jmstate 0.1.0__tar.gz

jmstate-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$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
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# 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/

jmstate-0.1.0/.gitlab-ci.yml

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+stages:
+  - lint
+  - deploy
+  - publish
+
+lint:
+  image: python:latest
+  stage: lint
+  script:
+    - pip install ruff
+    - ruff format jmstate
+    - ruff check jmstate
+  rules:
+    - if: $CI_COMMIT_BRANCH
+
+pages:
+  image: python:latest
+  stage: deploy
+  script:
+    - apt-get update && apt-get install -y git
+    - pip install sphinx furo
+    - pip install . --extra-index-url https://download.pytorch.org/whl/cpu
+    - sphinx-build -b html docs/source public
+  artifacts:
+    paths:
+      - public
+  rules:
+    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
+
+publish-to-pypi:
+  image: python:latest
+  stage: publish
+  script:
+    - python -m pip install --upgrade pip build twine setuptools-scm
+    - python -m build
+    - TWINE_PASSWORD=${PYPI_TOKEN} TWINE_USERNAME=__token__ python -m twine upload --verbose dist/*
+  rules: 
+    - if: '$CI_COMMIT_TAG =~ /^v.*$/'
+

jmstate-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 Felix Laplante <felixlaplante0@proton.me>
+
+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.

jmstate-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: jmstate
+Version: 0.1.0
+Summary: Joint modeling with automatic differentiation
+Author-email: Félix Laplante <felixlaplante0@proton.me>
+Requires-Python: >=3.10
+License-File: LICENSE
+Requires-Dist: torch
+Requires-Dist: numpy
+Requires-Dist: tqdm
+Requires-Dist: pydantic
+Requires-Dist: xxhash
+Dynamic: license-file

jmstate-0.1.0/README.md

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+# 📦 jmstate
+
+**jmstate** is a Python package for **multi-state nonlinear joint modeling**.  
+It leverages **PyTorch** for automatic differentiation and vectorized computation, making it efficient and scalable. The package provides a flexible framework where you can use **neural networks as regression and link functions**, while still offering simpler built-in options like parametric baseline hazards.
+
+With **jmstate**, you can model longitudinal data jointly with multi-state transitions (e.g. health progression), capture nonlinear effects, and perform inference in complex real-world settings.
+
+👉 Full documentation, tutorials, and API reference are hosted here:  
+[**jmstate Documentation**](https://felixlaplante0.gitlab.io/jmstate)
+
+---
+
+## ✨ Features
+
+- **Multi-State Joint Modeling**  
+  Supports subjects moving through multiple states with transition intensities that depend on longitudinal trajectories and covariates.
+
+- **Nonlinear Flexibility**  
+  Use neural networks (or any PyTorch model) as regression or link functions.
+
+- **Built-in Tools**  
+  Includes default baseline hazards, regression, link functions, and analysis utilities.
+
+- **Automatic Differentiation & GPU Support**  
+  Powered by PyTorch for efficient gradient computation and vectorization.
+
+- **Analysis & Visualization**  
+  Tools for state occupancy probabilities, hazard estimation, and residual diagnostics.
+
+---
+
+## 🚀 Installation
+
+```bash
+pip install jmstate
+```
+
+---
+
+## 📖 Learn More
+
+For tutorials, API reference, visit the official site:  
+👉 [jmstate Documentation](https://felixlaplante0.gitlab.io/jmstate)

jmstate-0.1.0/docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

jmstate-0.1.0/docs/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

jmstate-0.1.0/docs/source/_templates/autosummary/class.rst

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+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+
+   .. automethod:: __init__

jmstate-0.1.0/docs/source/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+
+import os
+
+release = os.getenv("CI_COMMIT_TAG", "v0.0.0")
+version = release.lstrip("v")
+
+
+project = "jmstate"
+copyright = "2025, Félix Laplante"
+author = "Félix Laplante"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.autosummary",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = []
+
+autodoc_member_order = "bysource"
+autodoc_typehints = "description"
+autodoc_typehints_format = "short"
+autodoc_inherit_docstrings = True
+autosummary_generate = True
+add_module_names = False
+napoleon_use_ivar = True
+napoleon_attr_annotations = True
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "furo"
+html_static_path = ["_static"]

jmstate-0.1.0/docs/source/functions.rst

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+Functions
+=========
+
+.. automodule:: jmstate.functions
+   :no-members:
+   :no-undoc-members:
+   :no-index:
+
+.. autosummary::
+   :toctree: generated/
+   :recursive:
+
+   Exponential
+   Gompertz
+   LogNormal
+   Net
+   Weibull
+   clock_forward
+   clock_reset
+   gamma_plus_b
+   gamma_x_plus_b
+   identity
+   linear

jmstate-0.1.0/docs/source/index.rst

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+Welcome to jmstate's Documentation!
+===================================
+
+This is a comprehensive guide to the jmstate package, a tool for multistate joint modeling with PyTorch.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   modules

jmstate-0.1.0/docs/source/jobs.rst

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+Jobs
+====
+
+.. automodule:: jmstate.jobs
+   :no-members:
+   :no-undoc-members:
+   :no-index:
+
+.. autosummary::
+   :toctree: generated/
+   :recursive:
+
+   AdamL1Proximal
+   ComputeCriteria
+   ComputeEBEs
+   ComputeFIM
+   Fit
+   GradStop
+   LogParamsHistory
+   MCMCDiagnostics
+   NoStop
+   ParamStop
+   PredictSurvLogps
+   PredictTrajectories
+   PredictY
+   Scheduling
+   SwitchParams
+   ValueStop

