chore: Update pre-commit (#435)

.github/CONTRIBUTING.md

@@ -4,14 +4,13 @@ If you are interested in contributing to PyTorch Frame, your contributions will
 
 1. You want to implement a new feature:
    - In general, we accept any features as long as they fit the scope of this package. If you are unsure about this or need help on the design/implementation of your feature, post about it in an issue.
-2. You want to fix a bug:
+1. You want to fix a bug:
    - Feel free to send a Pull Request (PR) any time you encounter a bug. Please provide a clear and concise description of what the bug was. If you are unsure about if this is a bug at all or how to fix, post about it in an issue.
 
 Once you finish implementing a feature or bug-fix, please send a PR to https://github.com/pyg-team/pytorch-frame.
 
 Your PR will be merged after one or more rounds of reviews by the [pyg-team](https://github.com/pyg-team).
 
-
 ## Developing PyTorch Frame
 
 To develop PyTorch Frame on your machine, here are some tips:
@@ -23,26 +22,28 @@ To develop PyTorch Frame on your machine, here are some tips:
    print(torch.__version__)
    ```
 
-2. Uninstall all existing PyTorch Frame installations.
+1. Uninstall all existing PyTorch Frame installations.
    It is advised to run this command repeatedly to confirm that installations across all locations are properly removed.
 
    ```bash
    pip uninstall pytorch_frame
    ```
 
-3. Fork and clone the PyTorch Frame repository:
+1. Fork and clone the PyTorch Frame repository:
 
    ```bash
    git clone https://github.com/<your_username>/pytorch-frame.git
    cd pytorch-frame
 
