.43__tar.gz → 8.0.45__tar.gz

{mcli_framework-8.0.43 → mcli_framework-8.0.45}/MANIFEST.in

@@ -17,12 +17,8 @@ recursive-include src/mcli *.toml
 graft mcli_rust/src
 include mcli_rust/Cargo.toml
 
-# Include GitHub workflows and configuration
-recursive-include .github *.yml *.yaml
-
-# Include tests (optional, for development)
-recursive-include tests *.py
-include tests/*.ini
+# Exclude CI/test files from distribution (not needed for end users)
+# GitHub workflows and test files are available in the source repository
 
 # Exclude build artifacts
 prune build/

{mcli_framework-8.0.43 → mcli_framework-8.0.45}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mcli-framework
-Version: 8.0.43
+Version: 8.0.45
 Summary: Portable workflow framework - transform any script into a versioned, schedulable command. Store in ~/.mcli/workflows/, version with lockfile, run as daemon or cron job.
 Author-email: Luis Fernandez de la Vara <luis@lefv.io>
 Maintainer-email: Luis Fernandez de la Vara <luis@lefv.io>
@@ -37,10 +37,12 @@ Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: click<9.0.0,>=8.1.7
-Requires-Dist: rich>=14.0.0
+Requires-Dist: rich<15.0.0,>=14.0.0
 Requires-Dist: requests<3.0.0,>=2.31.0
-Requires-Dist: tomli>=2.2.1
-Requires-Dist: python-dotenv>=1.1.1
+Requires-Dist: tomli<3.0.0,>=2.2.1
+Requires-Dist: python-dotenv<2.0.0,>=1.1.1
+Requires-Dist: pydantic<3.0.0,>=2.0.0
+Requires-Dist: pydantic-settings<3.0.0,>=2.0.0
 Requires-Dist: watchdog<4.0.0,>=3.0.0
 Requires-Dist: tqdm<5.0.0,>=4.66.1
 Requires-Dist: humanize<5.0.0,>=4.9.0
@@ -48,118 +50,22 @@ Requires-Dist: psutil<6.0.0,>=5.9.0
 Requires-Dist: inquirerpy<0.4.0,>=0.3.4
 Requires-Dist: gitpython<4.0.0,>=3.1.40
 Requires-Dist: prompt-toolkit<4.0.0,>=3.0.0
-Requires-Dist: aiohttp>=3.13.3
-Requires-Dist: httpx>=0.28.1
-Requires-Dist: websockets>=12.0
-Requires-Dist: beautifulsoup4>=4.13.5
-Requires-Dist: fuzzywuzzy>=0.18.0
+Requires-Dist: aiohttp<4.0.0,>=3.13.3
+Requires-Dist: httpx<1.0.0,>=0.28.1
+Requires-Dist: websockets<14.0.0,>=12.0
+Requires-Dist: beautifulsoup4<5.0.0,>=4.13.5
+Requires-Dist: fuzzywuzzy<1.0.0,>=0.18.0
 Requires-Dist: openai<2.0.0,>=1.3.0
-Requires-Dist: anthropic>=0.60.0
-Requires-Dist: ollama>=0.5.3
+Requires-Dist: anthropic<1.0.0,>=0.60.0
+Requires-Dist: ollama<1.0.0,>=0.5.3
 Requires-Dist: ipython<9.0.0,>=8.12.0
