hybrax 0.1.0__tar.gz

hybrax-0.1.0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          # setuptools-scm needs the tags to work out the version.
+          fetch-depth: 0
+
+      - uses: astral-sh/setup-uv@v6
+
+      - name: Build sdist and wheel
+        run: uv build
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/hybrax
+    permissions:
+      # Lets this job request an OIDC token for PyPI trusted publishing.
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - uses: pypa/gh-action-pypi-publish@release/v1

hybrax-0.1.0/.gitignore

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+# local dev files
+*.override.*
+dev/
+.vscode/
+reference/
+AGENTS.md
+CLAUDE.md
+
+# docs build output (regenerated by docs/docs_rebuild.sh)
+# docs/html/
+docs/jupyter_execute/
+docs/source/autoapi/
+docs/source/_data/out/
+docs/_scratch/
+
+# hidden files
+.*
+# except for the below
+!.github/
+!.python-version
+!.readthedocs.yaml
+
+# 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
+.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
+# ignore .pixi.toml as well (since we're only using pixi for local dev)
+pixi.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
+
+# 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/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Shitty Windows files
+*:Zone.Identifier
+
+# Local scratch directories
+tmp/
+**/tmp/
+
+# MemPalace per-project files
+mempalace.yaml
+entities.json

hybrax-0.1.0/.python-version

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+3.13.15

hybrax-0.1.0/.readthedocs.yaml

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+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.13"
+  jobs:
+    build:
+      html:
+        - mkdir -p "$READTHEDOCS_OUTPUT/html"
+        - cp -a docs/html/. "$READTHEDOCS_OUTPUT/html/"
+

hybrax-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Mathias Gotsmy and Julian Libiseller-Egger
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

hybrax-0.1.0/MANIFEST.in

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+# Keep the sdist small: built docs and example data are not needed to
+# build or test the package.
+prune docs
+prune examples

