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README.md

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-# Research_Legacy_Codes
-This repository stores code used in my previous research projects. The scripts are archived for reference and are not actively maintained, except when needed for review or specific requests.
+# ResearchCodes
+
+ResearchCodes is a personal research code vault. Everything lives under `Projects/` as self contained project folders (example data, Python modules, notebooks, notes). The goal is to make it easy to clone anywhere, reproduce the environment, and reuse code later.
+
+## Quick start
+
+### 1) Clone
+
+```bash
+git clone git@github.com:Yong2Sheng/ResearchCodes.git
+cd ResearchCodes
+```
+
+### 2) Create the conda environment from `environment.yml`
+
+Create a fresh environment:
+
+```bash
+conda env create -f environment.yml
+conda activate researchcode
+```
+Notes:
+- `environment.yml` is the source of truth for dependencies.
+- If you add a new import in any project module, update `environment.yml` accordingly.
+- Prefer keeping the environment reproducible on a clean machine, because CI will validate it.
+
+During developing, you can update an existing environment to match `environment.yml` (and remove packages no longer listed):
+
+```bash
+conda env update -f environment.yml --prune
+conda activate researchcode
+```
+
+### 3) Install pre-push checks (optional but recommended for pushing changes)
+
+This repo is configured to run checks on `git push` (not on every commit).
+
+```bash
+pre-commit install -f
+```
+
+Manually run the same checks that would run on push:
+
+```bash
+pre-commit run --all-files --hook-stage pre-push
+```
+
+### 4) Run smoke tests locally
+
+Smoke tests are intentionally lightweight. They mainly validate that key modules can be imported in the current environment.
+
+```bash
+pytest -q -m smoke -x -ra
+```
+
+To see what smoke tests would be collected:
+
+```bash
+pytest -m smoke --collect-only
+```
+
+## Repository layout
+
+- `Projects/`
+  - Each subfolder is an independent project workspace.
+  - Typical contents: `*.py`, notebooks, configs, small example data.
+- `tests/`
+  - Smoke tests (import checks and minimal sanity checks).
+- `environment.yml`
+  - Conda environment specification (primary dependency source of truth).
+- `pyproject.toml`
+  - Pytest configuration (markers, test discovery).
+- `.pre-commit-config.yaml`
+  - Pre-push hooks (lint, hygiene checks, smoke test).
+- `.github/workflows/ci.yml`
+  - CI runs pre-commit (full repo) and smoke tests on a clean environment.
+
+## CI on GitHub
+
+GitHub Actions runs on push and pull requests:
+- A `pre-commit` job that runs repository hooks against the full repository.
+- A `smoke` job that builds the conda environment from `environment.yml` and runs `pytest -m smoke`.
+
+CI is useful because it runs in a clean environment. If something imports locally only because your machine already had an extra dependency installed, CI will catch it.
+
+## Important notes and conventions
+
+### Auto-fix hooks are restricted
+
+Some hooks can automatically edit files (for example trimming trailing whitespace). This repo restricts auto-fix hooks to code and configuration file extensions to prevent accidental edits to scientific data files.
+
+### Large data
+
+Avoid committing large raw datasets into git. Prefer small example inputs that are sufficient to reproduce a workflow, and store large data elsewhere.