symident 0.9.2__tar.gz

symident-0.9.2/.github/workflows/wheels.yml

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+# Wheels for Linux (manylinux x86_64 and aarch64), macOS (x86_64 and arm64) and Windows,
+# the sdist, tests of the Linux wheel on Fedora and Debian, and a source build on Fedora;
+# uploaded to PyPI only when a release is published. Documentation goes to Pages from master.
+name: wheels
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+  workflow_dispatch:
+  release:
+    types: [published]
+
+jobs:
+  wheels:
+    name: wheels ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, ubuntu-24.04-arm, macos-15-intel, macos-latest, windows-latest]
+    steps:
+      - uses: actions/checkout@v5
+      - uses: pypa/cibuildwheel@v3.4.1
+      - uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.os }}
+          path: wheelhouse/*.whl
+
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - run: pipx run build --sdist
+      - uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist/*.tar.gz
+
+  # the manylinux wheel on the distributions' own Python; Fedora also builds msolve with
+  # install_msolve() and runs the tests that need it
+  distro:
+    needs: wheels
+    # runs when another platform's wheels failed; it needs only the ubuntu-latest wheel
+    if: ${{ !cancelled() }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        image: ["fedora:latest", "debian:stable"]
+    container: ${{ matrix.image }}
+    steps:
+      - name: Install Python and build tools
+        run: |
+          if command -v dnf >/dev/null; then
+            dnf install -y --setopt=install_weak_deps=False python3 python3-pip gcc make m4 curl xz tar
+          else
+            apt-get update && apt-get install -y --no-install-recommends \
+              python3 python3-venv ca-certificates
+          fi
+      - uses: actions/checkout@v5
+      - uses: actions/download-artifact@v4
+        with:
+          name: wheels-ubuntu-latest
+          path: wheelhouse
+      - name: Install the wheel
+        run: |
+          python3 -m venv /opt/venv
+          /opt/venv/bin/pip install --upgrade pip pytest pytest-xdist
+          /opt/venv/bin/pip install --only-binary=:all: --find-links wheelhouse symident
+      - name: Build msolve
+        if: startsWith(matrix.image, 'fedora')
+        run: /opt/venv/bin/python -c "import symident; symident.install_msolve(ask=False, jobs=4)"
+      - name: Tests
+        run: cd /tmp && /opt/venv/bin/python -m pytest -q -n auto "$GITHUB_WORKSPACE/tests"
+
+  # a source install on Fedora's own Python and compilers, as dMod2's CI installs it
+  fedora:
+    name: fedora
+    runs-on: ubuntu-latest
+    container: fedora:latest
+    steps:
+      - name: Install Python and the compilers
+        run: dnf install -y --setopt=install_weak_deps=False python3 python3-devel python3-pip gcc-c++ cmake
+      - uses: actions/checkout@v5
+      - name: Install from source
+        run: |
+          python3 -m venv /opt/venv
+          /opt/venv/bin/pip install --upgrade pip pytest pytest-xdist
+          /opt/venv/bin/pip install .
+      - name: Tests
+        run: cd /tmp && /opt/venv/bin/python -m pytest -q -n auto "$GITHUB_WORKSPACE/tests"
+
+  # the documentation as HTML, built on every run and deployed to Pages from master
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+      - run: pip install ".[docs]"
+      - run: sphinx-build -W -b html docs docs/_build/html
+      - uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/_build/html
+
+  pages:
+    if: github.event_name == 'push' && github.ref == 'refs/heads/master'
+    needs: docs
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+    environment:
+      name: github-pages
+      url: ${{ steps.deploy.outputs.page_url }}
+    steps:
+      - id: deploy
+        uses: actions/deploy-pages@v4
+
+  publish:
+    if: github.event_name == 'release' && github.event.action == 'published'
+    needs: [wheels, sdist, distro]
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      # the wheels and the sdist only, not the documentation for Pages
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: wheels-*
+          path: dist
+          merge-multiple: true
+      - uses: actions/download-artifact@v4
+        with:
+          name: sdist
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@release/v1

symident-0.9.2/.gitignore

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+build/
+*.so
+__pycache__/
+*.egg-info/
+.pytest_cache/
+.cmake/
+CMakeFiles/
+CMakeCache.txt
+CMakeInit.txt
+cmake_install.cmake
+build.ninja
+.ninja_*
+.skbuild-info.json
+.ruff_cache/
+docs/_build/
+docs/generated/

symident-0.9.2/CMakeLists.txt

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+cmake_minimum_required(VERSION 3.18)
+project(symident LANGUAGES CXX)
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE Release)
+endif()
+find_package(Python REQUIRED COMPONENTS Interpreter Development.Module)
+find_package(pybind11 CONFIG REQUIRED)
+find_package(OpenMP COMPONENTS CXX)
+pybind11_add_module(_core cpp/bindings.cpp cpp/kernel.cpp)
+if(OpenMP_CXX_FOUND)
+  target_link_libraries(_core PRIVATE OpenMP::OpenMP_CXX)
+else()
+  message(WARNING "OpenMP not found: the kernel runs on one thread")
+endif()
+if(NOT MSVC)
+  target_compile_options(_core PRIVATE -O2)
+endif()
+install(TARGETS _core DESTINATION symident)

symident-0.9.2/LICENSE

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+MIT License
+
+Copyright (c) 2026 Simon Beyer
+
+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.

symident-0.9.2/NEWS.md

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+# symident 0.9.2
+
+* `log(x, b)` and `atan2(y, x)` parse: the commas between the arguments were dropped.
+* `atanh()` of an argument whose logarithms cancel in part, such as `atanh(x/(1 + x))`,
+  no longer stops with a `KeyError`.
+
+# symident 0.9.1
+
+* Wheels for Python 3.14.
+* Linux wheels are built on manylinux_2_28 and need glibc 2.28 or newer; on the older
+  manylinux2014 base, installing the wheel built SciPy from source.
+* The tests pass on Windows: they read their data as UTF-8, and the msolve tests that run a
+  shell script are skipped there.
+
+# symident 0.9.0
+
+First release.
+
+* `Model`, `detect()` and `reduce()`: non-identifiable directions of ODE models with
+  observables, conditions, events and inputs, as exact generators where they close, and the
+  reparametrisation that removes them.
+* Observability rank over finite fields in a C++ kernel, with a certified Lie order, exact
+  scaling symmetries and rank proofs by scalings or invariant fields.
+* Elementary functions of states (logarithms, inverse trigonometric and hyperbolic
+  functions, powers of sums, nested) recast into rational form; their transcendental
+  initial values become generic leaves.
+* Steady-state constraints (`equilibrate`) through the joint resting-state system.
+  Directions that no sampling route closes are fitted along parameter lines through the
+  continued resting state, in the parameters and, where needed, the resting states
+  (`reconst_control(homotopy=)`).
+* Switches in right-hand sides and observables: `piecewise()` in SBML order, `ifelse()`,
+  comparisons, `&&`, `||`, `!`, `Heaviside()`, `sign()`, `abs()`, `max()` and `min()`, and
+  events with a `root`. A direction is reported when the observables of every regime
+  that the declared signs do not exclude stay unchanged along it, it maps every surface
+  of a visible switch to itself and keeps the events; a switch hidden from the
+  observables may move. `Model(regimes=)` restricts the analysis to the regimes an
+  experiment visits. The rank is certified between the stacked rows of the regimes and
+  directions proven symbolically, and an error is raised where they do not meet.
+* Reduction by scaling transversals, module reduction and invariants (monomial, polynomial,
+  rational, Darboux, exponential), with positivity certificates and face sections.
+* `reduce()` returns the best admissible chart and lists the others under `alternatives`
+  (`reduce(alternatives=True)`); dependent directions are named under `dependent`.
+* `install_msolve()` builds msolve, used for coupled steady states, into a per-user cache.
+* `symident.rjson`: JSON interface for host languages.

