ci: add linter for markdown, yaml, CSS, html

.pre-commit-config.yaml

@@ -2,93 +2,94 @@
 # See https://pre-commit.com/hooks.html for more hooks
 exclude: ^reacnetgenerator/static/webpack/\.yarn/releases/.*$
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
     hooks:
-    # there are many log files in tests
-    # TODO: seperate py files and log files
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
         exclude: ^conda/recipe/meta\.yaml$
-    -   id: check-json
-    -   id: check-added-large-files
-    -   id: check-merge-conflict
-    -   id: check-symlinks
-    -   id: check-toml
-    -   id: mixed-line-ending
-# Python
--   repo: https://github.com/astral-sh/ruff-pre-commit
+      - id: check-json
+      - id: check-added-large-files
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-toml
+      - id: mixed-line-ending
+  # Python
+  - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.3.3
     hooks:
-    - id: ruff
-      args: ["--fix"]
-      types_or: [python, pyi, jupyter]
-    - id: ruff-format
-      types_or: [python, pyi, jupyter]
-- repo: https://github.com/tox-dev/tox-ini-fmt
-  rev: "1.3.1"
-  hooks:
-    - id: tox-ini-fmt
-# numpydoc
--   repo: https://github.com/Carreau/velin
+      - id: ruff
+        args: ["--fix"]
+        types_or: [python, pyi, jupyter]
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+  - repo: https://github.com/tox-dev/tox-ini-fmt
+    rev: "1.3.1"
+    hooks:
+      - id: tox-ini-fmt
+  # numpydoc
+  - repo: https://github.com/Carreau/velin
     rev: 0.0.12
     hooks:
-    - id: velin
-      args: ["--write"]
-# C++
--   repo: https://github.com/pre-commit/mirrors-clang-format
+      - id: velin
+        args: ["--write"]
+  # C++
+  - repo: https://github.com/pre-commit/mirrors-clang-format
     rev: v18.1.1
     hooks:
-    -   id: clang-format
-# Cython
--   repo: https://github.com/MarcoGorelli/cython-lint
+      - id: clang-format
+  # Cython
+  - repo: https://github.com/MarcoGorelli/cython-lint
     rev: v0.16.0
     hooks:
-    -   id: cython-lint
-    -   id: double-quote-cython-strings
-# CSS
--   repo: https://github.com/pre-commit/mirrors-csslint
-    rev: v1.0.5
+      - id: cython-lint
+      - id: double-quote-cython-strings
+  # markdown, json, yaml, CSS, javascript, html
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
     hooks:
-    -   id: csslint
-# license header
--   repo: https://github.com/Lucas-C/pre-commit-hooks
+      - id: prettier
+        types_or: [markdown, json, yaml, css, javascript, html]
+        # workflow files cannot be modified by pre-commit.ci
+        exclude: ^conda/recipe/meta\.yaml|\.github/workflows
+  # license header
+  - repo: https://github.com/Lucas-C/pre-commit-hooks
     rev: v1.5.5
     hooks:
-    # C++, js
-    -   id: insert-license
+      # C++, js
+      - id: insert-license
         files: \.(c|cc|cpp|js|ts)$
         args:
-        - --license-filepath
-        - .license-header.txt
-        - --comment-style
-        - //
-        - --no-extra-eol
-    # CSS
-    -   id: insert-license
+          - --license-filepath
+          - .license-header.txt
+          - --comment-style
+          - //
+          - --no-extra-eol
+      # CSS
+      - id: insert-license
         files: \.(css|scss)$
         args:
-        - --license-filepath
-        - .license-header.txt
-        - --comment-style
-        - /*| *| */
-        - --no-extra-eol
-    # Python
-    -   id: insert-license
+          - --license-filepath
+          - .license-header.txt
+          - --comment-style
+          - /*| *| */
+          - --no-extra-eol
+      # Python
+      - id: insert-license
         files: \.(py|pyx)$
         args:
-        - --license-filepath
-        - .license-header.txt
-        - --comment-style
-        - "#"
-        - --no-extra-eol
-    # HTML
-    -   id: insert-license
+          - --license-filepath
+          - .license-header.txt
+          - --comment-style
+          - "#"
+          - --no-extra-eol
+      # HTML
+      - id: insert-license
         files: \.(html|vue|xml)$
         args:
-        - --license-filepath
-        - .license-header.txt
-        - --comment-style
-        - <!--|  ~|  -->
-        - --no-extra-eol
+          - --license-filepath
+          - .license-header.txt
+          - --comment-style
+          - <!--|  ~|  -->
+          - --no-extra-eol

