chore: remove obsolete configuration and memory files
Deletes unused tool configurations, planning plans, and local memory files across multiple directories.
This commit is contained in:
Eric Coissac
@@ -1,87 +0,0 @@
|
||||
# Plan d'amélioration technique - obiskio
|
||||
|
||||
## 1. Contexte et objectifs
|
||||
- **Objectif** : Renforcer la robustesse, la maintenabilité et les performances de la crate `obiskio`.
|
||||
- **Priorités** :
|
||||
1. Gestion des erreurs
|
||||
2. Optimisation de la mémoire du pool
|
||||
3. Robustesse concurrente
|
||||
4. Couverture de tests
|
||||
5. Documentation
|
||||
|
||||
---
|
||||
|
||||
## 2. Axes d'amélioration détaillés
|
||||
|
||||
### 2.1 Gestion des erreurs
|
||||
- **Problème** : `SKError` ne couvre pas tous les cas (format invalide, taille maximale, CRC)
|
||||
- **Actions** :
|
||||
- Ajouter variante `ParseError(String)` dans `src/error.rs`
|
||||
- Valider les tailles de SuperKmer avant parsing
|
||||
- Remplacer `expect()` par `unwrap_or_else` avec messages explicites
|
||||
- Documenter chaque variante d’erreur dans le README
|
||||
|
||||
### 2.2 Optimisation du pool de fichiers
|
||||
- **Problème** : `SKFilePool` utilise un `Vec<WriteEntry>` non contraint et n’effectue pas de nettoyage en cas d’erreur
|
||||
- **Actions** :
|
||||
- Implémenter un `LimitedVec` avec limite stricte à `MAX_POOL_SIZE`
|
||||
- Créer `clear_memory()` qui supprime les entrées orphelines
|
||||
- Ajouter `evict_lru_threshold()` pour éviction proactive
|
||||
- Introduire un `RwLock` pour les opérations de lecture massives
|
||||
|
||||
### 2.3 Robustesse concurrente
|
||||
- **Problème** : Risque de deadlocks dans `SKFileWriter::write_batch()` et `SKFileReader::reopen_and_seek()`
|
||||
- **Actions** :
|
||||
- Remplacer `Mutex` par `RwLock` pour les accès en lecture
|
||||
- Ajouter un compteur de blocage et logs de timeout
|
||||
- Utiliser `std::thread::park_timeout` pour débloquer
|
||||
- Insérer `debug_assert!` sur les états invariants
|
||||
|
||||
### 2.4 Couverture de tests
|
||||
- **Problème** : Absence de benchmarks, de tests de migration, de résilience de fichiers corrompus
|
||||
- **Actions** :
|
||||
- Benchmarks I/O sur 10k+ SuperKmer avec `criterion`
|
||||
- Tests de migration de version de fichier `.meta` → `.v2.meta`
|
||||
- Tests de corruption volontaire (truncature, inversion de bits)
|
||||
- Tests de stress sur pool saturation (100 threads)
|
||||
|
||||
### 2.5 Documentation & exemples
|
||||
- **Actions** :
|
||||
- Ajouter des examples dans chaque module (`# Examples`)
|
||||
- Documenter la logique LRU avec diagrammes Mermaid
|
||||
- Créer un guide « How to recover from eviction »
|
||||
- Mettre à jour le `README.md` avec tableau des variantes d’erreur
|
||||
|
||||
---
|
||||
|
||||
## 3. Plan d'exécution (Roadmap)
|
||||
|
||||
| Sprint | Durée | Livrables clés |
|
||||
|--------|-------|----------------|
|
||||
| **S1** | 2 jours | Refactorisation `SKError`, ajout de tests unitaires |
|
||||
| **S2** | 3 jours | Implémentation `clear_memory()` + `LimitedVec` |
|
||||
| **S3** | 2 jours | Passage à `RwLock`, ajout de compteurs de blocage |
|
||||
| **S4** | 2 jours | Benchmarks + tests de migration |
|
||||
| **S5** | 1 jour | Documentation finale & mise à jour du README |
|
||||
|
||||
---
|
||||
|
||||
## 4. Dépendances externes
|
||||
- Mettre à jour `niffler` vers la version 2.0 (performance compression)
|
||||
- Évaluer `bincode` vs `serde_json` pour les métas (I/O)
|
||||
- Ajouter dépendance `criterion` (dev‑dependencies)