symident-0.9.2/PKG-INFO

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+Metadata-Version: 2.4
+Name: symident
+Version: 0.9.2
+Summary: Structural identifiability of ODE models by Lie symmetries over finite fields
+Keywords: structural identifiability,Lie symmetries,ODE models,systems biology,finite fields,reparametrisation
+Author-Email: Simon Beyer <simon.beyer@fdm.uni-freiburg.de>
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Programming Language :: C++
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Project-URL: Homepage, https://github.com/dModverse/symident
+Project-URL: Documentation, https://dmodverse.github.io/symident/
+Project-URL: Source, https://github.com/dModverse/symident
+Project-URL: Issues, https://github.com/dModverse/symident/issues
+Requires-Python: >=3.10
+Requires-Dist: numpy>=1.24
+Requires-Dist: sympy>=1.12
+Requires-Dist: scipy>=1.11
+Provides-Extra: test
+Requires-Dist: pytest>=7; extra == "test"
+Requires-Dist: pytest-xdist; extra == "test"
+Provides-Extra: docs
+Requires-Dist: sphinx>=8; extra == "docs"
+Requires-Dist: numpydoc; extra == "docs"
+Requires-Dist: pydata-sphinx-theme; extra == "docs"
+Requires-Dist: myst-parser; extra == "docs"
+Description-Content-Type: text/markdown
+
+# symident
+
+[![wheels](https://github.com/dModverse/symident/actions/workflows/wheels.yml/badge.svg)](https://github.com/dModverse/symident/actions/workflows/wheels.yml)
+[![docs](https://img.shields.io/badge/docs-dmodverse.github.io%2Fsymident-blue)](https://dmodverse.github.io/symident/)
+[![License: MIT](https://img.shields.io/badge/license-MIT-green)](LICENSE)
+
+Structural identifiability of ODE models by Lie symmetries over finite fields.
+
+symident finds the non-identifiable directions of an ODE model with observables,
+conditions and events, returns them as exact generators where possible, and reduces
+the model to identifiable parameters. The observability rank is computed modulo
+primes in a C++ kernel; closed forms are reconstructed by sparse interpolation and
+verified at fresh primes.
+
+## Installation
+
+```sh
+pip install git+https://github.com/dModverse/symident
+```
+
+This builds from source and needs a C++17 compiler and CMake; with OpenMP the kernel runs
+on several threads. Once symident is on PyPI, `pip install symident` installs a wheel.
+Wheels are built for Linux (x86_64, aarch64; tested on Ubuntu, Debian and Fedora), macOS
+(x86_64, arm64) and Windows (x86_64).
+
+Steady-state analyses (`equilibrate=True`) whose resting state is a coupled nonlinear
+polynomial system use [msolve](https://msolve.lip6.fr). On Linux and macOS
+
+```python
+import symident
+symident.install_msolve()
+```
+
+builds it with GMP, MPFR and FLINT into a per-user cache (needs a C compiler, `make`, `m4`
+and `curl` or `wget`), where symident finds it. Alternatively point `SYMIDENT_MSOLVE` at an
+msolve executable; on Windows that is the only way.
+
+## Example
+
+```python
+import symident as si
+
+m = si.Model({"A": "-k1*A", "B": "k1*A - k2*B"}, {"y": "s*B"})
+res = si.detect(m, reconstruct=True)
+print(res)
+#> Result:  rank 4 / 5  |  1 non-identifiable direction
+res.symmetries[0].generator
+#> {'A': 'A', 'B': 'B', 's': '-s'}
+print(res.reduce())
+#> Reduced 1 of 1 direction.
+#> Trafo (non-identity entries)
+#>   A = 1
+```
+
+## Interface
+
+| | |
+|---|---|
+| `Model(odes, observables, ...)` | ODEs or a reaction network, observables, `trafo`, `conditions`, `events`, `inputs`, `fixed` |
+| `detect(model, ...)` | rank, identifiability and the non-identifiable directions (`Symmetries`) |
+| `reduce(result, ...)`, `result.reduce()` | reparametrisation that removes the directions (`Reduction`) |
+| `reconst_control(...)` | settings of the saturation and the reconstruction |
+
+Both results print a report; `summary()` adds the computation details and
+`to_dict()` returns the raw result.
+
+## Contact
+
+Simon Beyer, simon.beyer@fdm.uni-freiburg.de. Requests for further functions in model
+equations, questions and bug reports are welcome by e-mail or as an
+[issue](https://github.com/dModverse/symident/issues); the supported functions are listed
+in the [user guide](https://dmodverse.github.io/symident/guide.html#expressions).
+
+## License
+
+MIT

