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222f123
Add ipykernel; new docs extras, adjust dev deps
edvinskis Jun 4, 2026
fecb144
Remove an extra line break
edvinskis Jun 4, 2026
eaa075c
Ignore Quarto build files in .gitignore
edvinskis Jun 4, 2026
f9444a5
Expand .gitignore for Python and tooling artifacts
edvinskis Jun 4, 2026
deaff6f
Fix typo
edvinskis Jun 4, 2026
0605a3d
Update README installation instructions
edvinskis Jun 4, 2026
65d433e
Move old docs to temp archive
edvinskis Jun 4, 2026
cbd7e74
Delete styles.css_
edvinskis Jun 4, 2026
c9de967
Delete custom.scss_
edvinskis Jun 4, 2026
3cd1dca
Delete transport-model.ipynb
edvinskis Jun 4, 2026
9e38715
Delete transport-with-pymc.ipynb
edvinskis Jun 4, 2026
84b72e4
Delete transport-with-pymc.qmd
edvinskis Jun 4, 2026
3f18712
Adjust headings; modify list
edvinskis Jun 4, 2026
c2a3a3e
Reconfigure `_quarto.yml`; update all fields; add quartodoc
edvinskis Jun 5, 2026
19972be
Add contributing guide
edvinskis Jun 5, 2026
3445ba9
Reorder sections
edvinskis Jun 5, 2026
4d3013a
Add docs/_freeze/ to .gitignore
edvinskis Jun 5, 2026
22a6881
Revise docs index
edvinskis Jun 5, 2026
a731c2a
Simplify API section in index.md
edvinskis Jun 5, 2026
0422619
Add visual separators in the sidebar
edvinskis Jun 5, 2026
ce3b96c
Revise installation guide
edvinskis Jun 5, 2026
f6e2bdc
Add generated API documentation pages from quartodoc
edvinskis Jun 5, 2026
2764087
Add examples index page
edvinskis Jun 5, 2026
55a6aeb
Convert and adjust new transport example
edvinskis Jun 9, 2026
c317359
Use old example; rename kinetix to reactix
edvinskis Jun 9, 2026
60e96aa
Remove redundant docs/.gitignore
edvinskis Jun 11, 2026
2db5602
Remove old documentation
edvinskis Jun 11, 2026
880f69b
Add developer instructions
edvinskis Jun 11, 2026
fe0eeed
Add GitHub Action to build and deploy docs
edvinskis Jun 12, 2026
604d179
Map out reactix code structure and workflow
aysunrhn Jun 15, 2026
7f22dfe
Update GitHub Action checkout and cache versions
edvinskis Jun 18, 2026
15dcfc5
Update GitHub Action checkout and cache versions
edvinskis Jun 18, 2026
975b410
Update GitHub Actions workflows to use setup-python v6
edvinskis Jun 18, 2026
7a68f0d
Use actions/checkout@v6 in CI workflows
edvinskis Jun 18, 2026
e0f692a
Update actions/setup-python to v6
edvinskis Jun 18, 2026
ac75bd5
Turn the System class into MixedSystem and TransportSystem classes to…
aysunrhn Jun 18, 2026
dd5fd9e
Merge pull request #47 from astoeriko/46-update-actions-to-nodejs-24
aysunrhn Jun 18, 2026
dc395df
Remove TransportClass and MixedClass from the transport.py file
aysunrhn Jun 24, 2026
83b944d
Move TransportSystem and MixedSystem to a separate systems.py file
aysunrhn Jun 24, 2026
e6abdff