hybrax-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: hybrax
+Version: 0.1.0
+Summary: Bioprocess hybrid models and data management in JAX
+Author: Mathias Gotsmy, Julian Libiseller-Egger
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/hybrax/hybrax
+Project-URL: Repository, https://github.com/hybrax/hybrax
+Project-URL: Documentation, https://hybrax.readthedocs.io
+Keywords: bioprocess,fermentation,upstream modeling,hybrid modeling,jax,diffrax,neural ODE,UDE,universal differential equations,data structures
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: jax<0.10.1,>=0.4.30
+Requires-Dist: jaxlib>=0.4.0
+Requires-Dist: numpy>=1.26
+Requires-Dist: pandas<3.1,>=3.0.5
+Requires-Dist: equinox<0.14,>=0.13.8
+Requires-Dist: scipy>=1.15.0
+Requires-Dist: clarabel>=0.11
+Requires-Dist: diffrax<0.8,>=0.7.2
+Requires-Dist: sympy<1.15,>=1.14.0
+Requires-Dist: ijson>=3.5.1
+Requires-Dist: matplotlib>=3.8
+Requires-Dist: optax<0.3,>=0.2.8
+Requires-Dist: optimistix>=0.1.0
+Requires-Dist: pydantic>=2.5.2
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0; extra == "dev"
+Requires-Dist: pytest-cov>=3.0.0; extra == "dev"
+Requires-Dist: pytest-xdist>=3.6; extra == "dev"
+Requires-Dist: black>=22.0.0; extra == "dev"
+Requires-Dist: flake8>=4.0.0; extra == "dev"
+Requires-Dist: mypy>=0.950; extra == "dev"
+Requires-Dist: ruff>=0.17.2; extra == "dev"
+Requires-Dist: ipdb>=0.13.13; extra == "dev"
+Requires-Dist: jupyter>=1.1.1; extra == "dev"
+Requires-Dist: ipykernel>=7.2.0; extra == "dev"
+Requires-Dist: openpyxl>=3.1.5; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx>=7.2; extra == "docs"
+Requires-Dist: furo>=2024.1; extra == "docs"
+Requires-Dist: myst-nb>=1.1; extra == "docs"
+Requires-Dist: linkify-it-py>=2.0; extra == "docs"
+Requires-Dist: sphinx-autoapi>=3.1; extra == "docs"
+Requires-Dist: sphinx-copybutton>=0.5; extra == "docs"
+Requires-Dist: sphinx-design>=0.6; extra == "docs"
+Requires-Dist: jupyter-cache>=1.0; extra == "docs"
+Requires-Dist: ipykernel>=6.29; extra == "docs"
+Requires-Dist: matplotlib==3.11.1; extra == "docs"
+Dynamic: license-file
+
+# Hybrax
+
+Bioprocess hybrid models and data management in JAX.
+
+Hybrid models, also known as universal differential equations (UDEs) or
+grey-box models, embed learned components such as neural networks in a
+mechanistic ODE.
+
+Hybrax combines bioprocess data interchange and hybrid model training in one
+package. `hybrax.format` provides the data model, validation, serialization,
+and mechanistic right-hand side. `hybrax.train` provides preparation,
+augmentation, training, prediction, and leave-one-out cross-validation.
+
+Read the [documentation](https://hybrax.readthedocs.io) for tutorials, gallery
+examples, and API reference.
+
+## Motivation
+
+Bioprocess modeling research lacks standardized data formats, making it
+difficult to compare modeling approaches across labs and publications.
+`hybrax.format` provides a common hierarchical data structure with
+built-in validation, serialization, and mechanistic modeling support.
+Built on JAX and Equinox, it enables automatic differentiation through
+ODE integration for gradient-based hybrid model training.
+
+## Installation
+
+For local development, create the uv environment with the development extras:
+
+```bash
+uv sync --extra dev
+```
+
+Run tests with `uv run pytest`. Add `-n 12` to use 12 pytest-xdist workers.
+
+## Quick start
+
+```python
+import hybrax.format as bp
+
+# Load a process collection from JSON
+collection = bp.serialization.load_process_collection("data.json")
+
+# Explore the collection
+bp.print_collection_structure(collection, verbosity=1)
+
+# Access a specific process
+process = collection.processes["run_1"]
+
+# Validate data integrity
+is_valid, messages = bp.validate_process(process)
+
+# Inspect a single process
+bp.print_process_structure(process, verbosity=3)
+
+# Plot
+fig = bp.plot_process(process)
+```
+
+## Modules
+
+| Module | Description |
+|--------|-------------|
+| `hybrax.format.dataclasses` | Hierarchical data structures (`BioProcessCollection`, `BioProcess`, etc.) |
+| `hybrax.format.time_series` | Time-series container with optional fitted spline coefficients (JAX pytree) |
+| `hybrax.format.splines` | Pseudobatch transform, segmented spline fitting |
+| `hybrax.format.mechanistic` | ODE right-hand side and control splines (integration lives in `hybrax.train`) |
+| `hybrax.format.serialization` | JSON save/load for the full data hierarchy |
+| `hybrax.format.validate` | Data integrity checks |
+| `hybrax.format.inspect` | Text printing and matplotlib visualization |
+| `hybrax.format.simulation` | Event bookkeeping for synthetic datasets |
+| `hybrax.train` | Preparation, hybrid model training, prediction, and cross-validation |
+
+See the [documentation](https://hybrax.readthedocs.io) for the data structure
+and the training workflow.

hybrax-0.1.0/README.md

@@ -0,0 +1,75 @@
+# Hybrax
+
+Bioprocess hybrid models and data management in JAX.
+
+Hybrid models, also known as universal differential equations (UDEs) or
+grey-box models, embed learned components such as neural networks in a
+mechanistic ODE.
+
+Hybrax combines bioprocess data interchange and hybrid model training in one
+package. `hybrax.format` provides the data model, validation, serialization,
+and mechanistic right-hand side. `hybrax.train` provides preparation,
+augmentation, training, prediction, and leave-one-out cross-validation.
+
+Read the [documentation](https://hybrax.readthedocs.io) for tutorials, gallery
+examples, and API reference.
+
+## Motivation
+
+Bioprocess modeling research lacks standardized data formats, making it
+difficult to compare modeling approaches across labs and publications.
+`hybrax.format` provides a common hierarchical data structure with
+built-in validation, serialization, and mechanistic modeling support.
+Built on JAX and Equinox, it enables automatic differentiation through
+ODE integration for gradient-based hybrid model training.
+
+## Installation
+
+For local development, create the uv environment with the development extras:
+
+```bash
+uv sync --extra dev
+```
+
+Run tests with `uv run pytest`. Add `-n 12` to use 12 pytest-xdist workers.
+
+## Quick start
+
+```python
+import hybrax.format as bp
+
+# Load a process collection from JSON
+collection = bp.serialization.load_process_collection("data.json")
+
+# Explore the collection
+bp.print_collection_structure(collection, verbosity=1)
+
+# Access a specific process
+process = collection.processes["run_1"]
+
+# Validate data integrity
+is_valid, messages = bp.validate_process(process)
+
+# Inspect a single process
+bp.print_process_structure(process, verbosity=3)
+
+# Plot
+fig = bp.plot_process(process)
+```
+
+## Modules
+
+| Module | Description |
+|--------|-------------|
+| `hybrax.format.dataclasses` | Hierarchical data structures (`BioProcessCollection`, `BioProcess`, etc.) |
+| `hybrax.format.time_series` | Time-series container with optional fitted spline coefficients (JAX pytree) |
+| `hybrax.format.splines` | Pseudobatch transform, segmented spline fitting |
+| `hybrax.format.mechanistic` | ODE right-hand side and control splines (integration lives in `hybrax.train`) |
+| `hybrax.format.serialization` | JSON save/load for the full data hierarchy |
+| `hybrax.format.validate` | Data integrity checks |
+| `hybrax.format.inspect` | Text printing and matplotlib visualization |
+| `hybrax.format.simulation` | Event bookkeeping for synthetic datasets |
+| `hybrax.train` | Preparation, hybrid model training, prediction, and cross-validation |
+
+See the [documentation](https://hybrax.readthedocs.io) for the data structure
+and the training workflow.

