chore(docs): improve nagivation

Author: yuxizama

tfhe/docs/README.md

@@ -22,18 +22,27 @@ layout:
 
 Learn the basics of TFHE-rs, set it up, and make it run with ease.
 
-<table data-view="cards"><thead><tr><th></th><th></th><th data-hidden data-card-target data-type="content-ref"></th><th data-hidden data-card-cover data-type="files"></th></tr></thead><tbody><tr><td><strong>What is TFHE-rs?</strong></td><td>Understand TFHE-rs library and basic cryptographic concepts</td><td><a href="getting_started/readme.md">getting_started.md</a></td><td><a href=".gitbook/assets/start1.png">start1.png</a></td></tr><tr><td><strong>Installation</strong></td><td>Follow the step by step guide to import TFHE-rs in your project</td><td><a href="getting_started/installation.md">installation.md</a></td><td><a href=".gitbook/assets/start2.png">start2.png</a></td></tr><tr><td><strong>Quick start</strong></td><td>See a full example of using TFHE-rs to compute on encrypted data</td><td><a href="getting_started/quick_start.md">quick_start.md</a></td><td><a href=".gitbook/assets/start3.png">start3.png</a></td></tr></tbody></table>
+<table data-view="cards"><thead><tr><th></th><th></th><th data-hidden data-card-target data-type="content-ref"></th><th data-hidden data-card-cover data-type="files"></th></tr></thead><tbody><tr><td><strong>What is TFHE-rs?</strong></td><td>Understand TFHE-rs library and basic cryptographic concepts</td><td><a href="getting_started/">getting_started</a></td><td><a href=".gitbook/assets/start1.png">start1.png</a></td></tr><tr><td><strong>Installation</strong></td><td>Follow the step by step guide to import TFHE-rs in your project</td><td><a href="getting_started/installation.md">installation.md</a></td><td><a href=".gitbook/assets/start2.png">start2.png</a></td></tr><tr><td><strong>Quick start</strong></td><td>See a full example of using TFHE-rs to compute on encrypted data</td><td><a href="getting_started/quick_start.md">quick_start.md</a></td><td><a href=".gitbook/assets/start3.png">start3.png</a></td></tr></tbody></table>
 
 ## Build with TFHE-rs
 
 Start building with TFHE-rs by exploring its core features, discovering essential guides, and learning more with user-friendly tutorials.
 
-<table data-view="cards"><thead><tr><th></th><th></th><th></th><th data-hidden data-card-cover data-type="files"></th></tr></thead><tbody><tr><td><strong>Fundamentals</strong></td><td>Explore the core features.</td><td><ul><li><a href="fundamentals/configure-and-generate-keys.md">Configure</a></li><li><a href="fundamentals/encrypt-data.md">Encrypt data</a></li></ul></td><td><a href=".gitbook/assets/build1.png">build1.png</a></td></tr><tr><td><strong>Guides</strong></td><td>Deploy your project.</td><td><ul><li><a href="guides/run_on_gpu.md">Run on GPU</a></li><li><a href="guides/rust_configuration.md">Configure Rust</a></li></ul></td><td><a href=".gitbook/assets/build2.png">build2.png</a></td></tr><tr><td><strong>Tutorials</strong></td><td>Learn more with tutorials.</td><td><ul><li><a href="tutorials/see-all-tutorials.md#start-here">Start here</a></li><li><a href="tutorials/see-all-tutorials.md#go-further">Go further</a></li></ul></td><td><a href=".gitbook/assets/build3.png">build3.png</a></td></tr></tbody></table>
+<table data-view="cards"><thead><tr><th></th><th></th><th></th><th data-hidden data-card-cover data-type="files"></th></tr></thead><tbody><tr><td><strong>FHE Computations</strong></td><td>Run FHE computation on encrypted data.</td><td><ul><li><a href="fhe-computation/types/">Types </a></li><li><a href="fhe-computation/operations/">Operations</a></li></ul></td><td><a href=".gitbook/assets/build1.png">build1.png</a></td></tr><tr><td><strong>Configuration</strong></td><td>Advanced configuration for better performance.</td><td><ul><li><a href="configuration/rust_configuration.md">Advanced Rust </a></li><li><a href="configuration/run_on_gpu.md">GPU acceleration</a></li></ul></td><td><a href=".gitbook/assets/build2.png">build2.png</a></td></tr><tr><td><strong>Integration</strong></td><td>Use TFHE-rs in different contexts or platforms..</td><td><ul><li><a href="integration/c_api.md">C API</a></li><li><a href="integration/js_on_wasm_api.md">JS on WASM API</a></li></ul></td><td><a href=".gitbook/assets/build3.png">build3.png</a></td></tr></tbody></table>
 
 ## Explore more
 
 Access to additional resources and join the Zama community.
 