-Requires-Dist: fastapi>=0.110.0
-Requires-Dist: uvicorn>=0.27.0
-Requires-Dist: uvloop>=0.19.0
-Requires-Dist: aiosqlite>=0.20.0
-Requires-Dist: redis>=5.0.0
-Requires-Dist: aiohttp-sse-client>=0.2.1
-Requires-Dist: aiomqtt>=2.0.0
-Requires-Dist: opencv-python>=4.11.0.86
-Requires-Dist: pillow>=11.2.1
-Requires-Dist: numpy<2.0.0,>=1.24.0
-Requires-Dist: scikit-image>=0.24.0
-Requires-Dist: scipy>=1.10.0
-Requires-Dist: pypdf2>=3.0.1
-Requires-Dist: pymupdf>=1.26.3
-Requires-Dist: pandas>=2.3.1
-Requires-Dist: openpyxl>=3.1.5
-Requires-Dist: matplotlib>=3.9.4
-Requires-Dist: pydot>=4.0.1
-Requires-Dist: graphviz>=0.21
-Requires-Dist: seaborn>=0.13.0
-Requires-Dist: plotly>=5.17.0
-Requires-Dist: supabase>=2.8.1
-Requires-Dist: sqlalchemy>=2.0.0
-Requires-Dist: alembic>=1.12.0
-Requires-Dist: psycopg2-binary>=2.9.7
-Requires-Dist: asyncpg>=0.29.0
-Requires-Dist: torch>=2.0.0
-Requires-Dist: torchvision>=0.15.0
-Requires-Dist: pytorch-lightning>=2.0.0
-Requires-Dist: scikit-learn<2.0.0,>=1.3.0
-Requires-Dist: mlflow>=2.9.0
-Requires-Dist: dvc>=3.0.0
-Requires-Dist: polars>=0.19.0
-Requires-Dist: pyarrow>=14.0.0
-Requires-Dist: yfinance>=0.2.18
-Requires-Dist: alpha-vantage>=2.3.1
-Requires-Dist: alpaca-py==0.43.2
-Requires-Dist: cvxpy>=1.4.0
-Requires-Dist: python-jose[cryptography]>=3.3.0
-Requires-Dist: passlib[bcrypt]>=1.7.4
-Requires-Dist: pydantic-settings>=2.1.0
-Requires-Dist: dynaconf>=3.2.0
-Requires-Dist: pandera>=0.17.0
-Requires-Dist: pendulum>=2.1.2
-Requires-Dist: optuna>=3.4.0
-Requires-Dist: PyPortfolioOpt>=1.5.5
-Requires-Dist: jupyter>=1.0.0
-Requires-Dist: jupyterlab>=4.0.0
-Requires-Dist: ipykernel>=6.27.0
-Requires-Dist: prometheus-client>=0.19.0
-Requires-Dist: structlog>=23.2.0
-Requires-Dist: gunicorn>=21.2.0
-Requires-Dist: newrelic>=9.2.0
-Requires-Dist: datadog>=0.49.0
-Requires-Dist: orjson>=3.9.0
-Requires-Dist: kafka-python>=2.0.2
-Requires-Dist: streamlit>=1.50.0
-Requires-Dist: altair<5.0.0,>=4.2.1
-Requires-Dist: streamlit-autorefresh>=1.0.1
-Requires-Dist: typer>=0.9.0
-Requires-Dist: flask<3.0.0,>=2.3.0
-Provides-Extra: gpu
-Requires-Dist: cupy-cuda12x>=12.3.0; extra == "gpu"
-Requires-Dist: nvidia-ml-py>=12.535.0; extra == "gpu"
-Provides-Extra: ml-plugin
-Requires-Dist: torch>=2.0.0; extra == "ml-plugin"
-Requires-Dist: torchvision>=0.15.0; extra == "ml-plugin"