-5. If you already cloned PyTorch Frame from source, update it:
+   ```
+
+1. If you already cloned PyTorch Frame from source, update it:
 
    ```bash
    git pull
    ```
 
-6. Install PyTorch Frame in editable mode:
+1. Install PyTorch Frame in editable mode:
 
    ```bash
    pip install -e ".[dev,full]"
@@ -51,13 +52,13 @@ To develop PyTorch Frame on your machine, here are some tips:
    This mode will symlink the Python files from the current local source tree into the Python install.
    Hence, if you modify a Python file, you do not need to re-install PyTorch Frame again.
 
-7. Ensure that you have a working PyTorch Frame installation by running the entire test suite with
+1. Ensure that you have a working PyTorch Frame installation by running the entire test suite with
 
    ```bash
    pytest
    ```
 
-8. Install pre-commit hooks:
+1. Install pre-commit hooks:
 
    ```bash
     pre-commit install
@@ -91,7 +92,7 @@ Everytime you send a Pull Request, your commit will be built and checked against
 
    If you do not want to format your code manually, we recommend to use [`yapf`](https://github.com/google/yapf).
 
-2. Ensure that the entire test suite passes and that code coverage roughly stays the same.
+1. Ensure that the entire test suite passes and that code coverage roughly stays the same.
    Please feel encouraged to provide a test with your submitted code.
    To test, either run
 
@@ -101,19 +102,19 @@ Everytime you send a Pull Request, your commit will be built and checked against
 
    (which runs a set of additional but time-consuming tests) dependening on your needs.
 
-3. Add your feature/bugfix to the [`CHANGELOG.md`](https://github.com/pyg-team/pyotrch-frame/blob/master/CHANGELOG.md?plain=1).
+1. Add your feature/bugfix to the [`CHANGELOG.md`](https://github.com/pyg-team/pyotrch-frame/blob/master/CHANGELOG.md?plain=1).
    If multiple PRs move towards integrating a single feature, it is advised to group them together into one bullet point.
 
 ## Building Documentation
 
 To build the documentation:
 
 1. [Build and install](#developing-pytorch-frame) PyTorch Frame from source.
-2. Install [Sphinx](https://www.sphinx-doc.org/en/master/) theme via
+1. Install [Sphinx](https://www.sphinx-doc.org/en/master/) theme via
    ```bash
    pip install git+https://github.com/pyg-team/pyg_sphinx_theme.git
    ```
-3. Generate the documentation via:
+1. Generate the documentation via:
    ```bash
    cd docs
    make html

.pre-commit-config.yaml

@@ -33,6 +33,26 @@ repos:
         name: Lint yaml
         args: [-d, '{extends: default, rules: {line-length: disable, document-start: disable, truthy: {level: error}, braces: {max-spaces-inside: 1}}}']
 
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.17.0
+    hooks:
+      - id: pyupgrade
+        name: Upgrade Python syntax
+        args: [--py38-plus]
+
+  - repo: https://github.com/PyCQA/autoflake
+    rev: v2.3.1
+    hooks:
+      - id: autoflake
+        name: Remove unused imports and variables
+        args: [
+          --remove-all-unused-imports,
+          --remove-unused-variables,
+          --remove-duplicate-keys,
+          --ignore-init-module-imports,
+          --in-place,
+        ]
+
   - repo: https://github.com/google/yapf
     rev: v0.40.2
     hooks:
@@ -65,5 +85,15 @@ repos:
     hooks:
       - id: mypy
         name: Check types
-        additional_dependencies: [torch==2.2.0]
+        additional_dependencies: [torch==2.4.0]
         exclude: "^test/|^examples/|^benchmark/"
+
+  - repo: https://github.com/executablebooks/mdformat
+    rev: 0.7.17
+    hooks:
+      - id: mdformat
+        name: Format Markdown
+        additional_dependencies:
+          - mdformat-gfm
+          - mdformat_frontmatter
+          - mdformat_footnote

CHANGELOG.md

@@ -3,8 +3,7 @@
 All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
-
-## [Unreleased]
+## \[Unreleased\]
 
 ### Added
 
@@ -21,7 +20,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 - Removed CUDA synchronizations from `nn.LinearEmbeddingEncoder` ([#432](https://github.com/pyg-team/pytorch-frame/pull/432))
 - Removed CUDA synchronizations from N/A imputation logic in `nn.StypeEncoder` ([#433](https://github.com/pyg-team/pytorch-frame/pull/433), [#434](https://github.com/pyg-team/pytorch-frame/pull/434))
 
-## [0.2.3] - 2024-07-08
+## \[0.2.3\] - 2024-07-08
 
 ### Added
 
@@ -33,8 +32,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 - Updated `ExcelFormer` implementation and related scripts ([#391](https://github.com/pyg-team/pytorch-frame/pull/391))
 
-
-## [0.2.2] - 2024-03-04
+## \[0.2.2\] - 2024-03-04
 
 ### Added
 
@@ -60,14 +58,16 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 - Fixed the split of `DataFrameTextBenchmark` ([#358](https://github.com/pyg-team/pytorch-frame/pull/358))
 - Fixed empty `MultiNestedTensor` col indexing ([#355](https://github.com/pyg-team/pytorch-frame/pull/355))
 
-## [0.2.1] - 2024-01-16
+## \[0.2.1\] - 2024-01-16
 
 ### Added
+
 - Support more stypes in `LinearModelEncoder` ([#325](https://github.com/pyg-team/pytorch-frame/pull/325))
 - Added `stype_encoder_dict` to some models ([#319](https://github.com/pyg-team/pytorch-frame/pull/319))
 - Added `HuggingFaceDatasetDict` ([#287](https://github.com/pyg-team/pytorch-frame/pull/287))
 
 ### Changed
+
 - Supported decoder embedding model in `examples/transformers_text.py` ([#333](https://github.com/pyg-team/pytorch-frame/pull/333))
 - Removed implicit clones in `StypeEncoder` ([#286](https://github.com/pyg-team/pytorch-frame/pull/286))
 
@@ -76,10 +76,11 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 ### Removed
 
 ### Fixed
+
 - Fixed `TimestampEncoder` not applying `CyclicEncoder` to cyclic features ([#311](https://github.com/pyg-team/pytorch-frame/pull/311))
 - Fixed NaN masking in `multicateogrical` stype ([#307](https://github.com/pyg-team/pytorch-frame/pull/307))
 
-## [0.2.0] - 2023-12-15
+## \[0.2.0\] - 2023-12-15
 
 ### Added
 
@@ -104,7 +105,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 - Added `Timestamp` stype ([#212](https://github.com/pyg-team/pytorch-frame/pull/212))
 - Added `multicategorical` to `MultimodalTextBenchmark` ([#208](https://github.com/pyg-team/pytorch-frame/pull/208))
 - Added support for saving and loading of `TensorFrame` with complex `stypes`. ([#197](https://github.com/pyg-team/pytorch-frame/pull/197))
-- Added `stype.embedding` ((#194)[https://github.com/pyg-team/pytorch-frame/pull/194])
+- Added `stype.embedding` ([#194](https://github.com/pyg-team/pytorch-frame/pull/194))
 - Added `TensorFrame` concatenation of complex stypes. ([#190](https://github.com/pyg-team/pytorch-frame/pull/190))
 - Added `text_tokenized` example ([#174](https://github.com/pyg-team/pytorch-frame/pull/174))
 - Added Cohere embedding example ([#186](https://github.com/pyg-team/pytorch-frame/pull/186))
@@ -131,8 +132,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 - No manual passing of `in_channels` to `LinearEmbeddingEncoder` for `stype.text_embedded` ([#222](https://github.com/pyg-team/pytorch-frame/pull/222))
 
-
-## [0.1.0] - 2023-10-23
+## \[0.1.0\] - 2023-10-23
 
 ### Added