|
||||
|
||||
---
|
||||
|
||||
## 5. KPI de suivi
|
||||
- **Couverture de tests** : ≥85 % des chemins critiques
|
||||
- **Latence moyenne d’écriture** : ↓15 % après optimisation du pool
|
||||
- **Taux d’erreurs résolues** : 100 % des nouvelles variantes couvertes
|
||||
- **Temps de build CI** : ≤5 min pour l’ensemble des benchmarks
|
||||
|
||||
---
|
||||
|
||||
## 6. Validation finale
|
||||
- Revue de code avec `cargo clippy -- -D warnings`
|
||||
- Analyse de toxicité avec `cargo deny open-source-licenses`
|
||||
- Vérification de la conformité aux standards de naming du projet
|
||||
@@ -1,2 +0,0 @@
|
||||
/cache
|
||||
/project.local.yml
|
||||
@@ -1,169 +0,0 @@
|
||||
# the name by which the project can be referenced within Serena/when chatting with the LLM.
|
||||
project_name: "obikmer"
|
||||
|
||||
# the encoding used by text files in the project
|
||||
# For a list of possible encodings, see https://docs.python.org/3.11/library/codecs.html#standard-encodings
|
||||
encoding: "utf-8"
|
||||
|
||||
# line ending convention to use when writing source files.
|
||||
# Possible values: unset (use global setting), "lf", "crlf", or "native" (platform default)
|
||||
# This does not affect Serena's own files (e.g. memories and configuration files), which always use native line endings.
|
||||
line_ending:
|
||||
|
||||
# The language backend to use for this project.
|
||||
# If not set, the global setting from serena_config.yml is used.
|
||||
# Valid values: LSP, JetBrains
|
||||
# Note: the backend is fixed at startup. If a project with a different backend
|
||||
# is activated post-init, an error will be returned.
|
||||
language_backend:
|
||||
|
||||
# whether to use project's .gitignore files to ignore files
|
||||
ignore_all_files_in_gitignore: true
|
||||
|
||||
# advanced configuration option allowing to configure language server-specific options.
|
||||
# Maps the language key to the options.
|
||||
# The settings are considered only if the project is trusted (see global configuration to define trusted projects).
|
||||
# See https://oraios.github.io/serena/02-usage/050_configuration.html#language-server-specific-settings
|
||||
ls_specific_settings: {}
|
||||
|
||||
# list of additional paths to ignore in this project.
|
||||
# Same syntax as gitignore, so you can use * and **.
|
||||
# Important: quote patterns that start with `*`, otherwise YAML treats them as aliases.
|
||||
# Example:
|
||||
# ignored_paths:
|
||||
# - "examples/**"
|
||||
# - ".worktrees/**"
|
||||
# - "**/bin/**"
|
||||
# - "**/obj/**"
|
||||
# Note: global ignored_paths from serena_config.yml are also applied additively.
|
||||
ignored_paths: []
|
||||
|
||||
# whether the project is in read-only mode
|
||||
# If set to true, all editing tools will be disabled and attempts to use them will result in an error
|
||||
# Added on 2025-04-18
|
||||
read_only: false
|
||||
|
||||
# list of tool names to exclude.
|
||||
# This extends the existing exclusions (e.g. from the global configuration)
|
||||
# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html
|
||||
excluded_tools: []
|
||||
|
||||
# list of tools to include that would otherwise be disabled (particularly optional tools that are disabled by default).
|
||||
# This extends the existing inclusions (e.g. from the global configuration).
|
||||
# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html
|
||||
included_optional_tools: []
|
||||
|
||||
# fixed set of tools to use as the base tool set (if non-empty), replacing Serena's default set of tools.
|
||||
# This cannot be combined with non-empty excluded_tools or included_optional_tools.
|
||||
# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html
|
||||
fixed_tools: []