-Requires-Dist: pytorch-lightning>=2.0.0; extra == "ml-plugin"
-Requires-Dist: scikit-learn<2.0.0,>=1.3.0; extra == "ml-plugin"
-Requires-Dist: mlflow>=2.9.0; extra == "ml-plugin"
-Requires-Dist: dvc>=3.0.0; extra == "ml-plugin"
-Requires-Dist: optuna>=3.4.0; extra == "ml-plugin"
-Requires-Dist: streamlit>=1.50.0; extra == "ml-plugin"
-Requires-Dist: altair<5.0.0,>=4.2.1; extra == "ml-plugin"
-Requires-Dist: streamlit-autorefresh>=1.0.1; extra == "ml-plugin"
-Requires-Dist: pandas>=2.3.1; extra == "ml-plugin"
-Requires-Dist: numpy<2.0.0,>=1.24.0; extra == "ml-plugin"
-Requires-Dist: polars>=0.19.0; extra == "ml-plugin"
-Requires-Dist: pyarrow>=14.0.0; extra == "ml-plugin"
-Provides-Extra: video-plugin
-Requires-Dist: opencv-python>=4.11.0.86; extra == "video-plugin"
-Requires-Dist: pillow>=11.2.1; extra == "video-plugin"
-Requires-Dist: numpy<2.0.0,>=1.24.0; extra == "video-plugin"
-Requires-Dist: scikit-image>=0.24.0; extra == "video-plugin"
-Requires-Dist: scipy>=1.10.0; extra == "video-plugin"
-Provides-Extra: trading-plugin
-Requires-Dist: yfinance>=0.2.18; extra == "trading-plugin"
-Requires-Dist: alpha-vantage>=2.3.1; extra == "trading-plugin"
-Requires-Dist: alpaca-py==0.43.2; extra == "trading-plugin"
-Requires-Dist: cvxpy>=1.4.0; extra == "trading-plugin"
-Requires-Dist: PyPortfolioOpt>=1.5.5; extra == "trading-plugin"
-Requires-Dist: pandas>=2.3.1; extra == "trading-plugin"
-Requires-Dist: numpy<2.0.0,>=1.24.0; extra == "trading-plugin"
-Provides-Extra: async-extras
-Provides-Extra: video
-Provides-Extra: documents
-Provides-Extra: viz
-Provides-Extra: database
-Provides-Extra: ml
-Provides-Extra: monitoring
-Provides-Extra: streaming
-Provides-Extra: dashboard
-Provides-Extra: web
+Requires-Dist: fastapi<1.0.0,>=0.110.0
+Requires-Dist: uvicorn<1.0.0,>=0.27.0
+Requires-Dist: uvloop<1.0.0,>=0.19.0
+Requires-Dist: aiosqlite<1.0.0,>=0.20.0
+Requires-Dist: redis<6.0.0,>=5.0.0
+Requires-Dist: aiohttp-sse-client<1.0.0,>=0.2.1
+Requires-Dist: aiomqtt<3.0.0,>=2.0.0
 Provides-Extra: dev
 Requires-Dist: pytest>=8.4.1; extra == "dev"
 Requires-Dist: pytest-cov<5.0.0,>=4.1.0; extra == "dev"
@@ -182,7 +88,6 @@ Requires-Dist: pre-commit>=4.5.1; extra == "dev"
 Requires-Dist: build>=1.2.2.post1; extra == "dev"
 Requires-Dist: maturin>=1.9.3; extra == "dev"
 Requires-Dist: twine>=4.0.0; extra == "dev"
-Provides-Extra: all
 Dynamic: license-file
 