hybrax-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=64", "setuptools-scm>=8", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "hybrax"
+dynamic = ["version"]
+description = "Bioprocess hybrid models and data management in JAX"
+readme = "README.md"
+requires-python = ">=3.12"
+license = "MIT"
+authors = [{ name = "Mathias Gotsmy" }, { name = "Julian Libiseller-Egger" }]
+keywords = [
+    "bioprocess",
+    "fermentation",
+    "upstream modeling",
+    "hybrid modeling",
+    "jax",
+    "diffrax",
+    "neural ODE",
+    "UDE",
+    "universal differential equations",
+    "data structures",
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering",
+]
+
+dependencies = [
+    "jax>=0.4.30,<0.10.1",
+    "jaxlib>=0.4.0",
+    "numpy>=1.26",
+    "pandas>=3.0.5,<3.1",
+    "equinox>=0.13.8,<0.14",
+    "scipy>=1.15.0",
+    "clarabel>=0.11",
+    "diffrax>=0.7.2,<0.8",
+    "sympy>=1.14.0,<1.15",
+    "ijson>=3.5.1",
+    "matplotlib>=3.8",
+    "optax>=0.2.8,<0.3",
+    "optimistix>=0.1.0",
+    "pydantic>=2.5.2",
+]
+
+[project.scripts]
+hybrax = "hybrax.train.cli:main"
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=8.0",
+    "pytest-cov>=3.0.0",
+    "pytest-xdist>=3.6",
+    "black>=22.0.0",
+    "flake8>=4.0.0",
+    "mypy>=0.950",
+    "ruff>=0.17.2",
+    "ipdb>=0.13.13",
+    "jupyter>=1.1.1",
+    "ipykernel>=7.2.0",
+    "openpyxl>=3.1.5",
+]
+docs = [
+    "sphinx>=7.2",
+    "furo>=2024.1",
+    "myst-nb>=1.1",
+    "linkify-it-py>=2.0",
+    "sphinx-autoapi>=3.1",
+    "sphinx-copybutton>=0.5",
+    "sphinx-design>=0.6",
+    "jupyter-cache>=1.0",
+    "ipykernel>=6.29",
+    # Pinned so the docs plots look the same on every rebuild.
+    "matplotlib==3.11.1",
+]
+
+[project.urls]
+Homepage = "https://github.com/hybrax/hybrax"
+Repository = "https://github.com/hybrax/hybrax"
+Documentation = "https://hybrax.readthedocs.io"
+
+[tool.ruff.lint]
+extend-select = ["E501"]
+# Schema validation uses ValueError, including Pydantic field validators.
+ignore = ["TRY004"]
+
+[tool.ruff.format]
+exclude = ["*.md"]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+# Version comes from the latest git tag (e.g. v0.2.0 -> 0.2.0).
+[tool.setuptools_scm]
+fallback_version = "0.0.0"
+
+# Rebuild the editable install when the commit or tags change, so the
+# reported version stays current.
+[tool.uv]
+cache-keys = [{ file = "pyproject.toml" }, { git = { commit = true, tags = true } }]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+markers = ["integration: end-to-end tests that exercise the training pipeline"]
+filterwarnings = [
+    "ignore:jax.core.mapped_aval is deprecated:DeprecationWarning",
+    "ignore:jax.core.unmapped_aval is deprecated:DeprecationWarning",
+]
+
+[tool.mypy]
+python_version = "3.12"
+warn_return_any = true
+warn_unused_configs = true
+disallow_untyped_defs = false

hybrax-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+