Rolling out markdownlint-cli to lint Markdown

.pre-commit-config.yaml

@@ -65,6 +65,11 @@ repos:
     rev: 1.19.1
     hooks:
       - id: blacken-docs
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.45.0
+    hooks:
+      - id: markdownlint
+        args: [--config=pyproject.toml, --configPointer=/tool/markdownlint]
   - repo: https://github.com/jsh9/markdown-toc-creator
     rev: 0.0.10
     hooks:

README.md

@@ -1,10 +1,12 @@
+# ether0 Reward Model
+
 [![GitHub](https://img.shields.io/badge/github-%23121011.svg?style=for-the-badge&logo=github&logoColor=white)](https://github.com/Future-House/ether0)
 [![arXiv](https://img.shields.io/badge/arXiv-2506.17238-b31b1b.svg)](https://arxiv.org/abs/2506.17238)
 [![Project Status: Active](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 ![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)
 
 [![Tests](https://github.com/Future-House/ether0/actions/workflows/lint-test.yaml/badge.svg)](https://github.com/Future-House/ether0/actions)
-<a href="https://github.com/psf/black"><img alt="Code style: black" src="https://img.shields.io/badge/code%20style-black-000000.svg"></a>
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![python](https://img.shields.io/badge/python-3.11+-blue?style=flat&logo=python&logoColor=white)](https://www.python.org)
 [![Model on HF](https://huggingface.co/datasets/huggingface/badges/resolve/main/model-on-hf-md-dark.svg)](https://huggingface.co/futurehouse/ether0)
 [![Dataset on HF](https://huggingface.co/datasets/huggingface/badges/resolve/main/dataset-on-hf-md-dark.svg)](https://huggingface.co/datasets/futurehouse/ether0-benchmark)
@@ -13,9 +15,9 @@
 
 _ether0: a scientific reasoning model, dataset, and reward functions for chemistry._
 
-# ether0 Reward Model
-
-This repo contains the reward model for evaluating ether0 and similar models, along with utilities for working with the verifiable rewards in [our benchmark](https://huggingface.co/datasets/futurehouse/ether0-benchmark).
+This repo contains the reward model for evaluating ether0 and similar models,
+along with utilities for working with the verifiable rewards in
+[our benchmark](https://huggingface.co/datasets/futurehouse/ether0-benchmark).
 
 ## Overview
 
@@ -51,7 +53,8 @@ This repo contains several packages:
 
 ### Open Weights
 
-Please see our open-source weights on Hugging Face: https://huggingface.co/futurehouse/ether0
+Please see our open-source weights on Hugging Face:
+<https://huggingface.co/futurehouse/ether0>
 
 ```python
 from transformers import AutoModelForCausalLM, AutoTokenizer
@@ -62,7 +65,8 @@ tokenizer = AutoTokenizer.from_pretrained("futurehouse/ether0")
 
 ### Open Test Set
 
-Please see our open-source benchmark (test set) on Hugging Face: https://huggingface.co/datasets/futurehouse/ether0-benchmark
+Please see our open-source benchmark (test set) on Hugging Face:
+<https://huggingface.co/datasets/futurehouse/ether0-benchmark>
 
 ```python
 from datasets import load_dataset
@@ -148,7 +152,8 @@ ETHER0_REMOTES_API_TOKEN=abc123 ether0-serve
 Next, start `ipython` with the relevant environment variables set:
 
 ```bash
-ETHER0_REMOTES_API_BASE_URL="http://127.0.0.1:8000" ETHER0_REMOTES_API_TOKEN=abc123 ipython
+ETHER0_REMOTES_API_BASE_URL="http://127.0.0.1:8000" ETHER0_REMOTES_API_TOKEN=abc123 \
+    ipython
 ```
 
 And run the following Python code:

packages/remotes/README.md

@@ -14,14 +14,16 @@ curl --location --output src/ether0/USPTO480k_model_step_400000.pt \
 
 Or more manually:
 
-1. Go to this notebook: https://github.com/schwallergroup/ai4chem_course/blob/main/notebooks/07%20-%20Reaction%20Prediction/template_free.ipynb
+1. Go to [this notebook][1]
 2. Download the `USPTO480k_model_step_400000.pt`
    linked in the `trained_model_url` variable's linked Google Drive file:
-   https://drive.google.com/uc?id=1ywJCJHunoPTB5wr6KdZ8aLv7tMFMBHNy
+   <https://drive.google.com/uc?id=1ywJCJHunoPTB5wr6KdZ8aLv7tMFMBHNy>
 3. Set the environment variable `ETHER0_REMOTES_MOLTRANS_MODEL_PATH`
    to the downloaded PyTorch model's location,
    or place the model in the default checked `ether0` source code folder (`src/ether0`).
 
+[1]: https://github.com/schwallergroup/ai4chem_course/blob/main/notebooks/07%20-%20Reaction%20Prediction/template_free.ipynb
+
 ## Serving
 
 To run the server:
@@ -31,6 +33,6 @@ To run the server:
 
 ```bash
 ETHER0_REMOTES_API_TOKEN="abc123" \
-ETHER0_REMOTES_MOLTRANS_MODEL_PATH="/path/to/downloaded/USPTO480k_model_step_400000.pt" \
+ETHER0_REMOTES_MOLTRANS_MODEL_PATH="/path/to/USPTO480k_model_step_400000.pt" \
 ether0-serve
 ```

pyproject.toml

@@ -105,6 +105,15 @@ branch = true
 # This is designed to be invoked from within the test directory
 command_line = "-m pytest"
 
+[tool.markdownlint]
+no-inline-html = false
+
+[tool.markdownlint.line-length]
+code_block_line_length = 88  # Match ruff line-length
+line_length = 120  # Match ruff max-doc-length
+stern = true
+tables = false
+
 [tool.mypy]
 # Type-checks the interior of functions without type annotations.
 check_untyped_defs = true