 # MCLI - Universal Script Runner & Workflow Framework

{mcli_framework-8.0.43 → mcli_framework-8.0.45}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mcli-framework"
-version = "8.0.43"
+version = "8.0.45"
 description = "Portable workflow framework - transform any script into a versioned, schedulable command. Store in ~/.mcli/workflows/, version with lockfile, run as daemon or cron job."
 readme = "README.md"
  requires-python = ">=3.10"
@@ -37,10 +37,12 @@ classifiers = [
 dependencies = [
   # Core CLI dependencies
   "click>=8.1.7,<9.0.0",
-  "rich>=14.0.0",
+  "rich>=14.0.0,<15.0.0",
   "requests>=2.31.0,<3.0.0",
-  "tomli>=2.2.1",
-  "python-dotenv>=1.1.1",
+  "tomli>=2.2.1,<3.0.0",
+  "python-dotenv>=1.1.1,<2.0.0",
+  "pydantic>=2.0.0,<3.0.0",
+  "pydantic-settings>=2.0.0,<3.0.0",
   # Core utilities
   "watchdog>=3.0.0,<4.0.0",
   "tqdm>=4.66.1,<5.0.0",
@@ -50,88 +52,25 @@ dependencies = [
   "gitpython>=3.1.40,<4.0.0",
   "prompt-toolkit>=3.0.0,<4.0.0",
   # Basic HTTP/async support
-  "aiohttp>=3.13.3",  # CVE-2025-69223 through CVE-2025-69230 fixes
-  "httpx>=0.28.1",
-  "websockets>=12.0",
+  "aiohttp>=3.13.3,<4.0.0",  # CVE-2025-69223 through CVE-2025-69230 fixes
+  "httpx>=0.28.1,<1.0.0",
+  "websockets>=12.0,<14.0.0",
   # Data parsing
-  "beautifulsoup4>=4.13.5",
-  "fuzzywuzzy>=0.18.0",
+  "beautifulsoup4>=4.13.5,<5.0.0",
+  "fuzzywuzzy>=0.18.0,<1.0.0",
   # Chat and AI capabilities
   "openai>=1.3.0,<2.0.0",
-  "anthropic>=0.60.0",
-  "ollama>=0.5.3",
+  "anthropic>=0.60.0,<1.0.0",
+  "ollama>=0.5.3,<1.0.0",
   "ipython>=8.12.0,<9.0.0",
   # Enhanced async/performance features
-  "fastapi>=0.110.0",
-  "uvicorn>=0.27.0",
-  "uvloop>=0.19.0",
-  "aiosqlite>=0.20.0",
-  "redis>=5.0.0",
-  "aiohttp-sse-client>=0.2.1",
-  "aiomqtt>=2.0.0",
-  # Video processing
-  "opencv-python>=4.11.0.86",
-  "pillow>=11.2.1",
-  "numpy>=1.24.0,<2.0.0",
-  "scikit-image>=0.24.0",
-  "scipy>=1.10.0",
-  # Document processing
-  "pypdf2>=3.0.1",
-  "pymupdf>=1.26.3",
-  "pandas>=2.3.1",
-  "openpyxl>=3.1.5",
-  # Visualization
-  "matplotlib>=3.9.4",
-  "pydot>=4.0.1",
-  "graphviz>=0.21",
-  "seaborn>=0.13.0",
-  "plotly>=5.17.0",
-  # Database support
-  "supabase>=2.8.1",
-  "sqlalchemy>=2.0.0",
-  "alembic>=1.12.0",
-  "psycopg2-binary>=2.9.7",
-  "asyncpg>=0.29.0",
-  # ML/Trading features
-  "torch>=2.0.0",
-  "torchvision>=0.15.0",
-  "pytorch-lightning>=2.0.0",
-  "scikit-learn>=1.3.0,<2.0.0",
-  "mlflow>=2.9.0",
-  "dvc>=3.0.0",
-  "polars>=0.19.0",
-  "pyarrow>=14.0.0",
-  "yfinance>=0.2.18",
-  "alpha-vantage>=2.3.1",
-  "alpaca-py==0.43.2",
-  "cvxpy>=1.4.0",
-  "python-jose[cryptography]>=3.3.0",
-  "passlib[bcrypt]>=1.7.4",
-  "pydantic-settings>=2.1.0",
-  "dynaconf>=3.2.0",
-  "pandera>=0.17.0",
-  "pendulum>=2.1.2",
-  "optuna>=3.4.0",
-  "PyPortfolioOpt>=1.5.5",
-  "jupyter>=1.0.0",
-  "jupyterlab>=4.0.0",
-  "ipykernel>=6.27.0",
-  # Production monitoring
-  "prometheus-client>=0.19.0",
-  "structlog>=23.2.0",
-  "gunicorn>=21.2.0",
-  "newrelic>=9.2.0",
-  "datadog>=0.49.0",
-  "orjson>=3.9.0",
-  # Streaming/messaging
-  "kafka-python>=2.0.2",
-  # Dashboard
-  "streamlit>=1.50.0",
-  "altair>=4.2.1,<5.0.0",
-  "streamlit-autorefresh>=1.0.1",
-  "typer>=0.9.0",
-  # Web framework
-  "flask>=2.3.0,<3.0.0",
+  "fastapi>=0.110.0,<1.0.0",
+  "uvicorn>=0.27.0,<1.0.0",
+  "uvloop>=0.19.0,<1.0.0",
+  "aiosqlite>=0.20.0,<1.0.0",
+  "redis>=5.0.0,<6.0.0",
+  "aiohttp-sse-client>=0.2.1,<1.0.0",
+  "aiomqtt>=2.0.0,<3.0.0",
 ]
 
 [project.urls]
@@ -143,68 +82,6 @@ dependencies = [
 "Source" = "https://github.com/gwicho38/mcli"
 