Update imports in the init file
aysunrhn Jun 24, 2026
54561ad
Update mixed_rhs in systems.py
aysunrhn Jun 25, 2026
823c97d
Add inflow outflow calculation to mixed_rhs
aysunrhn Jun 25, 2026
a926f2a
Update test_tranport.py to be consistent with the new TransportSystem…
aysunrhn Jun 25, 2026
653dac0
Add __version__ using importlib
edvinskis Jun 25, 2026
162db5c
Add initial tests for the MixedSystem in test_systems.py
aysunrhn Jun 25, 2026
f90c2b4
Add installation verification to README
edvinskis Jun 25, 2026
aead8d5
Make installation verification section collapsible
edvinskis Jun 25, 2026
bd0e0cc
Update transport.py to change System to TransportSystem typing
aysunrhn Jun 25, 2026
bb13a81
Merge pull request #48 from astoeriko/45-set-up-code-coverage-report-…
aysunrhn Jun 29, 2026
3ffc890
Revise quickstart example and fix code cells
astoeriko Jun 29, 2026
d966211
Add simple usage example to the README
astoeriko Jun 29, 2026
1ed6345
Merge pull request #42 from astoeriko/prj-docs
edvinskis Jun 30, 2026
2ffe27a
Merge pull request #53 from astoeriko/52-installationexecution-verifi…
edvinskis Jun 30, 2026
ff7a4bb
Remove archived docs in docsarchive/docs
edvinskis Jun 30, 2026
815889d
Merge pull request #57 from astoeriko/56-remove-old-documentation
edvinskis Jun 30, 2026
9df05c9
Move rhs definition for each system to the respective class
astoeriko Jun 30, 2026
8b1d99e
Add missing decorator in MixedSystem class
astoeriko Jun 30, 2026
7f45b76
Ensure correct behavior for different argument types in MixedSystem
astoeriko Jun 30, 2026
1ed15fb
Add notebook with mixed reactor example
astoeriko Jun 30, 2026
9b73ae2
Add tests for MixedSystem class
astoeriko Jun 30, 2026
93e48f4
Update transport-model.ipynb to use new TransportModel class
astoeriko Jun 30, 2026
1470780
Add logo to the repository
astoeriko Jul 2, 2026
a8cada2
Convert font to path in SVG logo file
astoeriko Jul 2, 2026
9a021c4
Clarify JAX GPU support
edvinskis Jul 2, 2026
c761250
Update pathogen-model.ipynb to rename System class
aysunrhn Jul 2, 2026
4be0f2b
Update README: GPU note, API & notebooks links
edvinskis Jul 2, 2026
59bc7e7
Merge pull request #59 from astoeriko/11-polish-readmemd
edvinskis Jul 2, 2026
9e1dc89
Move solve_fn_dense outside of the solve_pt function to avoid redefin…
aysunrhn Jul 3, 2026
5eeb70e
Move the solve_fn_dense function back inside the solve_pt method
aysunrhn Jul 6, 2026
fdee950
Merge pull request #54 from astoeriko/system-class
aysunrhn Jul 6, 2026
2c97edf
Merge pull request #58 from astoeriko/logo
astoeriko Jul 20, 2026
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47 changes: 47 additions & 0 deletions .github/workflows/docs.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,47 @@
name: Publish docs

