Autoreduce v0.9

.coveragerc

@@ -1,6 +1,6 @@
 [run]
 branch = True
-source = autoreduce 
+source = autoreduce
 
 [report]
 exclude_lines =
@@ -10,4 +10,4 @@ exclude_lines =
     if __name__ == .__main__.:
 ignore_errors = True
 omit =
-    tests/*
+    tests/*

.github/workflows/build.yml

@@ -1,37 +1,33 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-
 name: build
 
 on:
   push:
-    branches: [ "master" ]
-  pull_request:
-    branches: [ "master" ]
+    branches: ["main"]
 
 jobs:
   build:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [windows-latest, ubuntu-latest, macos-latest]
-        python-version: [3.9, 3.11, 3.12]
+        python-version: ["3.10", "3.13"]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+        cache: "pip"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
     - name: Install autoreduce
-      run: pip install ".[all, test]"
+      run: pip install -e ".[test]"
     - name: Test autoreduce
-      run: pytest --cov --junitxml=junit.xml -o junit_family=legacy
-    - name: Upload test results to Codecov
+      run: pytest --cov=autoreduce --cov-report=xml --junitxml=junit.xml -o junit_family=legacy
+    - name: Upload coverage to Codecov
       if: ${{ !cancelled() }}
-      uses: codecov/test-results-action@v1
+      uses: codecov/codecov-action@v4
       with:
+        fail_ci_if_error: false
         token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/lint.yml

@@ -2,6 +2,9 @@ name: Lint
 
 on:
   push:
+    branches: ["main"]
+  pull_request:
+    branches: ["main"]
 
 jobs:
   lint:
@@ -12,13 +15,13 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: "3.11"
+        python-version: "3.13"
         cache: 'pip'
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8
+        pip install ruff
 
-    - name: Run flake8
-      run: flake8 autoreduce tests 
+    - name: Run ruff
+      run: ruff check autoreduce tests

.github/workflows/pypi-deploy.yml

@@ -2,14 +2,23 @@ name: PyPI Deploy
 
 on:
   workflow_dispatch:
+    inputs:
+      ref:
+        description: "Tag, branch, or commit to build. Leave blank to use the selected ref."
+        required: false
+        default: ""
 
 jobs:
   pypi-publish:
     runs-on: ubuntu-latest
     permissions:
       id-token: write
+    environment: Release Deploy
     steps:
       - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          ref: ${{ inputs.ref || github.ref }}
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
@@ -18,7 +27,6 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements.txt
           pip install build
 
       - name: Build the package

.github/workflows/test.yml

@@ -2,33 +2,30 @@ name: test
 
 on:
   push:
-    branches: ["*","!master"]
+    branches: ["*", "!main"]
+  pull_request:
+    branches: ["main"]
 jobs:
   test:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.9", "3.12"]
 
     steps:
     - uses: actions/checkout@v4
-    - name: show directory tree
-      run: ls -R .
-    - name: Set up Python ${{ matrix.python-version }}
+    - name: Set up Python 3.13
       uses: actions/setup-python@v5
       with:
-        python-version: ${{ matrix.python-version }}
-        cache: 'pip'
+        python-version: "3.13"
+        cache: "pip"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
     - name: Install autoreduce
-      run: pip install ".[all, test]"
+      run: pip install -e ".[test]"
     - name: Test autoreduce
-      run: pytest --cov --junitxml=junit.xml -o junit_family=legacy
-    - name: Upload test results to Codecov
+      run: pytest --cov=autoreduce --cov-report=xml --junitxml=junit.xml -o junit_family=legacy
+    - name: Upload coverage to Codecov
       if: ${{ !cancelled() }}
-      uses: codecov/test-results-action@v1
+      uses: codecov/codecov-action@v4
       with:
+        fail_ci_if_error: false
         token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -61,6 +61,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/generated/
 
 # PyBuilder
 target/
@@ -107,3 +108,12 @@ dmypy.json
 
 # Package specific
 examples/reduced_gene_expression.xml
+autoreduce/_version.py
+examples/biological/models/design1_regulated_promoter.xml
+examples/biological/models/example_1.xml
+examples/biological/models/example1.xml
+examples/biological/models/reduced_gene_expression.xml
+examples/biological/models/reduced_gfp_expression.xml
+*.xml
+*.pptx
+*.png

.readthedocs.yaml

@@ -9,12 +9,15 @@ version: 2
 build:
   os: ubuntu-24.04
   tools:
-    python: "3.13"
+    python: "3.12"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
 
 python:
-   install:
-   - requirements: docs/requirements.txt
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

.vscode/settings.json

@@ -1,5 +1,6 @@
 {
-    "python.pythonPath": "C:\\Users\\apand\\Anaconda3\\python.exe",
+    "python.pythonPath": "C:\\Users\\ayush\\anaconda3\\Scripts\\conda.exe",
+    "python.condaPath": "C:\\Users\\ayush\\anaconda3\\Scripts\\conda.exe",
     "python.linting.enabled": true,
     "python.linting.pylintEnabled": false,
     "python.linting.pycodestyleEnabled": true,
@@ -36,5 +37,7 @@
     "black-formatter.args": [
         "--line-length",
         "79"
-    ]
+    ],
+    "python-envs.defaultEnvManager": "ms-python.python:conda",
+    "python-envs.defaultPackageManager": "ms-python.python:conda"
 }

README.md

@@ -1,6 +1,10 @@
-# AutoReduce: An automated model reduction tool
+# AutoReduce: An Automated Model Reduction Toolbox
 
-Python toolbox to automatically obtain reduced model expressions using time-scale separation, conservation laws, and other assumptions.
+![AutoReduce banner](graphics/autoreduce_banner.png)
+
+Python toolbox to obtain reduced model expressions using time-scale
+separation, conservation laws, sensitivity analysis, and projection-based
+interfaces to established reduction libraries.
 