+### Tutorials
+
+Explore step-by-step guides that walk you through real-world uses of TFHE-rs.&#x20;
+
+* [Homomorphic parity bit](tutorials/parity_bit.md): Learn how to implement a parity bit calculation over encrypted data
+* [Homomorphic case changing on ASCII string](tutorials/ascii_fhe_string.md): See how to process string data securely by changing cases while keeping the data encrypted.
+* [SHA256 with Boolean API](tutorials/sha256_bool.md): Delve into a more complex example: implementing the SHA256 hash function entirely on encrypted boolean values.
+* [All tutorials](tutorials/see-all-tutorials.md): A complete list of all available tutorials in one place.tutorials: A complete list of all available tutorials in one place.
+
 ### References & Explanations
 
 Take a deep dive into TFHE-rs, exploring APIs from the highest to the lowest level of abstraction and accessing additional resources for in-depth explanations.
@@ -56,8 +65,8 @@ Collaborate with us to advance the FHE spaces and drive innovation together.
 
 * [Contribute to TFHE-rs](dev/contributing.md)
 * [Check the latest release note](https://github.com/zama-ai/tfhe-rs/releases)
-* [Request a feature](https://github.com/zama-ai/tfhe-rs/issues/new?assignees=\&labels=feature\_request\&projects=\&template=feature\_request.md\&title=)
-* [Report a bug](https://github.com/zama-ai/tfhe-rs/issues/new?assignees=\&labels=triage\_required\&projects=\&template=bug\_report.md\&title=)
+* [Request a feature](https://github.com/zama-ai/tfhe-rs/issues/new?assignees=\&labels=feature_request\&projects=\&template=feature_request.md\&title=)
+* [Report a bug](https://github.com/zama-ai/tfhe-rs/issues/new?assignees=\&labels=triage_required\&projects=\&template=bug_report.md\&title=)
 
 ***
 

tfhe/docs/SUMMARY.md

@@ -4,58 +4,73 @@
 
 ## Get Started
 
-* [What is TFHE-rs?](getting\_started/readme.md)
-* [Installation](getting\_started/installation.md)
-* [Quick start](getting\_started/quick\_start.md)
-* [Types & Operations](getting\_started/operations.md)
-* [Benchmarks](getting\_started/benchmarks/summary.md)
-  * [CPU Benchmarks](getting\_started/benchmarks/cpu\_benchmarks.md)
-  * [GPU Benchmarks](getting\_started/benchmarks/gpu\_benchmarks.md)
+* [What is TFHE-rs?](getting_started/readme.md)
+* [Installation](getting_started/installation.md)
+* [Quick start](getting_started/quick_start.md)
+* [Benchmarks](getting_started/benchmarks/summary.md)
+  * [CPU Benchmarks](getting_started/benchmarks/cpu_benchmarks.md)
+  * [GPU Benchmarks](getting_started/benchmarks/gpu_benchmarks.md)
   * [Zero-knowledge proof benchmarks](getting_started/benchmarks/zk_proof_benchmarks.md)
-* [Security and cryptography](getting\_started/security\_and\_cryptography.md)
-
-## Fundamentals
-
-* [Configuration and key generation](fundamentals/configure-and-generate-keys.md)
-* [Server key](fundamentals/set-the-server-key.md)
-* [Encryption](fundamentals/encrypt-data.md)
-* [Computation on encrypted data](fundamentals/compute.md)
-* [Decryption](fundamentals/decrypt-data.md)
-* [Encrypted pseudo random values](fundamentals/encrypted-prf.md)
-* [Serialization/deserialization](fundamentals/serialization.md)
-* [Compressing ciphertexts/keys](fundamentals/compress.md)
-* [Debugging](fundamentals/debug.md)
-
-## Guides
-
-* [Rust configuration](guides/rust\_configuration.md)
-* [GPU acceleration](guides/run\_on\_gpu.md)
-* [Overflow detection](guides/overflow\_operations.md)
-* [Data versioning](guides/data\_versioning.md)
-* [Public key encryption](guides/public\_key.md)
-* [Zero-knowledge proofs](guides/zk-pok.md)
-* [Generic trait bounds](guides/trait\_bounds.md)
-* [Parallelized PBS](guides/parallelized\_pbs.md)
-* [High-level API in C](guides/c\_api.md)
-* [JS on WASM API](guides/js\_on\_wasm\_api.md)
-* [Multi-threading with Rayon crate](guides/rayon\_crate.md)
-* [Trivial ciphertexts](guides/trivial\_ciphertext.md)
-* [PBS statistics](guides/pbs-stats.md)
-* [Array](guides/array.md)
-* [Strings](guides/strings.md)
+* [Security and cryptography](getting_started/security_and_cryptography.md)
+
+## FHE Computation
+
+* [Types](fhe-computation/types/README.md)
+  * [Integer](fhe-computation/types/integer.md)
+  * [Strings](fhe-computation/types/strings.md)
+  * [Array](fhe-computation/types/array.md)
+* [Operations](fhe-computation/operations/README.md)
+  * [Arithmetic operations](fhe-computation/operations/arithmetic-operations.md)
+  * [Bitwise operations](fhe-computation/operations/bitwise-operations.md)
+  * [Comparison operations](fhe-computation/operations/comparison-operations.md)
+  * [Min/Max operations](fhe-computation/operations/min-max-operations.md)
+  * [Ternary conditional operations](fhe-computation/operations/ternary-conditional-operations.md)
+  * [Casting operations](fhe-computation/operations/casting-operations.md)
+  * [Boolean Operations](fhe-computation/operations/boolean-operations.md)
+* [Core workflow](fhe-computation/compute/README.md)
+  * [Configuration and key generation](fhe-computation/compute/configure-and-generate-keys.md)
+  * [Server key](fhe-computation/compute/set-the-server-key.md)
+  * [Encryption](fhe-computation/compute/encrypt-data.md)
+  * [Decryption](fhe-computation/compute/decrypt-data.md)
+* [Data handling](fhe-computation/data-handling/README.md)
+  * [Compressing ciphertexts/keys](fhe-computation/data-handling/compress.md)
+  * [Serialization/deserialization](fhe-computation/data-handling/serialization.md)
+  * [Data versioning](fhe-computation/data-handling/data_versioning.md)
+* [Advanced features](fhe-computation/advanced-features/README.md)
+  * [Encrypted pseudo random values](fhe-computation/advanced-features/encrypted-prf.md)
+  * [Overflow detection](fhe-computation/advanced-features/overflow_operations.md)
+  * [Public key encryption](fhe-computation/advanced-features/public_key.md)
+  * [Trivial ciphertexts](fhe-computation/advanced-features/trivial_ciphertext.md)
+  * [Zero-knowledge proofs](fhe-computation/advanced-features/zk-pok.md)
+  * [Multi-threading with Rayon crate](fhe-computation/advanced-features/rayon_crate.md)
+* [Tooling](fhe-computation/tooling/README.md)
+  * [PBS statistics](fhe-computation/tooling/pbs-stats.md)
+  * [Generic trait bounds](fhe-computation/tooling/trait_bounds.md)
+  * [Debugging](fhe-computation/tooling/debug.md)
+
+## Configuration
+
+* [Advanced Rust setup](configuration/rust_configuration.md)
+* [GPU acceleration](configuration/run_on_gpu.md)
+* [Parallelized PBS](configuration/parallelized_pbs.md)
+
+## Integration
+
+* [JS on WASM API](integration/js_on_wasm_api.md)
+* [High-level API in C](integration/c_api.md)
 
 ## Tutorials
 
+* [Homomorphic parity bit](tutorials/parity_bit.md)
+* [Homomorphic case changing on Ascii string](tutorials/ascii_fhe_string.md)
+* [SHA256 with Boolean API](tutorials/sha256_bool.md)
 * [All tutorials](tutorials/see-all-tutorials.md)
-* [Homomorphic parity bit](tutorials/parity\_bit.md)
-* [Homomorphic case changing on Ascii string](tutorials/ascii\_fhe\_string.md)
-* [SHA256 with Boolean API](tutorials/sha256\_bool.md)
 
 ## References
 
 * [API references](https://docs.rs/tfhe/latest/tfhe/)
 * [Fine-grained APIs](references/fine-grained-apis/README.md)
-  * [Quick start](references/fine-grained-apis/quick\_start.md)
+  * [Quick start](references/fine-grained-apis/quick_start.md)
   * [Boolean](references/fine-grained-apis/boolean/README.md)
     * [Operations](references/fine-grained-apis/boolean/operations.md)
     * [Cryptographic parameters](references/fine-grained-apis/boolean/parameters.md)
@@ -80,5 +95,5 @@
 
 * [Contributing](dev/contributing.md)
 * [Release note](https://github.com/zama-ai/tfhe-rs/releases)
-* [Feature request](https://github.com/zama-ai/tfhe-rs/issues/new?assignees=\&labels=feature\_request\&projects=\&template=feature\_request.md\&title=)
-* [Bug report](https://github.com/zama-ai/tfhe-rs/issues/new?assignees=\&labels=triage\_required\&projects=\&template=bug\_report.md\&title=)
+* [Feature request](https://github.com/zama-ai/tfhe-rs/issues/new?assignees=\&labels=feature_request\&projects=\&template=feature_request.md\&title=)
+* [Bug report](https://github.com/zama-ai/tfhe-rs/issues/new?assignees=\&labels=triage_required\&projects=\&template=bug_report.md\&title=)

tfhe/docs/guides/parallelized_pbs.md renamed to tfhe/docs/configuration/parallelized_pbs.md

@@ -1,6 +1,6 @@
 # Parallelized PBS
 
-This document describes the implementation and benefits of parallelized [Programmable Bootstrapping](../getting\_started/security\_and\_cryptography.md) (PBS) in **TFHE-rs**, including code examples for using multi-bit PBS parameters and ensuring deterministic execution.
+This document describes the implementation and benefits of parallelized [Programmable Bootstrapping](../getting_started/security_and_cryptography.md) (PBS) in **TFHE-rs**, including code examples for using multi-bit PBS parameters and ensuring deterministic execution.
 
 ## Parallelized Programmable Bootstrapping
 

tfhe/docs/guides/run_on_gpu.md renamed to tfhe/docs/configuration/run_on_gpu.md

@@ -11,13 +11,12 @@ This guide explains how to update your existing program to leverage GPU accelera
 * [gcc](https://gcc.gnu.org/) >= 8.0 - check this [page](https://gist.github.com/ax3l/9489132) for more details about nvcc/gcc compatible versions
 * [cmake](https://cmake.org/) >= 3.24
 * libclang, to match Rust bingen [requirements](https://rust-lang.github.io/rust-bindgen/requirements.html) >= 9.0
-* Rust version - check this [page](rust\_configuration.md)
+* Rust version - check this [page](rust_configuration.md)
 
 ## Importing to your project
 
 To use the **TFHE-rs** GPU backend in your project, add the following dependency in your `Cargo.toml`.
 
-
 ```toml
 tfhe = { version = "1.0.0", features = ["boolean", "shortint", "integer", "gpu"] }
 ```
@@ -31,7 +30,7 @@ For optimal performance when using **TFHE-rs**, run your code in release mode wi
 **TFHE-rs** GPU backend is supported on Linux (x86, aarch64).
 
 | OS      | x86         | aarch64       |
-|---------|-------------|---------------|
+| ------- | ----------- | ------------- |
 | Linux   | Supported   | Supported\*   |
 | macOS   | Unsupported | Unsupported\* |
 | Windows | Unsupported | Unsupported   |
@@ -40,7 +39,7 @@ For optimal performance when using **TFHE-rs**, run your code in release mode wi
 
 ### Configuring and creating keys.
 
-Comparing to the [CPU example](../getting\_started/quick\_start.md), GPU set up differs in the key creation, as detailed [here](run\_on\_gpu.md#Setting-the-keys)
+Comparing to the [CPU example](../getting_started/quick_start.md), GPU set up differs in the key creation, as detailed [here](./run_on_gpu.md#setting-the-keys)
 
 Here is a full example (combining the client and server parts):
 
@@ -77,9 +76,7 @@ fn main() {
 }
 ```
 
-Beware that when the GPU feature is activated, when calling: `let config = ConfigBuilder::default().build();`,
-the cryptographic parameters differ from the CPU ones, used when the GPU feature is not activated.
-Indeed, TFHE-rs uses dedicated parameters for the GPU in order to achieve better performance.
+Beware that when the GPU feature is activated, when calling: `let config = ConfigBuilder::default().build();`, the cryptographic parameters differ from the CPU ones, used when the GPU feature is not activated. Indeed, TFHE-rs uses dedicated parameters for the GPU in order to achieve better performance.
 
 ### Setting the keys
 
@@ -103,7 +100,7 @@ On the client-side, the method to encrypt the data is exactly the same than the
 
 The server first need to set up its keys with `set_server_key(gpu_key)`.
 
-Then, homomorphic computations are performed using the same approach as the [CPU operations](../getting\_started/operations.md).
+Then, homomorphic computations are performed using the same approach as the [CPU operations](../fhe-computation/operations/README.md).
 
 ```Rust
     //Server-side
@@ -131,7 +128,7 @@ Finally, the client decrypts the results using:
 The GPU backend includes the following operations for both signed and unsigned encrypted integers:
 
 | name                  | symbol         | `Enc`/`Enc`                | `Enc`/ `Int`               |
-|-----------------------|----------------|----------------------------|----------------------------|
+| --------------------- | -------------- | -------------------------- | -------------------------- |
 | Neg                   | `-`            | :heavy\_check\_mark:       | N/A                        |
 | Add                   | `+`            | :heavy\_check\_mark:       | :heavy\_check\_mark:       |
 | Sub                   | `-`            | :heavy\_check\_mark:       | :heavy\_check\_mark:       |
@@ -157,31 +154,32 @@ The GPU backend includes the following operations for both signed and unsigned e
 | Cast (from src type)  | `cast_from`    | :heavy\_multiplication\_x: | N/A                        |
 | Ternary operator      | `select`       | :heavy\_check\_mark:       | :heavy\_multiplication\_x: |
 
-
 {% hint style="info" %}
-All operations follow the same syntax than the one described in [here](../getting\_started/operations.md).
+All operations follow the same syntax than the one described in [here](../fhe-computation/operations/README.md).
 {% endhint %}
 
 ## Multi-GPU support
 
 TFHE-rs supports platforms with multiple GPUs. There is **nothing to change in the code to execute on such platforms**. To keep the API as user-friendly as possible, the configuration is automatically set, i.e., the user has no fine-grained control over the number of GPUs to be used.
 
-## Benchmark 
+## Benchmark
+
 Please refer to the [GPU benchmarks](../getting_started/benchmarks/gpu_benchmarks.md) for detailed performance benchmark results.
 
 ## Warning
+
 When measuring GPU times on your own on Linux, set the environment variable `CUDA_MODULE_LOADING=EAGER` to avoid CUDA API overheads during the first kernel execution.
 
 ## Compressing ciphertexts after some homomorphic computation on the GPU
 
-You can compress ciphertexts using the GPU, even after computations, just like on the [CPU](../fundamentals/compress.md#compression-ciphertexts-after-some-homomorphic-computation).
+You can compress ciphertexts using the GPU, even after computations, just like on the [CPU](../fhe-computation/data-handling/compress.md#compression-ciphertexts-after-some-homomorphic-computation).
+
+The way to do it is very similar to how it's done on the CPU. The following example shows how to compress and decompress a list containing 4 messages:
 
-The way to do it is very similar to how it's done on the CPU.
-The following example shows how to compress and decompress a list containing 4 messages:
-- One 32-bits integer
-- One 64-bit integer
-- One Boolean
-- One 2-bit integer
+* One 32-bits integer
+* One 64-bit integer
+* One Boolean
+* One 2-bit integer
 
 ```rust
 use tfhe::prelude::*;
@@ -246,7 +244,8 @@ fn main() {
 
 ## Array types
 
-It is possible to use array types on GPU, just as [on CPU](array.md). Here is an example showing how to do it:
+It is possible to use array types on GPU, just as [on CPU](../fhe-computation/types/array.md). Here is an example showing how to do it:
+
 ```rust
 use tfhe::{ConfigBuilder, set_server_key, ClearArray, ClientKey, CompressedServerKey};
 use tfhe::array::GpuFheUint32Array;

tfhe/docs/guides/rust_configuration.md renamed to tfhe/docs/configuration/rust_configuration.md

@@ -0,0 +1 @@
+# Advanced features