.readthedocs.yml

@@ -1,10 +1,10 @@
-version: 2
-build:
-  os: ubuntu-22.04
-  tools:
-    python: "3.12"
-sphinx:
-   configuration: docs/conf.py
-python:
-   install:
-   - requirements: docs/requirements.txt
+version: 2
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+sphinx:
+  configuration: docs/conf.py
+python:
+  install:
+    - requirements: docs/requirements.txt

README.md

@@ -1,4 +1,4 @@
-# <img src=docs/_static/reacnetgen.svg height=40/>  ReacNetGenerator
+# <img src=docs/_static/reacnetgen.svg height=40/> ReacNetGenerator
 
 [![DOI:10.1039/C9CP05091D](https://img.shields.io/badge/DOI-10.1039%2FC9CP05091D-blue)](https://doi.org/10.1039/C9CP05091D)
 [![Citations](https://citations.njzjz.win/10.1039/C9CP05091D)](https://doi.org/10.1039/C9CP05091D)
@@ -12,11 +12,11 @@ [email protected] (Jinzhe Zeng), [email protected] (Tong Zhu)
 
 ## Features
 
--   Processing of MD trajectory containing atomic coordinates or bond orders
--   Hidden Markov Model (HMM) based noise filtering
--   Isomers identifying accoarding to SMILES
--   Generation of reaction network for visualization using force-directed algorithm
--   Parallel computing
+- Processing of MD trajectory containing atomic coordinates or bond orders
+- Hidden Markov Model (HMM) based noise filtering
+- Isomers identifying accoarding to SMILES
+- Generation of reaction network for visualization using force-directed algorithm
+- Parallel computing
 
 ## Guide and Tutorial
 
@@ -31,10 +31,12 @@ reacnetgenerator -h
 See [the guide](https://docs.deepmodeling.com/projects/reacnetgenerator/en/latest/guide/) to learn how to install and use ReacNetGenerattor. We also provide [a series of tutorials](https://docs.deepmodeling.com/projects/reacnetgenerator/en/latest/tutorial/) to help you learn ReacNetGenerator.
 
 ## Awards
-* The First Prize in 2019 (the 11th Session) Shanghai Computer Application Competition for College Students
-* The First Prize in 2019 (the 12th Session) Chinese Computer Design Competition for College Students
+
+- The First Prize in 2019 (the 11th Session) Shanghai Computer Application Competition for College Students
+- The First Prize in 2019 (the 12th Session) Chinese Computer Design Competition for College Students
 
 ## Acknowledge
-* National Natural Science Foundation of China (Grants No. 91641116)
-* National Innovation and Entrepreneurship Training Program for Undergraduate (201910269080)
-* ECNU Multifunctional Platform for Innovation (No. 001)
+
+- National Natural Science Foundation of China (Grants No. 91641116)
+- National Innovation and Entrepreneurship Training Program for Undergraduate (201910269080)
+- ECNU Multifunctional Platform for Innovation (No. 001)

docs/_static/css/custom.css

@@ -2,69 +2,72 @@
  * SPDX-License-Identifier: LGPL-3.0-or-later
  */
 .bilitube iframe {
-    width: 100%;
-    aspect-ratio: 1.2877;
+  width: 100%;
+  aspect-ratio: 1.2877;
 }
 
 .hero {
-    text-align: center;
+  text-align: center;
 }
 
-.hero .action, .hero p, .hero img, .hero h1 {
-    margin: 1.8rem auto;
+.hero .action,
+.hero p,
+.hero img,
+.hero h1 {
+  margin: 1.8rem auto;
 }
 
 .hero img {
-    max-width: 100%;
-    max-height: 280px;
-    display: block;
-    margin: 3rem auto 1.5rem;
-    background: none!important;
+  max-width: 100%;
+  max-height: 280px;
+  display: block;
+  margin: 3rem auto 1.5rem;
+  background: none !important;
 }
 