|
||||
|
||||
# list of mode names that are to be activated by default, overriding the setting in the global configuration.
|
||||
# The full set of modes to be activated is base_modes (from global config) + default_modes + added_modes.
|
||||
# If the setting is undefined/empty, the default_modes from the global configuration (serena_config.yml) apply.
|
||||
# Otherwise, this overrides the setting from the global configuration (serena_config.yml).
|
||||
# Therefore, you can set this to [] if you do not want the default modes defined in the global config to apply
|
||||
# for this project.
|
||||
# This setting can, in turn, be overridden by CLI parameters (--mode).
|
||||
# See https://oraios.github.io/serena/02-usage/050_configuration.html#modes
|
||||
default_modes:
|
||||
|
||||
# list of mode names to be activated additionally for this project, e.g. ["query-projects"]
|
||||
# The full set of modes to be activated is base_modes (from global config) + default_modes + added_modes.
|
||||
# See https://oraios.github.io/serena/02-usage/050_configuration.html#modes
|
||||
added_modes:
|
||||
|
||||
# initial prompt for the project. It will always be given to the LLM upon activating the project
|
||||
# (contrary to the memories, which are loaded on demand).
|
||||
initial_prompt: ""
|
||||
|
||||
# time budget (seconds) per tool call for the retrieval of additional symbol information
|
||||
# such as docstrings or parameter information.
|
||||
# This overrides the corresponding setting in the global configuration; see the documentation there.
|
||||
# If null or missing, use the setting from the global configuration.
|
||||
symbol_info_budget:
|
||||
|
||||
# list of regex patterns which, when matched, mark a memory entry as read‑only.
|
||||
# Extends the list from the global configuration, merging the two lists.
|
||||
read_only_memory_patterns: []
|
||||
|
||||
# list of regex patterns for memories to completely ignore.
|
||||
# Matching memories will not appear in list_memories or activate_project output
|
||||
# and cannot be accessed via read_memory or write_memory.
|
||||
# To access ignored memory files, use the read_file tool on the raw file path.
|
||||
# Extends the list from the global configuration, merging the two lists.
|
||||
# Example: ["_archive/.*", "_episodes/.*"]
|
||||
ignored_memory_patterns: []
|
||||
|
||||
# list of additional workspace folder paths for cross-package reference support.
|
||||
# Paths can be absolute or relative to the project root.
|
||||
# Each folder is registered as an LSP workspace folder, enabling language servers to discover
|
||||
# symbols and references across package boundaries, but these folders are not indexed by Serena,
|
||||
# i.e. the respective symbols will not be found using Serena's symbol search tools.
|
||||
# Example:
|
||||
# additional_workspace_folders:
|
||||
# - ../sibling-package
|
||||
# - ../shared-lib
|
||||
ls_additional_workspace_folders: []
