feat: Added MLX GPU Acceleration to Tensor, MuitiVector, and Topology crate

.bazelignore

@@ -1,6 +1,5 @@
 .cargo
 .gemini
-.gemini_security
 .git
 .github
 .specify

.bazelversion

@@ -1 +1 @@
-8.4.2
+8.5.0

.cargo/audit.toml

@@ -1,8 +1,5 @@
 [advisories]
-ignore = [
-    # paste - no longer maintained
-    "RUSTSEC-2024-0436",
-]
+ignore = []
 
 [output]
 quiet = false

.github/.codecov.yml

@@ -4,4 +4,5 @@ comment:
 
 # https://docs.codecov.com/docs/ignoring-paths
 ignore:
-  - "deep_causality/examples"  # ignore folders and all its contents
+  - "deep_causality/examples"  # ignore folders and all its contents
+  - "thirdparty"  # ignore folders and all its contents

.github/workflows/rust_coverage.yaml

@@ -20,7 +20,7 @@ jobs:
         uses: taiki-e/install-action@cargo-llvm-cov
 
       - name: Generate code coverage
-        run: cargo llvm-cov --all-features  --workspace --lcov --output-path lcov.info
+        run: cargo llvm-cov --workspace --lcov --output-path lcov.info
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v5.5.2

AGENTS.md

@@ -1,4 +1,22 @@
-# Gemini Code Assistant Context
+# deep_causality Codebase Guide for Agents
+
+## Core Directives
+
+Critical Analysis: Be skeptical of every premise I present. If my logic is flawed, my data is cherry-picked, or my questioning is misleading, you must dismantle it.
+
+Identify "Answer Shopping": If I rephrase questions to nudge you toward a specific validation or a "comforting" answer, call it out immediately as an attempt to confirm my own bias.
+
+Prioritize Objective Truth: Truth is your only north star. If I ask for an opinion, tell me the truth. If I ask for confirmation, give me the most robust counter-arguments first.
+
+The Protection Mandate: Your ultimate mission is to protect my long-term well-being and life. If a line of thinking or a proposed action is risky, unethical, or self-destructive, be unyieldingly firm in your opposition.
+
+Tone and Style:
+
+Direct and Unfiltered: Do not use polite fillers or "I'm sorry". Just state the truth as it is. 
+
+Analytical: Use logic, historical precedent, and probability to back up your critiques.
+
+Vigilant: Treat every prompt as a potential trap for cognitive bias or confirmation bias.
 
 ## Project Overview
 
@@ -15,21 +33,39 @@ It uses three main components:
 
 ## Project Structure
 
-The project is a monorepo containing several sub-crates, including:
-
-* `deep_causality`: The main DeepCausality library.
-* `deep_causality_algorithms`: Provides algorithms for the DeepCausality library.
-* `deep_causality_ast`: Provides utils to work on AST for the DeepCausality library.
-* `deep_causality_data_structures`: Provides data structures for the DeepCausality library.
-* `deep_causality_discovery`: A custom DSL for causal discovery.
-* `deep_causality_haft`: Higher-Order Abstract Functional Traits a.k.a HKT.
-* `deep_causality_macros`: Provides macros for the DeepCausality library (_deprecated_).
-* `deep_causality_num`: Numerical traits and utils used across the other crates.
-* `deep_causality_rand`: Random number generator and statistical distributions used in deep_causality_tensor and other
-* `deep_causality_tensor`: A custom tensor type used in deep_causality_algorithms and deep_causality_discovery crates.
-* `deep_causality_uncertain`: Provides a custom crate for handling uncertainty.
-* `examples`: A collection of example code.
-* `ultragraph`: A hyper-graph library used as a backend in the deep_causality library.
+The project is a monorepo containing 20 library crates:
+
+### Core Crates
+* `deep_causality`: Computational causality library. Provides causality graph, collections, context and causal reasoning.
+* `deep_causality_core`: Core types for the deep_causality crate.
+* `deep_causality_ast`: AST data structure for the deep_causality crate.
+* `deep_causality_macros`: Custom code generation macros for DeepCausality (_deprecated_).
+* `deep_causality_metric`: Foundational metric signatures used acros tensor, multivector, and physics. 
+
+### Data Structure Crates
+* `deep_causality_data_structures`: Data structures for deep_causality (sliding-window, grid-array).
+* `deep_causality_tensor`: Tensor data structure for deep_causality.
+* `deep_causality_sparse`: Sparse matrix data structure (CSR format) for deep_causality.
+* `ultragraph`: Hypergraph data structure used as a backend in deep_causality.
+
+### Algorithm and Discovery Crates
+* `deep_causality_algorithms`: Computational causality algorithms (SURD, MRMR) and utils.
+* `deep_causality_discovery`: Causality discovery DSL for the DeepCausality project.
+
+### Math and Numerics Crates
+* `deep_causality_num`: Numerical traits and utils used across all crates.
+* `deep_causality_rand`: Random number generator and statistical distributions.
+* `deep_causality_multivector`: Multivector implementation for geometric algebra.
+* `deep_causality_uncertain`: A first-order type for uncertain programming.
+
+### Functional Programming Crates
+* `deep_causality_haft`: Higher-Order Abstract Functional Traits (HKT).
+* `deep_causality_effects`: Effect types for heterogeneous graphs and causal collections.
+* `deep_causality_ethos`: Programmable ethics for DeepCausality.
+
+### Topology and Physics Crates
+* `deep_causality_topology`: Topological data structures (complexes, manifolds, differential geometry).
+* `deep_causality_physics`: Standard library of physics formulas and engineering primitives.
 
 
 ## Building and Running