 [project.optional-dependencies]
-# GPU support (optional - system specific)
-gpu = [
-  "cupy-cuda12x>=12.3.0",
-  "nvidia-ml-py>=12.535.0",
-]
-
-# Plugin-style optional dependencies (for migrated features)
-# These will be required ONLY if using the corresponding workflows from mcli-commands repo
-
-ml-plugin = [
-  # ML/Training dependencies
-  "torch>=2.0.0",
-  "torchvision>=0.15.0",
-  "pytorch-lightning>=2.0.0",
-  "scikit-learn>=1.3.0,<2.0.0",
-  "mlflow>=2.9.0",
-  "dvc>=3.0.0",
-  "optuna>=3.4.0",
-  # Dashboard dependencies
-  "streamlit>=1.50.0",
-  "altair>=4.2.1,<5.0.0",
-  "streamlit-autorefresh>=1.0.1",
-  # Data science
-  "pandas>=2.3.1",
-  "numpy>=1.24.0,<2.0.0",
-  "polars>=0.19.0",
-  "pyarrow>=14.0.0",
-]
-
-video-plugin = [
-  # Video processing dependencies
-  "opencv-python>=4.11.0.86",
-  "pillow>=11.2.1",
-  "numpy>=1.24.0,<2.0.0",
-  "scikit-image>=0.24.0",
-  "scipy>=1.10.0",
-]
-
-trading-plugin = [
-  # Trading/Finance dependencies
-  "yfinance>=0.2.18",
-  "alpha-vantage>=2.3.1",
-  "alpaca-py==0.43.2",
-  "cvxpy>=1.4.0",
-  "PyPortfolioOpt>=1.5.5",
-  "pandas>=2.3.1",
-  "numpy>=1.24.0,<2.0.0",
-]
-
-# Legacy extras for backward compatibility (all features now included by default)
-# TODO: Remove in v8.0.0
-async-extras = []
-video = []
-documents = []
-viz = []
-database = []
-ml = []
-monitoring = []
-streaming = []
-dashboard = []
-web = []
-
 # Development tools
 dev = [
   # Testing framework
@@ -235,9 +112,6 @@ dev = [
   "twine>=4.0.0",                 # Package upload
 ]
 
-# All optional features (all features now included by default)
-all = []
-
 [tool.black]
 line-length = 100
 include = '\.pyi?$'
@@ -263,11 +137,9 @@ known_first_party = ["mcli"]
 known_third_party = [
     "click", "rich", "requests", "tomli", "openai", "anthropic",
     "fastapi", "uvicorn", "uvloop", "aiosqlite", "redis", "watchdog",
-    "tqdm", "humanize", "psutil", "ipython", "inquirerpy", "flask",
-    "gitpython", "maturin", "scikit-learn", "numpy", "pillow",
-    "opencv", "scikit-image", "pypdf2", "pymupdf", "pydot", "graphviz",
-    "fuzzywuzzy", "pandas", "openpyxl", "ollama", "pytest", "supabase",
-    "httpx", "aiohttp", "beautifulsoup4", "python-dotenv", "matplotlib"
+    "tqdm", "humanize", "psutil", "ipython", "inquirerpy",
+    "gitpython", "maturin", "fuzzywuzzy", "ollama", "pytest",
+    "httpx", "aiohttp", "beautifulsoup4", "python-dotenv"
 ]
 sections = ["FUTURE", "STDLIB", "THIRDPARTY", "FIRSTPARTY", "LOCALFOLDER"]
 force_grid_wrap = 0
@@ -307,20 +179,15 @@ disable_error_code = [
     "index",
     "type-arg",
     "override",
-    "comparison-overlap",
-    "redundant-expr",
     "no-any-return",
     "has-type",
     "valid-type",
     "type-var",
     "dict-item",
     "call-overload",
-    "empty-body",
     "no-redef",
     "abstract",
     "list-item",
-    "str-bytes-safe",
-    "func-returns-value",
 ]
 
 # Module discovery
@@ -374,19 +241,6 @@ module = [
 warn_return_any = false
 ignore_errors = false
 
-# Ignore missing imports for optional dependencies
-[[tool.mypy.overrides]]
-module = [
-    "ollama.*",
-    "streamlit.*",
-    "torch.*",
-    "transformers.*",
-    "plotly.*",
-    "supabase.*",
-]
-warn_return_any = false
-ignore_missing_imports = true
-
 # Core modules - enable stricter type checking
 [[tool.mypy.overrides]]
 module = [
@@ -397,17 +251,13 @@ disallow_untyped_defs = true
 check_untyped_defs = true
 strict_optional = true
 