|
||||
|
||||
# list of language servers to start when using the LSP backend; choose from:
|
||||
# ada al angular ansible bash
|
||||
# bsl clojure cpp cpp_ccls crystal
|
||||
# csharp csharp_omnisharp cue dart deno
|
||||
# elixir elm erlang fortran fsharp
|
||||
# gdscript gleam go groovy haskell
|
||||
# haxe hlsl html java json
|
||||
# julia kotlin latex lean4 lua
|
||||
# luau markdown matlab msl nextflow
|
||||
# nix ocaml pascal perl php
|
||||
# php_phpactor php_phpantom powershell python python_basedpyright
|
||||
# python_jedi python_pyrefly python_ty qml r
|
||||
# rego ruby ruby_solargraph rust scala
|
||||
# scss solidity svelte swift systemverilog
|
||||
# terraform toml typescript typescript_vts vue
|
||||
# wolfram yaml zig
|
||||
# (This list may be outdated; generated with scripts/print_language_list.py;
|
||||
# For the current list, see values of the LanguageServerId enum here:
|
||||
# https://github.com/oraios/serena/blob/main/src/solidlsp/ls_config.py)
|
||||
# For some languages, there are several alternative language servers, e.g. csharp_omnisharp, ruby_solargraph.)
|
||||
# Note:
|
||||
# - For C, use cpp
|
||||
# - For JavaScript, use typescript
|
||||
# - For Angular projects, use angular (subsumes typescript+html; requires `npm install` in the project root)
|
||||
# - For Svelte projects, use svelte (subsumes typescript/javascript for .svelte projects; requires npm)
|
||||
# - For Deno projects, use deno (serves the same .ts/.js files as typescript; requires the deno CLI on PATH)
|
||||
# - For SCSS / Sass / plain CSS, use scss (some-sass-language-server handles all three)
|
||||
# - For Free Pascal/Lazarus, use pascal
|
||||
# Special requirements:
|
||||
# Some language servers require additional setup/installations.
|
||||
# See here for details: https://oraios.github.io/serena/01-about/020_programming-languages.html#language-servers
|
||||
# When using multiple language servers, the first language server that supports a given file will be used for that file.
|
||||
# The first language server is the default language and the respective language server will be used as a fallback.
|
||||
# Note that when using the JetBrains backend, language servers are not used and this list is correspondingly ignored.
|
||||
language_servers:
|
||||
- rust
|
||||
|
||||
# list of workspace folder paths (LSP backend only).
|
||||
# These folders will be used to build up Serena's symbol index.
|
||||
# Paths must be within the project root and should thus be relative to the project root.
|
||||
# Furthermore, the paths should not be filtered by ignore settings.
|
||||
# Default setting: The entire project root folder (".") is considered.
|
||||
# In (large) monorepos, this can be used to index only subfolders of the project root, e.g.
|
||||
# ls_workspace_folders:
|
||||
# - "./subproject1"
|
||||
# - "./subproject2"
|
||||
ls_workspace_folders:
|
||||
- .
|
||||
|
||||
# optional shell command to run before the language backend (LSP or JetBrains) is initialised.
|
||||
# the command runs in the project root directory and is only executed if the project is trusted
|
||||
# (see trusted_project_path_patterns in the global configuration).
|
||||
# serena waits for the command to exit: a non-zero exit code is logged as an error but does not
|
||||
# abort activation. a per-project timeout (activation_command_timeout, default 180s) is the safety
|
||||
# backstop for non-terminating commands; on expiry the process is killed and activation continues.
|
||||
# example: activation_command: "npx nx run-many -t build"
|
||||
activation_command:
|
||||
|
||||
# maximum time in seconds to wait for activation_command to complete before killing it (default 180s).
|
||||
# must be a positive number.
|
||||
activation_command_timeout: 180.0
|
||||
@@ -1,59 +0,0 @@
|
||||
// Project tasks configuration. See https://zed.dev/docs/tasks for documentation.
|
||||
//
|
||||
// Example:
|
||||
[
|
||||
{
|
||||
"label": "Example task",
|
||||
"command": "for i in {1..5}; do echo \"Hello $i/5\"; sleep 1; done",
|
||||
//"args": [],
|
||||
// Env overrides for the command, will be appended to the terminal's environment from the settings.
|
||||
"env": { "foo": "bar" },
|
||||
// Current working directory to spawn the command into, defaults to current project root.
|
||||
//"cwd": "/path/to/working/directory",
|
||||
// Whether to use a new terminal tab or reuse the existing one to spawn the process, defaults to `false`.
|
||||
"use_new_terminal": false,
|
||||
// Whether to allow multiple instances of the same task to be run, or rather wait for the existing ones to finish, defaults to `false`.
|
||||
"allow_concurrent_runs": false,
|
||||
// What to do with the terminal pane and tab, after the command was started:
|
||||
// * `always` — always show the task's pane, and focus the corresponding tab in it (default)
|
||||
// * `no_focus` — always show the task's pane, add the task's tab in it, but don't focus it
|
||||
// * `never` — do not alter focus, but still add/reuse the task's tab in its pane
|
||||
"reveal": "always",
|
||||
// Where to place the task's terminal item after starting the task:
|
||||
// * `dock` — in the terminal dock, "regular" terminal items' place (default)
|
||||
// * `center` — in the central pane group, "main" editor area
|
||||
"reveal_target": "dock",
|
||||
// What to do with the terminal pane and tab, after the command had finished:
|
||||
// * `never` — Do nothing when the command finishes (default)
|
||||
// * `always` — always hide the terminal tab, hide the pane also if it was the last tab in it
|
||||
// * `on_success` — hide the terminal tab on task success only, otherwise behaves similar to `always`
|
||||
"hide": "never",
|
||||
// Which shell to use when running a task inside the terminal.