symident-0.9.2/README.md

@@ -0,0 +1,76 @@
+# symident
+
+[![wheels](https://github.com/dModverse/symident/actions/workflows/wheels.yml/badge.svg)](https://github.com/dModverse/symident/actions/workflows/wheels.yml)
+[![docs](https://img.shields.io/badge/docs-dmodverse.github.io%2Fsymident-blue)](https://dmodverse.github.io/symident/)
+[![License: MIT](https://img.shields.io/badge/license-MIT-green)](LICENSE)
+
+Structural identifiability of ODE models by Lie symmetries over finite fields.
+
+symident finds the non-identifiable directions of an ODE model with observables,
+conditions and events, returns them as exact generators where possible, and reduces
+the model to identifiable parameters. The observability rank is computed modulo
+primes in a C++ kernel; closed forms are reconstructed by sparse interpolation and
+verified at fresh primes.
+
+## Installation
+
+```sh
+pip install git+https://github.com/dModverse/symident
+```
+
+This builds from source and needs a C++17 compiler and CMake; with OpenMP the kernel runs
+on several threads. Once symident is on PyPI, `pip install symident` installs a wheel.
+Wheels are built for Linux (x86_64, aarch64; tested on Ubuntu, Debian and Fedora), macOS
+(x86_64, arm64) and Windows (x86_64).
+
+Steady-state analyses (`equilibrate=True`) whose resting state is a coupled nonlinear
+polynomial system use [msolve](https://msolve.lip6.fr). On Linux and macOS
+
+```python
+import symident
+symident.install_msolve()
+```
+
+builds it with GMP, MPFR and FLINT into a per-user cache (needs a C compiler, `make`, `m4`
+and `curl` or `wget`), where symident finds it. Alternatively point `SYMIDENT_MSOLVE` at an
+msolve executable; on Windows that is the only way.
+
+## Example
+
+```python
+import symident as si
+
+m = si.Model({"A": "-k1*A", "B": "k1*A - k2*B"}, {"y": "s*B"})
+res = si.detect(m, reconstruct=True)
+print(res)
+#> Result:  rank 4 / 5  |  1 non-identifiable direction
+res.symmetries[0].generator
+#> {'A': 'A', 'B': 'B', 's': '-s'}
+print(res.reduce())
+#> Reduced 1 of 1 direction.
+#> Trafo (non-identity entries)
+#>   A = 1
+```
+
+## Interface
+
+| | |
+|---|---|
+| `Model(odes, observables, ...)` | ODEs or a reaction network, observables, `trafo`, `conditions`, `events`, `inputs`, `fixed` |
+| `detect(model, ...)` | rank, identifiability and the non-identifiable directions (`Symmetries`) |
+| `reduce(result, ...)`, `result.reduce()` | reparametrisation that removes the directions (`Reduction`) |
+| `reconst_control(...)` | settings of the saturation and the reconstruction |
+
+Both results print a report; `summary()` adds the computation details and
+`to_dict()` returns the raw result.
+
+## Contact
+
+Simon Beyer, simon.beyer@fdm.uni-freiburg.de. Requests for further functions in model
+equations, questions and bug reports are welcome by e-mail or as an
+[issue](https://github.com/dModverse/symident/issues); the supported functions are listed
+in the [user guide](https://dmodverse.github.io/symident/guide.html#expressions).
+
+## License
+
+MIT