jmstate-0.1.0/docs/source/model.rst

@@ -0,0 +1,13 @@
+Model
+=====
+
+.. automodule:: jmstate.model
+   :members:
+   :undoc-members:
+   :no-index:
+
+.. autosummary::
+   :toctree: generated/
+   :recursive:
+
+   MultiStateJointModel

jmstate-0.1.0/docs/source/modules.rst

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+API Reference
+=============
+
+This page provides an overview of the main modules and their members within the `jmstate` package.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Subpackages:
+
+   model
+   typedefs
+   functions
+   jobs
+   utils

jmstate-0.1.0/docs/source/typedefs.rst

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+Typedefs
+========
+
+.. automodule:: jmstate.typedefs
+   :no-members:
+   :no-undoc-members:
+   :no-index:
+
+.. autosummary::
+   :toctree: generated/
+   :recursive:
+
+   BaseHazardFn
+   BucketData
+   ClockMethod
+   IndividualEffectsFn
+   Info
+   Job
+   LinkFn
+   MatRepr
+   Metrics
+   ModelData
+   ModelDesign
+   ModelParams
+   RegressionFn
+   SampleData

jmstate-0.1.0/docs/source/utils.rst

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+Utils
+=====
+
+.. automodule:: jmstate.utils
+   :no-members:
+   :no-undoc-members:
+   :no-index:
+
+.. autosummary::
+   :toctree: generated/
+   :recursive:
+
+   build_buckets
+   cov_from_repr
+   get_dtype
+   repr_from_cov
+   set_dtype

jmstate-0.1.0/jmstate/__init__.py

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+"""multistate joint modeling package.
+
+This package provides tools for multistate joint modeling with PyTorch.
+"""
+
+from .functions import (
+    Exponential,
+    Gompertz,
+    LogNormal,
+    Net,
+    Weibull,
+    clock_forward,
+    clock_reset,
+    gamma_plus_b,
+    gamma_x_plus_b,
+    identity,
+    linear,
+)
+from .jobs import (
+    AdamL1Proximal,
+    ComputeCriteria,
+    ComputeEBEs,
+    ComputeFIM,
+    Fit,
+    GradStop,
+    LogParamsHistory,
+    MCMCDiagnostics,
+    ParamStop,
+    PredictSurvLogps,
+    PredictTrajectories,
+    PredictY,
+    Scheduling,
+    SwitchParams,
+    ValueStop,
+)
+from .model._base import MultiStateJointModel
+from .typedefs import (
+    BaseHazardFn,
+    BucketData,
+    ClockMethod,
+    IndividualEffectsFn,
+    Info,
+    Job,
+    LinkFn,
+    MatRepr,
+    Metrics,
+    ModelData,
+    ModelDesign,
+    ModelParams,
+    RegressionFn,
+    SampleData,
+)
+from .utils import build_buckets, cov_from_repr, get_dtype, repr_from_cov, set_dtype
+
+__author__ = "Félix Laplante"
+__email__ = "felixlaplante0@gmail.com"
+__license__ = "MIT"
+
+__all__ = [
+    "AdamL1Proximal",
+    "BaseHazardFn",
+    "BucketData",
+    "ClockMethod",
+    "ComputeCriteria",
+    "ComputeEBEs",
+    "ComputeFIM",
+    "Exponential",
+    "Fit",
+    "Gompertz",
+    "GradStop",
+    "IndividualEffectsFn",
+    "Info",
+    "Job",
+    "LinkFn",
+    "LogNormal",
+    "LogParamsHistory",
+    "MCMCDiagnostics",
+    "MatRepr",
+    "Metrics",
+    "ModelData",
+    "ModelDesign",
+    "ModelParams",
+    "MultiStateJointModel",
+    "Net",
+    "ParamStop",
+    "PredictSurvLogps",
+    "PredictTrajectories",
+    "PredictY",
+    "RegressionFn",
+    "SampleData",
+    "Scheduling",
+    "SwitchParams",
+    "ValueStop",
+    "Weibull",
+    "build_buckets",
+    "clock_forward",
+    "clock_reset",
+    "cov_from_repr",
+    "gamma_plus_b",
+    "gamma_x_plus_b",
+    "get_dtype",
+    "identity",
+    "linear",
+    "repr_from_cov",
+    "set_dtype",
+]

jmstate-0.1.0/jmstate/functions/__init__.py

@@ -0,0 +1,26 @@
+"""Functions for the jmstate package."""
+
+from ._base_hazards import (
+    Exponential,
+    Gompertz,
+    LogNormal,
+    Weibull,
+    clock_forward,
+    clock_reset,
+)
+from ._individual_effects import gamma_plus_b, gamma_x_plus_b, identity
+from ._regression_and_link import Net, linear
+
+__all__ = [
+    "Exponential",
+    "Gompertz",
+    "LogNormal",
+    "Net",
+    "Weibull",
+    "clock_forward",
+    "clock_reset",
+    "gamma_plus_b",
+    "gamma_x_plus_b",
+    "identity",
+    "linear",
+]