on:
push:
branches:
- main
workflow_dispatch:

permissions:
contents: write

jobs:
build-and-deploy:
runs-on: ubuntu-latest

steps:
- name: Checkout repository
uses: actions/checkout@v4

- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: "3.13"

- name: Install Quarto
uses: quarto-dev/quarto-actions/setup@v2

- name: Install package and docs dependencies
run: |
pip install uv
uv pip install --system -e ".[dev,docs]"

- name: Build API reference
working-directory: docs
run: quartodoc build

- name: Render site
uses: quarto-dev/quarto-actions/render@v2
with:
path: docs

- name: Deploy to GitHub Pages
uses: peaceiris/actions-gh-pages@v4
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
publish_dir: docs/_site
publish_branch: gh-pages
12 changes: 6 additions & 6 deletions .github/workflows/pytest.yml
Original file line number Diff line number Diff line change
Expand Up @@ -16,15 +16,15 @@ jobs:

steps:
- name: Checkout code
uses: actions/checkout@v4
uses: actions/checkout@v6

- name: Set up Python 3.13
uses: actions/setup-python@v5
uses: actions/setup-python@v6
with:
python-version: "3.13"

- name: Cache pip dependencies
uses: actions/cache@v4
uses: actions/cache@v5
with:
path: ~/.cache/pip
key: ${{ runner.os }}-python3.13-pip-${{ hashFiles('pyproject.toml') }}
Expand All @@ -48,15 +48,15 @@ jobs:

steps:
- name: Checkout code
uses: actions/checkout@v4
uses: actions/checkout@v6

- name: Set up Python 3.13
uses: actions/setup-python@v5
uses: actions/setup-python@v6
with:
python-version: "3.13"

- name: Cache pip dependencies
uses: actions/cache@v4
uses: actions/cache@v5
with:
path: ~/.cache/pip
key: ${{ runner.os }}-python3.13-pip-${{ hashFiles('pyproject.toml') }}
Expand Down
6 changes: 3 additions & 3 deletions .github/workflows/ruff.yml
Original file line number Diff line number Diff line change
Expand Up @@ -16,14 +16,14 @@ jobs:
matrix:
python-version: ["3.13"]
steps:
- uses: actions/checkout@v4
- uses: actions/checkout@v6
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
uses: actions/setup-python@v6
with:
python-version: ${{ matrix.python-version }}

- name: Cache pip dependencies
uses: actions/cache@v4
uses: actions/cache@v5
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }}
Expand Down
225 changes: 225 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -8,4 +8,229 @@ __pycache__
Untitled*.ipynb
notebooks-local
data_Qu_2015.nc

# Quarto
docs/.quarto/
docs/_site/
docs/_freeze/

# Byte-compiled / optimized / DLL files
__pycache__/
*.py[codz]
*$py.class

# C extensions
*.so

# 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
*.lcov
.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

# UV
# Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
# This is especially recommended for binary packages to ensure reproducibility, and is more
# commonly ignored for libraries.
# uv.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
# poetry.toml

# pdm
# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
# pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
# https://pdm-project.org/en/latest/usage/project/#working-with-version-control
# pdm.lock
# pdm.toml
.pdm-python
.pdm-build/

# pixi
# Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
# pixi.lock
# Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
# in the .venv directory. It is recommended not to include this directory in version control.
.pixi/*
!.pixi/config.toml

# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
__pypackages__/

# Celery stuff
celerybeat-schedule*
celerybeat.pid

# Redis
*.rdb
*.aof
*.pid

# RabbitMQ
mnesia/
rabbitmq/
rabbitmq-data/

# ActiveMQ
activemq-data/

# SageMath parsed files
*.sage.py

# Environments
.env
.envrc
.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/

# Abstra
# Abstra is an AI-powered process automation framework.
# Ignore directories containing user credentials, local state, and settings.
# Learn more at https://abstra.io/docs
.abstra/

# Visual Studio Code
# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
# that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
# and can be added to the global gitignore or merged into this file. However, if you prefer,
# you could uncomment the following to ignore the entire vscode folder
# .vscode/
# Temporary file for partial code execution
tempCodeRunnerFile.py

# Ruff stuff:
.ruff_cache/

# PyPI configuration file
.pypirc

# Marimo
marimo/_static/
marimo/_lsp/
__marimo__/

# Streamlit
.streamlit/secrets.toml
2 changes: 1 addition & 1 deletion CONTRIBUTING.md
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ If you find a bug, encounter unexpected behavior, or want to propose a feature,

## Share examples

If you are using Reactix, we are curious to hear about it! You are welcome to share examples in the [Github Discussions under the _Show and tell_ category](https://github.com/astoeriko/reactix/discussions/categories/show-and-tell).
If you are using Reactix, we are curious to hear about it! You are welcome to share examples in the [GitHub Discussions under the _Show and tell_ category](https://github.com/astoeriko/reactix/discussions/categories/show-and-tell).

## Contribute code

Expand Down
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