 [![Build](https://github.com/ayush9pandey/autoreduce/actions/workflows/build.yml/badge.svg)](https://github.com/ayush9pandey/autoreduce/actions/workflows/build.yml)
 [![Lint](https://github.com/ayush9pandey/autoreduce/actions/workflows/lint.yml/badge.svg)](https://github.com/ayush9pandey/autoreduce/actions/workflows/lint.yml)
@@ -10,41 +14,67 @@ Python toolbox to automatically obtain reduced model expressions using time-scal
 
 ## Overview
 
-AutoReduce is a Python package for automated model reduction of SBML models. It provides tools for:
+AutoReduce is a Python package for automated model reduction of nonlinear
+dynamical systems. It provides tools for:
+
 - Automated model reduction using QSSA (Quasi-Steady State Approximation)
-- Hill function approximation
+- Conservation-law based reductions
+- Local sensitivity analysis
+- SBML import/export through python-libsbml
 - Integration with [BioCRNPyler](https://biocrnpyler.readthedocs.io/) for synthetic biology models
-- Analysis of gene expression models
+- Optional python-control and PyDMD interfaces
 
-Refer to the [bioRxiv paper](https://www.biorxiv.org/content/10.1101/2020.02.15.950840v2.full.pdf) and [Journal of Robust and Nonlinear Control paper](https://onlinelibrary.wiley.com/doi/full/10.1002/rnc.6013) for more details.
+See the [bioRxiv paper](https://doi.org/10.1101/2020.02.15.950840)
+and [International Journal of Robust and Nonlinear Control paper](https://doi.org/10.1002/rnc.6013)
+for the model-reduction background.
 
 ## Quick Start
 
 ```python
-from autoreduce.converters import load_sbml
-
-# Load your SBML model
-sys = load_sbml('your_sbml_file.xml', outputs=['your_output'])
-
-# Solve conservation laws
-conservation_laws = sys.solve_conservation_laws(
-    conserved_sets=[
-        ['species1', 'species2', 'species3'],  # First conserved set
-        ['species4', 'species5']               # Second conserved set
-    ],
-    states_to_eliminate=['species_to_eliminate1', 'species_to_eliminate2']
+import numpy as np
+from sympy import symbols
+
+from autoreduce import System, solve_timescale_separation
+
+S, C, P, k1, k2, k3, E_total = symbols("S C P k1 k2 k3 E_total")
+
+E = E_total - C
+x = [S, C, P]
+f = [
+    -k1 * E * S + k2 * C,
+    k1 * E * S - (k2 + k3) * C,
+    k3 * C,
+]
+
+system = System(
+    x,
+    f,
+    params_dict={k1: 1.0, k2: 0.5, k3: 0.25, E_total: 1.0},
+    x_init=[10.0, 0.0, 0.0],
+    C=np.array([[1, 0, 0], [0, 0, 1]]),
+)
+
+reduced_system, collapsed_system = solve_timescale_separation(
+    system,
+    [S, P],
+    fast_states=[C],
 )
+```
+
+`params_dict` can be used to set, get, and update parameters:
 
-# Solve timescale separation using QSSA
-reduced_qssa_model = sys.solve_timescale_separation(
-    ['fast_species1', 'fast_species2']
-    )
+```python
+system.set_param(k1, 2.0)
+system.get_param(k1)
+system.set_param_dict({k2: 1.0, k3: 0.1})
 ```
 
 For more examples, check out the [documentation](https://autoreduce.readthedocs.io/en/latest/examples.html).
 
 ## Installation
 
+Supported Python versions are 3.9 - 3.13.
+
 Install the latest version of AutoReduce:
 
 ```bash
@@ -57,12 +87,20 @@ Install with all optional dependencies:
 pip install autoreduce[all]
 ```
 
+Install optional integrations explicitly:
+
+```bash
+pip install "autoreduce[bio]"
+pip install "autoreduce[control]"
+pip install "autoreduce[dmd]"
+```
+
 For development installation:
 
 ```bash
 git clone https://github.com/ayush9pandey/autoreduce.git
 cd autoreduce
-pip install -e ".[all]"
+pip install -e ".[dev]"
 ```
 
 ## Documentation
@@ -71,14 +109,8 @@ Full documentation is available at [autoreduce.readthedocs.io](https://autoreduc
 
 ## Contributing
 
-We welcome contributions! Please see our [contributing guide](https://autoreduce.readthedocs.io/en/latest/contributing.html) for details.
-
-## Versions
-
-AutoReduce versions:
-- 0.3.0 (current release): Major updates including improved API and documentation
-- 0.2.0 (alpha release): `pip install autoreduce==0.2.0`
-- 0.1.0 (alpha release): `pip install autoreduce==0.1.0`
+We welcome contributions. Developer notes and release instructions are in the
+[documentation](https://autoreduce.readthedocs.io/en/latest/develop.html).
 
 ## Contact
 
@@ -89,5 +121,3 @@ For questions, feedback, or suggestions, please contact:
 ## License
 
 Released under the BSD 3-Clause License (see `LICENSE`)
-
-Copyright (c) 2025, Ayush Pandey. All rights reserved.