Merge pull request #52 from MDverse/setup-precommit

Setup precommit

Author: pierrepo

.github/workflows/ci.yml

@@ -0,0 +1,29 @@
+name: CI
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+
+  pre-commit:
+    runs-on: ubuntu-24.04
+    timeout-minutes: 15
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v6
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v7
+      with:
+        enable-cache: true
+
+    - name: Install Python
+      run: uv python install
+    
+    - name: Install python dependencies
+      run: uv sync --locked --dev
+
+    - name: Run pre-commit hooks
+      run: uv run prek

.pre-commit-config.yaml

@@ -0,0 +1,31 @@
+# Install pre-commit hooks with:
+# prek install
+exclude: "scripts/*|tmp/*|.*.mdp|"
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v6.0.0
+  hooks:
+    - id: end-of-file-fixer
+    - id: mixed-line-ending
+    - id: trailing-whitespace
+    - id: check-json
+    - id: check-yaml
+    - id: check-added-large-files
+      args: ['--maxkb=5000']
+
+- repo: https://github.com/asottile/pyupgrade
+  rev: v3.21.2
+  hooks:
+  - id: pyupgrade
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.14.13
+  hooks:
+    # Run the linter.
+    - id: ruff-check
+      types_or: [ python, pyi ]
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format
+      types_or: [ python, pyi ]

CONTRIBUTING.md

@@ -0,0 +1,70 @@
+# Contributing guidelines
+
+## Setup your environment
+
+1. Install [uv](https://docs.astral.sh/uv/getting-started/installation/).
+
+2. [Fork](https://github.com/mdverse/mdws/fork) this repository.
+
+3. Clone your fork of thr project on your machine:
+
+    ```sh
+    git clone https://github.com/<your-github-username>/mdws.git
+    ```
+
+4. Get into the new directory:
+
+    ```sh
+    cd mdws
+    ```
+
+5. Install dependencies:
+
+    ```sh
+    uv sync --dev
+    ```
+
+6. Install pre-commit hook:
+
+    ```sh
+    uv run prek install
+    ```
+
+7. Create a new branch:
+
+    ```sh
+    git sw -c <your-branch-name>
+    ```
+
+8. Make changes and commit:
+
+    ```sh
+    git add
+    git commit -m "<your-commit-message>"
+    git push origin "<your-branch-name>"
+    ```
+
+9. Create a [pull request](https://github.com/mdverse/mdws/compare).
+
+    Click compare across forks if you don't see your branch.
+
+## Conventional commits
+
+For commit messages, please use Conventional Commits.
+
+See:
+- [Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0/): reference guide
+- Cheatsheet of [Sample Conventional Commit Verbs](https://gkarthiks.github.io/quick-commands-cheat-sheet/conventional-commit-verbs)
+- [Conventional Commit](https://blog.stephane-robert.info/docs/developper/conventional-commits/) (FR)
+
+Examples of valid commit messages:
+
+- `feat: Valide metadata with model`
+- `fix(http): Resolve multiple errors on HTTP queries`
+- `fix: Verify directory exists before writing in (#45)`
+- `docs: Update installation instructions`
+- `style: Format code according with ruff`
+- `refactor: Move CLI argument management into separate module`
+- `test: Add unit tests for the new scraper`
+- `chore: Update dependencies to latest versions`
+

README.md

@@ -2,6 +2,8 @@
 
 Parquet files and codebook are available on Zenodo: [10.5281/zenodo.7856523](https://doi.org/10.5281/zenodo.7856523)
 
+see [CONTRIBUTING](CONTRIBUTING.md) if you want to contribute to this repo.
+
 ## Setup your environment
 
 Install [uv](https://docs.astral.sh/uv/getting-started/installation/).
@@ -12,12 +14,6 @@ Clone this repository:
 git clone https://github.com/MDverse/mdws.git
 ```
 
-> [!TIP]
-> For maintainers only:
-> ```bash
-> git clone git@github.com:MDverse/mdws.git
-> ```
-
 Move to the new directory:
 
 ```bash
@@ -34,7 +30,7 @@ uv sync
 
 Have a look to the notes regarding [Zenodo](docs/zenodo.md) and how its API works.
 
-Create a token here: <https://zenodo.org/account/settings/applications/tokens/new/>  
+Create a token here: <https://zenodo.org/account/settings/applications/tokens/new/>
 and store it in the file `.env`:
 
 ```none
@@ -79,7 +75,7 @@ uv run scrape-figshare --query-file params/query_dev.yml --output-dir tmp
 
 The scraping takes some time (about 5 hours). Be patient.
 
-Eventually, the scraper will produce two files: `figshare_datasets.parquet` and `figshare_files.parquet` :sparkles: 
+Eventually, the scraper will produce two files: `figshare_datasets.parquet` and `figshare_files.parquet` :sparkles:
 
 ## Scrape OSF
 
@@ -265,7 +261,7 @@ bash run_all.sh
 Update metadata:
 
 ```bash
-uv run scripts/upload_datasets_to_zenodo.py --record 7856524 --metadata params/zenodo_metadata.json 
+uv run scripts/upload_datasets_to_zenodo.py --record 7856524 --metadata params/zenodo_metadata.json
 ```
 
 Update files: