Merge pull request #1 from kausalflow/init

Initialize the repo

.github/workflows/docs-publish.yaml

@@ -0,0 +1,36 @@
+name: Publish Docs
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+    inputs:
+      directory:
+        description: 'Build docs'
+        default: 'build it now'
+        required: false
+
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+    - uses: pre-commit/[email protected]
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.10
+      - name: Setup Poetry
+        uses: abatilo/actions-poetry@v2
+        with:
+          poetry-version: 1.3.2
+      - name: Install Packages
+        run: poetry install --with docs
+      - run: git config user.name 'github-actions[bot]' && git config user.email 'github-actions[bot]@users.noreply.github.com'
+      - name: Deploy
+        run: poetry run mkdocs gh-deploy --force

.github/workflows/publish.yaml

@@ -0,0 +1,50 @@
+name: Build and Publish Package to Pypi
+
+on:
+  push:
+    branches:
+        - "main"
+
+jobs:
+  tests:
+    strategy:
+      matrix:
+        python-version: [3.9,3.10]
+        os: [ubuntu-latest, macos-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Setup Poetry
+        uses: abatilo/actions-poetry@v2
+        with:
+          poetry-version: 1.3.2
+      - name: Install Packages
+        run: poetry install --with docs,test
+      - name: Build coverage file
+        run: |
+          pytest --cache-clear --cov=app tests/ > pytest-coverage.txt
+      - name: Comment coverage
+        uses: coroo/[email protected]
+  build-n-publish:
+    needs: tests
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.10
+      # - name: Generate dist
+      #   run: python setup.py sdist
+      # - name: Publish package
+      #   if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+      #   uses: pypa/gh-action-pypi-publish@release/v1
+      #   with:
+      #     user: __token__
+      #     password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/tests.yaml

@@ -0,0 +1,42 @@
+name: Test Code with Pip
+
+on:
+  push:
+    branches:
+      - "**"
+      - "!gh-pages"
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+    inputs:
+      name:
+        description: 'Test It'
+        required: false
+        default: 'I Just wanna test it'
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        python-version: [3.9, "3.10"]
+        os: [ubuntu-latest, macos-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Setup Poetry
+        uses: abatilo/actions-poetry@v2
+        with:
+          poetry-version: 1.3.2
+      - name: Install Packages
+        run: poetry install --with docs
+      - name: Build coverage file
+        run: |
+          poetry run pytest --cache-clear --cov=app tests/ > pytest-coverage.txt
+      - name: Comment coverage
+        uses: coroo/[email protected]

.pre-commit-config.yaml

@@ -0,0 +1,28 @@
+exclude: "^notebooks/|^notes/"
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.2.0
+    hooks:
+      - id: check-added-large-files
+      - id: debug-statements
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.960
+    hooks:
+      - id: mypy
+        args: [--no-strict-optional, --ignore-missing-imports]
+        files: ^(hamiltonian_flow/|tests/)
+  - repo: https://github.com/ambv/black
+    rev: 22.10.0
+    hooks:
+    - id: black
+      language: python
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        name: isort (python)
+        args: ["--multi-line", "3", "--profile", "black"]

MANIFEST.in

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+include README.md
+include pyproject.toml
+include LICENSE

README.md

@@ -1,2 +1,3 @@
 # hamiltonian_flow
+
 Dataset of simple physical systems.

docs/changelog.md

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+# hamiltonian_flow Changelog
+
+## 2024-02-18, 0.0.1
+
+Setting up repository.

docs/index.md

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+# Documentation for `hamiltonian_flow`
+
+Generating dataset for physical systems.
+
+## Development
+
+We use `poetry` to manage our python environment. Use
+
+```sh
+poetry install
+```
+
+to install the requirements. Or run
+
+```sh
+poetry install --with test
+```
+
+to install the base environment and test environment for development.
+
+
+If this is the first you clone the repo and committing code, run
+
+```sh
+pre-commit install
+```
+
+first.

docs/references/index.md

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+# References

docs/tutorials/index.md

@@ -0,0 +1 @@
+# Tutorials

mkdocs.yml

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+# mkdocs.yml
+site_name: "Hamiltonian Flow"
+site_author: ""
+site_description: "Dataset of simple physical systems."
+site_url: "https://kausalflow.github.io/hamiltonian_flow"
+repo_url: "https://github.com/kausalflow/hamiltonian_flow"
+edit_uri: "blob/main/docs/"
+repo_name: "kausalflow/hamiltonian_flow"
+
+
+theme:
+  name: "material"
+  # Don't include MkDocs' JavaScript
+  include_search_page: false
+  search_index_only: true
+
+  # Default values, taken from mkdocs_theme.yml
+  language: en
+  features:
+    # - navigation.instant
+    - navigation.sections
+    - navigation.tabs
+  palette:
+    - scheme: default
+      primary: indigo
+      accent: indigo
+      toggle:
+        icon: material/toggle-switch-off-outline
+        name: Switch to dark mode
+    - scheme: slate
+      primary: red
+      accent: red
+      toggle:
+        icon: material/toggle-switch
+        name: Switch to light mode
+  font:
+    text: Roboto
+    code: Roboto Mono
+  # favicon: assets/logo.png
+  # logo: assets/logo_transparent.png
+
+
+
+markdown_extensions:
+  - admonition
+  - pymdownx.details
+  - pymdownx.emoji
+  - pymdownx.magiclink
+  - pymdownx.snippets:
+      check_paths: true
+  - pymdownx.superfences
+  - pymdownx.tabbed
+  - pymdownx.tasklist
+  - pymdownx.arithmatex:
+      generic: true
+  - toc:
+      permalink: "¤"
+
+plugins:
+  - autorefs
+  - search
+  - mkdocstrings:
+      handlers:
+        python:
+          selection:
+            docstring_style: sphinx
+      watch:
+        - docs
+
+extra_javascript:
+  - javascripts/mathjax.js
+  - https://polyfill.io/v3/polyfill.min.js?features=es6
+  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
+
+nav:
+  - "Home": index.md
+  - "Tutorials":
+    - "Introduction": tutorials/index.md
+  - References:
+    - "Introduction": references/index.md
+  - "Changelog": changelog.md