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Add and run pretty-format-yaml
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‎.github/workflows/build.yml

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name: Build
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on:
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push:
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branches: main
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pull_request:
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branches: '*'
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push: # Only run on merges into master that modify files under pyscriptjs/
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branches: main
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paths:
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- pyscriptjs/**
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- .github/workflows/** # Test that workflows work when changed
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pull_request: # Run on any PR that modifies files in pyscriptjs/
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paths:
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- pyscriptjs/**
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- .github/workflows/**
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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- name: Install node
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uses: actions/setup-node@v3
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with:
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node-version: '12.x'
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- name: Cache node modules
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uses: actions/cache@v3
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env:
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cache-name: cache-node-modules
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with:
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build:
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runs-on: ubuntu-latest # Will be self hosted soon
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defaults:
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run:
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working-directory: ./pyscriptjs
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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- name: Install node
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uses: actions/setup-node@v3
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with:
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node-version: 12.x
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- name: Cache node modules
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uses: actions/cache@v3
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env:
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cache-name: cache-node-modules
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with:
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# npm cache files are stored in `~/.npm` on Linux/macOS
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path: ~/.npm
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key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('**/package-lock.json') }}
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restore-keys: |
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${{ runner.os }}-build-${{ env.cache-name }}-
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${{ runner.os }}-build-
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${{ runner.os }}-
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- name: Install dependencies
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run: |
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cd pyscriptjs
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npm install
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- name: Build pyscript
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run: |
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cd pyscriptjs
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npm run build
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path: ~/.npm
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key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('**/package-lock.json') }}
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restore-keys: |
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${{ runner.os }}-build-${{ env.cache-name }}-
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${{ runner.os }}-build-
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${{ runner.os }}-
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- name: Install dependencies
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run: |
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npm install
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- name: Build pyscript
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run: |
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npm run build

‎.github/workflows/lint.yml

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@@ -2,40 +2,40 @@ name: Lint
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on:
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push: # Only run on merges into master that modify files under pyscriptjs/
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branches:
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- main
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push: # Only run on merges into master that modify files under pyscriptjs/
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branches:
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- main
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pull_request: # Run on any PR that modifies files in pyscriptjs/
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pull_request: # Run on any PR that modifies files in pyscriptjs/
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jobs:
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build:
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runs-on: ubuntu-latest
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defaults:
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run:
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working-directory: ./pyscriptjs
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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- name: Install node
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uses: actions/setup-node@v3
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with:
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node-version: '12.x'
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- name: Cache node modules
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uses: actions/cache@v3
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env:
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cache-name: cache-node-modules
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with:
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build:
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runs-on: ubuntu-latest
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defaults:
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run:
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working-directory: ./pyscriptjs
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steps:
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- name: Checkout
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uses: actions/checkout@v3
20+
- name: Install node
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uses: actions/setup-node@v3
22+
with:
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node-version: 12.x
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- name: Cache node modules
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uses: actions/cache@v3
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env:
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cache-name: cache-node-modules
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with:
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# npm cache files are stored in `~/.npm` on Linux/macOS
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path: ~/.npm
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key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('**/package-lock.json') }}
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restore-keys: |
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${{ runner.os }}-build-${{ env.cache-name }}-
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${{ runner.os }}-build-
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${{ runner.os }}-
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- name: Install dependencies
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run: |
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npm install
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- name: Run linter
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run: |
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npm run lint
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path: ~/.npm
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key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('**/package-lock.json') }}
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restore-keys: |
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${{ runner.os }}-build-${{ env.cache-name }}-
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${{ runner.os }}-build-
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${{ runner.os }}-
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- name: Install dependencies
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run: |
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npm install
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- name: Run linter
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run: |
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npm run lint

‎.pre-commit-config.yaml

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default_stages: [commit]
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.2.0
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hooks:
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- id: end-of-file-fixer
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exclude: ".*.min.js"
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exclude: .*.min.js
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- id: trailing-whitespace
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- id: check-json
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exclude: .*/tsconfig.json
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- id: check-yaml
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- repo: https://github.com/psf/black
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- repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
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rev: v2.3.0
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hooks:
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- id: pretty-format-yaml
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args: [--autofix, --indent, '4']
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- repo: https://github.com/psf/black
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rev: 22.3.0
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hooks:
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- id: black
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- repo: https://github.com/pycqa/isort
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- id: black
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- repo: https://github.com/pycqa/isort
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rev: 5.10.1
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hooks:
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- id: isort
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- id: isort
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name: isort (python)
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args: [--profile, black]