-# Skip mlflow entirely due to Python version syntax issues
-[[tool.mypy.overrides]]
-module = ["mlflow", "mlflow.*"]
-ignore_errors = true
-follow_imports = "skip"
-
 [build-system]
 requires = ["setuptools>=65.0.0", "wheel>=0.40.0"]
 build-backend = "setuptools.build_meta"
 
 [dependency-groups]
+# NOTE: This is the primary dev dependency specification (PEP 735).
+# [project.optional-dependencies] dev is kept for pip compatibility.
 dev = [
     "black>=25.0.0,<26.0.0",  # Pin to 25.x to match lockfile
     "isort>=5.13.2",
@@ -469,7 +319,7 @@ precision = 2
 skip_covered = false
 skip_empty = false
 # Fail if coverage is below threshold
-fail_under = 25.0
+fail_under = 50.0
 
 [tool.coverage.html]
 directory = "htmlcov"
@@ -487,7 +337,7 @@ addopts = [
     "--cov-report=html",
     "--cov-report=xml",
     "--cov-branch",
-    "--cov-fail-under=80",
+    "--cov-fail-under=50",
 ]
 testpaths = ["tests"]
 python_files = ["test_*.py", "*_test.py"]
@@ -512,11 +362,6 @@ filterwarnings = [
 
 [project.scripts]
 mcli = "mcli.app.main:main"
-mcli-train = "mcli.ml.training.train:main"
-mcli-serve = "mcli.ml.serving.serve:main"
-mcli-backtest = "mcli.ml.backtesting.run:main"
-mcli-optimize = "mcli.ml.optimization.optimize:main"
-mcli-dashboard = "mcli.ml.dashboard:main"
 
 [tool.bandit]
 # Skip these test IDs - acceptable in this CLI tool context

{mcli_framework-8.0.43 → mcli_framework-8.0.45}/src/mcli/app/commands_cmd.py

@@ -353,7 +353,9 @@ def init_store(path, remote):
         # Initialize git if not already initialized
         git_dir = store_path / ".git"
         if not git_dir.exists():
-            subprocess.run(["git", "init"], cwd=store_path, check=True, capture_output=True)
+            subprocess.run(
+                ["git", "init"], cwd=store_path, check=True, capture_output=True, timeout=60
+            )
             success(f"Initialized git repository at {store_path}")
 
             # Create .gitignore
@@ -395,7 +397,10 @@ Last updated: {datetime.now().isoformat()}
             # Add remote if provided
             if remote:
                 subprocess.run(
-                    ["git", "remote", "add", "origin", remote], cwd=store_path, check=True
+                    ["git", "remote", "add", "origin", remote],
+                    cwd=store_path,
+                    check=True,
+                    timeout=60,
                 )
                 success(f"Added remote: {remote}")
         else:
@@ -455,11 +460,15 @@ def push_commands(message, all, is_global):
         success(f"Copied {copied_count} items to store")
 
         # Git add, commit, push
-        subprocess.run(["git", "add", "."], cwd=store_path, check=True)
+        subprocess.run(["git", "add", "."], cwd=store_path, check=True, timeout=60)
 
         # Check if there are changes
         result = subprocess.run(
-            ["git", "status", "--porcelain"], cwd=store_path, capture_output=True, text=True
+            ["git", "status", "--porcelain"],
+            cwd=store_path,
+            capture_output=True,
+            text=True,
+            timeout=60,
         )
 
         if not result.stdout.strip():
@@ -468,12 +477,14 @@ def push_commands(message, all, is_global):
 
         # Commit with message
         commit_msg = message or f"Update commands {datetime.now().strftime('%Y-%m-%d %H:%M:%S')}"
-        subprocess.run(["git", "commit", "-m", commit_msg], cwd=store_path, check=True)
+        subprocess.run(["git", "commit", "-m", commit_msg], cwd=store_path, check=True, timeout=60)
         success(f"Committed changes: {commit_msg}")
 
         # Push to remote if configured
         try:
-            subprocess.run(["git", "push"], cwd=store_path, check=True, capture_output=True)
+            subprocess.run(
+                ["git", "push"], cwd=store_path, check=True, capture_output=True, timeout=60
+            )
             success("Pushed to remote")
         except subprocess.CalledProcessError:
             warning("No remote configured or push failed. Commands committed locally.")
@@ -502,7 +513,7 @@ def pull_commands(force, is_global):
 