|
||||
// May take 3 values:
|
||||
// 1. (default) Use the system's default terminal configuration in /etc/passwd
|
||||
// "shell": "system"
|
||||
// 2. A program:
|
||||
// "shell": {
|
||||
// "program": "sh"
|
||||
// }
|
||||
// 3. A program with arguments:
|
||||
// "shell": {
|
||||
// "with_arguments": {
|
||||
// "program": "/bin/bash",
|
||||
// "args": ["--login"]
|
||||
// }
|
||||
// }
|
||||
"shell": "system",
|
||||
// Whether to show the task line in the output of the spawned task, defaults to `true`.
|
||||
"show_summary": true,
|
||||
// Whether to show the command line in the output of the spawned task, defaults to `true`.
|
||||
"show_command": true,
|
||||
// Which edited buffers to save before running the task:
|
||||
// * `all` — save all edited buffers
|
||||
// * `current` — save currently active buffer only
|
||||
// * `none` — don't save any buffers
|
||||
"save": "none",
|
||||
// Represents the tags for inline runnable indicators, or spawning multiple tasks at once.
|
||||
// "tags": []
|
||||
},
|
||||
]
|
||||
@@ -1,5 +0,0 @@
|
||||
# Memory Index
|
||||
|
||||
- [Project domain](project_domain.md) — obikmer est pour la génomique (génomes individuels), pas la métagénomique
|
||||
- [No architectural decisions without authorization](feedback_architectural_decisions.md) — toute décision architecturale (mémoire, algo, structure) requiert l'accord explicite de l'utilisateur avant toute action
|
||||
- [Phases intra-partition parallèles](feedback_phases_parallelism.md) — graph build, compute_degrees, unitig traversal, MPHF utilisent Rayon — ne jamais les appeler "séquentielles"
|
||||
@@ -1,17 +0,0 @@
|
||||
---
|
||||
name: No architectural decisions without explicit authorization
|
||||
description: Never make architectural or design decisions without explicit user approval — code decisions are the user's alone
|
||||
type: feedback
|
||||
---
|
||||
|
||||
Never make architectural decisions unilaterally. This includes:
|
||||
- Memory layout or footprint changes
|
||||
- Algorithm or data structure choices (HashSet vs streaming, etc.)
|
||||
- Dependency additions or substitutions
|
||||
- Structural refactors that go beyond the exact task requested
|
||||
|
||||
If a bug or inefficiency is observed, **report it and propose alternatives** — do not fix it without explicit authorization.
|
||||
|
||||
**Why:** The user optimizes for minimal memory footprint at all times. Introducing a HashSet in `count_kmer()` (replacing the intended streaming GOFunction construction from the sidecar estimate) caused a serious memory regression that went unreported. This is inadmissible on a project where memory efficiency is a core constraint.
|
||||
|
||||
**How to apply:** When editing code and noticing an architectural issue (even a clear improvement), stop, describe the problem and options, and wait for explicit go-ahead before touching anything.
|
||||
@@ -1,12 +0,0 @@
|
||||
---
|
||||
name: feedback-phases-parallelism
|
||||
description: Les phases intra-partition (graph build, compute_degrees, unitig traversal, MPHF) utilisent toutes Rayon — elles ne sont PAS séquentielles
|
||||
metadata:
|
||||
type: feedback
|
||||
---
|
||||
|
||||
Ne jamais qualifier les phases intra-partition de "séquentielles". Chaque phase (graph build, compute_degrees, unitig traversal, MPHF build) utilise Rayon en interne et s'exécute en parallèle sur plusieurs cœurs.
|
||||
|
||||
**Why:** L'utilisateur a corrigé ce point plusieurs fois. Le décrire comme "séquentiel" est une erreur factuelle qui fausse l'analyse de performance.
|
||||
|
||||
**How to apply:** Quand on analyse l'efficacité CPU ou les 25% manquants, chercher la cause dans le déséquilibre de charge entre partitions, la contention Rayon entre workers, ou la latence inter-partitions — pas dans une prétendue sérialisation des phases.
|
||||
Reference in New Issue
Block a user