‎pyscriptjs/environment.yml

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channels:
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- defaults
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- conda-forge
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- defaults
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- conda-forge
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dependencies:
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- python=3.9
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- pip=20.2.2
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- pytest=7
8-
- nodejs=16
9-
- black
10-
- isort
11-
- codespell
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- python=3.9
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- pip=20.2.2
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- pytest=7
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- nodejs=16
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- black
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- isort
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- codespell

‎pyscriptjs/examples/micrograd_ai.html

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<link rel="stylesheet" href="../build/pyscript.css" />
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<script defer src="../build/pyscript.js"></script>
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11+
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<py-env>
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- micrograd
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- numpy
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- matplotlib
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</py-env>
17-
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<link href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
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</head>
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<body style="padding-top: 20px; padding-right: 20px; padding-bottom: 20px; padding-left: 20px">
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<h1>Micrograd - A tiny Autograd engine (with a bite! :))</h1><br>
2323
<div>
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<p>
25-
<a href="https://github.com/karpathy/micrograd">Micrograd</a> is a tiny Autograd engine created
26-
by <a href="https://twitter.com/karpathy">Andrej Karpathy</a>. This app recreates the
27-
<a href="https://github.com/karpathy/micrograd/blob/master/demo.ipynb">demo</a>
28-
he prepared for this package using pyscript to train a basic model, written in Python, natively in
25+
<a href="https://github.com/karpathy/micrograd">Micrograd</a> is a tiny Autograd engine created
26+
by <a href="https://twitter.com/karpathy">Andrej Karpathy</a>. This app recreates the
27+
<a href="https://github.com/karpathy/micrograd/blob/master/demo.ipynb">demo</a>
28+
he prepared for this package using pyscript to train a basic model, written in Python, natively in
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the browser. <br>
3030
</p>
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</div>
3232
<div>
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<p>
34-
You may run each Python REPL cell interactively by pressing (Shift + Enter) or (Ctrl + Enter).
34+
You may run each Python REPL cell interactively by pressing (Shift + Enter) or (Ctrl + Enter).
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You can also modify the code directly as you wish. If you want to run all the code at once,
36-
not each cell individually, you may instead click the 'Run All' button. Training the model
36+
not each cell individually, you may instead click the 'Run All' button. Training the model
3737
takes between 1-2 min if you decide to 'Run All' at once. 'Run All' is your only option if
38-
you are running this on a mobile device where you cannot press (Shift + Enter). After the
39-
model is trained, a plot image should be displayed depicting the model's ability to
38+
you are running this on a mobile device where you cannot press (Shift + Enter). After the
39+
model is trained, a plot image should be displayed depicting the model's ability to
4040
classify the data. <br>
4141
</p>
4242
<p>
43-
Currently the <code>&gt;</code> symbol is being imported incorrectly as <code>&ampgt;</code> into the REPL's.
43+
Currently the <code>&gt;</code> symbol is being imported incorrectly as <code>&ampgt;</code> into the REPL's.
4444
In this app the <code>&gt;</code> symbol has been replaced with <code>().__gt__()</code> so you can run the code
4545
without issue. Ex: intead of <code>a &gt; b</code>, you will see <code>(a).__gt__(b)</code> instead. <br>
4646
</p>
@@ -99,7 +99,7 @@ <h1>Micrograd - A tiny Autograd engine (with a bite! :))</h1><br>
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</py-repl><br>
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101101
<div>
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Line 24 has been changed from: <br>
103103
<code>accuracy = [(yi &gt; 0) == (scorei.data &gt; 0) for yi, scorei in zip(yb, scores)]</code><br>
104104
to: <br>
105105
<code>accuracy = [((yi).__gt__(0)) == ((scorei.data).__gt__(0)) for yi, scorei in zip(yb, scores)]</code><br>
@@ -108,26 +108,26 @@ <h1>Micrograd - A tiny Autograd engine (with a bite! :))</h1><br>
108108
<py-repl auto-generate="true">
109109
# loss function
110110
def loss(batch_size=None):
111-
111+
112112
# inline DataLoader :)
113113
if batch_size is None:
114114
Xb, yb = X, y
115115
else:
116116
ri = np.random.permutation(X.shape[0])[:batch_size]
117117
Xb, yb = X[ri], y[ri]
118118
inputs = [list(map(Value, xrow)) for xrow in Xb]
119-
119+
120120
# forward the model to get scores
121121
scores = list(map(model, inputs))
122-
122+
123123
# svm "max-margin" loss
124124
losses = [(1 + -yi*scorei).relu() for yi, scorei in zip(yb, scores)]
125125
data_loss = sum(losses) * (1.0 / len(losses))
126126
# L2 regularization
127127
alpha = 1e-4
128128
reg_loss = alpha * sum((p*p for p in model.parameters()))
129129
total_loss = data_loss + reg_loss
130-
130+
131131
# also get accuracy
132132
accuracy = [((yi).__gt__(0)) == ((scorei.data).__gt__(0)) for yi, scorei in zip(yb, scores)]
133133
return total_loss, sum(accuracy) / len(accuracy)
@@ -138,25 +138,25 @@ <h1>Micrograd - A tiny Autograd engine (with a bite! :))</h1><br>
138138
<py-repl auto-generate="true">
139139
# optimization
140140
for k in range(20): #was 100. Accuracy can be further improved w/ more epochs (to 100%).
141-
141+
142142
# forward
143143
total_loss, acc = loss()
144-
144+
145145
# backward
146146
model.zero_grad()
147147
total_loss.backward()
148-
148+
149149
# update (sgd)
150150
learning_rate = 1.0 - 0.9*k/100
151151
for p in model.parameters():
152152
p.data -= learning_rate * p.grad
153-
153+
154154
if k % 1 == 0:
155155
print(f"step {k} loss {total_loss.data}, accuracy {acc*100}%")
156156
</py-repl><br>
157157
<div>
158158
<p>
159-
Please wait for the training loop above to complete. It will not print out stats until it
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Please wait for the training loop above to complete. It will not print out stats until it
160160
has completely finished. This typically takes 1-2 min. <br><br>
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Line 9 has been changed from: <br>

‎pyscriptjs/examples/simple_bioinformatics_tool.html

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<div class="hero-body">
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<p class="title is-3">PyScript — Simple Bioinformatics Example <span class="tag is-white">v.1</span></p>
1818
<p class="subtitle is-6">
19-
Demonstrates the simple use of <a href="https://pyscript.net/" target="_blank"><code>PyScript</code></a>
19+
Demonstrates the simple use of <a href="https://pyscript.net/" target="_blank"><code>PyScript</code></a>
2020
in <strong>Bioinformatics/Computational Biology</strong> fields!
2121
</p>
2222
</div>
@@ -58,7 +58,7 @@
5858
<!--- DNA Sequence Output -->
5959
<label class="label">Output for the <code id="operation_name_output">given operation</code></label>
6060
<div id="output"></div>
61-
</div>
61+
</div>
6262

6363
<br><br>
6464
<!-- Footer -->
@@ -84,15 +84,15 @@
8484
operation_name_output_element = Element("operation_name_output")
8585

8686
# DNA Sequene Operations
87-
def return_reverse(dna_seq):
87+
def return_reverse(dna_seq):
8888
return dna_seq[::-1]
89-
def return_complement(dna_seq):
89+
def return_complement(dna_seq):
9090
return dna_seq.translate(str.maketrans("ATCG", "TAGC"))
91-
def return_reverse_complement(dna_seq):
91+
def return_reverse_complement(dna_seq):
9292
return dna_seq.translate(str.maketrans("ATCG", "TAGC"))[::-1]
9393

9494
# Check DNA seq is valid
95-
def check_dna_seq(dna_seq):
95+
def check_dna_seq(dna_seq):
9696
return all(letter in dna_alphabet for letter in dna_seq.upper())
9797

9898
# Clear the form and output
@@ -115,7 +115,7 @@
115115
output_dna_seq = return_complement(dna_seq)
116116
elif operation_name == "ReverseComplement":
117117
output_dna_seq = return_reverse_complement(dna_seq)
118-
118+
119119
# Output the result
120120
output.write(output_dna_seq)
121121
elif (dna_seq.strip() == "") or (dna_seq is None):

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