         # Pull from remote
         try:
-            subprocess.run(["git", "pull"], cwd=store_path, check=True)
+            subprocess.run(["git", "pull"], cwd=store_path, check=True, timeout=60)
             success("Pulled latest changes from remote")
         except subprocess.CalledProcessError:
             warning("No remote configured or pull failed. Using local store.")
@@ -561,7 +572,9 @@ def sync_commands(message, is_global):
         # First pull
         info("Pulling latest changes...")
         try:
-            subprocess.run(["git", "pull"], cwd=store_path, check=True, capture_output=True)
+            subprocess.run(
+                ["git", "pull"], cwd=store_path, check=True, capture_output=True, timeout=60
+            )
             success("Pulled from remote")
         except subprocess.CalledProcessError:
             warning("No remote or pull failed")
@@ -581,7 +594,11 @@ def sync_commands(message, is_global):
 
         # Check for changes
         result = subprocess.run(
-            ["git", "status", "--porcelain"], cwd=store_path, capture_output=True, text=True
+            ["git", "status", "--porcelain"],
+            cwd=store_path,
+            capture_output=True,
+            text=True,
+            timeout=60,
         )
 
         if not result.stdout.strip():
@@ -589,12 +606,14 @@ def sync_commands(message, is_global):
             return
 
         # Commit and push
-        subprocess.run(["git", "add", "."], cwd=store_path, check=True)
+        subprocess.run(["git", "add", "."], cwd=store_path, check=True, timeout=60)
         commit_msg = message or f"Sync commands {datetime.now().strftime('%Y-%m-%d %H:%M:%S')}"
-        subprocess.run(["git", "commit", "-m", commit_msg], cwd=store_path, check=True)
+        subprocess.run(["git", "commit", "-m", commit_msg], cwd=store_path, check=True, timeout=60)
 
         try:
-            subprocess.run(["git", "push"], cwd=store_path, check=True, capture_output=True)
+            subprocess.run(
+                ["git", "push"], cwd=store_path, check=True, capture_output=True, timeout=60
+            )
             success("Synced and pushed to remote")
         except subprocess.CalledProcessError:
             success("Synced locally (no remote configured)")
@@ -614,7 +633,11 @@ def store_status():
 
         # Git status
         result = subprocess.run(
-            ["git", "status", "--short", "--branch"], cwd=store_path, capture_output=True, text=True
+            ["git", "status", "--short", "--branch"],
+            cwd=store_path,
+            capture_output=True,
+            text=True,
+            timeout=60,
         )
 
         if result.stdout:
@@ -622,7 +645,7 @@ def store_status():
 
         # Show remote
         result = subprocess.run(
-            ["git", "remote", "-v"], cwd=store_path, capture_output=True, text=True
+            ["git", "remote", "-v"], cwd=store_path, capture_output=True, text=True, timeout=60
         )
 
         if result.stdout:
@@ -656,17 +679,23 @@ def configure_store(remote, path):
         if remote:
             # Check if remote exists
             result = subprocess.run(
-                ["git", "remote"], cwd=store_path, capture_output=True, text=True
+                ["git", "remote"], cwd=store_path, capture_output=True, text=True, timeout=60
             )
 
             if "origin" in result.stdout:
                 subprocess.run(
-                    ["git", "remote", "set-url", "origin", remote], cwd=store_path, check=True
+                    ["git", "remote", "set-url", "origin", remote],
+                    cwd=store_path,
+                    check=True,
+                    timeout=60,
                 )
                 success(f"Updated remote URL: {remote}")
             else:
                 subprocess.run(
-                    ["git", "remote", "add", "origin", remote], cwd=store_path, check=True
+                    ["git", "remote", "add", "origin", remote],
+                    cwd=store_path,
+                    check=True,
+                    timeout=60,
                 )
                 success(f"Added remote URL: {remote}")
 
@@ -1391,9 +1420,7 @@ def add_command(command_name, group, description, template, language, shell, is_
         if language != "ipynb":
             import stat
 
-            script_path.chmod(
-                script_path.stat().st_mode | stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH
-            )
+            script_path.chmod(script_path.stat().st_mode | stat.S_IXUSR | stat.S_IXGRP)
 
         logger.info(f"Created script: {script_path}")
     except Exception as e: