big refactor of the fink-fat-eval crate (#183)

* big refactor of the fink-fat-eval crate

* update gitignore

* enabling seed parallel construction

* add seeding evaluation

* add plots for seeding

* fix an overflow error bug

* add edges stats

* move dev profile in the workspace cargo toml

* improve edge generation

* forgotten files

* optimize edge generation

* add tests, add solver evaluation

* add an edge features exporter

* fix docs and missing system dep

* clean edge ml prediction project, add a ml model evaluation in rust

* add rust ml eval plots

* add optuna optimization

* add fink-fat-eval readme

* add evaluation compilation profile note in readme

* add a new edges generation benchmark

* change ml behavior in the pipeline, ml is not a ranking anymore, it is now a filtering

* add engine readme, remove units file, put content in lib.rs

* add main doc page

* refactor fink fat main

* skip code coverage for fink-fat-eval

Author: FusRoman

.github/agents/code-generation.agent.md

@@ -0,0 +1,76 @@
+---
+name: code-generation
+description: >
+  Code generation and programming problem solving agent for the Fink-FAT project.
+  Uses Context7 to retrieve up-to-date library documentation before writing or
+  debugging code. Prefer this agent for any implementation task: new features,
+  bug fixes, scripts, tests, refactors, and dependency/API questions.
+argument-hint: Describe the programming task or problem to solve
+tools: [vscode/getProjectSetupInfo, vscode/memory, vscode/extensions, vscode/askQuestions, execute/runNotebookCell, execute/testFailure, execute/getTerminalOutput, execute/awaitTerminal, execute/killTerminal, execute/createAndRunTask, execute/runInTerminal, execute/runTests, read/getNotebookSummary, read/problems, read/readFile, read/readNotebookCellOutput, read/terminalSelection, read/terminalLastCommand, agent/runSubagent, edit/createDirectory, edit/createFile, edit/createJupyterNotebook, edit/editFiles, edit/editNotebook, edit/rename, search/changes, search/codebase, search/fileSearch, search/listDirectory, search/searchResults, search/textSearch, search/searchSubagent, search/usages, web/fetch, web/githubRepo, browser/openBrowserPage, io.github.upstash/context7/get-library-docs, io.github.upstash/context7/resolve-library-id, ms-python.python/getPythonEnvironmentInfo, ms-python.python/getPythonExecutableCommand, todo]
+---
+
+# Code Generation Agent
+
+## Role
+
+Implement, debug, and improve code across the Fink-FAT project.
+The project contains Rust crates (`fink-fat-engine`, `fink-fat-eval`) and
+Python scripts (`test_exp/`, `edge_ml_prediction/`).
+
+## Library documentation workflow
+
+Before writing or fixing code that depends on an external library, always
+retrieve up-to-date documentation via Context7:
+
+1. Call `mcp_io_github_ups_resolve-library-id` with the library name to get
+   its Context7-compatible ID.
+2. Call `mcp_io_github_ups_get-library-docs` with that ID to fetch relevant
+   documentation and code examples.
+3. Use the retrieved documentation to write correct, idiomatic code.
+
+Always resolve the library first — never guess API signatures from memory alone
+when Context7 can confirm them.
+
+## Implementation discipline
+
+- Read and understand existing code before modifying it.
+- Make only changes that are directly requested or clearly necessary.
+- Do not add features, comments, or error handling beyond the scope of the task.
+- Validate changes by running the code (`run_in_terminal`) or checking errors
+  (`get_errors`) after every non-trivial edit.
+- Use `manage_todo_list` for multi-step tasks.
+- Ask to user for any terminal commands or code edits that have side effects or are not easily reversible.
+
+## Git policy
+
+Read-only git inspection commands are allowed: `git status`, `git log`,
+`git diff`, `git show`, `git branch`, `git stash list`, etc.
+
+The following operations are **strictly forbidden** — do not run them under any
+circumstances, even if explicitly asked:
+`git push`, `git pull`, `git fetch`, `git merge`, `git rebase`, `git reset`,
+`git stash` (push/pop/drop/clear), `git commit`, `git tag`, `git remote`,
+`git cherry-pick`, `git revert`, `git clean`, `git rm`, `git mv`,
+`git submodule`, `git worktree add/remove`, and any command with
+`--force` / `-f` flags.
+
+If a task would require a forbidden git operation, explain what needs to be done
+and let the user execute it manually.
+
+## Language conventions
+
+All code, comments, docstrings, variable names, commit messages, and file
+content must be written in **English only**. Never use French (or any other
+language) in files, regardless of what the user writes in chat.
+
+### Rust
+- Follow standard Rust idioms: `?` for error propagation, iterators over loops,
+  `clippy`-clean code.
+- Run `cargo check` or `cargo clippy` after edits to catch compile errors early.
+
+### Python
+- Target Python 3.12.
+- Use `pathlib.Path` over `os.path`.
+- Prefer numpy vectorised operations over Python loops on large arrays.
+- Format with `black` when editing existing files that already use it.
+- Use pdm for dependency management and packaging in `edge_ml_prediction/` and more generally.

.github/workflows/CI.yml

@@ -37,6 +37,10 @@ jobs:
         with:
           components: clippy
 
+      - name: Install system dependencies
+        # Note: Needed for plotters in the fink-fat-eval crate
+        run: sudo apt-get update && sudo apt-get install -y libfontconfig1-dev
+
       - name: Cache Rust
         uses: Swatinem/rust-cache@v2
         with:
@@ -55,6 +59,10 @@ jobs:
       - name: Install Rust (stable)
         uses: dtolnay/rust-toolchain@stable
 
+      - name: Install system dependencies
+        # Note: Needed for plotters in the fink-fat-eval crate
+        run: sudo apt-get update && sudo apt-get install -y libfontconfig1-dev
+
       - name: Cache Rust
         uses: Swatinem/rust-cache@v2
         with:
@@ -73,6 +81,10 @@ jobs:
       - name: Install Rust (stable)
         uses: dtolnay/rust-toolchain@stable
 
+      - name: Install system dependencies
+        # Note: Needed for plotters in the fink-fat-eval crate
+        run: sudo apt-get update && sudo apt-get install -y libfontconfig1-dev
+
       - name: Cache Rust
         uses: Swatinem/rust-cache@v2
         with:
@@ -94,6 +106,10 @@ jobs:
         with:
           components: llvm-tools-preview
 
+      - name: Install system dependencies
+        # Note: Needed for plotters in the fink-fat-eval crate
+        run: sudo apt-get update && sudo apt-get install -y libfontconfig1-dev
+
       - name: Cache Rust
         uses: Swatinem/rust-cache@v2
         with:

.gitignore

@@ -12,7 +12,7 @@ __pycache__/
 .Python
 .venv/
 env/
-bin/
+# bin/
 build/
 develop-eggs/
 dist/
@@ -86,3 +86,6 @@ test_config.toml
 test_exp/
 
 crates/fink-fat-engine/.github/agents/
+docs/
+edge_plots/
+model_eval_plots/