Repackage hydrochns to use pyproject.toml

Change package from HydroCNHS to hydrocnhs
Update tutorials

.github/workflows/docs.yml

@@ -0,0 +1,42 @@
+name: Docs
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.12'
+
+    - name: Install dependencies
+      run: |
+        pip install sphinx sphinx_rtd_theme sphinx-autodoc-typehints nbsphinx
+
+    - name: Install hydrocnhs
+      run: |
+        pip install .
+
+    - name: Generate API documentation
+      run: |
+        sphinx-apidoc -o docs/source/api src/hydrocnhs
+
+    - name: Build documentation
+      run: |
+        cd docs
+        make html
+
+    - name: Deploy to GitHub Pages
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GH_PAT }}
+        publish_dir: ./docs/_build/html

.gitignore

@@ -1,2 +1,178 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# VS Code
 .vscode/
-!to_do_list.txt
+
+# outputs
+#outputs/
+
+# Archive folders
+**/Archive/*
+
+# R
+*.Rhistory
+scenarios/*.RData
+
+# Ignore any .py file with prefix "debug_"
+debug_*.py
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

.pre-commit-config.yaml

@@ -0,0 +1,28 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.4.0  # Use the latest version
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+-   repo: https://github.com/psf/black
+    rev: 23.9.1
+    hooks:
+    -   id: black
+    # By default, targets Python files only
+#-   repo: https://github.com/lorenzwalthert/precommit
+#    rev: v0.4.2  # Use the latest release from the repository
+#    hooks:
+#    -   id: style-files
+    # R package styler to format R files according to the tidyverse style guide.
+
+# Instrunctions to install pre-commit
+# To auto run pre-commit on every commit, do the following:
+# 1. Install pre-commit: `pip install pre-commit`
+# 2. Install the pre-commit hooks: `pre-commit install`
+# [optional] Run pre-commit on all files: `pre-commit run --all-files`
+#            (manually run pre-commit on all files)
+# The detailed configurations for black are defined in pyproject.toml
+# To just run pre-commit when pushing to the remote repository, do the following:
+# pre-commit uninstall (if the pre-commit hooks are already installed)
+# pre-commit install --hook-type pre-push