 .hero p {
-    max-width: 35rem;
-    font-size: 1.6rem;
-    line-height: 1.3;
-    color: #6a8bad;
+  max-width: 35rem;
+  font-size: 1.6rem;
+  line-height: 1.3;
+  color: #6a8bad;
 }
 
 .hero .action-button {
-    display: inline-block;
-    font-size: 1.2rem;
-    color: #fff;
-    background-color: #3eaf7c;
-    padding: .8rem 1.6rem;
-    border-radius: 4px;
-    transition: background-color .1s ease;
-    box-sizing: border-box;
-    border-bottom: 1px solid #389d70;
+  display: inline-block;
+  font-size: 1.2rem;
+  color: #fff;
+  background-color: #3eaf7c;
+  padding: 0.8rem 1.6rem;
+  border-radius: 4px;
+  transition: background-color 0.1s ease;
+  box-sizing: border-box;
+  border-bottom: 1px solid #389d70;
 }
 
 .features {
-    border-top: 1px solid #eaecef;
-    padding: 1.2rem 0;
-    margin-top: 2.5rem;
-    display: flex;
-    flex-wrap: wrap;
-    align-items: flex-start;
-    align-content: stretch;
-    justify-content: space-between;
+  border-top: 1px solid #eaecef;
+  padding: 1.2rem 0;
+  margin-top: 2.5rem;
+  display: flex;
+  flex-wrap: wrap;
+  align-items: flex-start;
+  align-content: stretch;
+  justify-content: space-between;
 }
 
 .features section {
-    flex-grow: 1;
-    flex-basis: 30%;
-    max-width: 30%;
+  flex-grow: 1;
+  flex-basis: 30%;
+  max-width: 30%;
 }
 
 @media (max-width: 719px) {
-    .features {
-        flex-direction: column;
-    }
+  .features {
+    flex-direction: column;
+  }
 
-    .features section {
-        max-width: 100%;
-        padding: 0 2.5rem;
-    }
+  .features section {
+    max-width: 100%;
+    padding: 0 2.5rem;
+  }
 }

docs/guide/build.md

@@ -12,13 +12,15 @@ Then build ReacNetGenerator with one of the following guides:
 ## Installing via pip
 
 Use `pip` to install in the main directory of ReacNetGenerator. Note that a C/C++ compiler must be installed.
+
 ```bash
 # upgrade pip as old pip may not be supported
 pip install -U pip
 pip install .
 ```
 
 Test installation by
+
 ```bash
 reacnetgenerator -h
 ```

docs/guide/run.md

@@ -5,6 +5,7 @@ After a [trajectory file](format.md) is prepared, you can process the file using
 ```bash
 reacnetgenerator --type dump -i dump.reaxc -a C H O --nohmm
 ```
+
 where C, H, and O are atomic names in the input file.
 `--type` decides the [format](format.md) of the trajectory file `dump.reaxc`.
 `--nohmm` controls whether [HMM filter](hmm.md) is enabled.

docs/overall.md

@@ -63,10 +63,12 @@ reacnetgenerator -h
 See [the guide](guide/index) to learn how to install and use ReacNetGenerattor. We also provide [a series of tutorials](tutorial/index) to help you learn ReacNetGenerator.
 
 # Awards
-* The First Prize in 2019 (the 11th Session) Shanghai Computer Application Competition for College Students
-* The First Prize in 2019 (the 12th Session) Chinese Computer Design Competition for College Students
+
+- The First Prize in 2019 (the 11th Session) Shanghai Computer Application Competition for College Students
+- The First Prize in 2019 (the 12th Session) Chinese Computer Design Competition for College Students
 
 # Acknowledge
-* National Natural Science Foundation of China (Grants No. 91641116)
-* National Innovation and Entrepreneurship Training Program for Undergraduate (201910269080)
-* ECNU Multifunctional Platform for Innovation (No. 001)
+
+- National Natural Science Foundation of China (Grants No. 91641116)
+- National Innovation and Entrepreneurship Training Program for Undergraduate (201910269080)
+- ECNU Multifunctional Platform for Innovation (No. 001)